Merge remote-tracking branch 'upstream/master'

157 files changed, 21683 insertions, 11834 deletions

diff --git a/.gitignore b/.gitignore
index bde0f6a5..d963db32 100644
--- a/.gitignore
+++ b/.gitignore
@@ -69,6 +69,9 @@ extools/filter_score_grammar
 extools/mr_stripe_rule_reduce
 extools/score_grammar
 extools/sg_lexer.cc
+extractor/*_test
+extractor/compile
+extractor/run_extractor
 gi/clda/src/clda
 gi/markov_al/ml
 gi/pf/align-lexonly
@@ -100,7 +103,9 @@ jam-files/bjam
 jam-files/engine/bin.*
 jam-files/engine/bootstrap/
 klm/lm/bin/
+klm/lm/builder/builder
 klm/lm/build_binary
+klm/lm/ngram_query
 klm/lm/query
 klm/util/bin/
 libtool
@@ -122,6 +127,7 @@ phrasinator/gibbs_train_plm_notables
 previous.sh
 pro-train/mr_pro_map
 pro-train/mr_pro_reduce
+python/build
 python/setup.py
 rampion/rampion_cccp
 rst_parser/mst_train
@@ -182,6 +188,7 @@ utils/small_vector_test
 utils/ts
 utils/weights_test
 training/crf/mpi_batch_optimize
+training/crf/mpi_baum_welch
 training/crf/mpi_compute_cllh
 training/crf/mpi_extract_features
 training/crf/mpi_extract_reachable
diff --git a/.travis.yml b/.travis.yml
index d2d25903..1f0f2eee 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,6 +2,7 @@ language: python
 python:
  - "2.7"
 before_script:
+ - sudo apt-get install libboost-filesystem1.48-dev
  - sudo apt-get install libboost-program-options1.48-dev
  - sudo apt-get install libboost-serialization1.48-dev
  - sudo apt-get install libboost-regex1.48-dev
diff --git a/Makefile.am b/Makefile.am
index e017fba7..1c30a6ff 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -14,7 +14,8 @@ SUBDIRS = \
   training \
   training/liblbfgs \
   word-aligner \
-  example_extff
+  example_extff \
+  extractor
 
 #gi/pyp-topics/src gi/clda/src gi/posterior-regularisation/prjava
 
diff --git a/configure.ac b/configure.ac
index 98deac86..8cbdb4fa 100644
--- a/configure.ac
+++ b/configure.ac
@@ -10,8 +10,11 @@ esac
 # CPPFLAGS="$CPPFLAGS -std=c++0x"
 AC_PROG_CC
 AC_PROG_CXX
+AX_CXX_COMPILE_STDCXX_11
 AC_LANG_CPLUSPLUS
+AC_OPENMP
 BOOST_REQUIRE([1.44])
+BOOST_FILESYSTEM
 BOOST_PROGRAM_OPTIONS
 BOOST_SYSTEM
 BOOST_SERIALIZATION
@@ -87,11 +90,94 @@ then
   AM_CONDITIONAL([HAVE_CMPH], true)
 fi
 
+AM_CONDITIONAL([HAVE_GTEST], false)
+AC_ARG_WITH(gtest,
+            [AC_HELP_STRING([--with-gtest=DIR], [(optional) path to Google Test library])],
+            [with_gtest=$withval],
+            [with_gtest=no]
+           )
+
+AM_CONDITIONAL([HAVE_GMOCK], false)
+AC_ARG_WITH(gmock,
+            [AC_HELP_STRING([--with-gmock=DIR], [(optional) path to Google Mock library])],
+            [with_gmock=$withval],
+            [with_gmock=no]
+           )
+
+if test "x$with_gtest" != 'xno'
+then
+  gtest_CPPFLAGS="-I${with_gtest}/include"
+  gtest_LDFLAGS="-L${with_gtest} -L${with_gtest}/lib"
+  gtest_LIBS="-lgtest_main -lgtest -lpthread"
+
+  SAVECPP_FLAGS="$CPPFLAGS"
+  CPPFLAGS="$CPPFLAGS $gtest_CPPFLAGS"
+  AC_CHECK_HEADER(${with_gtest}/include/gtest/gtest.h,
+                  [AC_DEFINE([HAVE_GTEST], [1], [flag for Google Test header])],
+                  [AC_MSG_ERROR([Cannot find Google Test headers!])]
+                 )
+
+  SAVE_LDFLAGS="$LDFLAGS"
+  LDFLAGS="$LDFLAGS $gtest_LDFLAGS"
+  SAVE_LIBS="$LIBS"
+  # Google Test needs pthreads.
+  AC_CHECK_LIB([pthread],
+               [pthread_mutex_init],
+               [],
+               [AC_MSG_ERROR([Cannot find pthread library])]
+              )
+  AX_CXX_CHECK_LIB([gtest],
+                   [testing::TestInfo::name() const],
+                   [],
+                   [AC_MSG_ERROR([Cannot find Google Test library libgtest])]
+                  )
+  AC_CHECK_LIB([gtest_main],
+               [main],
+               [],
+               [AC_MSG_ERROR([Cannot find Google Test library libgtest_main])]
+              )
+
+  AC_SUBST(AS_TR_CPP([GTEST_CPPFLAGS]), ["$gtest_CPPFLAGS"])
+  AC_SUBST(AS_TR_CPP([GTEST_LDFLAGS]), ["$gtest_LDFLAGS"])
+  AC_SUBST(AS_TR_CPP([GTEST_LIBS]), ["$gtest_LIBS"])
+
+
+  if test "x$with_gmock" != 'xno'
+  then
+    gmock_CPPFLAGS="-I${with_gmock}/include"
+    gmock_LDFLAGS="-L${with_gmock} -L${with_gmock}/lib"
+    gmock_LIBS="-lgmock"
+
+    CPPFLAGS="$CPPFLAGS $gmock_CPPFLAGS"
+    AC_CHECK_HEADER(${with_gmock}/include/gmock/gmock.h,
+                    [AC_DEFINE([HAVE_GMOCK], [1], [flag for Google Mock header])],
+                    [AC_MSG_ERROR([Cannot find Google Mock headers!])]
+                   )
+
+    LDFLAGS="$LDFLAGS $gmock_LDFLAGS"
+    AX_CXX_CHECK_LIB([gmock],
+                     [testing::Expectation],
+                     [],
+                     [AC_MSG_ERROR([Cannot find Google Mock library libgmock])]
+                    )
+
+    AC_SUBST(AS_TR_CPP([GMOCK_CPPFLAGS]), ["$gmock_CPPFLAGS"])
+    AC_SUBST(AS_TR_CPP([GMOCK_LDFLAGS]), ["$gmock_LDFLAGS"])
+    AC_SUBST(AS_TR_CPP([GMOCK_LIBS]), ["$gmock_LIBS"])
+    AM_CONDITIONAL([HAVE_GMOCK], true)
+  fi
+
+  CPPFLAGS="$SAVE_CPPFLAGS"
+  LDFLAGS="$SAVE_LDFLAGS"
+  LIBS="$SAVE_LIBS"
+  AM_CONDITIONAL([HAVE_GTEST], true)
+fi
+
 #BOOST_THREADS
 CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
-LDFLAGS="$LDFLAGS $BOOST_PROGRAM_OPTIONS_LDFLAGS $BOOST_SERIALIZATION_LDFLAGS $BOOST_SYSTEM_LDFLAGS"
+LDFLAGS="$LDFLAGS $BOOST_PROGRAM_OPTIONS_LDFLAGS $BOOST_SERIALIZATION_LDFLAGS $BOOST_SYSTEM_LDFLAGS $BOOST_FILESYSTEM_LDFLAGS"
 # $BOOST_THREAD_LDFLAGS"
-LIBS="$LIBS $BOOST_PROGRAM_OPTIONS_LIBS $BOOST_SERIALIZATION_LIBS $BOOST_SYSTEM_LIBS $ZLIBS"
+LIBS="$LIBS $BOOST_PROGRAM_OPTIONS_LIBS $BOOST_SERIALIZATION_LIBS $BOOST_SYSTEM_LIBS $BOOST_FILESYSTEM_LIBS $ZLIBS"
 # $BOOST_THREAD_LIBS"
 
 AC_CHECK_HEADER(google/dense_hash_map,
@@ -108,6 +194,7 @@ AC_CONFIG_FILES([mteval/Makefile])
 AC_CONFIG_FILES([mteval/meteor_jar.cc])
 AC_CONFIG_FILES([decoder/Makefile])
 AC_CONFIG_FILES([python/setup.py])
+AC_CONFIG_FILES([extractor/Makefile])
 AC_CONFIG_FILES([word-aligner/Makefile])
 
 # KenLM stuff
@@ -128,6 +215,7 @@ AC_CONFIG_FILES([training/pro/Makefile])
 AC_CONFIG_FILES([training/rampion/Makefile])
 AC_CONFIG_FILES([training/minrisk/Makefile])
 AC_CONFIG_FILES([training/mira/Makefile])
+AC_CONFIG_FILES([training/latent_svm/Makefile])
 AC_CONFIG_FILES([training/dtrain/Makefile])
 
 # external feature function example code
diff --git a/corpus/lowercase.pl b/corpus/lowercase.pl
index 688e493b..9fd91dac 100755
--- a/corpus/lowercase.pl
+++ b/corpus/lowercase.pl
@@ -2,7 +2,7 @@
 use strict;
 binmode(STDIN,":utf8");
 binmode(STDOUT,":utf8");
-while(<>) {
+while(<STDIN>) {
   $_ = lc $_;
   print;
 }
diff --git a/corpus/support/token_list b/corpus/support/token_list
index 366cd7ff..43dd80d9 100644
--- a/corpus/support/token_list
+++ b/corpus/support/token_list
@@ -294,3 +294,155 @@ Z.
 т.н.
 т.ч.
 н.э.
+# Swahili
+A.D.
+Afr.
+A.G.
+agh.
+A.H.
+A.M.
+a.s.
+B.A.
+B.C.
+Bi.
+B.J.
+B.K.
+B.O.M.
+Brig.
+Bro.
+bt.
+bw.
+Bw.
+Cap.
+C.C.
+cCM.
+C.I.A.
+cit.
+C.M.S.
+Co.
+Corp.
+C.S.Sp.
+C.W.
+D.C.
+Dk.
+Dkt.
+Dk.B.
+Dr.
+E.C.
+e.g.
+E.M.
+E.n.
+etc.
+Feb.
+F.F.U.
+F.M.
+Fr.
+F.W.
+I.C.O.
+i.e.
+I.L.C.
+Inc.
+Jan.
+J.F.
+Jr.
+J.S.
+J.V.W.A.
+K.A.R.
+K.A.U.
+K.C.M.C.
+K.k.
+K.K.
+k.m.
+km.
+K.m.
+K.N.C.U.
+K.O.
+K.S.
+Ksh.
+kt.
+kumb.
+k.v.
+kv.
+L.G.
+ltd.
+Ltd.
+M.A.
+M.D.
+mf.
+Mh.
+Mhe.
+mil.
+m.m.
+M.m.
+Mm.
+M.M.
+Mr.
+Mrs.
+M.S.
+Mt.
+Mw.
+M.W.
+Mwl.
+na.
+Na.
+N.F.
+N.J.
+n.k.
+nk.
+n.k.w.
+N.N.
+Nov.
+O.C.D.
+op.
+P.C.
+Phd.
+Ph.D.
+P.J.
+P.o.
+P.O.
+P.O.P.
+P.P.F.
+Prof.
+P.s.
+P.S.
+Q.C.
+Rd.
+s.a.w.
+S.A.W.
+S.D.
+Sept.
+sh.
+Sh.
+SH.
+shs.
+Shs.
+S.J.
+S.L.
+S.L.P.
+S.s.
+S.S.
+St.
+s.w.
+s.w.T.
+taz.
+Taz.
+T.C.
+T.E.C.
+T.L.P.
+T.O.H.S.
+Tsh.
+T.V.
+tz.
+uk.
+Uk.
+U.M.C.A.
+U.N.
+U.S.
+Ush.
+U.W.T.
+Viii.
+Vol.
+V.T.C.
+W.H.
+yamb.
+Y.M.C.A.
diff --git a/corpus/support/tokenizer.pl b/corpus/support/tokenizer.pl
index 0350a894..acc537fb 100755
--- a/corpus/support/tokenizer.pl
+++ b/corpus/support/tokenizer.pl
@@ -226,7 +226,7 @@ sub proc_token {
     }
 
     ## step 1: check the most common case
-    if($token =~ /^[a-z0-9\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}]+$/i){
+    if($token =~ /^[a-z0-9\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}\p{Devanagari}]+$/i){
 	### most common cases
 	return $token;
     }
@@ -246,7 +246,7 @@ sub proc_token {
 	## number
 	return $token;
     }
-    if($token =~ /^(@|#)[A-Za-z0-9_\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}]+.*$/){
+    if($token =~ /^(@|#)[A-Za-z0-9_\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}\p{Devanagari}]+.*$/){
         ## twitter hashtag or address
         return proc_rightpunc($token);
     }
@@ -277,7 +277,7 @@ sub proc_token {
     }
 
     #my $t1 = '[\x{0600}-\x{06ff}a-z\d\_\.\-]';
-    my $t1 = '[a-z\d\_\-\.\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}]';
+    my $t1 = '[a-z\d\_\-\.\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}\p{Devanagari}]';
     if($token =~ /^\/(($t1)+\/)+($t1)+\/?$/i){
 	### /nls/p/....
 	return $token;
@@ -361,7 +361,7 @@ sub deep_proc_token {
     }
 
     ##### step 0: if it mades up of all puncts, remove one punct at a time.
-    if($line !~ /[\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}a-zA-Z\d]/){
+    if($line !~ /[\p{Cyrillic}\p{Greek}\p{Hebrew}\p{Han}\p{Arabic}\p{Devanagari}a-zA-Z\d]/){
 	if($line =~ /^(\!+|\@+|\++|\=+|\*+|\<+|\>+|\|+|\?+|\.+|\-+|\_+|\&+)$/){
 	    ## ++ @@@@ !!! ....
 	    return $line;
diff --git a/decoder/ff_klm.cc b/decoder/ff_klm.cc
index fefa90bd..c8ca917a 100644
--- a/decoder/ff_klm.cc
+++ b/decoder/ff_klm.cc
@@ -1,6 +1,7 @@
 #include "ff_klm.h"
 
 #include <cstring>
+#include <cstdlib>
 #include <iostream>
 
 #include <boost/scoped_ptr.hpp>
@@ -151,8 +152,9 @@ template <class Model> class BoundaryRuleScore {
 template <class Model>
 class KLanguageModelImpl {
  public:
-  double LookupWords(const TRule& rule, const vector<const void*>& ant_states, double* oovs, void* remnant) {
+  double LookupWords(const TRule& rule, const vector<const void*>& ant_states, double* oovs, double* emit, void* remnant) {
     *oovs = 0;
+    *emit = 0;
     const vector<WordID>& e = rule.e();
     BoundaryRuleScore<Model> ruleScore(*ngram_, *static_cast<BoundaryAnnotatedState*>(remnant));
     unsigned i = 0;
@@ -169,8 +171,9 @@ class KLanguageModelImpl {
       if (e[i] <= 0) {
         ruleScore.NonTerminal(*static_cast<const BoundaryAnnotatedState*>(ant_states[-e[i]]));
       } else {
-        const WordID cdec_word_or_class = ClassifyWordIfNecessary(e[i]);  // in future,
-                                                                          // maybe handle emission
+        float ep = 0.f;
+        const WordID cdec_word_or_class = ClassifyWordIfNecessary(e[i], &ep);
+        if (ep) { *emit += ep; }
         const lm::WordIndex cur_word = MapWord(cdec_word_or_class); // map to LM's id
         if (cur_word == 0) (*oovs) += 1.0;
         ruleScore.Terminal(cur_word);
@@ -205,12 +208,14 @@ class KLanguageModelImpl {
   // if this is not a class-based LM, returns w untransformed,
   // otherwise returns a word class mapping of w,
   // returns TD::Convert("<unk>") if there is no mapping for w
-  WordID ClassifyWordIfNecessary(WordID w) const {
+  WordID ClassifyWordIfNecessary(WordID w, float* emitp) const {
     if (word2class_map_.empty()) return w;
     if (w >= word2class_map_.size())
       return kCDEC_UNK;
-    else
-      return word2class_map_[w];
+    else {
+      *emitp = word2class_map_[w].second;
+      return word2class_map_[w].first;
+    }
   }
 
   // converts to cdec word id's to KenLM's id space, OOVs and <unk> end up at 0
@@ -256,32 +261,32 @@ class KLanguageModelImpl {
     int lc = 0;
     if (!SILENT)
       cerr << "  Loading word classes from " << file << " ...\n";
-    AddWordToClassMapping_(TD::Convert("<s>"), TD::Convert("<s>"));
-    AddWordToClassMapping_(TD::Convert("</s>"), TD::Convert("</s>"));
-    while(in) {
-      getline(in, line);
-      if (!in) continue;
+    AddWordToClassMapping_(TD::Convert("<s>"), TD::Convert("<s>"), 0.0);
+    AddWordToClassMapping_(TD::Convert("</s>"), TD::Convert("</s>"), 0.0);
+    while(getline(in, line)) {
       dummy.clear();
       TD::ConvertSentence(line, &dummy);
       ++lc;
-      if (dummy.size() != 2) {
+      if (dummy.size() != 3) {
+        cerr << "    Class map file expects: CLASS WORD logp(WORD|CLASS)\n";
         cerr << "    Format error in " << file << ", line " << lc << ": " << line << endl;
         abort();
       }
-      AddWordToClassMapping_(dummy[0], dummy[1]);
+      AddWordToClassMapping_(dummy[1], dummy[0], strtof(TD::Convert(dummy[2]).c_str(), NULL));
     }
   }
 
-  void AddWordToClassMapping_(WordID word, WordID cls) {
+  void AddWordToClassMapping_(WordID word, WordID cls, float emit) {
     if (word2class_map_.size() <= word) {
-      word2class_map_.resize((word + 10) * 1.1, kCDEC_UNK);
+      word2class_map_.resize((word + 10) * 1.1, pair<WordID,float>(kCDEC_UNK,0.f));
       assert(word2class_map_.size() > word);
     }
-    if(word2class_map_[word] != kCDEC_UNK) {
+    if(word2class_map_[word].first != kCDEC_UNK) {
       cerr << "Multiple classes for symbol " << TD::Convert(word) << endl;
       abort();
     }
-    word2class_map_[word] = cls;
+    word2class_map_[word].first = cls;
+    word2class_map_[word].second = emit;
   }
 
   ~KLanguageModelImpl() {
@@ -304,7 +309,9 @@ class KLanguageModelImpl {
 
   int order_;
   vector<lm::WordIndex> cdec2klm_map_;
-  vector<WordID> word2class_map_;        // if this is a class-based LM, this is the word->class mapping
+  vector<pair<WordID,float> > word2class_map_; // if this is a class-based LM,
+          // .first is the word->class mapping
+          // .second is the emission log probability
 };
 
 template <class Model>
@@ -322,6 +329,7 @@ KLanguageModel<Model>::KLanguageModel(const string& param) {
   }
   fid_ = FD::Convert(featname);
   oov_fid_ = FD::Convert(featname+"_OOV");
+  emit_fid_ = FD::Convert(featname+"_Emit");
   // cerr << "FID: " << oov_fid_ << endl;
   SetStateSize(pimpl_->ReserveStateSize());
 }
@@ -340,9 +348,12 @@ void KLanguageModel<Model>::TraversalFeaturesImpl(const SentenceMetadata& /* sme
                                           void* state) const {
   double est = 0;
   double oovs = 0;
-  features->set_value(fid_, pimpl_->LookupWords(*edge.rule_, ant_states, &oovs, state));
+  double emit = 0;
+  features->set_value(fid_, pimpl_->LookupWords(*edge.rule_, ant_states, &oovs, &emit, state));
   if (oovs && oov_fid_)
     features->set_value(oov_fid_, oovs);
+  if (emit && emit_fid_)
+    features->set_value(emit_fid_, emit);
 }
 
 template <class Model>
diff --git a/decoder/ff_klm.h b/decoder/ff_klm.h
index b5ceffd0..db4032f7 100644
--- a/decoder/ff_klm.h
+++ b/decoder/ff_klm.h
@@ -28,8 +28,9 @@ class KLanguageModel : public FeatureFunction {
                                      SparseVector<double>* estimated_features,
                                      void* out_context) const;
  private:
-  int fid_; // conceptually const; mutable only to simplify constructor
-  int oov_fid_; // will be zero if extra OOV feature is not configured by decoder
+  int fid_;        // LanguageModel
+  int oov_fid_;    // LanguageModel_OOV
+  int emit_fid_;   // LanguageModel_Emit [only used for class-based LMs]
   KLanguageModelImpl<Model>* pimpl_;
 };
 
diff --git a/decoder/ff_ngrams.cc b/decoder/ff_ngrams.cc
index 9c13fdbb..d337b28b 100644
--- a/decoder/ff_ngrams.cc
+++ b/decoder/ff_ngrams.cc
@@ -60,7 +60,7 @@ namespace {
   }
 }
 
-static bool ParseArgs(string const& in, bool* explicit_markers, unsigned* order, vector<string>& prefixes, string& target_separator) {
+static bool ParseArgs(string const& in, bool* explicit_markers, unsigned* order, vector<string>& prefixes, string& target_separator, string* cluster_file) {
   vector<string> const& argv=SplitOnWhitespace(in);
   *explicit_markers = false;
   *order = 3;
@@ -103,6 +103,10 @@ static bool ParseArgs(string const& in, bool* explicit_markers, unsigned* order,
 	LMSPEC_NEXTARG;
 	prefixes[5] = *i;
 	break;
+      case 'c':
+        LMSPEC_NEXTARG;
+        *cluster_file = *i;
+        break;
       case 'S':
 	LMSPEC_NEXTARG;
 	target_separator = *i;
@@ -124,6 +128,7 @@ usage:
 
        << "NgramFeatures Usage: \n"			     
        << " feature_function=NgramFeatures filename.lm [-x] [-o <order>] \n"
+       << " [-c <cluster-file>]\n"
        << " [-U <unigram-prefix>] [-B <bigram-prefix>][-T <trigram-prefix>]\n"
        << " [-4 <4-gram-prefix>] [-5 <5-gram-prefix>] [-S <separator>]\n\n" 
     
@@ -203,6 +208,12 @@ class NgramDetectorImpl {
     SetFlag(flag, HAS_FULL_CONTEXT, state);
   }
 
+  WordID MapToClusterIfNecessary(WordID w) const {
+    if (cluster_map.size() == 0) return w;
+    if (w >= cluster_map.size()) return kCDEC_UNK;
+    return cluster_map[w];
+  }
+
   void FireFeatures(const State<5>& state, WordID cur, SparseVector<double>* feats) {
     FidTree* ft = &fidroot_;
     int n = 0;
@@ -285,7 +296,7 @@ class NgramDetectorImpl {
           context_complete = true;
         }
       } else {   // handle terminal
-        const WordID cur_word = e[j];
+        const WordID cur_word = MapToClusterIfNecessary(e[j]);
         SparseVector<double> p;
         if (cur_word == kSOS_) {
           state = BeginSentenceState();
@@ -348,9 +359,52 @@ class NgramDetectorImpl {
     }
   }
 
+  void ReadClusterFile(const string& clusters) {
+    ReadFile rf(clusters);
+    istream& in = *rf.stream();
+    string line;
+    int lc = 0;
+    string cluster;
+    string word;
+    while(getline(in, line)) {
+      ++lc;
+      if (line.size() == 0) continue;
+      if (line[0] == '#') continue;
+      unsigned cend = 1;
+      while((line[cend] != ' ' && line[cend] != '\t') && cend < line.size()) {
+        ++cend;
+      }
+      if (cend == line.size()) {
+        cerr << "Line " << lc << " in " << clusters << " malformed: " << line << endl;
+        abort();
+      }
+      unsigned wbeg = cend + 1;
+      while((line[wbeg] == ' ' || line[wbeg] == '\t') && wbeg < line.size()) {
+        ++wbeg;
+      }
+      if (wbeg == line.size()) {
+        cerr << "Line " << lc << " in " << clusters << " malformed: " << line << endl;
+        abort();
+      }
+      unsigned wend = wbeg + 1;
+      while((line[wend] != ' ' && line[wend] != '\t') && wend < line.size()) {
+        ++wend;
+      }
+      const WordID clusterid = TD::Convert(line.substr(0, cend));
+      const WordID wordid = TD::Convert(line.substr(wbeg, wend - wbeg));
+      if (wordid >= cluster_map.size())
+        cluster_map.resize(wordid + 10, kCDEC_UNK);
+      cluster_map[wordid] = clusterid;
+    }
+    cluster_map[kSOS_] = kSOS_;
+    cluster_map[kEOS_] = kEOS_;
+  }
+
+  vector<WordID> cluster_map;
+
  public:
   explicit NgramDetectorImpl(bool explicit_markers, unsigned order,
-			     vector<string>& prefixes, string& target_separator) :
+			     vector<string>& prefixes, string& target_separator, const string& clusters) :
       kCDEC_UNK(TD::Convert("<unk>")) ,
       add_sos_eos_(!explicit_markers) {
     order_ = order;
@@ -369,6 +423,9 @@ class NgramDetectorImpl {
     dummy_rule_.reset(new TRule("[DUMMY] ||| [BOS] [DUMMY] ||| [1] [2] </s> ||| X=0"));
     kSOS_ = TD::Convert("<s>");
     kEOS_ = TD::Convert("</s>");
+
+    if (clusters.size())
+      ReadClusterFile(clusters);
   }
 
   ~NgramDetectorImpl() {
@@ -409,9 +466,10 @@ NgramDetector::NgramDetector(const string& param) {
   vector<string> prefixes;
   bool explicit_markers = false;
   unsigned order = 3;
-  ParseArgs(param, &explicit_markers, &order, prefixes, target_separator);
+  string clusters;
+  ParseArgs(param, &explicit_markers, &order, prefixes, target_separator, &clusters);
   pimpl_ = new NgramDetectorImpl(explicit_markers, order, prefixes, 
-				 target_separator);
+				 target_separator, clusters);
   SetStateSize(pimpl_->ReserveStateSize());
 }
 
diff --git a/decoder/ff_rules.cc b/decoder/ff_rules.cc
index 6716d3da..410e083c 100644
--- a/decoder/ff_rules.cc
+++ b/decoder/ff_rules.cc
@@ -107,7 +107,12 @@ void RuleSourceBigramFeatures::TraversalFeaturesImpl(const SentenceMetadata& sme
   (*features) += it->second;
 }
 
-RuleTargetBigramFeatures::RuleTargetBigramFeatures(const std::string& param) {
+RuleTargetBigramFeatures::RuleTargetBigramFeatures(const std::string& param) : inds(1000) {
+  for (unsigned i = 0; i < inds.size(); ++i) {
+    ostringstream os;
+    os << (i + 1);
+    inds[i] = os.str();
+  }
 }
 
 void RuleTargetBigramFeatures::PrepareForInput(const SentenceMetadata& smeta) {
@@ -126,11 +131,18 @@ void RuleTargetBigramFeatures::TraversalFeaturesImpl(const SentenceMetadata& sme
     it = rule2_feats_.insert(make_pair(&rule, SparseVector<double>())).first;
     SparseVector<double>& f = it->second;
     string prev = "<r>";
+    vector<WordID> nt_types(rule.Arity());
+    unsigned ntc = 0;
+    for (int i = 0; i < rule.f_.size(); ++i)
+      if (rule.f_[i] < 0) nt_types[ntc++] = -rule.f_[i];
     for (int i = 0; i < rule.e_.size(); ++i) {
       WordID w = rule.e_[i];
-      if (w < 0) w = -w;
-      if (w == 0) return;
-      const string& cur = TD::Convert(w);
+      string cur;
+      if (w > 0) {
+        cur = TD::Convert(w);
+      } else {
+        cur = TD::Convert(nt_types[-w]) + inds[-w];
+      }
       ostringstream os;
       os << "RBT:" << prev << '_' << cur;
       const int fid = FD::Convert(Escape(os.str()));
diff --git a/decoder/ff_rules.h b/decoder/ff_rules.h
index b100ec34..f210dc65 100644
--- a/decoder/ff_rules.h
+++ b/decoder/ff_rules.h
@@ -51,6 +51,7 @@ class RuleTargetBigramFeatures : public FeatureFunction {
                                      void* context) const;
   virtual void PrepareForInput(const SentenceMetadata& smeta);
  private:
+  std::vector<std::string> inds;
   mutable std::map<const TRule*, SparseVector<double> > rule2_feats_;
 };
 
diff --git a/decoder/kbest.h b/decoder/kbest.h
index 9a55f653..44c23151 100644
--- a/decoder/kbest.h
+++ b/decoder/kbest.h
@@ -6,6 +6,7 @@
 #include <tr1/unordered_set>
 
 #include <boost/shared_ptr.hpp>
+#include <boost/type_traits.hpp>
 
 #include "wordid.h"
 #include "hg.h"
@@ -134,7 +135,7 @@ namespace KBest {
         }
         add_next = false;
 
-        if (cand.size() > 0) {
+        while (!add_next && cand.size() > 0) {
           std::pop_heap(cand.begin(), cand.end(), HeapCompare());
           Derivation* d = cand.back();
           cand.pop_back();
@@ -145,10 +146,15 @@ namespace KBest {
           if (!filter(d->yield)) {
             D.push_back(d);
             add_next = true;
+          } else {
+            // just because a node already derived a string (or whatever
+            // equivalent derivation class), you need to add its successors
+            // to the node's candidate pool
+            LazyNext(d, &cand, &s.ds);
           }
-        } else {
-          break;
         }
+        if (!add_next)
+          break;
       }
       if (k < D.size()) return D[k]; else return NULL;
     }
@@ -184,7 +190,11 @@ namespace KBest {
         s.cand.push_back(d);
       }
 
-      const unsigned effective_k = std::min(k_prime, s.cand.size());
+      unsigned effective_k = s.cand.size();
+      if (boost::is_same<DerivationFilter,NoFilter<T> >::value) {
+        // if there's no filter you can use this optimization
+        effective_k = std::min(k_prime, s.cand.size());
+      }
       const typename CandidateHeap::iterator kth = s.cand.begin() + effective_k;
       std::nth_element(s.cand.begin(), kth, s.cand.end(), DerivationCompare());
       s.cand.resize(effective_k);
diff --git a/environment/LocalConfig.pm b/environment/LocalConfig.pm
index 627f7f8c..f7c3b1c7 100644
--- a/environment/LocalConfig.pm
+++ b/environment/LocalConfig.pm
@@ -34,7 +34,7 @@ my $CCONFIG = {
     #'QSubQueue' => '-q long',
   },
   'UMIACS' => {
-    'HOST_REGEXP' => qr/^d.*\.umiacs\.umd\.edu$/,
+    'HOST_REGEXP' => qr/^(n|s|d).*\.umiacs\.umd\.edu$/,
     'JobControl'  => 'qsub',
     'QSubMemFlag' => '-l pmem=',
     'QSubQueue' => '-q batch',
diff --git a/extractor/Makefile.am b/extractor/Makefile.am
new file mode 100644
index 00000000..e94a9b91
--- /dev/null
+++ b/extractor/Makefile.am
@@ -0,0 +1,152 @@
+if HAVE_CXX11
+
+bin_PROGRAMS = compile run_extractor
+
+EXTRA_PROGRAMS = alignment_test \
+    data_array_test \
+    fast_intersector_test \
+    feature_count_source_target_test \
+    feature_is_source_singleton_test \
+    feature_is_source_target_singleton_test \
+    feature_max_lex_source_given_target_test \
+    feature_max_lex_target_given_source_test \
+    feature_sample_source_count_test \
+    feature_target_given_source_coherent_test \
+    grammar_extractor_test \
+    matchings_finder_test \
+    phrase_test \
+    precomputation_test \
+    rule_extractor_helper_test \
+    rule_extractor_test \
+    rule_factory_test \
+    sampler_test \
+    scorer_test \
+    suffix_array_test \
+    target_phrase_extractor_test \
+    translation_table_test
+
+if HAVE_GTEST
+  RUNNABLE_TESTS = alignment_test \
+    data_array_test \
+    fast_intersector_test \
+    feature_count_source_target_test \
+    feature_is_source_singleton_test \
+    feature_is_source_target_singleton_test \
+    feature_max_lex_source_given_target_test \
+    feature_max_lex_target_given_source_test \
+    feature_sample_source_count_test \
+    feature_target_given_source_coherent_test \
+    grammar_extractor_test \
+    matchings_finder_test \
+    phrase_test \
+    precomputation_test \
+    rule_extractor_helper_test \
+    rule_extractor_test \
+    rule_factory_test \
+    sampler_test \
+    scorer_test \
+    suffix_array_test \
+    target_phrase_extractor_test \
+    translation_table_test
+endif
+
+noinst_PROGRAMS = $(RUNNABLE_TESTS)
+
+TESTS = $(RUNNABLE_TESTS)
+
+alignment_test_SOURCES = alignment_test.cc
+alignment_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+data_array_test_SOURCES = data_array_test.cc
+data_array_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+fast_intersector_test_SOURCES = fast_intersector_test.cc
+fast_intersector_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+feature_count_source_target_test_SOURCES = features/count_source_target_test.cc
+feature_count_source_target_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+feature_is_source_singleton_test_SOURCES = features/is_source_singleton_test.cc
+feature_is_source_singleton_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+feature_is_source_target_singleton_test_SOURCES = features/is_source_target_singleton_test.cc
+feature_is_source_target_singleton_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+feature_max_lex_source_given_target_test_SOURCES = features/max_lex_source_given_target_test.cc
+feature_max_lex_source_given_target_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+feature_max_lex_target_given_source_test_SOURCES = features/max_lex_target_given_source_test.cc
+feature_max_lex_target_given_source_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+feature_sample_source_count_test_SOURCES = features/sample_source_count_test.cc
+feature_sample_source_count_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+feature_target_given_source_coherent_test_SOURCES = features/target_given_source_coherent_test.cc
+feature_target_given_source_coherent_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) libextractor.a
+grammar_extractor_test_SOURCES = grammar_extractor_test.cc
+grammar_extractor_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+matchings_finder_test_SOURCES = matchings_finder_test.cc
+matchings_finder_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+phrase_test_SOURCES = phrase_test.cc
+phrase_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+precomputation_test_SOURCES = precomputation_test.cc
+precomputation_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+rule_extractor_helper_test_SOURCES = rule_extractor_helper_test.cc
+rule_extractor_helper_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+rule_extractor_test_SOURCES = rule_extractor_test.cc
+rule_extractor_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+rule_factory_test_SOURCES = rule_factory_test.cc
+rule_factory_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+sampler_test_SOURCES = sampler_test.cc
+sampler_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+scorer_test_SOURCES = scorer_test.cc
+scorer_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+suffix_array_test_SOURCES = suffix_array_test.cc
+suffix_array_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+target_phrase_extractor_test_SOURCES = target_phrase_extractor_test.cc
+target_phrase_extractor_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+translation_table_test_SOURCES = translation_table_test.cc
+translation_table_test_LDADD = $(GTEST_LDFLAGS) $(GTEST_LIBS) $(GMOCK_LDFLAGS) $(GMOCK_LIBS) libextractor.a
+
+noinst_LIBRARIES = libextractor.a libcompile.a
+
+compile_SOURCES = compile.cc
+compile_LDADD = libcompile.a
+run_extractor_SOURCES = run_extractor.cc
+run_extractor_LDADD = libextractor.a
+
+libcompile_a_SOURCES = \
+  alignment.cc \
+  data_array.cc \
+  phrase_location.cc \
+  precomputation.cc \
+  suffix_array.cc \
+  time_util.cc \
+  translation_table.cc
+
+libextractor_a_SOURCES = \
+  alignment.cc \
+  data_array.cc \
+  fast_intersector.cc \
+  features/count_source_target.cc \
+  features/feature.cc \
+  features/is_source_singleton.cc \
+  features/is_source_target_singleton.cc \
+  features/max_lex_source_given_target.cc \
+  features/max_lex_target_given_source.cc \
+  features/sample_source_count.cc \
+  features/target_given_source_coherent.cc \
+  grammar.cc \
+  grammar_extractor.cc \
+  matchings_finder.cc \
+  matchings_trie.cc \
+  phrase.cc \
+  phrase_builder.cc \
+  phrase_location.cc \
+  precomputation.cc \
+  rule.cc \
+  rule_extractor.cc \
+  rule_extractor_helper.cc \
+  rule_factory.cc \
+  sampler.cc \
+  scorer.cc \
+  suffix_array.cc \
+  target_phrase_extractor.cc \
+  time_util.cc \
+  translation_table.cc \
+  vocabulary.cc
+
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(CXX11_SWITCH) -fopenmp $(GTEST_CPPFLAGS) $(GMOCK_CPPFLAGS)
+AM_LDFLAGS = -fopenmp
+endif
diff --git a/extractor/README.md b/extractor/README.md
new file mode 100644
index 00000000..575f5ca5
--- /dev/null
+++ b/extractor/README.md
@@ -0,0 +1,14 @@
+C++ implementation of the online grammar extractor originally developed by [Adam Lopez](http://www.cs.jhu.edu/~alopez/).
+
+To run the extractor you need to:
+
+    cdec/extractor/run_extractor -a <alignment> -b <parallel_corpus> -g <grammar_output_path> < <input_sentences> > <sgm_file>
+
+To run unit tests you need first to configure `cdec` with the [Google Test](https://code.google.com/p/googletest/) and [Google Mock](https://code.google.com/p/googlemock/) libraries:
+
+    ./configure --with-gtest=</absolute/path/to/gtest> --with-gmock=</absolute/path/to/gmock>
+
+Then, you simply need to:
+
+    cd cdec/extractor
+    make check
diff --git a/extractor/alignment.cc b/extractor/alignment.cc
new file mode 100644
index 00000000..1aea34b3
--- /dev/null
+++ b/extractor/alignment.cc
@@ -0,0 +1,53 @@
+#include "alignment.h"
+
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <fcntl.h>
+#include <unistd.h>
+#include <vector>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/filesystem.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+Alignment::Alignment(const string& filename) {
+  ifstream infile(filename.c_str());
+  string line;
+  while (getline(infile, line)) {
+    vector<string> items;
+    boost::split(items, line, boost::is_any_of(" -"));
+    vector<pair<int, int> > alignment;
+    alignment.reserve(items.size() / 2);
+    for (size_t i = 0; i < items.size(); i += 2) {
+      alignment.push_back(make_pair(stoi(items[i]), stoi(items[i + 1])));
+    }
+    alignments.push_back(alignment);
+  }
+  alignments.shrink_to_fit();
+}
+
+Alignment::Alignment() {}
+
+Alignment::~Alignment() {}
+
+vector<pair<int, int> > Alignment::GetLinks(int sentence_index) const {
+  return alignments[sentence_index];
+}
+
+void Alignment::WriteBinary(const fs::path& filepath) {
+  FILE* file = fopen(filepath.string().c_str(), "w");
+  int size = alignments.size();
+  fwrite(&size, sizeof(int), 1, file);
+  for (vector<pair<int, int> > alignment: alignments) {
+    size = alignment.size();
+    fwrite(&size, sizeof(int), 1, file);
+    fwrite(alignment.data(), sizeof(pair<int, int>), size, file);
+  }
+}
+
+} // namespace extractor
diff --git a/extractor/alignment.h b/extractor/alignment.h
new file mode 100644
index 00000000..e9292121
--- /dev/null
+++ b/extractor/alignment.h
@@ -0,0 +1,39 @@
+#ifndef _ALIGNMENT_H_
+#define _ALIGNMENT_H_
+
+#include <string>
+#include <vector>
+
+#include <boost/filesystem.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Data structure storing the word alignments for a parallel corpus.
+ */
+class Alignment {
+ public:
+  // Reads alignment from text file.
+  Alignment(const string& filename);
+
+  // Returns the alignment for a given sentence.
+  virtual vector<pair<int, int> > GetLinks(int sentence_index) const;
+
+  // Writes alignment to file in binary format.
+  void WriteBinary(const fs::path& filepath);
+
+  virtual ~Alignment();
+
+ protected:
+  Alignment();
+
+ private:
+  vector<vector<pair<int, int> > > alignments;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/alignment_test.cc b/extractor/alignment_test.cc
new file mode 100644
index 00000000..a7defb66
--- /dev/null
+++ b/extractor/alignment_test.cc
@@ -0,0 +1,33 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include "alignment.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class AlignmentTest : public Test {
+ protected:
+  virtual void SetUp() {
+    alignment = make_shared<Alignment>("sample_alignment.txt");
+  }
+
+  shared_ptr<Alignment> alignment;
+};
+
+TEST_F(AlignmentTest, TestGetLinks) {
+  vector<pair<int, int> > expected_links = {
+    make_pair(0, 0), make_pair(1, 1), make_pair(2, 2)
+  };
+  EXPECT_EQ(expected_links, alignment->GetLinks(0));
+  expected_links = {make_pair(1, 0), make_pair(2, 1)};
+  EXPECT_EQ(expected_links, alignment->GetLinks(1));
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/compile.cc b/extractor/compile.cc
new file mode 100644
index 00000000..a9ae2cef
--- /dev/null
+++ b/extractor/compile.cc
@@ -0,0 +1,100 @@
+#include <iostream>
+#include <string>
+
+#include <boost/filesystem.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "alignment.h"
+#include "data_array.h"
+#include "precomputation.h"
+#include "suffix_array.h"
+#include "translation_table.h"
+
+namespace fs = boost::filesystem;
+namespace po = boost::program_options;
+using namespace std;
+using namespace extractor;
+
+int main(int argc, char** argv) {
+  po::options_description desc("Command line options");
+  desc.add_options()
+    ("help,h", "Show available options")
+    ("source,f", po::value<string>(), "Source language corpus")
+    ("target,e", po::value<string>(), "Target language corpus")
+    ("bitext,b", po::value<string>(), "Parallel text (source ||| target)")
+    ("alignment,a", po::value<string>()->required(), "Bitext word alignment")
+    ("output,o", po::value<string>()->required(), "Output path")
+    ("frequent", po::value<int>()->default_value(100),
+        "Number of precomputed frequent patterns")
+    ("super_frequent", po::value<int>()->default_value(10),
+        "Number of precomputed super frequent patterns")
+    ("max_rule_span,s", po::value<int>()->default_value(15),
+        "Maximum rule span")
+    ("max_rule_symbols,l", po::value<int>()->default_value(5),
+        "Maximum number of symbols (terminals + nontermals) in a rule")
+    ("min_gap_size,g", po::value<int>()->default_value(1), "Minimum gap size")
+    ("max_phrase_len,p", po::value<int>()->default_value(4),
+        "Maximum frequent phrase length")
+    ("min_frequency", po::value<int>()->default_value(1000),
+        "Minimum number of occurrences for a pharse to be considered frequent");
+
+  po::variables_map vm;
+  po::store(po::parse_command_line(argc, argv, desc), vm);
+
+  // Check for help argument before notify, so we don't need to pass in the
+  // required parameters.
+  if (vm.count("help")) {
+    cout << desc << endl;
+    return 0;
+  }
+
+  po::notify(vm);
+
+  if (!((vm.count("source") && vm.count("target")) || vm.count("bitext"))) {
+    cerr << "A paralel corpus is required. "
+         << "Use -f (source) with -e (target) or -b (bitext)."
+         << endl;
+    return 1;
+  }
+
+  fs::path output_dir(vm["output"].as<string>().c_str());
+  if (!fs::exists(output_dir)) {
+    fs::create_directory(output_dir);
+  }
+
+  shared_ptr<DataArray> source_data_array, target_data_array;
+  if (vm.count("bitext")) {
+    source_data_array = make_shared<DataArray>(
+        vm["bitext"].as<string>(), SOURCE);
+    target_data_array = make_shared<DataArray>(
+        vm["bitext"].as<string>(), TARGET);
+  } else {
+    source_data_array = make_shared<DataArray>(vm["source"].as<string>());
+    target_data_array = make_shared<DataArray>(vm["target"].as<string>());
+  }
+  shared_ptr<SuffixArray> source_suffix_array =
+      make_shared<SuffixArray>(source_data_array);
+  source_suffix_array->WriteBinary(output_dir / fs::path("f.bin"));
+  target_data_array->WriteBinary(output_dir / fs::path("e.bin"));
+
+  shared_ptr<Alignment> alignment =
+      make_shared<Alignment>(vm["alignment"].as<string>());
+  alignment->WriteBinary(output_dir / fs::path("a.bin"));
+
+  Precomputation precomputation(
+      source_suffix_array,
+      vm["frequent"].as<int>(),
+      vm["super_frequent"].as<int>(),
+      vm["max_rule_span"].as<int>(),
+      vm["max_rule_symbols"].as<int>(),
+      vm["min_gap_size"].as<int>(),
+      vm["max_phrase_len"].as<int>(),
+      vm["min_frequency"].as<int>());
+  precomputation.WriteBinary(output_dir / fs::path("precompute.bin"));
+
+  TranslationTable table(source_data_array, target_data_array, alignment);
+  table.WriteBinary(output_dir / fs::path("lex.bin"));
+
+  return 0;
+}
diff --git a/extractor/data_array.cc b/extractor/data_array.cc
new file mode 100644
index 00000000..203fe219
--- /dev/null
+++ b/extractor/data_array.cc
@@ -0,0 +1,161 @@
+#include "data_array.h"
+
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include <boost/filesystem.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+int DataArray::NULL_WORD = 0;
+int DataArray::END_OF_LINE = 1;
+string DataArray::NULL_WORD_STR = "__NULL__";
+string DataArray::END_OF_LINE_STR = "__END_OF_LINE__";
+
+DataArray::DataArray() {
+  InitializeDataArray();
+}
+
+DataArray::DataArray(const string& filename) {
+  InitializeDataArray();
+  ifstream infile(filename.c_str());
+  vector<string> lines;
+  string line;
+  while (getline(infile, line)) {
+    lines.push_back(line);
+  }
+  CreateDataArray(lines);
+}
+
+DataArray::DataArray(const string& filename, const Side& side) {
+  InitializeDataArray();
+  ifstream infile(filename.c_str());
+  vector<string> lines;
+  string line, delimiter = "|||";
+  while (getline(infile, line)) {
+    int position = line.find(delimiter);
+    if (side == SOURCE) {
+      lines.push_back(line.substr(0, position));
+    } else {
+      lines.push_back(line.substr(position + delimiter.size()));
+    }
+  }
+  CreateDataArray(lines);
+}
+
+void DataArray::InitializeDataArray() {
+  word2id[NULL_WORD_STR] = NULL_WORD;
+  id2word.push_back(NULL_WORD_STR);
+  word2id[END_OF_LINE_STR] = END_OF_LINE;
+  id2word.push_back(END_OF_LINE_STR);
+}
+
+void DataArray::CreateDataArray(const vector<string>& lines) {
+  for (size_t i = 0; i < lines.size(); ++i) {
+    sentence_start.push_back(data.size());
+
+    istringstream iss(lines[i]);
+    string word;
+    while (iss >> word) {
+      if (word2id.count(word) == 0) {
+        word2id[word] = id2word.size();
+        id2word.push_back(word);
+      }
+      data.push_back(word2id[word]);
+      sentence_id.push_back(i);
+    }
+    data.push_back(END_OF_LINE);
+    sentence_id.push_back(i);
+  }
+  sentence_start.push_back(data.size());
+
+  data.shrink_to_fit();
+  sentence_id.shrink_to_fit();
+  sentence_start.shrink_to_fit();
+}
+
+DataArray::~DataArray() {}
+
+const vector<int>& DataArray::GetData() const {
+  return data;
+}
+
+int DataArray::AtIndex(int index) const {
+  return data[index];
+}
+
+string DataArray::GetWordAtIndex(int index) const {
+  return id2word[data[index]];
+}
+
+int DataArray::GetSize() const {
+  return data.size();
+}
+
+int DataArray::GetVocabularySize() const {
+  return id2word.size();
+}
+
+int DataArray::GetNumSentences() const {
+  return sentence_start.size() - 1;
+}
+
+int DataArray::GetSentenceStart(int position) const {
+  return sentence_start[position];
+}
+
+int DataArray::GetSentenceLength(int sentence_id) const {
+  // Ignore end of line markers.
+  return sentence_start[sentence_id + 1] - sentence_start[sentence_id] - 1;
+}
+
+int DataArray::GetSentenceId(int position) const {
+  return sentence_id[position];
+}
+
+void DataArray::WriteBinary(const fs::path& filepath) const {
+  std::cerr << "File: " << filepath.string() << std::endl;
+  WriteBinary(fopen(filepath.string().c_str(), "w"));
+}
+
+void DataArray::WriteBinary(FILE* file) const {
+  int size = id2word.size();
+  fwrite(&size, sizeof(int), 1, file);
+  for (string word: id2word) {
+    size = word.size();
+    fwrite(&size, sizeof(int), 1, file);
+    fwrite(word.data(), sizeof(char), size, file);
+  }
+
+  size = data.size();
+  fwrite(&size, sizeof(int), 1, file);
+  fwrite(data.data(), sizeof(int), size, file);
+
+  size = sentence_id.size();
+  fwrite(&size, sizeof(int), 1, file);
+  fwrite(sentence_id.data(), sizeof(int), size, file);
+
+  size = sentence_start.size();
+  fwrite(&size, sizeof(int), 1, file);
+  fwrite(sentence_start.data(), sizeof(int), 1, file);
+}
+
+bool DataArray::HasWord(const string& word) const {
+  return word2id.count(word);
+}
+
+int DataArray::GetWordId(const string& word) const {
+  auto result = word2id.find(word);
+  return result == word2id.end() ? -1 : result->second;
+}
+
+string DataArray::GetWord(int word_id) const {
+  return id2word[word_id];
+}
+
+} // namespace extractor
diff --git a/extractor/data_array.h b/extractor/data_array.h
new file mode 100644
index 00000000..978a6931
--- /dev/null
+++ b/extractor/data_array.h
@@ -0,0 +1,110 @@
+#ifndef _DATA_ARRAY_H_
+#define _DATA_ARRAY_H_
+
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+#include <boost/filesystem.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+enum Side {
+  SOURCE,
+  TARGET
+};
+
+/**
+ * Data structure storing information about a single side of a parallel corpus.
+ *
+ * Each word is mapped to a unique integer (word_id). The data structure holds
+ * the corpus in the numberized format, together with the hash table mapping
+ * words to word_ids. It also holds additional information such as the starting
+ * index for each sentence and, for each token, the index of the sentence it
+ * belongs to.
+ *
+ * Note: This class has features for both the source and target data arrays.
+ * Maybe we can save some memory by having more specific implementations (not
+ * likely to save a lot of memory tough).
+ */
+class DataArray {
+ public:
+  static int NULL_WORD;
+  static int END_OF_LINE;
+  static string NULL_WORD_STR;
+  static string END_OF_LINE_STR;
+
+  // Reads data array from text file.
+  DataArray(const string& filename);
+
+  // Reads data array from bitext file where the sentences are separated by |||.
+  DataArray(const string& filename, const Side& side);
+
+  virtual ~DataArray();
+
+  // Returns a vector containing the word ids.
+  virtual const vector<int>& GetData() const;
+
+  // Returns the word id at the specified position.
+  virtual int AtIndex(int index) const;
+
+  // Returns the original word at the specified position.
+  virtual string GetWordAtIndex(int index) const;
+
+  // Returns the size of the data array.
+  virtual int GetSize() const;
+
+  // Returns the number of distinct words in the data array.
+  virtual int GetVocabularySize() const;
+
+  // Returns whether a word has ever been observed in the data array.
+  virtual bool HasWord(const string& word) const;
+
+  // Returns the word id for a given word or -1 if it the word has never been
+  // observed.
+  virtual int GetWordId(const string& word) const;
+
+  // Returns the word corresponding to a particular word id.
+  virtual string GetWord(int word_id) const;
+
+  // Returns the number of sentences in the data.
+  virtual int GetNumSentences() const;
+
+  // Returns the index where the sentence containing the given position starts.
+  virtual int GetSentenceStart(int position) const;
+
+  // Returns the length of the sentence.
+  virtual int GetSentenceLength(int sentence_id) const;
+
+  // Returns the number of the sentence containing the given position.
+  virtual int GetSentenceId(int position) const;
+
+  // Writes data array to file in binary format.
+  void WriteBinary(const fs::path& filepath) const;
+
+  // Writes data array to file in binary format.
+  void WriteBinary(FILE* file) const;
+
+ protected:
+  DataArray();
+
+ private:
+  // Sets up specific constants.
+  void InitializeDataArray();
+
+  // Constructs the data array.
+  void CreateDataArray(const vector<string>& lines);
+
+  unordered_map<string, int> word2id;
+  vector<string> id2word;
+  vector<int> data;
+  vector<int> sentence_id;
+  vector<int> sentence_start;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/data_array_test.cc b/extractor/data_array_test.cc
new file mode 100644
index 00000000..71175fda
--- /dev/null
+++ b/extractor/data_array_test.cc
@@ -0,0 +1,98 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include <boost/filesystem.hpp>
+
+#include "data_array.h"
+
+using namespace std;
+using namespace ::testing;
+namespace fs = boost::filesystem;
+
+namespace extractor {
+namespace {
+
+class DataArrayTest : public Test {
+ protected:
+  virtual void SetUp() {
+    string sample_test_file("sample_bitext.txt");
+    source_data = make_shared<DataArray>(sample_test_file, SOURCE);
+    target_data = make_shared<DataArray>(sample_test_file, TARGET);
+  }
+
+  shared_ptr<DataArray> source_data;
+  shared_ptr<DataArray> target_data;
+};
+
+TEST_F(DataArrayTest, TestGetData) {
+  vector<int> expected_source_data = {2, 3, 4, 5, 1, 2, 6, 7, 8, 5, 1};
+  vector<string> expected_source_words = {
+      "ana", "are", "mere", ".", "__END_OF_LINE__",
+      "ana", "bea", "mult", "lapte", ".", "__END_OF_LINE__"
+  };
+  EXPECT_EQ(expected_source_data, source_data->GetData());
+  EXPECT_EQ(expected_source_data.size(), source_data->GetSize());
+  for (size_t i = 0; i < expected_source_data.size(); ++i) {
+    EXPECT_EQ(expected_source_data[i], source_data->AtIndex(i));
+    EXPECT_EQ(expected_source_words[i], source_data->GetWordAtIndex(i));
+  }
+
+  vector<int> expected_target_data = {2, 3, 4, 5, 1, 2, 6, 7, 8, 9, 10, 5, 1};
+  vector<string> expected_target_words = {
+      "anna", "has", "apples", ".", "__END_OF_LINE__",
+      "anna", "drinks", "a", "lot", "of", "milk", ".", "__END_OF_LINE__"
+  };
+  EXPECT_EQ(expected_target_data, target_data->GetData());
+  EXPECT_EQ(expected_target_data.size(), target_data->GetSize());
+  for (size_t i = 0; i < expected_target_data.size(); ++i) {
+    EXPECT_EQ(expected_target_data[i], target_data->AtIndex(i));
+    EXPECT_EQ(expected_target_words[i], target_data->GetWordAtIndex(i));
+  }
+}
+
+TEST_F(DataArrayTest, TestVocabulary) {
+  EXPECT_EQ(9, source_data->GetVocabularySize());
+  EXPECT_TRUE(source_data->HasWord("mere"));
+  EXPECT_EQ(4, source_data->GetWordId("mere"));
+  EXPECT_EQ("mere", source_data->GetWord(4));
+  EXPECT_FALSE(source_data->HasWord("banane"));
+
+  EXPECT_EQ(11, target_data->GetVocabularySize());
+  EXPECT_TRUE(target_data->HasWord("apples"));
+  EXPECT_EQ(4, target_data->GetWordId("apples"));
+  EXPECT_EQ("apples", target_data->GetWord(4));
+  EXPECT_FALSE(target_data->HasWord("bananas"));
+}
+
+TEST_F(DataArrayTest, TestSentenceData) {
+  EXPECT_EQ(2, source_data->GetNumSentences());
+  EXPECT_EQ(0, source_data->GetSentenceStart(0));
+  EXPECT_EQ(5, source_data->GetSentenceStart(1));
+  EXPECT_EQ(11, source_data->GetSentenceStart(2));
+
+  EXPECT_EQ(4, source_data->GetSentenceLength(0));
+  EXPECT_EQ(5, source_data->GetSentenceLength(1));
+
+  vector<int> expected_source_ids = {0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1};
+  for (size_t i = 0; i < expected_source_ids.size(); ++i) {
+    EXPECT_EQ(expected_source_ids[i], source_data->GetSentenceId(i));
+  }
+
+  EXPECT_EQ(2, target_data->GetNumSentences());
+  EXPECT_EQ(0, target_data->GetSentenceStart(0));
+  EXPECT_EQ(5, target_data->GetSentenceStart(1));
+  EXPECT_EQ(13, target_data->GetSentenceStart(2));
+
+  EXPECT_EQ(4, target_data->GetSentenceLength(0));
+  EXPECT_EQ(7, target_data->GetSentenceLength(1));
+
+  vector<int> expected_target_ids = {0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1};
+  for (size_t i = 0; i < expected_target_ids.size(); ++i) {
+    EXPECT_EQ(expected_target_ids[i], target_data->GetSentenceId(i));
+  }
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/fast_intersector.cc b/extractor/fast_intersector.cc
new file mode 100644
index 00000000..2a7693b2
--- /dev/null
+++ b/extractor/fast_intersector.cc
@@ -0,0 +1,195 @@
+#include "fast_intersector.h"
+
+#include <cassert>
+
+#include "data_array.h"
+#include "phrase.h"
+#include "phrase_location.h"
+#include "precomputation.h"
+#include "suffix_array.h"
+#include "vocabulary.h"
+
+namespace extractor {
+
+FastIntersector::FastIntersector(shared_ptr<SuffixArray> suffix_array,
+                                 shared_ptr<Precomputation> precomputation,
+                                 shared_ptr<Vocabulary> vocabulary,
+                                 int max_rule_span,
+                                 int min_gap_size) :
+    suffix_array(suffix_array),
+    vocabulary(vocabulary),
+    max_rule_span(max_rule_span),
+    min_gap_size(min_gap_size) {
+  Index precomputed_collocations = precomputation->GetCollocations();
+  for (pair<vector<int>, vector<int> > entry: precomputed_collocations) {
+    vector<int> phrase = ConvertPhrase(entry.first);
+    collocations[phrase] = entry.second;
+  }
+}
+
+FastIntersector::FastIntersector() {}
+
+FastIntersector::~FastIntersector() {}
+
+vector<int> FastIntersector::ConvertPhrase(const vector<int>& old_phrase) {
+  vector<int> new_phrase;
+  new_phrase.reserve(old_phrase.size());
+  shared_ptr<DataArray> data_array = suffix_array->GetData();
+  for (int word_id: old_phrase) {
+    if (word_id < 0) {
+      new_phrase.push_back(word_id);
+    } else {
+      new_phrase.push_back(
+          vocabulary->GetTerminalIndex(data_array->GetWord(word_id)));
+    }
+  }
+  return new_phrase;
+}
+
+PhraseLocation FastIntersector::Intersect(
+    PhraseLocation& prefix_location,
+    PhraseLocation& suffix_location,
+    const Phrase& phrase) {
+  vector<int> symbols = phrase.Get();
+
+  // We should never attempt to do an intersect query for a pattern starting or
+  // ending with a non terminal. The RuleFactory should handle these cases,
+  // initializing the matchings list with the one for the pattern without the
+  // starting or ending terminal.
+  assert(vocabulary->IsTerminal(symbols.front())
+      && vocabulary->IsTerminal(symbols.back()));
+
+  if (collocations.count(symbols)) {
+    return PhraseLocation(collocations[symbols], phrase.Arity() + 1);
+  }
+
+  bool prefix_ends_with_x =
+      !vocabulary->IsTerminal(symbols[symbols.size() - 2]);
+  bool suffix_starts_with_x = !vocabulary->IsTerminal(symbols[1]);
+  if (EstimateNumOperations(prefix_location, prefix_ends_with_x) <=
+      EstimateNumOperations(suffix_location, suffix_starts_with_x)) {
+    return ExtendPrefixPhraseLocation(prefix_location, phrase,
+                                      prefix_ends_with_x, symbols.back());
+  } else {
+    return ExtendSuffixPhraseLocation(suffix_location, phrase,
+                                      suffix_starts_with_x, symbols.front());
+  }
+}
+
+int FastIntersector::EstimateNumOperations(
+    const PhraseLocation& phrase_location, bool has_margin_x) const {
+  int num_locations = phrase_location.GetSize();
+  return has_margin_x ? num_locations * max_rule_span : num_locations;
+}
+
+PhraseLocation FastIntersector::ExtendPrefixPhraseLocation(
+    PhraseLocation& prefix_location, const Phrase& phrase,
+    bool prefix_ends_with_x, int next_symbol) const {
+  ExtendPhraseLocation(prefix_location);
+  vector<int> positions = *prefix_location.matchings;
+  int num_subpatterns = prefix_location.num_subpatterns;
+
+  vector<int> new_positions;
+  shared_ptr<DataArray> data_array = suffix_array->GetData();
+  int data_array_symbol = data_array->GetWordId(
+      vocabulary->GetTerminalValue(next_symbol));
+  if (data_array_symbol == -1) {
+    return PhraseLocation(new_positions, num_subpatterns);
+  }
+
+  pair<int, int> range = GetSearchRange(prefix_ends_with_x);
+  for (size_t i = 0; i < positions.size(); i += num_subpatterns) {
+    int sent_id = data_array->GetSentenceId(positions[i]);
+    int sent_end = data_array->GetSentenceStart(sent_id + 1) - 1;
+    int pattern_end = positions[i + num_subpatterns - 1] + range.first;
+    if (prefix_ends_with_x) {
+      pattern_end += phrase.GetChunkLen(phrase.Arity() - 1) - 1;
+    } else {
+      pattern_end += phrase.GetChunkLen(phrase.Arity()) - 2;
+    }
+    // Searches for the last symbol in the phrase after each prefix occurrence.
+    for (int j = range.first; j < range.second; ++j) {
+      if (pattern_end >= sent_end ||
+          pattern_end - positions[i] >= max_rule_span) {
+        break;
+      }
+
+      if (data_array->AtIndex(pattern_end) == data_array_symbol) {
+        new_positions.insert(new_positions.end(), positions.begin() + i,
+                             positions.begin() + i + num_subpatterns);
+        if (prefix_ends_with_x) {
+          new_positions.push_back(pattern_end);
+        }
+      }
+      ++pattern_end;
+    }
+  }
+
+  return PhraseLocation(new_positions, phrase.Arity() + 1);
+}
+
+PhraseLocation FastIntersector::ExtendSuffixPhraseLocation(
+    PhraseLocation& suffix_location, const Phrase& phrase,
+    bool suffix_starts_with_x, int prev_symbol) const {
+  ExtendPhraseLocation(suffix_location);
+  vector<int> positions = *suffix_location.matchings;
+  int num_subpatterns = suffix_location.num_subpatterns;
+
+  vector<int> new_positions;
+  shared_ptr<DataArray> data_array = suffix_array->GetData();
+  int data_array_symbol = data_array->GetWordId(
+      vocabulary->GetTerminalValue(prev_symbol));
+  if (data_array_symbol == -1) {
+    return PhraseLocation(new_positions, num_subpatterns);
+  }
+
+  pair<int, int> range = GetSearchRange(suffix_starts_with_x);
+  for (size_t i = 0; i < positions.size(); i += num_subpatterns) {
+    int sent_id = data_array->GetSentenceId(positions[i]);
+    int sent_start = data_array->GetSentenceStart(sent_id);
+    int pattern_start = positions[i] - range.first;
+    int pattern_end = positions[i + num_subpatterns - 1] +
+        phrase.GetChunkLen(phrase.Arity()) - 1;
+    // Searches for the first symbol in the phrase before each suffix
+    // occurrence.
+    for (int j = range.first; j < range.second; ++j) {
+      if (pattern_start < sent_start ||
+          pattern_end - pattern_start >= max_rule_span) {
+        break;
+      }
+
+      if (data_array->AtIndex(pattern_start) == data_array_symbol) {
+        new_positions.push_back(pattern_start);
+        new_positions.insert(new_positions.end(),
+                             positions.begin() + i + !suffix_starts_with_x,
+                             positions.begin() + i + num_subpatterns);
+      }
+      --pattern_start;
+    }
+  }
+
+  return PhraseLocation(new_positions, phrase.Arity() + 1);
+}
+
+void FastIntersector::ExtendPhraseLocation(PhraseLocation& location) const {
+  if (location.matchings != NULL) {
+    return;
+  }
+
+  location.num_subpatterns = 1;
+  location.matchings = make_shared<vector<int> >();
+  for (int i = location.sa_low; i < location.sa_high; ++i) {
+    location.matchings->push_back(suffix_array->GetSuffix(i));
+  }
+  location.sa_low = location.sa_high = 0;
+}
+
+pair<int, int> FastIntersector::GetSearchRange(bool has_marginal_x) const {
+  if (has_marginal_x) {
+    return make_pair(min_gap_size + 1, max_rule_span);
+  } else {
+    return make_pair(1, 2);
+  }
+}
+
+} // namespace extractor
diff --git a/extractor/fast_intersector.h b/extractor/fast_intersector.h
new file mode 100644
index 00000000..f950a2a9
--- /dev/null
+++ b/extractor/fast_intersector.h
@@ -0,0 +1,96 @@
+#ifndef _FAST_INTERSECTOR_H_
+#define _FAST_INTERSECTOR_H_
+
+#include <memory>
+#include <unordered_map>
+#include <vector>
+
+#include <boost/functional/hash.hpp>
+
+using namespace std;
+
+namespace extractor {
+
+typedef boost::hash<vector<int> > VectorHash;
+typedef unordered_map<vector<int>, vector<int>, VectorHash> Index;
+
+class Phrase;
+class PhraseLocation;
+class Precomputation;
+class SuffixArray;
+class Vocabulary;
+
+/**
+ * Component for searching the training data for occurrences of source phrases
+ * containing nonterminals
+ *
+ * Given a source phrase containing a nonterminal, we first query the
+ * precomputed index containing frequent collocations. If the phrase is not
+ * frequent enough, we extend the matchings of either its prefix or its suffix,
+ * depending on which operation seems to require less computations.
+ *
+ * Note: This method for intersecting phrase locations is faster than both
+ * mergers (linear or Baeza Yates) described in Adam Lopez' dissertation.
+ */
+class FastIntersector {
+ public:
+  FastIntersector(shared_ptr<SuffixArray> suffix_array,
+                  shared_ptr<Precomputation> precomputation,
+                  shared_ptr<Vocabulary> vocabulary,
+                  int max_rule_span,
+                  int min_gap_size);
+
+  virtual ~FastIntersector();
+
+  // Finds the locations of a phrase given the locations of its prefix and
+  // suffix.
+  virtual PhraseLocation Intersect(PhraseLocation& prefix_location,
+                                   PhraseLocation& suffix_location,
+                                   const Phrase& phrase);
+
+ protected:
+  FastIntersector();
+
+ private:
+  // Uses the vocabulary to convert the phrase from the numberized format
+  // specified by the source data array to the numberized format given by the
+  // vocabulary.
+  vector<int> ConvertPhrase(const vector<int>& old_phrase);
+
+  // Estimates the number of computations needed if the prefix/suffix is
+  // extended. If the last/first symbol is separated from the rest of the phrase
+  // by a nonterminal, then for each occurrence of the prefix/suffix we need to
+  // check max_rule_span positions. Otherwise, we only need to check a single
+  // position for each occurrence.
+  int EstimateNumOperations(const PhraseLocation& phrase_location,
+                            bool has_margin_x) const;
+
+  // Uses the occurrences of the prefix to find the occurrences of the phrase.
+  PhraseLocation ExtendPrefixPhraseLocation(PhraseLocation& prefix_location,
+                                            const Phrase& phrase,
+                                            bool prefix_ends_with_x,
+                                            int next_symbol) const;
+
+  // Uses the occurrences of the suffix to find the occurrences of the phrase.
+  PhraseLocation ExtendSuffixPhraseLocation(PhraseLocation& suffix_location,
+                                            const Phrase& phrase,
+                                            bool suffix_starts_with_x,
+                                            int prev_symbol) const;
+
+  // Extends the prefix/suffix location to a list of subpatterns positions if it
+  // represents a suffix array range.
+  void ExtendPhraseLocation(PhraseLocation& location) const;
+
+  // Returns the range in which the search should be performed.
+  pair<int, int> GetSearchRange(bool has_marginal_x) const;
+
+  shared_ptr<SuffixArray> suffix_array;
+  shared_ptr<Vocabulary> vocabulary;
+  int max_rule_span;
+  int min_gap_size;
+  Index collocations;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/fast_intersector_test.cc b/extractor/fast_intersector_test.cc
new file mode 100644
index 00000000..76c3aaea
--- /dev/null
+++ b/extractor/fast_intersector_test.cc
@@ -0,0 +1,146 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "fast_intersector.h"
+#include "mocks/mock_data_array.h"
+#include "mocks/mock_precomputation.h"
+#include "mocks/mock_suffix_array.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase.h"
+#include "phrase_location.h"
+#include "phrase_builder.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class FastIntersectorTest : public Test {
+ protected:
+  virtual void SetUp() {
+    vector<string> words = {"EOL", "it", "makes", "him", "and", "mars", ",",
+                            "sets", "on", "takes", "off", "."};
+    vocabulary = make_shared<MockVocabulary>();
+    for (size_t i = 0; i < words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalIndex(words[i]))
+          .WillRepeatedly(Return(i));
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i))
+          .WillRepeatedly(Return(words[i]));
+    }
+
+    vector<int> data = {1, 2, 3, 4, 1, 5, 3, 6, 1,
+                        7, 3, 8, 4, 1, 9, 3, 10, 11, 0};
+    data_array = make_shared<MockDataArray>();
+    for (size_t i = 0; i < data.size(); ++i) {
+      EXPECT_CALL(*data_array, AtIndex(i)).WillRepeatedly(Return(data[i]));
+      EXPECT_CALL(*data_array, GetSentenceId(i))
+          .WillRepeatedly(Return(0));
+    }
+    EXPECT_CALL(*data_array, GetSentenceStart(0))
+        .WillRepeatedly(Return(0));
+    EXPECT_CALL(*data_array, GetSentenceStart(1))
+        .WillRepeatedly(Return(19));
+    for (size_t i = 0; i < words.size(); ++i) {
+      EXPECT_CALL(*data_array, GetWordId(words[i]))
+          .WillRepeatedly(Return(i));
+      EXPECT_CALL(*data_array, GetWord(i))
+          .WillRepeatedly(Return(words[i]));
+    }
+
+    vector<int> suffixes = {18, 0, 4, 8, 13, 1, 2, 6, 10, 15, 3, 12, 5, 7, 9,
+                            11, 14, 16, 17};
+    suffix_array = make_shared<MockSuffixArray>();
+    EXPECT_CALL(*suffix_array, GetData()).WillRepeatedly(Return(data_array));
+    for (size_t i = 0; i < suffixes.size(); ++i) {
+      EXPECT_CALL(*suffix_array, GetSuffix(i)).
+          WillRepeatedly(Return(suffixes[i]));
+    }
+
+    precomputation = make_shared<MockPrecomputation>();
+    EXPECT_CALL(*precomputation, GetCollocations())
+        .WillRepeatedly(ReturnRef(collocations));
+
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+    intersector = make_shared<FastIntersector>(suffix_array, precomputation,
+                                               vocabulary, 15, 1);
+  }
+
+  Index collocations;
+  shared_ptr<MockDataArray> data_array;
+  shared_ptr<MockSuffixArray> suffix_array;
+  shared_ptr<MockPrecomputation> precomputation;
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<FastIntersector> intersector;
+  shared_ptr<PhraseBuilder> phrase_builder;
+};
+
+TEST_F(FastIntersectorTest, TestCachedCollocation) {
+  vector<int> symbols = {8, -1, 9};
+  vector<int> expected_location = {11};
+  Phrase phrase = phrase_builder->Build(symbols);
+  PhraseLocation prefix_location(15, 16), suffix_location(16, 17);
+
+  collocations[symbols] = expected_location;
+  EXPECT_CALL(*precomputation, GetCollocations())
+      .WillRepeatedly(ReturnRef(collocations));
+  intersector = make_shared<FastIntersector>(suffix_array, precomputation,
+                                             vocabulary, 15, 1);
+
+  PhraseLocation result = intersector->Intersect(
+      prefix_location, suffix_location, phrase);
+
+  EXPECT_EQ(PhraseLocation(expected_location, 2), result);
+  EXPECT_EQ(PhraseLocation(15, 16), prefix_location);
+  EXPECT_EQ(PhraseLocation(16, 17), suffix_location);
+}
+
+TEST_F(FastIntersectorTest, TestIntersectaXbXcExtendSuffix) {
+  vector<int> symbols = {1, -1, 3, -1, 1};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> prefix_locs = {0, 2, 0, 6, 0, 10, 4, 6, 4, 10, 4, 15, 8, 10,
+                             8, 15, 3, 15};
+  vector<int> suffix_locs = {2, 4, 2, 8, 2, 13, 6, 8, 6, 13, 10, 13};
+  PhraseLocation prefix_location(prefix_locs, 2);
+  PhraseLocation suffix_location(suffix_locs, 2);
+
+  vector<int> expected_locs = {0, 2, 4, 0, 2, 8, 0, 2, 13, 4, 6, 8, 0, 6, 8,
+                               4, 6, 13, 0, 6, 13, 8, 10, 13, 4, 10, 13,
+                               0, 10, 13};
+  PhraseLocation result = intersector->Intersect(
+      prefix_location, suffix_location, phrase);
+  EXPECT_EQ(PhraseLocation(expected_locs, 3), result);
+}
+
+TEST_F(FastIntersectorTest, TestIntersectaXbExtendPrefix) {
+  vector<int> symbols = {1, -1, 3};
+  Phrase phrase = phrase_builder->Build(symbols);
+  PhraseLocation prefix_location(1, 5), suffix_location(6, 10);
+
+  vector<int> expected_prefix_locs = {0, 4, 8, 13};
+  vector<int> expected_locs = {0, 2, 0, 6, 0, 10, 4, 6, 4, 10, 4, 15, 8, 10,
+                               8, 15, 13, 15};
+  PhraseLocation result = intersector->Intersect(
+      prefix_location, suffix_location, phrase);
+  EXPECT_EQ(PhraseLocation(expected_locs, 2), result);
+  EXPECT_EQ(PhraseLocation(expected_prefix_locs, 1), prefix_location);
+}
+
+TEST_F(FastIntersectorTest, TestIntersectCheckEstimates) {
+  // The suffix matches in fewer positions, but because it starts with an X
+  // it requires more operations and we prefer extending the prefix.
+  vector<int> symbols = {1, -1, 4, 1};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> prefix_locs = {0, 3, 0, 12, 4, 12, 8, 12};
+  PhraseLocation prefix_location(prefix_locs, 2), suffix_location(10, 12);
+
+  vector<int> expected_locs = {0, 3, 0, 12, 4, 12, 8, 12};
+  PhraseLocation result = intersector->Intersect(
+      prefix_location, suffix_location, phrase);
+  EXPECT_EQ(PhraseLocation(expected_locs, 2), result);
+  EXPECT_EQ(PhraseLocation(10, 12), suffix_location);
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/features/count_source_target.cc b/extractor/features/count_source_target.cc
new file mode 100644
index 00000000..db0385e0
--- /dev/null
+++ b/extractor/features/count_source_target.cc
@@ -0,0 +1,17 @@
+#include "count_source_target.h"
+
+#include <cmath>
+
+namespace extractor {
+namespace features {
+
+double CountSourceTarget::Score(const FeatureContext& context) const {
+  return log10(1 + context.pair_count);
+}
+
+string CountSourceTarget::GetName() const {
+  return "CountEF";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/count_source_target.h b/extractor/features/count_source_target.h
new file mode 100644
index 00000000..8747fa60
--- /dev/null
+++ b/extractor/features/count_source_target.h
@@ -0,0 +1,22 @@
+#ifndef _COUNT_SOURCE_TARGET_H_
+#define _COUNT_SOURCE_TARGET_H_
+
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+/**
+ * Feature for the number of times a word pair was found in the bitext.
+ */
+class CountSourceTarget : public Feature {
+ public:
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/count_source_target_test.cc b/extractor/features/count_source_target_test.cc
new file mode 100644
index 00000000..1fd0c2aa
--- /dev/null
+++ b/extractor/features/count_source_target_test.cc
@@ -0,0 +1,36 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include "count_source_target.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class CountSourceTargetTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature = make_shared<CountSourceTarget>();
+  }
+
+  shared_ptr<CountSourceTarget> feature;
+};
+
+TEST_F(CountSourceTargetTest, TestGetName) {
+  EXPECT_EQ("CountEF", feature->GetName());
+}
+
+TEST_F(CountSourceTargetTest, TestScore) {
+  Phrase phrase;
+  FeatureContext context(phrase, phrase, 0.5, 9, 13);
+  EXPECT_EQ(1.0, feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/feature.cc b/extractor/features/feature.cc
new file mode 100644
index 00000000..939bcc59
--- /dev/null
+++ b/extractor/features/feature.cc
@@ -0,0 +1,11 @@
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+const double Feature::MAX_SCORE = 99.0;
+
+Feature::~Feature() {}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/feature.h b/extractor/features/feature.h
new file mode 100644
index 00000000..36ea504a
--- /dev/null
+++ b/extractor/features/feature.h
@@ -0,0 +1,47 @@
+#ifndef _FEATURE_H_
+#define _FEATURE_H_
+
+#include <string>
+
+#include "phrase.h"
+
+using namespace std;
+
+namespace extractor {
+namespace features {
+
+/**
+ * Structure providing context for computing feature scores.
+ */
+struct FeatureContext {
+  FeatureContext(const Phrase& source_phrase, const Phrase& target_phrase,
+                 double source_phrase_count, int pair_count, int num_samples) :
+    source_phrase(source_phrase), target_phrase(target_phrase),
+    source_phrase_count(source_phrase_count), pair_count(pair_count),
+    num_samples(num_samples) {}
+
+  Phrase source_phrase;
+  Phrase target_phrase;
+  double source_phrase_count;
+  int pair_count;
+  int num_samples;
+};
+
+/**
+ * Base class for features.
+ */
+class Feature {
+ public:
+  virtual double Score(const FeatureContext& context) const = 0;
+
+  virtual string GetName() const = 0;
+
+  virtual ~Feature();
+
+  static const double MAX_SCORE;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/is_source_singleton.cc b/extractor/features/is_source_singleton.cc
new file mode 100644
index 00000000..1abb486f
--- /dev/null
+++ b/extractor/features/is_source_singleton.cc
@@ -0,0 +1,17 @@
+#include "is_source_singleton.h"
+
+#include <cmath>
+
+namespace extractor {
+namespace features {
+
+double IsSourceSingleton::Score(const FeatureContext& context) const {
+  return fabs(context.source_phrase_count - 1) < 1e-6;
+}
+
+string IsSourceSingleton::GetName() const {
+  return "IsSingletonF";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/is_source_singleton.h b/extractor/features/is_source_singleton.h
new file mode 100644
index 00000000..b8352d0e
--- /dev/null
+++ b/extractor/features/is_source_singleton.h
@@ -0,0 +1,22 @@
+#ifndef _IS_SOURCE_SINGLETON_H_
+#define _IS_SOURCE_SINGLETON_H_
+
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+/**
+ * Boolean feature checking if the source phrase occurs only once in the data.
+ */
+class IsSourceSingleton : public Feature {
+ public:
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/is_source_singleton_test.cc b/extractor/features/is_source_singleton_test.cc
new file mode 100644
index 00000000..f4266671
--- /dev/null
+++ b/extractor/features/is_source_singleton_test.cc
@@ -0,0 +1,39 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include "is_source_singleton.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class IsSourceSingletonTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature = make_shared<IsSourceSingleton>();
+  }
+
+  shared_ptr<IsSourceSingleton> feature;
+};
+
+TEST_F(IsSourceSingletonTest, TestGetName) {
+  EXPECT_EQ("IsSingletonF", feature->GetName());
+}
+
+TEST_F(IsSourceSingletonTest, TestScore) {
+  Phrase phrase;
+  FeatureContext context(phrase, phrase, 0.5, 3, 31);
+  EXPECT_EQ(0, feature->Score(context));
+
+  context = FeatureContext(phrase, phrase, 1, 3, 25);
+  EXPECT_EQ(1, feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/is_source_target_singleton.cc b/extractor/features/is_source_target_singleton.cc
new file mode 100644
index 00000000..03b3c62c
--- /dev/null
+++ b/extractor/features/is_source_target_singleton.cc
@@ -0,0 +1,17 @@
+#include "is_source_target_singleton.h"
+
+#include <cmath>
+
+namespace extractor {
+namespace features {
+
+double IsSourceTargetSingleton::Score(const FeatureContext& context) const {
+  return context.pair_count == 1;
+}
+
+string IsSourceTargetSingleton::GetName() const {
+  return "IsSingletonFE";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/is_source_target_singleton.h b/extractor/features/is_source_target_singleton.h
new file mode 100644
index 00000000..dacfebba
--- /dev/null
+++ b/extractor/features/is_source_target_singleton.h
@@ -0,0 +1,22 @@
+#ifndef _IS_SOURCE_TARGET_SINGLETON_H_
+#define _IS_SOURCE_TARGET_SINGLETON_H_
+
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+/**
+ * Boolean feature checking if the phrase pair occurs only once in the data.
+ */
+class IsSourceTargetSingleton : public Feature {
+ public:
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/is_source_target_singleton_test.cc b/extractor/features/is_source_target_singleton_test.cc
new file mode 100644
index 00000000..929635b0
--- /dev/null
+++ b/extractor/features/is_source_target_singleton_test.cc
@@ -0,0 +1,39 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include "is_source_target_singleton.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class IsSourceTargetSingletonTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature = make_shared<IsSourceTargetSingleton>();
+  }
+
+  shared_ptr<IsSourceTargetSingleton> feature;
+};
+
+TEST_F(IsSourceTargetSingletonTest, TestGetName) {
+  EXPECT_EQ("IsSingletonFE", feature->GetName());
+}
+
+TEST_F(IsSourceTargetSingletonTest, TestScore) {
+  Phrase phrase;
+  FeatureContext context(phrase, phrase, 0.5, 3, 7);
+  EXPECT_EQ(0, feature->Score(context));
+
+  context = FeatureContext(phrase, phrase, 2.3, 1, 28);
+  EXPECT_EQ(1, feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/max_lex_source_given_target.cc b/extractor/features/max_lex_source_given_target.cc
new file mode 100644
index 00000000..65d0ec68
--- /dev/null
+++ b/extractor/features/max_lex_source_given_target.cc
@@ -0,0 +1,37 @@
+#include "max_lex_source_given_target.h"
+
+#include <cmath>
+
+#include "data_array.h"
+#include "translation_table.h"
+
+namespace extractor {
+namespace features {
+
+MaxLexSourceGivenTarget::MaxLexSourceGivenTarget(
+    shared_ptr<TranslationTable> table) :
+    table(table) {}
+
+double MaxLexSourceGivenTarget::Score(const FeatureContext& context) const {
+  vector<string> source_words = context.source_phrase.GetWords();
+  vector<string> target_words = context.target_phrase.GetWords();
+  target_words.push_back(DataArray::NULL_WORD_STR);
+
+  double score = 0;
+  for (string source_word: source_words) {
+    double max_score = 0;
+    for (string target_word: target_words) {
+      max_score = max(max_score,
+          table->GetSourceGivenTargetScore(source_word, target_word));
+    }
+    score += max_score > 0 ? -log10(max_score) : MAX_SCORE;
+  }
+  return score;
+}
+
+string MaxLexSourceGivenTarget::GetName() const {
+  return "MaxLexFgivenE";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/max_lex_source_given_target.h b/extractor/features/max_lex_source_given_target.h
new file mode 100644
index 00000000..461b0ebf
--- /dev/null
+++ b/extractor/features/max_lex_source_given_target.h
@@ -0,0 +1,34 @@
+#ifndef _MAX_LEX_SOURCE_GIVEN_TARGET_H_
+#define _MAX_LEX_SOURCE_GIVEN_TARGET_H_
+
+#include <memory>
+
+#include "feature.h"
+
+using namespace std;
+
+namespace extractor {
+
+class TranslationTable;
+
+namespace features {
+
+/**
+ * Feature computing max(p(f | e)) across all pairs of words in the phrase pair.
+ */
+class MaxLexSourceGivenTarget : public Feature {
+ public:
+  MaxLexSourceGivenTarget(shared_ptr<TranslationTable> table);
+
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+
+ private:
+  shared_ptr<TranslationTable> table;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/max_lex_source_given_target_test.cc b/extractor/features/max_lex_source_given_target_test.cc
new file mode 100644
index 00000000..7f6aae41
--- /dev/null
+++ b/extractor/features/max_lex_source_given_target_test.cc
@@ -0,0 +1,78 @@
+#include <gtest/gtest.h>
+
+#include <cmath>
+#include <memory>
+#include <string>
+
+#include "data_array.h"
+#include "mocks/mock_translation_table.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase_builder.h"
+#include "max_lex_source_given_target.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class MaxLexSourceGivenTargetTest : public Test {
+ protected:
+  virtual void SetUp() {
+    vector<string> source_words = {"f1", "f2", "f3"};
+    vector<string> target_words = {"e1", "e2", "e3"};
+
+    vocabulary = make_shared<MockVocabulary>();
+    for (size_t i = 0; i < source_words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i))
+          .WillRepeatedly(Return(source_words[i]));
+    }
+    for (size_t i = 0; i < target_words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i + source_words.size()))
+          .WillRepeatedly(Return(target_words[i]));
+    }
+
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+
+    table = make_shared<MockTranslationTable>();
+    for (size_t i = 0; i < source_words.size(); ++i) {
+      for (size_t j = 0; j < target_words.size(); ++j) {
+        int value = i - j;
+        EXPECT_CALL(*table, GetSourceGivenTargetScore(
+            source_words[i], target_words[j])).WillRepeatedly(Return(value));
+      }
+    }
+
+    for (size_t i = 0; i < source_words.size(); ++i) {
+      int value = i * 3;
+      EXPECT_CALL(*table, GetSourceGivenTargetScore(
+          source_words[i], DataArray::NULL_WORD_STR))
+          .WillRepeatedly(Return(value));
+    }
+
+    feature = make_shared<MaxLexSourceGivenTarget>(table);
+  }
+
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<MockTranslationTable> table;
+  shared_ptr<MaxLexSourceGivenTarget> feature;
+};
+
+TEST_F(MaxLexSourceGivenTargetTest, TestGetName) {
+  EXPECT_EQ("MaxLexFgivenE", feature->GetName());
+}
+
+TEST_F(MaxLexSourceGivenTargetTest, TestScore) {
+  vector<int> source_symbols = {0, 1, 2};
+  Phrase source_phrase = phrase_builder->Build(source_symbols);
+  vector<int> target_symbols = {3, 4, 5};
+  Phrase target_phrase = phrase_builder->Build(target_symbols);
+  FeatureContext context(source_phrase, target_phrase, 0.3, 7, 11);
+  EXPECT_EQ(99 - log10(18), feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/max_lex_target_given_source.cc b/extractor/features/max_lex_target_given_source.cc
new file mode 100644
index 00000000..33783054
--- /dev/null
+++ b/extractor/features/max_lex_target_given_source.cc
@@ -0,0 +1,37 @@
+#include "max_lex_target_given_source.h"
+
+#include <cmath>
+
+#include "data_array.h"
+#include "translation_table.h"
+
+namespace extractor {
+namespace features {
+
+MaxLexTargetGivenSource::MaxLexTargetGivenSource(
+    shared_ptr<TranslationTable> table) :
+    table(table) {}
+
+double MaxLexTargetGivenSource::Score(const FeatureContext& context) const {
+  vector<string> source_words = context.source_phrase.GetWords();
+  source_words.push_back(DataArray::NULL_WORD_STR);
+  vector<string> target_words = context.target_phrase.GetWords();
+
+  double score = 0;
+  for (string target_word: target_words) {
+    double max_score = 0;
+    for (string source_word: source_words) {
+      max_score = max(max_score,
+          table->GetTargetGivenSourceScore(source_word, target_word));
+    }
+    score += max_score > 0 ? -log10(max_score) : MAX_SCORE;
+  }
+  return score;
+}
+
+string MaxLexTargetGivenSource::GetName() const {
+  return "MaxLexEgivenF";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/max_lex_target_given_source.h b/extractor/features/max_lex_target_given_source.h
new file mode 100644
index 00000000..c3c87327
--- /dev/null
+++ b/extractor/features/max_lex_target_given_source.h
@@ -0,0 +1,34 @@
+#ifndef _MAX_LEX_TARGET_GIVEN_SOURCE_H_
+#define _MAX_LEX_TARGET_GIVEN_SOURCE_H_
+
+#include <memory>
+
+#include "feature.h"
+
+using namespace std;
+
+namespace extractor {
+
+class TranslationTable;
+
+namespace features {
+
+/**
+ * Feature computing max(p(e | f)) across all pairs of words in the phrase pair.
+ */
+class MaxLexTargetGivenSource : public Feature {
+ public:
+  MaxLexTargetGivenSource(shared_ptr<TranslationTable> table);
+
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+
+ private:
+  shared_ptr<TranslationTable> table;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/max_lex_target_given_source_test.cc b/extractor/features/max_lex_target_given_source_test.cc
new file mode 100644
index 00000000..6d0efd9c
--- /dev/null
+++ b/extractor/features/max_lex_target_given_source_test.cc
@@ -0,0 +1,78 @@
+#include <gtest/gtest.h>
+
+#include <cmath>
+#include <memory>
+#include <string>
+
+#include "data_array.h"
+#include "mocks/mock_translation_table.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase_builder.h"
+#include "max_lex_target_given_source.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class MaxLexTargetGivenSourceTest : public Test {
+ protected:
+  virtual void SetUp() {
+    vector<string> source_words = {"f1", "f2", "f3"};
+    vector<string> target_words = {"e1", "e2", "e3"};
+
+    vocabulary = make_shared<MockVocabulary>();
+    for (size_t i = 0; i < source_words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i))
+          .WillRepeatedly(Return(source_words[i]));
+    }
+    for (size_t i = 0; i < target_words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i + source_words.size()))
+          .WillRepeatedly(Return(target_words[i]));
+    }
+
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+
+    table = make_shared<MockTranslationTable>();
+    for (size_t i = 0; i < source_words.size(); ++i) {
+      for (size_t j = 0; j < target_words.size(); ++j) {
+        int value = i - j;
+        EXPECT_CALL(*table, GetTargetGivenSourceScore(
+            source_words[i], target_words[j])).WillRepeatedly(Return(value));
+      }
+    }
+
+    for (size_t i = 0; i < target_words.size(); ++i) {
+      int value = i * 3;
+      EXPECT_CALL(*table, GetTargetGivenSourceScore(
+          DataArray::NULL_WORD_STR, target_words[i]))
+          .WillRepeatedly(Return(value));
+    }
+
+    feature = make_shared<MaxLexTargetGivenSource>(table);
+  }
+
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<MockTranslationTable> table;
+  shared_ptr<MaxLexTargetGivenSource> feature;
+};
+
+TEST_F(MaxLexTargetGivenSourceTest, TestGetName) {
+  EXPECT_EQ("MaxLexEgivenF", feature->GetName());
+}
+
+TEST_F(MaxLexTargetGivenSourceTest, TestScore) {
+  vector<int> source_symbols = {0, 1, 2};
+  Phrase source_phrase = phrase_builder->Build(source_symbols);
+  vector<int> target_symbols = {3, 4, 5};
+  Phrase target_phrase = phrase_builder->Build(target_symbols);
+  FeatureContext context(source_phrase, target_phrase, 0.3, 7, 19);
+  EXPECT_EQ(-log10(36), feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/sample_source_count.cc b/extractor/features/sample_source_count.cc
new file mode 100644
index 00000000..b110fc51
--- /dev/null
+++ b/extractor/features/sample_source_count.cc
@@ -0,0 +1,17 @@
+#include "sample_source_count.h"
+
+#include <cmath>
+
+namespace extractor {
+namespace features {
+
+double SampleSourceCount::Score(const FeatureContext& context) const {
+  return log10(1 + context.num_samples);
+}
+
+string SampleSourceCount::GetName() const {
+  return "SampleCountF";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/sample_source_count.h b/extractor/features/sample_source_count.h
new file mode 100644
index 00000000..ee6e59a0
--- /dev/null
+++ b/extractor/features/sample_source_count.h
@@ -0,0 +1,23 @@
+#ifndef _SAMPLE_SOURCE_COUNT_H_
+#define _SAMPLE_SOURCE_COUNT_H_
+
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+/**
+ * Feature scoring the number of times the source phrase occurs in the sampled
+ * set.
+ */
+class SampleSourceCount : public Feature {
+ public:
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/sample_source_count_test.cc b/extractor/features/sample_source_count_test.cc
new file mode 100644
index 00000000..63856b9d
--- /dev/null
+++ b/extractor/features/sample_source_count_test.cc
@@ -0,0 +1,40 @@
+#include <gtest/gtest.h>
+
+#include <cmath>
+#include <memory>
+#include <string>
+
+#include "sample_source_count.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class SampleSourceCountTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature = make_shared<SampleSourceCount>();
+  }
+
+  shared_ptr<SampleSourceCount> feature;
+};
+
+TEST_F(SampleSourceCountTest, TestGetName) {
+  EXPECT_EQ("SampleCountF", feature->GetName());
+}
+
+TEST_F(SampleSourceCountTest, TestScore) {
+  Phrase phrase;
+  FeatureContext context(phrase, phrase, 0, 3, 1);
+  EXPECT_EQ(log10(2), feature->Score(context));
+
+  context = FeatureContext(phrase, phrase, 3.2, 3, 9);
+  EXPECT_EQ(1.0, feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/target_given_source_coherent.cc b/extractor/features/target_given_source_coherent.cc
new file mode 100644
index 00000000..c4551d88
--- /dev/null
+++ b/extractor/features/target_given_source_coherent.cc
@@ -0,0 +1,18 @@
+#include "target_given_source_coherent.h"
+
+#include <cmath>
+
+namespace extractor {
+namespace features {
+
+double TargetGivenSourceCoherent::Score(const FeatureContext& context) const {
+  double prob = (double) context.pair_count / context.num_samples;
+  return prob > 0 ? -log10(prob) : MAX_SCORE;
+}
+
+string TargetGivenSourceCoherent::GetName() const {
+  return "EgivenFCoherent";
+}
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/features/target_given_source_coherent.h b/extractor/features/target_given_source_coherent.h
new file mode 100644
index 00000000..e66d70a5
--- /dev/null
+++ b/extractor/features/target_given_source_coherent.h
@@ -0,0 +1,23 @@
+#ifndef _TARGET_GIVEN_SOURCE_COHERENT_H_
+#define _TARGET_GIVEN_SOURCE_COHERENT_H_
+
+#include "feature.h"
+
+namespace extractor {
+namespace features {
+
+/**
+ * Feature computing the ratio of the phrase pair count over all source phrase
+ * occurrences (sampled).
+ */
+class TargetGivenSourceCoherent : public Feature {
+ public:
+  double Score(const FeatureContext& context) const;
+
+  string GetName() const;
+};
+
+} // namespace features
+} // namespace extractor
+
+#endif
diff --git a/extractor/features/target_given_source_coherent_test.cc b/extractor/features/target_given_source_coherent_test.cc
new file mode 100644
index 00000000..454105e1
--- /dev/null
+++ b/extractor/features/target_given_source_coherent_test.cc
@@ -0,0 +1,39 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+
+#include "target_given_source_coherent.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace features {
+namespace {
+
+class TargetGivenSourceCoherentTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature = make_shared<TargetGivenSourceCoherent>();
+  }
+
+  shared_ptr<TargetGivenSourceCoherent> feature;
+};
+
+TEST_F(TargetGivenSourceCoherentTest, TestGetName) {
+  EXPECT_EQ("EgivenFCoherent", feature->GetName());
+}
+
+TEST_F(TargetGivenSourceCoherentTest, TestScore) {
+  Phrase phrase;
+  FeatureContext context(phrase, phrase, 0.3, 2, 20);
+  EXPECT_EQ(1.0, feature->Score(context));
+
+  context = FeatureContext(phrase, phrase, 1.9, 0, 1);
+  EXPECT_EQ(99.0, feature->Score(context));
+}
+
+} // namespace
+} // namespace features
+} // namespace extractor
diff --git a/extractor/grammar.cc b/extractor/grammar.cc
new file mode 100644
index 00000000..b45a8261
--- /dev/null
+++ b/extractor/grammar.cc
@@ -0,0 +1,43 @@
+#include "grammar.h"
+
+#include <iomanip>
+
+#include "rule.h"
+
+using namespace std;
+
+namespace extractor {
+
+Grammar::Grammar(const vector<Rule>& rules,
+                 const vector<string>& feature_names) :
+  rules(rules), feature_names(feature_names) {}
+
+vector<Rule> Grammar::GetRules() const {
+  return rules;
+}
+
+vector<string> Grammar::GetFeatureNames() const {
+  return feature_names;
+}
+
+ostream& operator<<(ostream& os, const Grammar& grammar) {
+  vector<Rule> rules = grammar.GetRules();
+  vector<string> feature_names = grammar.GetFeatureNames();
+  os << setprecision(12);
+  for (Rule rule: rules) {
+    os << "[X] ||| " << rule.source_phrase << " ||| "
+                     << rule.target_phrase << " |||";
+    for (size_t i = 0; i < rule.scores.size(); ++i) {
+      os << " " << feature_names[i] << "=" << rule.scores[i];
+    }
+    os << " |||";
+    for (auto link: rule.alignment) {
+      os << " " << link.first << "-" << link.second;
+    }
+    os << '\n';
+  }
+
+  return os;
+}
+
+} // namespace extractor
diff --git a/extractor/grammar.h b/extractor/grammar.h
new file mode 100644
index 00000000..fed41b16
--- /dev/null
+++ b/extractor/grammar.h
@@ -0,0 +1,34 @@
+#ifndef _GRAMMAR_H_
+#define _GRAMMAR_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+class Rule;
+
+/**
+ * Grammar class wrapping the set of rules to be extracted.
+ */
+class Grammar {
+ public:
+  Grammar(const vector<Rule>& rules, const vector<string>& feature_names);
+
+  vector<Rule> GetRules() const;
+
+  vector<string> GetFeatureNames() const;
+
+  friend ostream& operator<<(ostream& os, const Grammar& grammar);
+
+ private:
+  vector<Rule> rules;
+  vector<string> feature_names;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/grammar_extractor.cc b/extractor/grammar_extractor.cc
new file mode 100644
index 00000000..8050ce7b
--- /dev/null
+++ b/extractor/grammar_extractor.cc
@@ -0,0 +1,62 @@
+#include "grammar_extractor.h"
+
+#include <iterator>
+#include <sstream>
+#include <vector>
+
+#include "grammar.h"
+#include "rule.h"
+#include "rule_factory.h"
+#include "vocabulary.h"
+
+using namespace std;
+
+namespace extractor {
+
+GrammarExtractor::GrammarExtractor(
+    shared_ptr<SuffixArray> source_suffix_array,
+    shared_ptr<DataArray> target_data_array,
+    shared_ptr<Alignment> alignment, shared_ptr<Precomputation> precomputation,
+    shared_ptr<Scorer> scorer, int min_gap_size, int max_rule_span,
+    int max_nonterminals, int max_rule_symbols, int max_samples,
+    bool require_tight_phrases) :
+    vocabulary(make_shared<Vocabulary>()),
+    rule_factory(make_shared<HieroCachingRuleFactory>(
+        source_suffix_array, target_data_array, alignment, vocabulary,
+        precomputation, scorer, min_gap_size, max_rule_span, max_nonterminals,
+        max_rule_symbols, max_samples, require_tight_phrases)) {}
+
+GrammarExtractor::GrammarExtractor(
+    shared_ptr<Vocabulary> vocabulary,
+    shared_ptr<HieroCachingRuleFactory> rule_factory) :
+    vocabulary(vocabulary),
+    rule_factory(rule_factory) {}
+
+Grammar GrammarExtractor::GetGrammar(const string& sentence) {
+  vector<string> words = TokenizeSentence(sentence);
+  vector<int> word_ids = AnnotateWords(words);
+  return rule_factory->GetGrammar(word_ids);
+}
+
+vector<string> GrammarExtractor::TokenizeSentence(const string& sentence) {
+  vector<string> result;
+  result.push_back("<s>");
+
+  istringstream buffer(sentence);
+  copy(istream_iterator<string>(buffer),
+       istream_iterator<string>(),
+       back_inserter(result));
+
+  result.push_back("</s>");
+  return result;
+}
+
+vector<int> GrammarExtractor::AnnotateWords(const vector<string>& words) {
+  vector<int> result;
+  for (string word: words) {
+    result.push_back(vocabulary->GetTerminalIndex(word));
+  }
+  return result;
+}
+
+} // namespace extractor
diff --git a/extractor/grammar_extractor.h b/extractor/grammar_extractor.h
new file mode 100644
index 00000000..b36ceeb9
--- /dev/null
+++ b/extractor/grammar_extractor.h
@@ -0,0 +1,62 @@
+#ifndef _GRAMMAR_EXTRACTOR_H_
+#define _GRAMMAR_EXTRACTOR_H_
+
+#include <memory>
+#include <string>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+class Alignment;
+class DataArray;
+class Grammar;
+class HieroCachingRuleFactory;
+class Precomputation;
+class Rule;
+class Scorer;
+class SuffixArray;
+class Vocabulary;
+
+/**
+ * Class wrapping all the logic for extracting the synchronous context free
+ * grammars.
+ */
+class GrammarExtractor {
+ public:
+  GrammarExtractor(
+      shared_ptr<SuffixArray> source_suffix_array,
+      shared_ptr<DataArray> target_data_array,
+      shared_ptr<Alignment> alignment,
+      shared_ptr<Precomputation> precomputation,
+      shared_ptr<Scorer> scorer,
+      int min_gap_size,
+      int max_rule_span,
+      int max_nonterminals,
+      int max_rule_symbols,
+      int max_samples,
+      bool require_tight_phrases);
+
+  // For testing only.
+  GrammarExtractor(shared_ptr<Vocabulary> vocabulary,
+                   shared_ptr<HieroCachingRuleFactory> rule_factory);
+
+  // Converts the sentence to a vector of word ids and uses the RuleFactory to
+  // extract the SCFG rules which may be used to decode the sentence.
+  Grammar GetGrammar(const string& sentence);
+
+ private:
+  // Splits the sentence in a vector of words.
+  vector<string> TokenizeSentence(const string& sentence);
+
+  // Maps the words to word ids.
+  vector<int> AnnotateWords(const vector<string>& words);
+
+  shared_ptr<Vocabulary> vocabulary;
+  shared_ptr<HieroCachingRuleFactory> rule_factory;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/grammar_extractor_test.cc b/extractor/grammar_extractor_test.cc
new file mode 100644
index 00000000..823bb8b4
--- /dev/null
+++ b/extractor/grammar_extractor_test.cc
@@ -0,0 +1,51 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "grammar.h"
+#include "grammar_extractor.h"
+#include "mocks/mock_rule_factory.h"
+#include "mocks/mock_vocabulary.h"
+#include "rule.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+TEST(GrammarExtractorTest, TestAnnotatingWords) {
+  shared_ptr<MockVocabulary> vocabulary = make_shared<MockVocabulary>();
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("<s>"))
+      .WillRepeatedly(Return(0));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("Anna"))
+      .WillRepeatedly(Return(1));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("has"))
+      .WillRepeatedly(Return(2));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("many"))
+      .WillRepeatedly(Return(3));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("apples"))
+      .WillRepeatedly(Return(4));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("."))
+      .WillRepeatedly(Return(5));
+  EXPECT_CALL(*vocabulary, GetTerminalIndex("</s>"))
+      .WillRepeatedly(Return(6));
+
+  shared_ptr<MockHieroCachingRuleFactory> factory =
+      make_shared<MockHieroCachingRuleFactory>();
+  vector<int> word_ids = {0, 1, 2, 3, 3, 4, 5, 6};
+  vector<Rule> rules;
+  vector<string> feature_names;
+  Grammar grammar(rules, feature_names);
+  EXPECT_CALL(*factory, GetGrammar(word_ids))
+      .WillOnce(Return(grammar));
+
+  GrammarExtractor extractor(vocabulary, factory);
+  string sentence = "Anna has many many apples .";
+  extractor.GetGrammar(sentence);
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/matchings_finder.cc b/extractor/matchings_finder.cc
new file mode 100644
index 00000000..ceed6891
--- /dev/null
+++ b/extractor/matchings_finder.cc
@@ -0,0 +1,25 @@
+#include "matchings_finder.h"
+
+#include "suffix_array.h"
+#include "phrase_location.h"
+
+namespace extractor {
+
+MatchingsFinder::MatchingsFinder(shared_ptr<SuffixArray> suffix_array) :
+    suffix_array(suffix_array) {}
+
+MatchingsFinder::MatchingsFinder() {}
+
+MatchingsFinder::~MatchingsFinder() {}
+
+PhraseLocation MatchingsFinder::Find(PhraseLocation& location,
+                                     const string& word, int offset) {
+  if (location.sa_low == -1 && location.sa_high == -1) {
+    location.sa_low = 0;
+    location.sa_high = suffix_array->GetSize();
+  }
+
+  return suffix_array->Lookup(location.sa_low, location.sa_high, word, offset);
+}
+
+} // namespace extractor
diff --git a/extractor/matchings_finder.h b/extractor/matchings_finder.h
new file mode 100644
index 00000000..451f4a4c
--- /dev/null
+++ b/extractor/matchings_finder.h
@@ -0,0 +1,37 @@
+#ifndef _MATCHINGS_FINDER_H_
+#define _MATCHINGS_FINDER_H_
+
+#include <memory>
+#include <string>
+
+using namespace std;
+
+namespace extractor {
+
+class PhraseLocation;
+class SuffixArray;
+
+/**
+ * Class wrapping the suffix array lookup for a contiguous phrase.
+ */
+class MatchingsFinder {
+ public:
+  MatchingsFinder(shared_ptr<SuffixArray> suffix_array);
+
+  virtual ~MatchingsFinder();
+
+  // Uses the suffix array to search only for the last word of the phrase
+  // starting from the range in which the prefix of the phrase occurs.
+  virtual PhraseLocation Find(PhraseLocation& location, const string& word,
+                              int offset);
+
+ protected:
+  MatchingsFinder();
+
+ private:
+  shared_ptr<SuffixArray> suffix_array;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/matchings_finder_test.cc b/extractor/matchings_finder_test.cc
new file mode 100644
index 00000000..d40e5191
--- /dev/null
+++ b/extractor/matchings_finder_test.cc
@@ -0,0 +1,44 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "matchings_finder.h"
+#include "mocks/mock_suffix_array.h"
+#include "phrase_location.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class MatchingsFinderTest : public Test {
+ protected:
+  virtual void SetUp() {
+    suffix_array = make_shared<MockSuffixArray>();
+    EXPECT_CALL(*suffix_array, Lookup(0, 10, _, _))
+        .Times(1)
+        .WillOnce(Return(PhraseLocation(3, 5)));
+
+    matchings_finder = make_shared<MatchingsFinder>(suffix_array);
+  }
+
+  shared_ptr<MatchingsFinder> matchings_finder;
+  shared_ptr<MockSuffixArray> suffix_array;
+};
+
+TEST_F(MatchingsFinderTest, TestFind) {
+  PhraseLocation phrase_location(0, 10), expected_result(3, 5);
+  EXPECT_EQ(expected_result, matchings_finder->Find(phrase_location, "bla", 2));
+}
+
+TEST_F(MatchingsFinderTest, ResizeUnsetRange) {
+  EXPECT_CALL(*suffix_array, GetSize()).Times(1).WillOnce(Return(10));
+
+  PhraseLocation phrase_location, expected_result(3, 5);
+  EXPECT_EQ(expected_result, matchings_finder->Find(phrase_location, "bla", 2));
+  EXPECT_EQ(PhraseLocation(0, 10), phrase_location);
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/matchings_trie.cc b/extractor/matchings_trie.cc
new file mode 100644
index 00000000..7fb7a529
--- /dev/null
+++ b/extractor/matchings_trie.cc
@@ -0,0 +1,29 @@
+#include "matchings_trie.h"
+
+namespace extractor {
+
+MatchingsTrie::MatchingsTrie() {
+  root = make_shared<TrieNode>();
+}
+
+MatchingsTrie::~MatchingsTrie() {
+  DeleteTree(root);
+}
+
+shared_ptr<TrieNode> MatchingsTrie::GetRoot() const {
+  return root;
+}
+
+void MatchingsTrie::DeleteTree(shared_ptr<TrieNode> root) {
+  if (root != NULL) {
+    for (auto child: root->children) {
+      DeleteTree(child.second);
+    }
+    if (root->suffix_link != NULL) {
+      root->suffix_link.reset();
+    }
+    root.reset();
+  }
+}
+
+} // namespace extractor
diff --git a/extractor/matchings_trie.h b/extractor/matchings_trie.h
new file mode 100644
index 00000000..1fb29693
--- /dev/null
+++ b/extractor/matchings_trie.h
@@ -0,0 +1,66 @@
+#ifndef _MATCHINGS_TRIE_
+#define _MATCHINGS_TRIE_
+
+#include <memory>
+#include <unordered_map>
+
+#include "phrase.h"
+#include "phrase_location.h"
+
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Trie node containing all the occurrences of the corresponding phrase in the
+ * source data.
+ */
+struct TrieNode {
+  TrieNode(shared_ptr<TrieNode> suffix_link = shared_ptr<TrieNode>(),
+           Phrase phrase = Phrase(),
+           PhraseLocation matchings = PhraseLocation()) :
+      suffix_link(suffix_link), phrase(phrase), matchings(matchings) {}
+
+  // Adds a trie node as a child of the current node.
+  void AddChild(int key, shared_ptr<TrieNode> child_node) {
+    children[key] = child_node;
+  }
+
+  // Checks if a child exists for a given key.
+  bool HasChild(int key) {
+    return children.count(key);
+  }
+
+  // Gets the child corresponding to the given key.
+  shared_ptr<TrieNode> GetChild(int key) {
+    return children[key];
+  }
+
+  shared_ptr<TrieNode> suffix_link;
+  Phrase phrase;
+  PhraseLocation matchings;
+  unordered_map<int, shared_ptr<TrieNode> > children;
+};
+
+/**
+ * Trie containing all the phrases that can be obtained from a sentence.
+ */
+class MatchingsTrie {
+ public:
+  MatchingsTrie();
+
+  virtual ~MatchingsTrie();
+
+  // Returns the root of the trie.
+  shared_ptr<TrieNode> GetRoot() const;
+
+ private:
+  // Recursively deletes a subtree of the trie.
+  void DeleteTree(shared_ptr<TrieNode> root);
+
+  shared_ptr<TrieNode> root;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/mocks/mock_alignment.h b/extractor/mocks/mock_alignment.h
new file mode 100644
index 00000000..299c3d1c
--- /dev/null
+++ b/extractor/mocks/mock_alignment.h
@@ -0,0 +1,14 @@
+#include <gmock/gmock.h>
+
+#include "alignment.h"
+
+namespace extractor {
+
+typedef vector<pair<int, int> > SentenceLinks;
+
+class MockAlignment : public Alignment {
+ public:
+  MOCK_CONST_METHOD1(GetLinks, SentenceLinks(int sentence_id));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_data_array.h b/extractor/mocks/mock_data_array.h
new file mode 100644
index 00000000..6f85abb4
--- /dev/null
+++ b/extractor/mocks/mock_data_array.h
@@ -0,0 +1,23 @@
+#include <gmock/gmock.h>
+
+#include "data_array.h"
+
+namespace extractor {
+
+class MockDataArray : public DataArray {
+ public:
+  MOCK_CONST_METHOD0(GetData, const vector<int>&());
+  MOCK_CONST_METHOD1(AtIndex, int(int index));
+  MOCK_CONST_METHOD1(GetWordAtIndex, string(int index));
+  MOCK_CONST_METHOD0(GetSize, int());
+  MOCK_CONST_METHOD0(GetVocabularySize, int());
+  MOCK_CONST_METHOD1(HasWord, bool(const string& word));
+  MOCK_CONST_METHOD1(GetWordId, int(const string& word));
+  MOCK_CONST_METHOD1(GetWord, string(int word_id));
+  MOCK_CONST_METHOD1(GetSentenceLength, int(int sentence_id));
+  MOCK_CONST_METHOD0(GetNumSentences, int());
+  MOCK_CONST_METHOD1(GetSentenceStart, int(int sentence_id));
+  MOCK_CONST_METHOD1(GetSentenceId, int(int position));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_fast_intersector.h b/extractor/mocks/mock_fast_intersector.h
new file mode 100644
index 00000000..f0b628d7
--- /dev/null
+++ b/extractor/mocks/mock_fast_intersector.h
@@ -0,0 +1,15 @@
+#include <gmock/gmock.h>
+
+#include "fast_intersector.h"
+#include "phrase.h"
+#include "phrase_location.h"
+
+namespace extractor {
+
+class MockFastIntersector : public FastIntersector {
+ public:
+  MOCK_METHOD3(Intersect, PhraseLocation(PhraseLocation&, PhraseLocation&,
+                                         const Phrase&));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_feature.h b/extractor/mocks/mock_feature.h
new file mode 100644
index 00000000..0b0f0ead
--- /dev/null
+++ b/extractor/mocks/mock_feature.h
@@ -0,0 +1,15 @@
+#include <gmock/gmock.h>
+
+#include "features/feature.h"
+
+namespace extractor {
+namespace features {
+
+class MockFeature : public Feature {
+ public:
+  MOCK_CONST_METHOD1(Score, double(const FeatureContext& context));
+  MOCK_CONST_METHOD0(GetName, string());
+};
+
+} // namespace features
+} // namespace extractor
diff --git a/extractor/mocks/mock_matchings_finder.h b/extractor/mocks/mock_matchings_finder.h
new file mode 100644
index 00000000..827526fd
--- /dev/null
+++ b/extractor/mocks/mock_matchings_finder.h
@@ -0,0 +1,13 @@
+#include <gmock/gmock.h>
+
+#include "matchings_finder.h"
+#include "phrase_location.h"
+
+namespace extractor {
+
+class MockMatchingsFinder : public MatchingsFinder {
+ public:
+  MOCK_METHOD3(Find, PhraseLocation(PhraseLocation&, const string&, int));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_precomputation.h b/extractor/mocks/mock_precomputation.h
new file mode 100644
index 00000000..8753343e
--- /dev/null
+++ b/extractor/mocks/mock_precomputation.h
@@ -0,0 +1,12 @@
+#include <gmock/gmock.h>
+
+#include "precomputation.h"
+
+namespace extractor {
+
+class MockPrecomputation : public Precomputation {
+ public:
+  MOCK_CONST_METHOD0(GetCollocations, const Index&());
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_rule_extractor.h b/extractor/mocks/mock_rule_extractor.h
new file mode 100644
index 00000000..aad11651
--- /dev/null
+++ b/extractor/mocks/mock_rule_extractor.h
@@ -0,0 +1,16 @@
+#include <gmock/gmock.h>
+
+#include "phrase.h"
+#include "phrase_builder.h"
+#include "rule.h"
+#include "rule_extractor.h"
+
+namespace extractor {
+
+class MockRuleExtractor : public RuleExtractor {
+ public:
+  MOCK_CONST_METHOD2(ExtractRules, vector<Rule>(const Phrase&,
+      const PhraseLocation&));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_rule_extractor_helper.h b/extractor/mocks/mock_rule_extractor_helper.h
new file mode 100644
index 00000000..468468f6
--- /dev/null
+++ b/extractor/mocks/mock_rule_extractor_helper.h
@@ -0,0 +1,82 @@
+#include <gmock/gmock.h>
+
+#include <vector>
+
+#include "rule_extractor_helper.h"
+
+using namespace std;
+
+namespace extractor {
+
+typedef unordered_map<int, int> Indexes;
+
+class MockRuleExtractorHelper : public RuleExtractorHelper {
+ public:
+  MOCK_CONST_METHOD5(GetLinksSpans, void(vector<int>&, vector<int>&,
+      vector<int>&, vector<int>&, int));
+  MOCK_CONST_METHOD4(CheckAlignedTerminals, bool(const vector<int>&,
+      const vector<int>&, const vector<int>&, int));
+  MOCK_CONST_METHOD4(CheckTightPhrases, bool(const vector<int>&,
+      const vector<int>&, const vector<int>&, int));
+  MOCK_CONST_METHOD1(GetGapOrder, vector<int>(const vector<pair<int, int> >&));
+  MOCK_CONST_METHOD4(GetSourceIndexes, Indexes(const vector<int>&,
+      const vector<int>&, int, int));
+
+  // We need to implement these methods, because Google Mock doesn't support
+  // methods with more than 10 arguments.
+  bool FindFixPoint(
+      int, int, const vector<int>&, const vector<int>&, int& target_phrase_low,
+      int& target_phrase_high, const vector<int>&, const vector<int>&,
+      int& source_back_low, int& source_back_high, int, int, int, int, bool,
+      bool, bool) const {
+    target_phrase_low = this->target_phrase_low;
+    target_phrase_high = this->target_phrase_high;
+    source_back_low = this->source_back_low;
+    source_back_high = this->source_back_high;
+    return find_fix_point;
+  }
+
+  bool GetGaps(vector<pair<int, int> >& source_gaps,
+               vector<pair<int, int> >& target_gaps,
+               const vector<int>&, const vector<int>&, const vector<int>&,
+               const vector<int>&, const vector<int>&, const vector<int>&,
+               int, int, int, int, int, int, int& num_symbols,
+               bool& met_constraints) const {
+    source_gaps = this->source_gaps;
+    target_gaps = this->target_gaps;
+    num_symbols = this->num_symbols;
+    met_constraints = this->met_constraints;
+    return get_gaps;
+  }
+
+  void SetUp(
+      int target_phrase_low, int target_phrase_high, int source_back_low,
+      int source_back_high, bool find_fix_point,
+      vector<pair<int, int> > source_gaps, vector<pair<int, int> > target_gaps,
+      int num_symbols, bool met_constraints, bool get_gaps) {
+    this->target_phrase_low = target_phrase_low;
+    this->target_phrase_high = target_phrase_high;
+    this->source_back_low = source_back_low;
+    this->source_back_high = source_back_high;
+    this->find_fix_point = find_fix_point;
+    this->source_gaps = source_gaps;
+    this->target_gaps = target_gaps;
+    this->num_symbols = num_symbols;
+    this->met_constraints = met_constraints;
+    this->get_gaps = get_gaps;
+  }
+
+ private:
+  int target_phrase_low;
+  int target_phrase_high;
+  int source_back_low;
+  int source_back_high;
+  bool find_fix_point;
+  vector<pair<int, int> > source_gaps;
+  vector<pair<int, int> > target_gaps;
+  int num_symbols;
+  bool met_constraints;
+  bool get_gaps;
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_rule_factory.h b/extractor/mocks/mock_rule_factory.h
new file mode 100644
index 00000000..7389b396
--- /dev/null
+++ b/extractor/mocks/mock_rule_factory.h
@@ -0,0 +1,13 @@
+#include <gmock/gmock.h>
+
+#include "grammar.h"
+#include "rule_factory.h"
+
+namespace extractor {
+
+class MockHieroCachingRuleFactory : public HieroCachingRuleFactory {
+ public:
+  MOCK_METHOD1(GetGrammar, Grammar(const vector<int>& word_ids));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_sampler.h b/extractor/mocks/mock_sampler.h
new file mode 100644
index 00000000..75c43c27
--- /dev/null
+++ b/extractor/mocks/mock_sampler.h
@@ -0,0 +1,13 @@
+#include <gmock/gmock.h>
+
+#include "phrase_location.h"
+#include "sampler.h"
+
+namespace extractor {
+
+class MockSampler : public Sampler {
+ public:
+  MOCK_CONST_METHOD1(Sample, PhraseLocation(const PhraseLocation& location));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_scorer.h b/extractor/mocks/mock_scorer.h
new file mode 100644
index 00000000..cc0c444d
--- /dev/null
+++ b/extractor/mocks/mock_scorer.h
@@ -0,0 +1,15 @@
+#include <gmock/gmock.h>
+
+#include "scorer.h"
+#include "features/feature.h"
+
+namespace extractor {
+
+class MockScorer : public Scorer {
+ public:
+  MOCK_CONST_METHOD1(Score, vector<double>(
+      const features::FeatureContext& context));
+  MOCK_CONST_METHOD0(GetFeatureNames, vector<string>());
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_suffix_array.h b/extractor/mocks/mock_suffix_array.h
new file mode 100644
index 00000000..7018acc7
--- /dev/null
+++ b/extractor/mocks/mock_suffix_array.h
@@ -0,0 +1,23 @@
+#include <gmock/gmock.h>
+
+#include <memory>
+#include <string>
+
+#include "data_array.h"
+#include "phrase_location.h"
+#include "suffix_array.h"
+
+using namespace std;
+
+namespace extractor {
+
+class MockSuffixArray : public SuffixArray {
+ public:
+  MOCK_CONST_METHOD0(GetSize, int());
+  MOCK_CONST_METHOD0(GetData, shared_ptr<DataArray>());
+  MOCK_CONST_METHOD0(BuildLCPArray, vector<int>());
+  MOCK_CONST_METHOD1(GetSuffix, int(int));
+  MOCK_CONST_METHOD4(Lookup, PhraseLocation(int, int, const string& word, int));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_target_phrase_extractor.h b/extractor/mocks/mock_target_phrase_extractor.h
new file mode 100644
index 00000000..6aad853c
--- /dev/null
+++ b/extractor/mocks/mock_target_phrase_extractor.h
@@ -0,0 +1,16 @@
+#include <gmock/gmock.h>
+
+#include "target_phrase_extractor.h"
+
+namespace extractor {
+
+typedef pair<Phrase, PhraseAlignment> PhraseExtract;
+
+class MockTargetPhraseExtractor : public TargetPhraseExtractor {
+ public:
+  MOCK_CONST_METHOD6(ExtractPhrases, vector<PhraseExtract>(
+      const vector<pair<int, int> > &, const vector<int>&, int, int,
+      const unordered_map<int, int>&, int));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_translation_table.h b/extractor/mocks/mock_translation_table.h
new file mode 100644
index 00000000..307e4282
--- /dev/null
+++ b/extractor/mocks/mock_translation_table.h
@@ -0,0 +1,13 @@
+#include <gmock/gmock.h>
+
+#include "translation_table.h"
+
+namespace extractor {
+
+class MockTranslationTable : public TranslationTable {
+ public:
+  MOCK_METHOD2(GetSourceGivenTargetScore, double(const string&, const string&));
+  MOCK_METHOD2(GetTargetGivenSourceScore, double(const string&, const string&));
+};
+
+} // namespace extractor
diff --git a/extractor/mocks/mock_vocabulary.h b/extractor/mocks/mock_vocabulary.h
new file mode 100644
index 00000000..042c9ce2
--- /dev/null
+++ b/extractor/mocks/mock_vocabulary.h
@@ -0,0 +1,13 @@
+#include <gmock/gmock.h>
+
+#include "vocabulary.h"
+
+namespace extractor {
+
+class MockVocabulary : public Vocabulary {
+ public:
+  MOCK_METHOD1(GetTerminalValue, string(int word_id));
+  MOCK_METHOD1(GetTerminalIndex, int(const string& word));
+};
+
+} // namespace extractor
diff --git a/extractor/phrase.cc b/extractor/phrase.cc
new file mode 100644
index 00000000..e619bfe5
--- /dev/null
+++ b/extractor/phrase.cc
@@ -0,0 +1,58 @@
+#include "phrase.h"
+
+namespace extractor {
+
+int Phrase::Arity() const {
+  return var_pos.size();
+}
+
+int Phrase::GetChunkLen(int index) const {
+  if (var_pos.size() == 0) {
+    return symbols.size();
+  } else if (index == 0) {
+    return var_pos[0];
+  } else if (index == var_pos.size()) {
+    return symbols.size() - var_pos.back() - 1;
+  } else {
+    return var_pos[index] - var_pos[index - 1] - 1;
+  }
+}
+
+vector<int> Phrase::Get() const {
+  return symbols;
+}
+
+int Phrase::GetSymbol(int position) const {
+  return symbols[position];
+}
+
+int Phrase::GetNumSymbols() const {
+  return symbols.size();
+}
+
+vector<string> Phrase::GetWords() const {
+  return words;
+}
+
+bool Phrase::operator<(const Phrase& other) const {
+  return symbols < other.symbols;
+}
+
+ostream& operator<<(ostream& os, const Phrase& phrase) {
+  int current_word = 0;
+  for (size_t i = 0; i < phrase.symbols.size(); ++i) {
+    if (phrase.symbols[i] < 0) {
+      os << "[X," << -phrase.symbols[i] << "]";
+    } else {
+      os << phrase.words[current_word];
+      ++current_word;
+    }
+
+    if (i + 1 < phrase.symbols.size()) {
+      os << " ";
+    }
+  }
+  return os;
+}
+
+} // namspace extractor
diff --git a/extractor/phrase.h b/extractor/phrase.h
new file mode 100644
index 00000000..a8e91e3c
--- /dev/null
+++ b/extractor/phrase.h
@@ -0,0 +1,52 @@
+#ifndef _PHRASE_H_
+#define _PHRASE_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "phrase_builder.h"
+
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Structure containing the data for a phrase.
+ */
+class Phrase {
+ public:
+  friend Phrase PhraseBuilder::Build(const vector<int>& phrase);
+
+  // Returns the number of nonterminals in the phrase.
+  int Arity() const;
+
+  // Returns the number of terminals (length) for the given chunk. (A chunk is a
+  // contiguous sequence of terminals in the phrase).
+  int GetChunkLen(int index) const;
+
+  // Returns the symbols (word ids) marking up the phrase.
+  vector<int> Get() const;
+
+  // Returns the symbol located at the given position in the phrase.
+  int GetSymbol(int position) const;
+
+  // Returns the number of symbols in the phrase.
+  int GetNumSymbols() const;
+
+  // Returns the words making up the phrase. (Nonterminals are stripped out.)
+  vector<string> GetWords() const;
+
+  bool operator<(const Phrase& other) const;
+
+  friend ostream& operator<<(ostream& os, const Phrase& phrase);
+
+ private:
+  vector<int> symbols;
+  vector<int> var_pos;
+  vector<string> words;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/phrase_builder.cc b/extractor/phrase_builder.cc
new file mode 100644
index 00000000..9faee4be
--- /dev/null
+++ b/extractor/phrase_builder.cc
@@ -0,0 +1,48 @@
+#include "phrase_builder.h"
+
+#include "phrase.h"
+#include "vocabulary.h"
+
+namespace extractor {
+
+PhraseBuilder::PhraseBuilder(shared_ptr<Vocabulary> vocabulary) :
+    vocabulary(vocabulary) {}
+
+Phrase PhraseBuilder::Build(const vector<int>& symbols) {
+  Phrase phrase;
+  phrase.symbols = symbols;
+  for (size_t i = 0; i < symbols.size(); ++i) {
+    if (vocabulary->IsTerminal(symbols[i])) {
+      phrase.words.push_back(vocabulary->GetTerminalValue(symbols[i]));
+    } else {
+      phrase.var_pos.push_back(i);
+    }
+  }
+  return phrase;
+}
+
+Phrase PhraseBuilder::Extend(const Phrase& phrase, bool start_x, bool end_x) {
+  vector<int> symbols = phrase.Get();
+  int num_nonterminals = 0;
+  if (start_x) {
+    num_nonterminals = 1;
+    symbols.insert(symbols.begin(),
+        vocabulary->GetNonterminalIndex(num_nonterminals));
+  }
+
+  for (size_t i = start_x; i < symbols.size(); ++i) {
+    if (!vocabulary->IsTerminal(symbols[i])) {
+      ++num_nonterminals;
+      symbols[i] = vocabulary->GetNonterminalIndex(num_nonterminals);
+    }
+  }
+
+  if (end_x) {
+    ++num_nonterminals;
+    symbols.push_back(vocabulary->GetNonterminalIndex(num_nonterminals));
+  }
+
+  return Build(symbols);
+}
+
+} // namespace extractor
diff --git a/extractor/phrase_builder.h b/extractor/phrase_builder.h
new file mode 100644
index 00000000..de86dbae
--- /dev/null
+++ b/extractor/phrase_builder.h
@@ -0,0 +1,33 @@
+#ifndef _PHRASE_BUILDER_H_
+#define _PHRASE_BUILDER_H_
+
+#include <memory>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+class Phrase;
+class Vocabulary;
+
+/**
+ * Component for constructing phrases.
+ */
+class PhraseBuilder {
+ public:
+  PhraseBuilder(shared_ptr<Vocabulary> vocabulary);
+
+  // Constructs a phrase starting from an array of symbols.
+  Phrase Build(const vector<int>& symbols);
+
+  // Extends a phrase with a leading and/or trailing nonterminal.
+  Phrase Extend(const Phrase& phrase, bool start_x, bool end_x);
+
+ private:
+  shared_ptr<Vocabulary> vocabulary;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/phrase_location.cc b/extractor/phrase_location.cc
new file mode 100644
index 00000000..678ae270
--- /dev/null
+++ b/extractor/phrase_location.cc
@@ -0,0 +1,43 @@
+#include "phrase_location.h"
+
+namespace extractor {
+
+PhraseLocation::PhraseLocation(int sa_low, int sa_high) :
+    sa_low(sa_low), sa_high(sa_high), num_subpatterns(0) {}
+
+PhraseLocation::PhraseLocation(const vector<int>& matchings,
+                               int num_subpatterns) :
+    sa_low(0), sa_high(0),
+    matchings(make_shared<vector<int> >(matchings)),
+    num_subpatterns(num_subpatterns) {}
+
+bool PhraseLocation::IsEmpty() const {
+  return GetSize() == 0;
+}
+
+int PhraseLocation::GetSize() const {
+  if (num_subpatterns > 0) {
+    return matchings->size();
+  } else {
+    return sa_high - sa_low;
+  }
+}
+
+bool operator==(const PhraseLocation& a, const PhraseLocation& b) {
+  if (a.sa_low != b.sa_low || a.sa_high != b.sa_high ||
+      a.num_subpatterns != b.num_subpatterns) {
+    return false;
+  }
+
+  if (a.matchings == NULL && b.matchings == NULL) {
+    return true;
+  }
+
+  if (a.matchings == NULL || b.matchings == NULL) {
+    return false;
+  }
+
+  return *a.matchings == *b.matchings;
+}
+
+} // namespace extractor
diff --git a/extractor/phrase_location.h b/extractor/phrase_location.h
new file mode 100644
index 00000000..91950e03
--- /dev/null
+++ b/extractor/phrase_location.h
@@ -0,0 +1,41 @@
+#ifndef _PHRASE_LOCATION_H_
+#define _PHRASE_LOCATION_H_
+
+#include <memory>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Structure containing information about the occurrences of a phrase in the
+ * source data.
+ *
+ * Every consecutive (disjoint) group of num_subpatterns entries in matchings
+ * vector encodes an occurrence of the phrase. The i-th entry of a group
+ * represents the start of the i-th subpattern of the phrase. If the phrase
+ * doesn't contain any nonterminals, then it may also be represented as the
+ * range in the suffix array which matches the phrase.
+ */
+struct PhraseLocation {
+  PhraseLocation(int sa_low = -1, int sa_high = -1);
+
+  PhraseLocation(const vector<int>& matchings, int num_subpatterns);
+
+  // Checks if a phrase has any occurrences in the source data.
+  bool IsEmpty() const;
+
+  // Returns the number of occurrences of a phrase in the source data.
+  int GetSize() const;
+
+  friend bool operator==(const PhraseLocation& a, const PhraseLocation& b);
+
+  int sa_low, sa_high;
+  shared_ptr<vector<int> > matchings;
+  int num_subpatterns;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/phrase_test.cc b/extractor/phrase_test.cc
new file mode 100644
index 00000000..3ba9368a
--- /dev/null
+++ b/extractor/phrase_test.cc
@@ -0,0 +1,83 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <vector>
+
+#include "mocks/mock_vocabulary.h"
+#include "phrase.h"
+#include "phrase_builder.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class PhraseTest : public Test {
+ protected:
+  virtual void SetUp() {
+    shared_ptr<MockVocabulary> vocabulary = make_shared<MockVocabulary>();
+    vector<string> words = {"w1", "w2", "w3", "w4"};
+    for (size_t i = 0; i < words.size(); ++i) {
+      EXPECT_CALL(*vocabulary, GetTerminalValue(i + 1))
+          .WillRepeatedly(Return(words[i]));
+    }
+    shared_ptr<PhraseBuilder> phrase_builder =
+        make_shared<PhraseBuilder>(vocabulary);
+
+    symbols1 = vector<int>{1, 2, 3};
+    phrase1 = phrase_builder->Build(symbols1);
+    symbols2 = vector<int>{1, 2, -1, 3, -2, 4};
+    phrase2 = phrase_builder->Build(symbols2);
+  }
+
+  vector<int> symbols1, symbols2;
+  Phrase phrase1, phrase2;
+};
+
+TEST_F(PhraseTest, TestArity) {
+  EXPECT_EQ(0, phrase1.Arity());
+  EXPECT_EQ(2, phrase2.Arity());
+}
+
+TEST_F(PhraseTest, GetChunkLen) {
+  EXPECT_EQ(3, phrase1.GetChunkLen(0));
+
+  EXPECT_EQ(2, phrase2.GetChunkLen(0));
+  EXPECT_EQ(1, phrase2.GetChunkLen(1));
+  EXPECT_EQ(1, phrase2.GetChunkLen(2));
+}
+
+TEST_F(PhraseTest, TestGet) {
+  EXPECT_EQ(symbols1, phrase1.Get());
+  EXPECT_EQ(symbols2, phrase2.Get());
+}
+
+TEST_F(PhraseTest, TestGetSymbol) {
+  for (size_t i = 0; i < symbols1.size(); ++i) {
+    EXPECT_EQ(symbols1[i], phrase1.GetSymbol(i));
+  }
+  for (size_t i = 0; i < symbols2.size(); ++i) {
+    EXPECT_EQ(symbols2[i], phrase2.GetSymbol(i));
+  }
+}
+
+TEST_F(PhraseTest, TestGetNumSymbols) {
+  EXPECT_EQ(3, phrase1.GetNumSymbols());
+  EXPECT_EQ(6, phrase2.GetNumSymbols());
+}
+
+TEST_F(PhraseTest, TestGetWords) {
+  vector<string> expected_words = {"w1", "w2", "w3"};
+  EXPECT_EQ(expected_words, phrase1.GetWords());
+  expected_words = {"w1", "w2", "w3", "w4"};
+  EXPECT_EQ(expected_words, phrase2.GetWords());
+}
+
+TEST_F(PhraseTest, TestComparator) {
+  EXPECT_FALSE(phrase1 < phrase2);
+  EXPECT_TRUE(phrase2 < phrase1);
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/precomputation.cc b/extractor/precomputation.cc
new file mode 100644
index 00000000..b3906943
--- /dev/null
+++ b/extractor/precomputation.cc
@@ -0,0 +1,189 @@
+#include "precomputation.h"
+
+#include <iostream>
+#include <queue>
+
+#include "data_array.h"
+#include "suffix_array.h"
+
+using namespace std;
+
+namespace extractor {
+
+int Precomputation::FIRST_NONTERMINAL = -1;
+int Precomputation::SECOND_NONTERMINAL = -2;
+
+Precomputation::Precomputation(
+    shared_ptr<SuffixArray> suffix_array, int num_frequent_patterns,
+    int num_super_frequent_patterns, int max_rule_span,
+    int max_rule_symbols, int min_gap_size,
+    int max_frequent_phrase_len, int min_frequency) {
+  vector<int> data = suffix_array->GetData()->GetData();
+  vector<vector<int> > frequent_patterns = FindMostFrequentPatterns(
+      suffix_array, data, num_frequent_patterns, max_frequent_phrase_len,
+      min_frequency);
+
+  // Construct sets containing the frequent and superfrequent contiguous
+  // collocations.
+  unordered_set<vector<int>, VectorHash> frequent_patterns_set;
+  unordered_set<vector<int>, VectorHash> super_frequent_patterns_set;
+  for (size_t i = 0; i < frequent_patterns.size(); ++i) {
+    frequent_patterns_set.insert(frequent_patterns[i]);
+    if (i < num_super_frequent_patterns) {
+      super_frequent_patterns_set.insert(frequent_patterns[i]);
+    }
+  }
+
+  vector<tuple<int, int, int> > matchings;
+  for (size_t i = 0; i < data.size(); ++i) {
+    // If the sentence is over, add all the discontiguous frequent patterns to
+    // the index.
+    if (data[i] == DataArray::END_OF_LINE) {
+      AddCollocations(matchings, data, max_rule_span, min_gap_size,
+          max_rule_symbols);
+      matchings.clear();
+      continue;
+    }
+    vector<int> pattern;
+    // Find all the contiguous frequent patterns starting at position i.
+    for (int j = 1; j <= max_frequent_phrase_len && i + j <= data.size(); ++j) {
+      pattern.push_back(data[i + j - 1]);
+      if (frequent_patterns_set.count(pattern)) {
+        int is_super_frequent = super_frequent_patterns_set.count(pattern);
+        matchings.push_back(make_tuple(i, j, is_super_frequent));
+      } else {
+        // If the current pattern is not frequent, any longer pattern having the
+        // current pattern as prefix will not be frequent.
+        break;
+      }
+    }
+  }
+}
+
+Precomputation::Precomputation() {}
+
+Precomputation::~Precomputation() {}
+
+vector<vector<int> > Precomputation::FindMostFrequentPatterns(
+    shared_ptr<SuffixArray> suffix_array, const vector<int>& data,
+    int num_frequent_patterns, int max_frequent_phrase_len, int min_frequency) {
+  vector<int> lcp = suffix_array->BuildLCPArray();
+  vector<int> run_start(max_frequent_phrase_len);
+
+  // Find all the patterns occurring at least min_frequency times.
+  priority_queue<pair<int, pair<int, int> > > heap;
+  for (size_t i = 1; i < lcp.size(); ++i) {
+    for (int len = lcp[i]; len < max_frequent_phrase_len; ++len) {
+      int frequency = i - run_start[len];
+      if (frequency >= min_frequency) {
+        heap.push(make_pair(frequency,
+            make_pair(suffix_array->GetSuffix(run_start[len]), len + 1)));
+      }
+      run_start[len] = i;
+    }
+  }
+
+  // Extract the most frequent patterns.
+  vector<vector<int> > frequent_patterns;
+  while (frequent_patterns.size() < num_frequent_patterns && !heap.empty()) {
+    int start = heap.top().second.first;
+    int len = heap.top().second.second;
+    heap.pop();
+
+    vector<int> pattern(data.begin() + start, data.begin() + start + len);
+    if (find(pattern.begin(), pattern.end(), DataArray::END_OF_LINE) ==
+        pattern.end()) {
+      frequent_patterns.push_back(pattern);
+    }
+  }
+  return frequent_patterns;
+}
+
+void Precomputation::AddCollocations(
+    const vector<tuple<int, int, int> >& matchings, const vector<int>& data,
+    int max_rule_span, int min_gap_size, int max_rule_symbols) {
+  // Select the leftmost subpattern.
+  for (size_t i = 0; i < matchings.size(); ++i) {
+    int start1, size1, is_super1;
+    tie(start1, size1, is_super1) = matchings[i];
+
+    // Select the second (middle) subpattern
+    for (size_t j = i + 1; j < matchings.size(); ++j) {
+      int start2, size2, is_super2;
+      tie(start2, size2, is_super2) = matchings[j];
+      if (start2 - start1 >= max_rule_span) {
+        break;
+      }
+
+      if (start2 - start1 - size1 >= min_gap_size
+          && start2 + size2 - start1 <= max_rule_span
+          && size1 + size2 + 1 <= max_rule_symbols) {
+        vector<int> pattern(data.begin() + start1,
+            data.begin() + start1 + size1);
+        pattern.push_back(Precomputation::FIRST_NONTERMINAL);
+        pattern.insert(pattern.end(), data.begin() + start2,
+            data.begin() + start2 + size2);
+        AddStartPositions(collocations[pattern], start1, start2);
+
+        // Try extending the binary collocation to a ternary collocation.
+        if (is_super2) {
+          pattern.push_back(Precomputation::SECOND_NONTERMINAL);
+          // Select the rightmost subpattern.
+          for (size_t k = j + 1; k < matchings.size(); ++k) {
+            int start3, size3, is_super3;
+            tie(start3, size3, is_super3) = matchings[k];
+            if (start3 - start1 >= max_rule_span) {
+              break;
+            }
+
+            if (start3 - start2 - size2 >= min_gap_size
+                && start3 + size3 - start1 <= max_rule_span
+                && size1 + size2 + size3 + 2 <= max_rule_symbols
+                && (is_super1 || is_super3)) {
+              pattern.insert(pattern.end(), data.begin() + start3,
+                  data.begin() + start3 + size3);
+              AddStartPositions(collocations[pattern], start1, start2, start3);
+              pattern.erase(pattern.end() - size3);
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+void Precomputation::AddStartPositions(
+    vector<int>& positions, int pos1, int pos2) {
+  positions.push_back(pos1);
+  positions.push_back(pos2);
+}
+
+void Precomputation::AddStartPositions(
+    vector<int>& positions, int pos1, int pos2, int pos3) {
+  positions.push_back(pos1);
+  positions.push_back(pos2);
+  positions.push_back(pos3);
+}
+
+void Precomputation::WriteBinary(const fs::path& filepath) const {
+  FILE* file = fopen(filepath.string().c_str(), "w");
+
+  // TODO(pauldb): Refactor this code.
+  int size = collocations.size();
+  fwrite(&size, sizeof(int), 1, file);
+  for (auto entry: collocations) {
+    size = entry.first.size();
+    fwrite(&size, sizeof(int), 1, file);
+    fwrite(entry.first.data(), sizeof(int), size, file);
+
+    size = entry.second.size();
+    fwrite(&size, sizeof(int), 1, file);
+    fwrite(entry.second.data(), sizeof(int), size, file);
+  }
+}
+
+const Index& Precomputation::GetCollocations() const {
+  return collocations;
+}
+
+} // namespace extractor
diff --git a/extractor/precomputation.h b/extractor/precomputation.h
new file mode 100644
index 00000000..e3c4d26a
--- /dev/null
+++ b/extractor/precomputation.h
@@ -0,0 +1,80 @@
+#ifndef _PRECOMPUTATION_H_
+#define _PRECOMPUTATION_H_
+
+#include <memory>
+#include <unordered_map>
+#include <unordered_set>
+#include <tuple>
+#include <vector>
+
+#include <boost/filesystem.hpp>
+#include <boost/functional/hash.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+typedef boost::hash<vector<int> > VectorHash;
+typedef unordered_map<vector<int>, vector<int>, VectorHash> Index;
+
+class SuffixArray;
+
+/**
+ * Data structure wrapping an index with all the occurrences of the most
+ * frequent discontiguous collocations in the source data.
+ *
+ * Let a, b, c be contiguous collocations. The index will contain an entry for
+ * every collocation of the form:
+ * - aXb, where a and b are frequent
+ * - aXbXc, where a and b are super-frequent and c is frequent or
+ *                b and c are super-frequent and a is frequent.
+ */
+class Precomputation {
+ public:
+  // Constructs the index using the suffix array.
+  Precomputation(
+      shared_ptr<SuffixArray> suffix_array, int num_frequent_patterns,
+      int num_super_frequent_patterns, int max_rule_span,
+      int max_rule_symbols, int min_gap_size,
+      int max_frequent_phrase_len, int min_frequency);
+
+  virtual ~Precomputation();
+
+  void WriteBinary(const fs::path& filepath) const;
+
+  // Returns a reference to the index.
+  virtual const Index& GetCollocations() const;
+
+  static int FIRST_NONTERMINAL;
+  static int SECOND_NONTERMINAL;
+
+ protected:
+  Precomputation();
+
+ private:
+  // Finds the most frequent contiguous collocations.
+  vector<vector<int> > FindMostFrequentPatterns(
+      shared_ptr<SuffixArray> suffix_array, const vector<int>& data,
+      int num_frequent_patterns, int max_frequent_phrase_len,
+      int min_frequency);
+
+  // Given the locations of the frequent contiguous collocations in a sentence,
+  // it adds new entries to the index for each discontiguous collocation
+  // matching the criteria specified in the class description.
+  void AddCollocations(
+      const vector<std::tuple<int, int, int> >& matchings, const vector<int>& data,
+      int max_rule_span, int min_gap_size, int max_rule_symbols);
+
+  // Adds an occurrence of a binary collocation.
+  void AddStartPositions(vector<int>& positions, int pos1, int pos2);
+
+  // Adds an occurrence of a ternary collocation.
+  void AddStartPositions(vector<int>& positions, int pos1, int pos2, int pos3);
+
+  Index collocations;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/precomputation_test.cc b/extractor/precomputation_test.cc
new file mode 100644
index 00000000..363febb7
--- /dev/null
+++ b/extractor/precomputation_test.cc
@@ -0,0 +1,106 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <vector>
+
+#include "mocks/mock_data_array.h"
+#include "mocks/mock_suffix_array.h"
+#include "precomputation.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class PrecomputationTest : public Test {
+ protected:
+  virtual void SetUp() {
+    data = {4, 2, 3, 5, 7, 2, 3, 5, 2, 3, 4, 2, 1};
+    data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*data_array, GetData()).WillRepeatedly(ReturnRef(data));
+
+    vector<int> suffixes{12, 8, 5, 1, 9, 6, 2, 0, 10, 7, 3, 4, 13};
+    vector<int> lcp{-1, 0, 2, 3, 1, 0, 1, 2, 0, 2, 0, 1, 0, 0};
+    suffix_array = make_shared<MockSuffixArray>();
+    EXPECT_CALL(*suffix_array, GetData()).WillRepeatedly(Return(data_array));
+    for (size_t i = 0; i < suffixes.size(); ++i) {
+      EXPECT_CALL(*suffix_array,
+                  GetSuffix(i)).WillRepeatedly(Return(suffixes[i]));
+    }
+    EXPECT_CALL(*suffix_array, BuildLCPArray()).WillRepeatedly(Return(lcp));
+  }
+
+  vector<int> data;
+  shared_ptr<MockDataArray> data_array;
+  shared_ptr<MockSuffixArray> suffix_array;
+};
+
+TEST_F(PrecomputationTest, TestCollocations) {
+  Precomputation precomputation(suffix_array, 3, 3, 10, 5, 1, 4, 2);
+  Index collocations = precomputation.GetCollocations();
+
+  vector<int> key = {2, 3, -1, 2};
+  vector<int> expected_value = {1, 5, 1, 8, 5, 8, 5, 11, 8, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, 3, -1, 2, 3};
+  expected_value = {1, 5, 1, 8, 5, 8};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, 3, -1, 3};
+  expected_value = {1, 6, 1, 9, 5, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 2};
+  expected_value = {2, 5, 2, 8, 2, 11, 6, 8, 6, 11, 9, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 3};
+  expected_value = {2, 6, 2, 9, 6, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 2, 3};
+  expected_value = {2, 5, 2, 8, 6, 8};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 2};
+  expected_value = {1, 5, 1, 8, 5, 8, 5, 11, 8, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 2, 3};
+  expected_value = {1, 5, 1, 8, 5, 8};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 3};
+  expected_value = {1, 6, 1, 9, 5, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+
+  key = {2, -1, 2, -2, 2};
+  expected_value = {1, 5, 8, 5, 8, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 2, -2, 3};
+  expected_value = {1, 5, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 3, -2, 2};
+  expected_value = {1, 6, 8, 5, 9, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {2, -1, 3, -2, 3};
+  expected_value = {1, 6, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 2, -2, 2};
+  expected_value = {2, 5, 8, 2, 5, 11, 2, 8, 11, 6, 8, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 2, -2, 3};
+  expected_value = {2, 5, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 3, -2, 2};
+  expected_value = {2, 6, 8, 2, 6, 11, 2, 9, 11, 6, 9, 11};
+  EXPECT_EQ(expected_value, collocations[key]);
+  key = {3, -1, 3, -2, 3};
+  expected_value = {2, 6, 9};
+  EXPECT_EQ(expected_value, collocations[key]);
+
+  // Exceeds max_rule_symbols.
+  key = {2, -1, 2, -2, 2, 3};
+  EXPECT_EQ(0, collocations.count(key));
+  // Contains non frequent pattern.
+  key = {2, -1, 5};
+  EXPECT_EQ(0, collocations.count(key));
+}
+
+} // namespace
+} // namespace extractor
+
diff --git a/extractor/rule.cc b/extractor/rule.cc
new file mode 100644
index 00000000..b6c7d783
--- /dev/null
+++ b/extractor/rule.cc
@@ -0,0 +1,14 @@
+#include "rule.h"
+
+namespace extractor {
+
+Rule::Rule(const Phrase& source_phrase,
+           const Phrase& target_phrase,
+           const vector<double>& scores,
+           const vector<pair<int, int> >& alignment) :
+  source_phrase(source_phrase),
+  target_phrase(target_phrase),
+  scores(scores),
+  alignment(alignment) {}
+
+} // namespace extractor
diff --git a/extractor/rule.h b/extractor/rule.h
new file mode 100644
index 00000000..bc95709e
--- /dev/null
+++ b/extractor/rule.h
@@ -0,0 +1,27 @@
+#ifndef _RULE_H_
+#define _RULE_H_
+
+#include <vector>
+
+#include "phrase.h"
+
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Structure containing the data for a SCFG rule.
+ */
+struct Rule {
+  Rule(const Phrase& source_phrase, const Phrase& target_phrase,
+       const vector<double>& scores, const vector<pair<int, int> >& alignment);
+
+  Phrase source_phrase;
+  Phrase target_phrase;
+  vector<double> scores;
+  vector<pair<int, int> > alignment;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/rule_extractor.cc b/extractor/rule_extractor.cc
new file mode 100644
index 00000000..fa7386a4
--- /dev/null
+++ b/extractor/rule_extractor.cc
@@ -0,0 +1,343 @@
+#include "rule_extractor.h"
+
+#include <map>
+
+#include "alignment.h"
+#include "data_array.h"
+#include "features/feature.h"
+#include "phrase_builder.h"
+#include "phrase_location.h"
+#include "rule.h"
+#include "rule_extractor_helper.h"
+#include "scorer.h"
+#include "target_phrase_extractor.h"
+
+using namespace std;
+
+namespace extractor {
+
+RuleExtractor::RuleExtractor(
+    shared_ptr<DataArray> source_data_array,
+    shared_ptr<DataArray> target_data_array,
+    shared_ptr<Alignment> alignment,
+    shared_ptr<PhraseBuilder> phrase_builder,
+    shared_ptr<Scorer> scorer,
+    shared_ptr<Vocabulary> vocabulary,
+    int max_rule_span,
+    int min_gap_size,
+    int max_nonterminals,
+    int max_rule_symbols,
+    bool require_aligned_terminal,
+    bool require_aligned_chunks,
+    bool require_tight_phrases) :
+    target_data_array(target_data_array),
+    source_data_array(source_data_array),
+    phrase_builder(phrase_builder),
+    scorer(scorer),
+    max_rule_span(max_rule_span),
+    min_gap_size(min_gap_size),
+    max_nonterminals(max_nonterminals),
+    max_rule_symbols(max_rule_symbols),
+    require_tight_phrases(require_tight_phrases) {
+  helper = make_shared<RuleExtractorHelper>(
+      source_data_array, target_data_array, alignment, max_rule_span,
+      max_rule_symbols, require_aligned_terminal, require_aligned_chunks,
+      require_tight_phrases);
+  target_phrase_extractor = make_shared<TargetPhraseExtractor>(
+      target_data_array, alignment, phrase_builder, helper, vocabulary,
+      max_rule_span, require_tight_phrases);
+}
+
+RuleExtractor::RuleExtractor(
+    shared_ptr<DataArray> source_data_array,
+    shared_ptr<PhraseBuilder> phrase_builder,
+    shared_ptr<Scorer> scorer,
+    shared_ptr<TargetPhraseExtractor> target_phrase_extractor,
+    shared_ptr<RuleExtractorHelper> helper,
+    int max_rule_span,
+    int min_gap_size,
+    int max_nonterminals,
+    int max_rule_symbols,
+    bool require_tight_phrases) :
+    source_data_array(source_data_array),
+    phrase_builder(phrase_builder),
+    scorer(scorer),
+    target_phrase_extractor(target_phrase_extractor),
+    helper(helper),
+    max_rule_span(max_rule_span),
+    min_gap_size(min_gap_size),
+    max_nonterminals(max_nonterminals),
+    max_rule_symbols(max_rule_symbols),
+    require_tight_phrases(require_tight_phrases) {}
+
+RuleExtractor::RuleExtractor() {}
+
+RuleExtractor::~RuleExtractor() {}
+
+vector<Rule> RuleExtractor::ExtractRules(const Phrase& phrase,
+                                         const PhraseLocation& location) const {
+  int num_subpatterns = location.num_subpatterns;
+  vector<int> matchings = *location.matchings;
+
+  // Calculate statistics for the (sampled) occurrences of the source phrase.
+  map<Phrase, double> source_phrase_counter;
+  map<Phrase, map<Phrase, map<PhraseAlignment, int> > > alignments_counter;
+  for (auto i = matchings.begin(); i != matchings.end(); i += num_subpatterns) {
+    vector<int> matching(i, i + num_subpatterns);
+    vector<Extract> extracts = ExtractAlignments(phrase, matching);
+
+    for (Extract e: extracts) {
+      source_phrase_counter[e.source_phrase] += e.pairs_count;
+      alignments_counter[e.source_phrase][e.target_phrase][e.alignment] += 1;
+    }
+  }
+
+  // Compute the feature scores and find the most likely (frequent) alignment
+  // for each pair of source-target phrases.
+  int num_samples = matchings.size() / num_subpatterns;
+  vector<Rule> rules;
+  for (auto source_phrase_entry: alignments_counter) {
+    Phrase source_phrase = source_phrase_entry.first;
+    for (auto target_phrase_entry: source_phrase_entry.second) {
+      Phrase target_phrase = target_phrase_entry.first;
+
+      int max_locations = 0, num_locations = 0;
+      PhraseAlignment most_frequent_alignment;
+      for (auto alignment_entry: target_phrase_entry.second) {
+        num_locations += alignment_entry.second;
+        if (alignment_entry.second > max_locations) {
+          most_frequent_alignment = alignment_entry.first;
+          max_locations = alignment_entry.second;
+        }
+      }
+
+      features::FeatureContext context(source_phrase, target_phrase,
+          source_phrase_counter[source_phrase], num_locations, num_samples);
+      vector<double> scores = scorer->Score(context);
+      rules.push_back(Rule(source_phrase, target_phrase, scores,
+                           most_frequent_alignment));
+    }
+  }
+  return rules;
+}
+
+vector<Extract> RuleExtractor::ExtractAlignments(
+    const Phrase& phrase, const vector<int>& matching) const {
+  vector<Extract> extracts;
+  int sentence_id = source_data_array->GetSentenceId(matching[0]);
+  int source_sent_start = source_data_array->GetSentenceStart(sentence_id);
+
+  // Get the span in the opposite sentence for each word in the source-target
+  // sentece pair.
+  vector<int> source_low, source_high, target_low, target_high;
+  helper->GetLinksSpans(source_low, source_high, target_low, target_high,
+                        sentence_id);
+
+  int num_subpatterns = matching.size();
+  vector<int> chunklen(num_subpatterns);
+  for (size_t i = 0; i < num_subpatterns; ++i) {
+    chunklen[i] = phrase.GetChunkLen(i);
+  }
+
+  // Basic checks to see if we can extract phrase pairs for this occurrence.
+  if (!helper->CheckAlignedTerminals(matching, chunklen, source_low,
+                                     source_sent_start) ||
+      !helper->CheckTightPhrases(matching, chunklen, source_low,
+                                 source_sent_start)) {
+    return extracts;
+  }
+
+  int source_back_low = -1, source_back_high = -1;
+  int source_phrase_low = matching[0] - source_sent_start;
+  int source_phrase_high = matching.back() + chunklen.back() -
+                           source_sent_start;
+  int target_phrase_low = -1, target_phrase_high = -1;
+  // Find target span and reflected source span for the source phrase.
+  if (!helper->FindFixPoint(source_phrase_low, source_phrase_high, source_low,
+                            source_high, target_phrase_low, target_phrase_high,
+                            target_low, target_high, source_back_low,
+                            source_back_high, sentence_id, min_gap_size, 0,
+                            max_nonterminals - matching.size() + 1, true, true,
+                            false)) {
+    return extracts;
+  }
+
+  // Get spans for nonterminal gaps.
+  bool met_constraints = true;
+  int num_symbols = phrase.GetNumSymbols();
+  vector<pair<int, int> > source_gaps, target_gaps;
+  if (!helper->GetGaps(source_gaps, target_gaps, matching, chunklen, source_low,
+                       source_high, target_low, target_high, source_phrase_low,
+                       source_phrase_high, source_back_low, source_back_high,
+                       sentence_id, source_sent_start, num_symbols,
+                       met_constraints)) {
+    return extracts;
+  }
+
+  // Find target phrases aligned with the initial source phrase.
+  bool starts_with_x = source_back_low != source_phrase_low;
+  bool ends_with_x = source_back_high != source_phrase_high;
+  Phrase source_phrase = phrase_builder->Extend(
+      phrase, starts_with_x, ends_with_x);
+  unordered_map<int, int> source_indexes = helper->GetSourceIndexes(
+      matching, chunklen, starts_with_x, source_sent_start);
+  if (met_constraints) {
+    AddExtracts(extracts, source_phrase, source_indexes, target_gaps,
+                target_low, target_phrase_low, target_phrase_high, sentence_id);
+  }
+
+  if (source_gaps.size() >= max_nonterminals ||
+      source_phrase.GetNumSymbols() >= max_rule_symbols ||
+      source_back_high - source_back_low + min_gap_size > max_rule_span) {
+    // Cannot add any more nonterminals.
+    return extracts;
+  }
+
+  // Extend the source phrase by adding a leading and/or trailing nonterminal
+  // and find target phrases aligned with the extended source phrase.
+  for (int i = 0; i < 2; ++i) {
+    for (int j = 1 - i; j < 2; ++j) {
+      AddNonterminalExtremities(extracts, matching, chunklen, source_phrase,
+          source_back_low, source_back_high, source_low, source_high,
+          target_low, target_high, target_gaps, sentence_id, source_sent_start,
+          starts_with_x, ends_with_x, i, j);
+    }
+  }
+
+  return extracts;
+}
+
+void RuleExtractor::AddExtracts(
+    vector<Extract>& extracts, const Phrase& source_phrase,
+    const unordered_map<int, int>& source_indexes,
+    const vector<pair<int, int> >& target_gaps, const vector<int>& target_low,
+    int target_phrase_low, int target_phrase_high, int sentence_id) const {
+  auto target_phrases = target_phrase_extractor->ExtractPhrases(
+      target_gaps, target_low, target_phrase_low, target_phrase_high,
+      source_indexes, sentence_id);
+
+  if (target_phrases.size() > 0) {
+    // Split the probability equally across all target phrases that can be
+    // aligned with a single occurrence of the source phrase.
+    double pairs_count = 1.0 / target_phrases.size();
+    for (auto target_phrase: target_phrases) {
+      extracts.push_back(Extract(source_phrase, target_phrase.first,
+                                 pairs_count, target_phrase.second));
+    }
+  }
+}
+
+void RuleExtractor::AddNonterminalExtremities(
+    vector<Extract>& extracts, const vector<int>& matching,
+    const vector<int>& chunklen, const Phrase& source_phrase,
+    int source_back_low, int source_back_high, const vector<int>& source_low,
+    const vector<int>& source_high, const vector<int>& target_low,
+    const vector<int>& target_high, vector<pair<int, int> > target_gaps,
+    int sentence_id, int source_sent_start, int starts_with_x, int ends_with_x,
+    int extend_left, int extend_right) const {
+  int source_x_low = source_back_low, source_x_high = source_back_high;
+
+  // Check if the extended source phrase will remain tight.
+  if (require_tight_phrases) {
+    if (source_low[source_back_low - extend_left] == -1 ||
+        source_low[source_back_high + extend_right - 1] == -1) {
+      return;
+    }
+  }
+
+  // Check if we can add a nonterminal to the left.
+  if (extend_left) {
+    if (starts_with_x || source_back_low < min_gap_size) {
+      return;
+    }
+
+    source_x_low = source_back_low - min_gap_size;
+    if (require_tight_phrases) {
+      while (source_x_low >= 0 && source_low[source_x_low] == -1) {
+        --source_x_low;
+      }
+    }
+    if (source_x_low < 0) {
+      return;
+    }
+  }
+
+  // Check if we can add a nonterminal to the right.
+  if (extend_right) {
+    int source_sent_len = source_data_array->GetSentenceLength(sentence_id);
+    if (ends_with_x || source_back_high + min_gap_size > source_sent_len) {
+      return;
+    }
+    source_x_high = source_back_high + min_gap_size;
+    if (require_tight_phrases) {
+      while (source_x_high <= source_sent_len &&
+             source_low[source_x_high - 1] == -1) {
+        ++source_x_high;
+      }
+    }
+
+    if (source_x_high > source_sent_len) {
+      return;
+    }
+  }
+
+  // More length checks.
+  int new_nonterminals = extend_left + extend_right;
+  if (source_x_high - source_x_low > max_rule_span ||
+      target_gaps.size() + new_nonterminals > max_nonterminals ||
+      source_phrase.GetNumSymbols() + new_nonterminals > max_rule_symbols) {
+    return;
+  }
+
+  // Find the target span for the extended phrase and the reflected source span.
+  int target_x_low = -1, target_x_high = -1;
+  if (!helper->FindFixPoint(source_x_low, source_x_high, source_low,
+                            source_high, target_x_low, target_x_high,
+                            target_low, target_high, source_x_low,
+                            source_x_high, sentence_id, 1, 1,
+                            new_nonterminals, extend_left, extend_right,
+                            true)) {
+    return;
+  }
+
+  // Check gap integrity for the leading nonterminal.
+  if (extend_left) {
+    int source_gap_low = -1, source_gap_high = -1;
+    int target_gap_low = -1, target_gap_high = -1;
+    if ((require_tight_phrases && source_low[source_x_low] == -1) ||
+        !helper->FindFixPoint(source_x_low, source_back_low, source_low,
+                              source_high, target_gap_low, target_gap_high,
+                              target_low, target_high, source_gap_low,
+                              source_gap_high, sentence_id, 0, 0, 0, false,
+                              false, false)) {
+      return;
+    }
+    target_gaps.insert(target_gaps.begin(),
+                       make_pair(target_gap_low, target_gap_high));
+  }
+
+  // Check gap integrity for the trailing nonterminal.
+  if (extend_right) {
+    int target_gap_low = -1, target_gap_high = -1;
+    int source_gap_low = -1, source_gap_high = -1;
+    if ((require_tight_phrases && source_low[source_x_high - 1] == -1) ||
+        !helper->FindFixPoint(source_back_high, source_x_high, source_low,
+                              source_high, target_gap_low, target_gap_high,
+                              target_low, target_high, source_gap_low,
+                              source_gap_high, sentence_id, 0, 0, 0, false,
+                              false, false)) {
+      return;
+    }
+    target_gaps.push_back(make_pair(target_gap_low, target_gap_high));
+  }
+
+  // Find target phrases aligned with the extended source phrase.
+  Phrase new_source_phrase = phrase_builder->Extend(source_phrase, extend_left,
+                                                    extend_right);
+  unordered_map<int, int> source_indexes = helper->GetSourceIndexes(
+      matching, chunklen, extend_left || starts_with_x, source_sent_start);
+  AddExtracts(extracts, new_source_phrase, source_indexes, target_gaps,
+              target_low, target_x_low, target_x_high, sentence_id);
+}
+
+} // namespace extractor
diff --git a/extractor/rule_extractor.h b/extractor/rule_extractor.h
new file mode 100644
index 00000000..26e6f21c
--- /dev/null
+++ b/extractor/rule_extractor.h
@@ -0,0 +1,124 @@
+#ifndef _RULE_EXTRACTOR_H_
+#define _RULE_EXTRACTOR_H_
+
+#include <memory>
+#include <unordered_map>
+#include <vector>
+
+#include "phrase.h"
+
+using namespace std;
+
+namespace extractor {
+
+typedef vector<pair<int, int> > PhraseAlignment;
+
+class Alignment;
+class DataArray;
+class PhraseBuilder;
+class PhraseLocation;
+class Rule;
+class RuleExtractorHelper;
+class Scorer;
+class TargetPhraseExtractor;
+
+/**
+ * Structure containing data about the occurrences of a source-target phrase pair
+ * in the parallel corpus.
+ */
+struct Extract {
+  Extract(const Phrase& source_phrase, const Phrase& target_phrase,
+          double pairs_count, const PhraseAlignment& alignment) :
+      source_phrase(source_phrase), target_phrase(target_phrase),
+      pairs_count(pairs_count), alignment(alignment) {}
+
+  Phrase source_phrase;
+  Phrase target_phrase;
+  double pairs_count;
+  PhraseAlignment alignment;
+};
+
+/**
+ * Component for extracting SCFG rules.
+ */
+class RuleExtractor {
+ public:
+  RuleExtractor(shared_ptr<DataArray> source_data_array,
+                shared_ptr<DataArray> target_data_array,
+                shared_ptr<Alignment> alingment,
+                shared_ptr<PhraseBuilder> phrase_builder,
+                shared_ptr<Scorer> scorer,
+                shared_ptr<Vocabulary> vocabulary,
+                int min_gap_size,
+                int max_rule_span,
+                int max_nonterminals,
+                int max_rule_symbols,
+                bool require_aligned_terminal,
+                bool require_aligned_chunks,
+                bool require_tight_phrases);
+
+  // For testing only.
+  RuleExtractor(shared_ptr<DataArray> source_data_array,
+                shared_ptr<PhraseBuilder> phrase_builder,
+                shared_ptr<Scorer> scorer,
+                shared_ptr<TargetPhraseExtractor> target_phrase_extractor,
+                shared_ptr<RuleExtractorHelper> helper,
+                int max_rule_span,
+                int min_gap_size,
+                int max_nonterminals,
+                int max_rule_symbols,
+                bool require_tight_phrases);
+
+  virtual ~RuleExtractor();
+
+  // Extracts SCFG rules given a source phrase and a set of its occurrences
+  // in the source data.
+  virtual vector<Rule> ExtractRules(const Phrase& phrase,
+                                    const PhraseLocation& location) const;
+
+ protected:
+  RuleExtractor();
+
+ private:
+  // Finds all target phrases that can be aligned with the source phrase for a
+  // particular occurrence in the data.
+  vector<Extract> ExtractAlignments(const Phrase& phrase,
+                                    const vector<int>& matching) const;
+
+  // Extracts all target phrases for a given occurrence of the source phrase in
+  // the data. Constructs a vector of Extracts using these target phrases.
+  void AddExtracts(
+      vector<Extract>& extracts, const Phrase& source_phrase,
+      const unordered_map<int, int>& source_indexes,
+      const vector<pair<int, int> >& target_gaps, const vector<int>& target_low,
+      int target_phrase_low, int target_phrase_high, int sentence_id) const;
+
+  // Adds a leading and/or trailing nonterminal to the source phrase and
+  // extracts target phrases that can be aligned with the extended source
+  // phrase.
+  void AddNonterminalExtremities(
+      vector<Extract>& extracts, const vector<int>& matching,
+      const vector<int>& chunklen, const Phrase& source_phrase,
+      int source_back_low, int source_back_high, const vector<int>& source_low,
+      const vector<int>& source_high, const vector<int>& target_low,
+      const vector<int>& target_high, vector<pair<int, int> > target_gaps,
+      int sentence_id, int source_sent_start, int starts_with_x,
+      int ends_with_x, int extend_left, int extend_right) const;
+
+ private:
+  shared_ptr<DataArray> target_data_array;
+  shared_ptr<DataArray> source_data_array;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<Scorer> scorer;
+  shared_ptr<TargetPhraseExtractor> target_phrase_extractor;
+  shared_ptr<RuleExtractorHelper> helper;
+  int max_rule_span;
+  int min_gap_size;
+  int max_nonterminals;
+  int max_rule_symbols;
+  bool require_tight_phrases;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/rule_extractor_helper.cc b/extractor/rule_extractor_helper.cc
new file mode 100644
index 00000000..8a9516f2
--- /dev/null
+++ b/extractor/rule_extractor_helper.cc
@@ -0,0 +1,362 @@
+#include "rule_extractor_helper.h"
+
+#include "data_array.h"
+#include "alignment.h"
+
+namespace extractor {
+
+RuleExtractorHelper::RuleExtractorHelper(
+    shared_ptr<DataArray> source_data_array,
+    shared_ptr<DataArray> target_data_array,
+    shared_ptr<Alignment> alignment,
+    int max_rule_span,
+    int max_rule_symbols,
+    bool require_aligned_terminal,
+    bool require_aligned_chunks,
+    bool require_tight_phrases) :
+    source_data_array(source_data_array),
+    target_data_array(target_data_array),
+    alignment(alignment),
+    max_rule_span(max_rule_span),
+    max_rule_symbols(max_rule_symbols),
+    require_aligned_terminal(require_aligned_terminal),
+    require_aligned_chunks(require_aligned_chunks),
+    require_tight_phrases(require_tight_phrases) {}
+
+RuleExtractorHelper::RuleExtractorHelper() {}
+
+RuleExtractorHelper::~RuleExtractorHelper() {}
+
+void RuleExtractorHelper::GetLinksSpans(
+    vector<int>& source_low, vector<int>& source_high,
+    vector<int>& target_low, vector<int>& target_high, int sentence_id) const {
+  int source_sent_len = source_data_array->GetSentenceLength(sentence_id);
+  int target_sent_len = target_data_array->GetSentenceLength(sentence_id);
+  source_low = vector<int>(source_sent_len, -1);
+  source_high = vector<int>(source_sent_len, -1);
+
+  target_low = vector<int>(target_sent_len, -1);
+  target_high = vector<int>(target_sent_len, -1);
+  vector<pair<int, int> > links = alignment->GetLinks(sentence_id);
+  for (auto link: links) {
+    if (source_low[link.first] == -1 || source_low[link.first] > link.second) {
+      source_low[link.first] = link.second;
+    }
+    source_high[link.first] = max(source_high[link.first], link.second + 1);
+
+    if (target_low[link.second] == -1 || target_low[link.second] > link.first) {
+      target_low[link.second] = link.first;
+    }
+    target_high[link.second] = max(target_high[link.second], link.first + 1);
+  }
+}
+
+bool RuleExtractorHelper::CheckAlignedTerminals(
+    const vector<int>& matching,
+    const vector<int>& chunklen,
+    const vector<int>& source_low,
+    int source_sent_start) const {
+  if (!require_aligned_terminal) {
+    return true;
+  }
+
+  int num_aligned_chunks = 0;
+  for (size_t i = 0; i < chunklen.size(); ++i) {
+    for (size_t j = 0; j < chunklen[i]; ++j) {
+      int sent_index = matching[i] - source_sent_start + j;
+      if (source_low[sent_index] != -1) {
+        ++num_aligned_chunks;
+        break;
+      }
+    }
+  }
+
+  if (num_aligned_chunks == 0) {
+    return false;
+  }
+
+  return !require_aligned_chunks || num_aligned_chunks == chunklen.size();
+}
+
+bool RuleExtractorHelper::CheckTightPhrases(
+    const vector<int>& matching,
+    const vector<int>& chunklen,
+    const vector<int>& source_low,
+    int source_sent_start) const {
+  if (!require_tight_phrases) {
+    return true;
+  }
+
+  // Check if the chunk extremities are aligned.
+  for (size_t i = 0; i + 1 < chunklen.size(); ++i) {
+    int gap_start = matching[i] + chunklen[i] - source_sent_start;
+    int gap_end = matching[i + 1] - 1 - source_sent_start;
+    if (source_low[gap_start] == -1 || source_low[gap_end] == -1) {
+      return false;
+    }
+  }
+
+  return true;
+}
+
+bool RuleExtractorHelper::FindFixPoint(
+    int source_phrase_low, int source_phrase_high,
+    const vector<int>& source_low, const vector<int>& source_high,
+    int& target_phrase_low, int& target_phrase_high,
+    const vector<int>& target_low, const vector<int>& target_high,
+    int& source_back_low, int& source_back_high, int sentence_id,
+    int min_source_gap_size, int min_target_gap_size,
+    int max_new_x, bool allow_low_x, bool allow_high_x,
+    bool allow_arbitrary_expansion) const {
+  int prev_target_low = target_phrase_low;
+  int prev_target_high = target_phrase_high;
+
+  FindProjection(source_phrase_low, source_phrase_high, source_low,
+                 source_high, target_phrase_low, target_phrase_high);
+
+  if (target_phrase_low == -1) {
+    // Note: Low priority corner case inherited from Adam's code:
+    // If w is unaligned, but we don't require aligned terminals, returning an
+    // error here prevents the extraction of the allowed rule
+    // X -> X_1 w X_2 / X_1 X_2
+    return false;
+  }
+
+  int source_sent_len = source_data_array->GetSentenceLength(sentence_id);
+  int target_sent_len = target_data_array->GetSentenceLength(sentence_id);
+  // Extend the target span to the left.
+  if (prev_target_low != -1 && target_phrase_low != prev_target_low) {
+    if (prev_target_low - target_phrase_low < min_target_gap_size) {
+      target_phrase_low = prev_target_low - min_target_gap_size;
+      if (target_phrase_low < 0) {
+        return false;
+      }
+    }
+  }
+
+  // Extend the target span to the right.
+  if (prev_target_high != -1 && target_phrase_high != prev_target_high) {
+    if (target_phrase_high - prev_target_high < min_target_gap_size) {
+      target_phrase_high = prev_target_high + min_target_gap_size;
+      if (target_phrase_high > target_sent_len) {
+        return false;
+      }
+    }
+  }
+
+  // Check target span length.
+  if (target_phrase_high - target_phrase_low > max_rule_span) {
+    return false;
+  }
+
+  // Find the initial reflected source span.
+  source_back_low = source_back_high = -1;
+  FindProjection(target_phrase_low, target_phrase_high, target_low, target_high,
+                 source_back_low, source_back_high);
+  int new_x = 0;
+  bool new_low_x = false, new_high_x = false;
+  while (true) {
+    source_back_low = min(source_back_low, source_phrase_low);
+    source_back_high = max(source_back_high, source_phrase_high);
+
+    // Stop if the reflected source span matches the previous source span.
+    if (source_back_low == source_phrase_low &&
+        source_back_high == source_phrase_high) {
+      return true;
+    }
+
+    if (!allow_low_x && source_back_low < source_phrase_low) {
+      // Extension on the left side not allowed.
+      return false;
+    }
+    if (!allow_high_x && source_back_high > source_phrase_high) {
+      // Extension on the right side not allowed.
+      return false;
+    }
+
+    // Extend left side.
+    if (source_back_low < source_phrase_low) {
+      if (new_low_x == false) {
+        if (new_x >= max_new_x) {
+          return false;
+        }
+        new_low_x = true;
+        ++new_x;
+      }
+      if (source_phrase_low - source_back_low < min_source_gap_size) {
+        source_back_low = source_phrase_low - min_source_gap_size;
+        if (source_back_low < 0) {
+          return false;
+        }
+      }
+    }
+
+    // Extend right side.
+    if (source_back_high > source_phrase_high) {
+      if (new_high_x == false) {
+        if (new_x >= max_new_x) {
+          return false;
+        }
+        new_high_x = true;
+        ++new_x;
+      }
+      if (source_back_high - source_phrase_high < min_source_gap_size) {
+        source_back_high = source_phrase_high + min_source_gap_size;
+        if (source_back_high > source_sent_len) {
+          return false;
+        }
+      }
+    }
+
+    if (source_back_high - source_back_low > max_rule_span) {
+      // Rule span too wide.
+      return false;
+    }
+
+    prev_target_low = target_phrase_low;
+    prev_target_high = target_phrase_high;
+    // Find the reflection including the left gap (if one was added).
+    FindProjection(source_back_low, source_phrase_low, source_low, source_high,
+                   target_phrase_low, target_phrase_high);
+    // Find the reflection including the right gap (if one was added).
+    FindProjection(source_phrase_high, source_back_high, source_low,
+                   source_high, target_phrase_low, target_phrase_high);
+    // Stop if the new re-reflected target span matches the previous target
+    // span.
+    if (prev_target_low == target_phrase_low &&
+        prev_target_high == target_phrase_high) {
+      return true;
+    }
+
+    if (!allow_arbitrary_expansion) {
+      // Arbitrary expansion not allowed.
+      return false;
+    }
+    if (target_phrase_high - target_phrase_low > max_rule_span) {
+      // Target side too wide.
+      return false;
+    }
+
+    source_phrase_low = source_back_low;
+    source_phrase_high = source_back_high;
+    // Re-reflect the target span.
+    FindProjection(target_phrase_low, prev_target_low, target_low, target_high,
+                   source_back_low, source_back_high);
+    FindProjection(prev_target_high, target_phrase_high, target_low,
+                   target_high, source_back_low, source_back_high);
+  }
+
+  return false;
+}
+
+void RuleExtractorHelper::FindProjection(
+    int source_phrase_low, int source_phrase_high,
+    const vector<int>& source_low, const vector<int>& source_high,
+    int& target_phrase_low, int& target_phrase_high) const {
+  for (size_t i = source_phrase_low; i < source_phrase_high; ++i) {
+    if (source_low[i] != -1) {
+      if (target_phrase_low == -1 || source_low[i] < target_phrase_low) {
+        target_phrase_low = source_low[i];
+      }
+      target_phrase_high = max(target_phrase_high, source_high[i]);
+    }
+  }
+}
+
+bool RuleExtractorHelper::GetGaps(
+     vector<pair<int, int> >& source_gaps, vector<pair<int, int> >& target_gaps,
+     const vector<int>& matching, const vector<int>& chunklen,
+     const vector<int>& source_low, const vector<int>& source_high,
+     const vector<int>& target_low, const vector<int>& target_high,
+     int source_phrase_low, int source_phrase_high, int source_back_low,
+     int source_back_high, int sentence_id, int source_sent_start,
+     int& num_symbols, bool& met_constraints) const {
+  if (source_back_low < source_phrase_low) {
+    source_gaps.push_back(make_pair(source_back_low, source_phrase_low));
+    if (num_symbols >= max_rule_symbols) {
+      // Source side contains too many symbols.
+      return false;
+    }
+    ++num_symbols;
+    if (require_tight_phrases && (source_low[source_back_low] == -1 ||
+        source_low[source_phrase_low - 1] == -1)) {
+      // Inside edges of preceding gap are not tight.
+      return false;
+    }
+  } else if (require_tight_phrases && source_low[source_phrase_low] == -1) {
+    // This is not a hard error. We can't extract this phrase, but we might
+    // still be able to extract a superphrase.
+    met_constraints = false;
+  }
+
+  for (size_t i = 0; i + 1 < chunklen.size(); ++i) {
+    int gap_start = matching[i] + chunklen[i] - source_sent_start;
+    int gap_end = matching[i + 1] - source_sent_start;
+    source_gaps.push_back(make_pair(gap_start, gap_end));
+  }
+
+  if (source_phrase_high < source_back_high) {
+    source_gaps.push_back(make_pair(source_phrase_high, source_back_high));
+    if (num_symbols >= max_rule_symbols) {
+      // Source side contains too many symbols.
+      return false;
+    }
+    ++num_symbols;
+    if (require_tight_phrases && (source_low[source_phrase_high] == -1 ||
+        source_low[source_back_high - 1] == -1)) {
+      // Inside edges of following gap are not tight.
+      return false;
+    }
+  } else if (require_tight_phrases &&
+             source_low[source_phrase_high - 1] == -1) {
+    // This is not a hard error. We can't extract this phrase, but we might
+    // still be able to extract a superphrase.
+    met_constraints = false;
+  }
+
+  target_gaps.resize(source_gaps.size(), make_pair(-1, -1));
+  for (size_t i = 0; i < source_gaps.size(); ++i) {
+    if (!FindFixPoint(source_gaps[i].first, source_gaps[i].second, source_low,
+                      source_high, target_gaps[i].first, target_gaps[i].second,
+                      target_low, target_high, source_gaps[i].first,
+                      source_gaps[i].second, sentence_id, 0, 0, 0, false, false,
+                      false)) {
+      // Gap fails integrity check.
+      return false;
+    }
+  }
+
+  return true;
+}
+
+vector<int> RuleExtractorHelper::GetGapOrder(
+    const vector<pair<int, int> >& gaps) const {
+  vector<int> gap_order(gaps.size());
+  for (size_t i = 0; i < gap_order.size(); ++i) {
+    for (size_t j = 0; j < i; ++j) {
+      if (gaps[gap_order[j]] < gaps[i]) {
+        ++gap_order[i];
+      } else {
+        ++gap_order[j];
+      }
+    }
+  }
+  return gap_order;
+}
+
+unordered_map<int, int> RuleExtractorHelper::GetSourceIndexes(
+    const vector<int>& matching, const vector<int>& chunklen,
+    int starts_with_x, int source_sent_start) const {
+ unordered_map<int, int> source_indexes;
+ int num_symbols = starts_with_x;
+ for (size_t i = 0; i < matching.size(); ++i) {
+   for (size_t j = 0; j < chunklen[i]; ++j) {
+     source_indexes[matching[i] + j - source_sent_start] = num_symbols;
+     ++num_symbols;
+   }
+   ++num_symbols;
+ }
+ return source_indexes;
+}
+
+} // namespace extractor
diff --git a/extractor/rule_extractor_helper.h b/extractor/rule_extractor_helper.h
new file mode 100644
index 00000000..d4ae45d4
--- /dev/null
+++ b/extractor/rule_extractor_helper.h
@@ -0,0 +1,101 @@
+#ifndef _RULE_EXTRACTOR_HELPER_H_
+#define _RULE_EXTRACTOR_HELPER_H_
+
+#include <memory>
+#include <unordered_map>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+class Alignment;
+class DataArray;
+
+/**
+ * Helper class for extracting SCFG rules.
+ */
+class RuleExtractorHelper {
+ public:
+  RuleExtractorHelper(shared_ptr<DataArray> source_data_array,
+                      shared_ptr<DataArray> target_data_array,
+                      shared_ptr<Alignment> alignment,
+                      int max_rule_span,
+                      int max_rule_symbols,
+                      bool require_aligned_terminal,
+                      bool require_aligned_chunks,
+                      bool require_tight_phrases);
+
+  virtual ~RuleExtractorHelper();
+
+  // Find the alignment span for each word in the source target sentence pair.
+  virtual void GetLinksSpans(vector<int>& source_low, vector<int>& source_high,
+                             vector<int>& target_low, vector<int>& target_high,
+                             int sentence_id) const;
+
+  // Check if one chunk (all chunks) is aligned at least in one point.
+  virtual bool CheckAlignedTerminals(const vector<int>& matching,
+                                     const vector<int>& chunklen,
+                                     const vector<int>& source_low,
+                                     int source_sent_start) const;
+
+  // Check if the chunks are tight.
+  virtual bool CheckTightPhrases(const vector<int>& matching,
+                                 const vector<int>& chunklen,
+                                 const vector<int>& source_low,
+                                 int source_sent_start) const;
+
+  // Find the target span and the reflected source span for a source phrase
+  // occurrence.
+  virtual bool FindFixPoint(
+      int source_phrase_low, int source_phrase_high,
+      const vector<int>& source_low, const vector<int>& source_high,
+      int& target_phrase_low, int& target_phrase_high,
+      const vector<int>& target_low, const vector<int>& target_high,
+      int& source_back_low, int& source_back_high, int sentence_id,
+      int min_source_gap_size, int min_target_gap_size,
+      int max_new_x, bool allow_low_x, bool allow_high_x,
+      bool allow_arbitrary_expansion) const;
+
+  // Find the gap spans for each nonterminal in the source phrase.
+  virtual bool GetGaps(
+      vector<pair<int, int> >& source_gaps, vector<pair<int, int> >& target_gaps,
+      const vector<int>& matching, const vector<int>& chunklen,
+      const vector<int>& source_low, const vector<int>& source_high,
+      const vector<int>& target_low, const vector<int>& target_high,
+      int source_phrase_low, int source_phrase_high, int source_back_low,
+      int source_back_high, int sentence_id, int source_sent_start,
+      int& num_symbols, bool& met_constraints) const;
+
+  // Get the order of the nonterminals in the target phrase.
+  virtual vector<int> GetGapOrder(const vector<pair<int, int> >& gaps) const;
+
+  // Map each terminal symbol with its position in the source phrase.
+  virtual unordered_map<int, int> GetSourceIndexes(
+      const vector<int>& matching, const vector<int>& chunklen,
+      int starts_with_x, int source_sent_start) const;
+
+ protected:
+  RuleExtractorHelper();
+
+ private:
+  // Find the projection of a source phrase in the target sentence. May also be
+  // used to find the projection of a target phrase in the source sentence.
+  void FindProjection(
+      int source_phrase_low, int source_phrase_high,
+      const vector<int>& source_low, const vector<int>& source_high,
+      int& target_phrase_low, int& target_phrase_high) const;
+
+  shared_ptr<DataArray> source_data_array;
+  shared_ptr<DataArray> target_data_array;
+  shared_ptr<Alignment> alignment;
+  int max_rule_span;
+  int max_rule_symbols;
+  bool require_aligned_terminal;
+  bool require_aligned_chunks;
+  bool require_tight_phrases;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/rule_extractor_helper_test.cc b/extractor/rule_extractor_helper_test.cc
new file mode 100644
index 00000000..9b82abb1
--- /dev/null
+++ b/extractor/rule_extractor_helper_test.cc
@@ -0,0 +1,645 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "mocks/mock_alignment.h"
+#include "mocks/mock_data_array.h"
+#include "rule_extractor_helper.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class RuleExtractorHelperTest : public Test {
+ protected:
+  virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+        .WillRepeatedly(Return(12));
+
+    target_data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+        .WillRepeatedly(Return(12));
+
+    vector<pair<int, int> > links = {
+      make_pair(0, 0), make_pair(0, 1), make_pair(2, 2), make_pair(3, 1)
+    };
+    alignment = make_shared<MockAlignment>();
+    EXPECT_CALL(*alignment, GetLinks(_)).WillRepeatedly(Return(links));
+  }
+
+  shared_ptr<MockDataArray> source_data_array;
+  shared_ptr<MockDataArray> target_data_array;
+  shared_ptr<MockAlignment> alignment;
+  shared_ptr<RuleExtractorHelper> helper;
+};
+
+TEST_F(RuleExtractorHelperTest, TestGetLinksSpans) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(4));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+
+  vector<int> source_low, source_high, target_low, target_high;
+  helper->GetLinksSpans(source_low, source_high, target_low, target_high, 0);
+
+  vector<int> expected_source_low = {0, -1, 2, 1};
+  EXPECT_EQ(expected_source_low, source_low);
+  vector<int> expected_source_high = {2, -1, 3, 2};
+  EXPECT_EQ(expected_source_high, source_high);
+  vector<int> expected_target_low = {0, 0, 2};
+  EXPECT_EQ(expected_target_low, target_low);
+  vector<int> expected_target_high = {1, 4, 3};
+  EXPECT_EQ(expected_target_high, target_high);
+}
+
+TEST_F(RuleExtractorHelperTest, TestCheckAlignedFalse) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, false, false, true);
+  EXPECT_CALL(*source_data_array, GetSentenceId(_)).Times(0);
+  EXPECT_CALL(*source_data_array, GetSentenceStart(_)).Times(0);
+
+  vector<int> matching, chunklen, source_low;
+  EXPECT_TRUE(helper->CheckAlignedTerminals(matching, chunklen,
+                                            source_low, 10));
+}
+
+TEST_F(RuleExtractorHelperTest, TestCheckAlignedTerminal) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, false, true);
+
+  vector<int> matching = {10, 12};
+  vector<int> chunklen = {1, 3};
+  vector<int> source_low = {-1, 1, -1, 3, -1};
+  EXPECT_TRUE(helper->CheckAlignedTerminals(matching, chunklen,
+                                            source_low, 10));
+  source_low = {-1, 1, -1, -1, -1};
+  EXPECT_FALSE(helper->CheckAlignedTerminals(matching, chunklen,
+                                             source_low, 10));
+}
+
+TEST_F(RuleExtractorHelperTest, TestCheckAlignedChunks) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+
+  vector<int> matching = {10, 12};
+  vector<int> chunklen = {1, 3};
+  vector<int> source_low = {2, 1, -1, 3, -1};
+  EXPECT_TRUE(helper->CheckAlignedTerminals(matching, chunklen,
+                                            source_low, 10));
+  source_low = {-1, 1, -1, 3, -1};
+  EXPECT_FALSE(helper->CheckAlignedTerminals(matching, chunklen,
+                                             source_low, 10));
+  source_low = {2, 1, -1, -1, -1};
+  EXPECT_FALSE(helper->CheckAlignedTerminals(matching, chunklen,
+                                             source_low, 10));
+}
+
+
+TEST_F(RuleExtractorHelperTest, TestCheckTightPhrasesFalse) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, false);
+  EXPECT_CALL(*source_data_array, GetSentenceId(_)).Times(0);
+  EXPECT_CALL(*source_data_array, GetSentenceStart(_)).Times(0);
+
+  vector<int> matching, chunklen, source_low;
+  EXPECT_TRUE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+}
+
+TEST_F(RuleExtractorHelperTest, TestCheckTightPhrases) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+
+  vector<int> matching = {10, 14, 18};
+  vector<int> chunklen = {2, 3, 1};
+  // No missing links.
+  vector<int> source_low = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+  EXPECT_TRUE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+
+  // Missing link at the beginning or ending of a gap.
+  source_low = {0, 1, -1, 3, 4, 5, 6, 7, 8};
+  EXPECT_FALSE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+  source_low = {0, 1, 2, -1, 4, 5, 6, 7, 8};
+  EXPECT_FALSE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+  source_low = {0, 1, 2, 3, 4, 5, 6, -1, 8};
+  EXPECT_FALSE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+
+  // Missing link inside the gap.
+  chunklen = {1, 3, 1};
+  source_low = {0, 1, -1, 3, 4, 5, 6, 7, 8};
+  EXPECT_TRUE(helper->CheckTightPhrases(matching, chunklen, source_low, 10));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointBadEdgeCase) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+
+  vector<int> source_low = {0, -1, 2};
+  vector<int> source_high = {1, -1, 3};
+  vector<int> target_low = {0, -1, 2};
+  vector<int> target_high = {1, -1, 3};
+  int source_phrase_low = 1, source_phrase_high = 2;
+  int source_back_low, source_back_high;
+  int target_phrase_low = -1, target_phrase_high = 1;
+
+  // This should be in fact true. See comment about the inherited bug.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 0, 0,
+                                    0, false, false, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointTargetSentenceOutOfBounds) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+
+  vector<int> source_low = {0, 0, 2};
+  vector<int> source_high = {1, 2, 3};
+  vector<int> target_low = {0, 1, 2};
+  vector<int> target_high = {2, 2, 3};
+  int source_phrase_low = 1, source_phrase_high = 2;
+  int source_back_low, source_back_high;
+  int target_phrase_low = 1, target_phrase_high = 2;
+
+  // Extend out of sentence to left.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 2, 2,
+                                    0, false, false, false));
+  source_low = {0, 1, 2};
+  source_high = {1, 3, 3};
+  target_low = {0, 1, 1};
+  target_high = {1, 2, 3};
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 2, 2,
+                                    0, false, false, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointTargetTooWide) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 5, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  vector<int> source_low = {0, 0, 0, 0, 0, 0, 0};
+  vector<int> source_high = {7, 7, 7, 7, 7, 7, 7};
+  vector<int> target_low = {0, -1, -1, -1, -1, -1, 0};
+  vector<int> target_high = {7, -1, -1, -1, -1, -1, 7};
+  int source_phrase_low = 2, source_phrase_high = 5;
+  int source_back_low, source_back_high;
+  int target_phrase_low = -1, target_phrase_high = -1;
+
+  // Projection is too wide.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    0, false, false, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPoint) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  vector<int> source_low = {1, 1, 1, 3, 4, 5, 5};
+  vector<int> source_high = {2, 2, 3, 4, 6, 6, 6};
+  vector<int> target_low = {-1, 0, 2, 3, 4, 4, -1};
+  vector<int> target_high = {-1, 3, 3, 4, 5, 7, -1};
+  int source_phrase_low = 2, source_phrase_high = 5;
+  int source_back_low, source_back_high;
+  int target_phrase_low = 2, target_phrase_high = 5;
+
+  EXPECT_TRUE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                   source_low, source_high, target_phrase_low,
+                                   target_phrase_high, target_low, target_high,
+                                   source_back_low, source_back_high, 1, 1, 1,
+                                   2, true, true, false));
+  EXPECT_EQ(1, target_phrase_low);
+  EXPECT_EQ(6, target_phrase_high);
+  EXPECT_EQ(0, source_back_low);
+  EXPECT_EQ(7, source_back_high);
+
+  source_low = {0, -1, 1, 3, 4, -1, 6};
+  source_high = {1, -1, 3, 4, 6, -1, 7};
+  target_low = {0, 2, 2, 3, 4, 4, 6};
+  target_high = {1, 3, 3, 4, 5, 5, 7};
+  source_phrase_low = 2, source_phrase_high = 5;
+  target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_TRUE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                   source_low, source_high, target_phrase_low,
+                                   target_phrase_high, target_low, target_high,
+                                   source_back_low, source_back_high, 1, 1, 1,
+                                   2, true, true, false));
+  EXPECT_EQ(1, target_phrase_low);
+  EXPECT_EQ(6, target_phrase_high);
+  EXPECT_EQ(2, source_back_low);
+  EXPECT_EQ(5, source_back_high);
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointExtensionsNotAllowed) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+
+  vector<int> source_low = {0, 0, 2};
+  vector<int> source_high = {1, 2, 3};
+  vector<int> target_low = {0, 1, 2};
+  vector<int> target_high = {2, 2, 3};
+  int source_phrase_low = 1, source_phrase_high = 2;
+  int source_back_low, source_back_high;
+  int target_phrase_low = -1, target_phrase_high = -1;
+
+  // Extension on the left side not allowed.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    1, false, true, false));
+  // Extension on the left side is allowed, but we can't add anymore X.
+  target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    0, true, true, false));
+  source_low = {0, 1, 2};
+  source_high = {1, 3, 3};
+  target_low = {0, 1, 1};
+  target_high = {1, 2, 3};
+  // Extension on the right side not allowed.
+  target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    1, true, false, false));
+  // Extension on the right side is allowed, but we can't add anymore X.
+  target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    0, true, true, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointSourceSentenceOutOfBounds) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(3));
+
+  vector<int> source_low = {0, 0, 2};
+  vector<int> source_high = {1, 2, 3};
+  vector<int> target_low = {0, 1, 2};
+  vector<int> target_high = {2, 2, 3};
+  int source_phrase_low = 1, source_phrase_high = 2;
+  int source_back_low, source_back_high;
+  int target_phrase_low = 1, target_phrase_high = 2;
+  // Extend out of sentence to left.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 2, 1,
+                                    1, true, true, false));
+  source_low = {0, 1, 2};
+  source_high = {1, 3, 3};
+  target_low = {0, 1, 1};
+  target_high = {1, 2, 3};
+  target_phrase_low = 1, target_phrase_high = 2;
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 2, 1,
+                                    1, true, true, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointTargetSourceWide) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 5, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  vector<int> source_low = {2, -1, 2, 3, 4, -1, 4};
+  vector<int> source_high = {3, -1, 3, 4, 5, -1, 5};
+  vector<int> target_low = {-1, -1, 0, 3, 4, -1, -1};
+  vector<int> target_high = {-1, -1, 3, 4, 7, -1, -1};
+  int source_phrase_low = 2, source_phrase_high = 5;
+  int source_back_low, source_back_high;
+  int target_phrase_low = -1, target_phrase_high = -1;
+
+  // Second projection (on source side) is too wide.
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    2, true, true, false));
+}
+
+TEST_F(RuleExtractorHelperTest, TestFindFixPointArbitraryExpansion) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 20, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(11));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(11));
+
+  vector<int> source_low = {1, 1, 2, 3, 4, 5, 6, 7, 7, 8, 9};
+  vector<int> source_high = {2, 3, 4, 5, 5, 6, 7, 8, 9, 10, 10};
+  vector<int> target_low = {-1, 0, 1, 2, 3, 5, 6, 7, 8, 9, -1};
+  vector<int> target_high = {-1, 2, 3, 4, 5, 6, 8, 9, 10, 11, -1};
+  int source_phrase_low = 4, source_phrase_high = 7;
+  int source_back_low, source_back_high;
+  int target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_FALSE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                    source_low, source_high, target_phrase_low,
+                                    target_phrase_high, target_low, target_high,
+                                    source_back_low, source_back_high, 0, 1, 1,
+                                    10, true, true, false));
+
+  source_phrase_low = 4, source_phrase_high = 7;
+  target_phrase_low = -1, target_phrase_high = -1;
+  EXPECT_TRUE(helper->FindFixPoint(source_phrase_low, source_phrase_high,
+                                   source_low, source_high, target_phrase_low,
+                                   target_phrase_high, target_low, target_high,
+                                   source_back_low, source_back_high, 0, 1, 1,
+                                   10, true, true, true));
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapOrder) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+
+  vector<pair<int, int> > gaps =
+      {make_pair(0, 3), make_pair(5, 8), make_pair(11, 12), make_pair(15, 17)};
+  vector<int> expected_gap_order = {0, 1, 2, 3};
+  EXPECT_EQ(expected_gap_order, helper->GetGapOrder(gaps));
+
+  gaps = {make_pair(15, 17), make_pair(8, 9), make_pair(5, 6), make_pair(0, 3)};
+  expected_gap_order = {3, 2, 1, 0};
+  EXPECT_EQ(expected_gap_order, helper->GetGapOrder(gaps));
+
+  gaps = {make_pair(8, 9), make_pair(5, 6), make_pair(0, 3), make_pair(15, 17)};
+  expected_gap_order = {2, 1, 0, 3};
+  EXPECT_EQ(expected_gap_order, helper->GetGapOrder(gaps));
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapsExceedNumSymbols) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {1, 1, 2, 3, 4, 5, 6};
+  vector<int> source_high = {2, 2, 3, 4, 5, 6, 7};
+  vector<int> target_low = {-1, 0, 2, 3, 4, 5, 6};
+  vector<int> target_high = {-1, 2, 3, 4, 5, 6, 7};
+  int source_phrase_low = 1, source_phrase_high = 6;
+  int source_back_low = 0, source_back_high = 6;
+  vector<int> matching = {11, 13, 15};
+  vector<int> chunklen = {1, 1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 5;
+  EXPECT_FALSE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                               source_low, source_high, target_low, target_high,
+                               source_phrase_low, source_phrase_high,
+                               source_back_low, source_back_high, 5, 10,
+                               num_symbols, met_constraints));
+
+  source_low = {0, 1, 2, 3, 4, 5, 5};
+  source_high = {1, 2, 3, 4, 5, 6, 6};
+  target_low = {0, 1, 2, 3, 4, 5, -1};
+  target_high = {1, 2, 3, 4, 5, 7, -1};
+  source_phrase_low = 1, source_phrase_high = 6;
+  source_back_low = 1, source_back_high = 7;
+  num_symbols = 5;
+  EXPECT_FALSE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                               source_low, source_high, target_low, target_high,
+                               source_phrase_low, source_phrase_high,
+                               source_back_low, source_back_high, 5, 10,
+                               num_symbols, met_constraints));
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapsExtensionsNotTight) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 7, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {-1, 1, 2, 3, 4, 5, -1};
+  vector<int> source_high = {-1, 2, 3, 4, 5, 6, -1};
+  vector<int> target_low = {-1, 1, 2, 3, 4, 5, -1};
+  vector<int> target_high = {-1, 2, 3, 4, 5, 6, -1};
+  int source_phrase_low = 1, source_phrase_high = 6;
+  int source_back_low = 0, source_back_high = 6;
+  vector<int> matching = {11, 13, 15};
+  vector<int> chunklen = {1, 1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 5;
+  EXPECT_FALSE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                               source_low, source_high, target_low, target_high,
+                               source_phrase_low, source_phrase_high,
+                               source_back_low, source_back_high, 5, 10,
+                               num_symbols, met_constraints));
+
+  source_phrase_low = 1, source_phrase_high = 6;
+  source_back_low = 1, source_back_high = 7;
+  num_symbols = 5;
+  EXPECT_FALSE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                               source_low, source_high, target_low, target_high,
+                               source_phrase_low, source_phrase_high,
+                               source_back_low, source_back_high, 5, 10,
+                               num_symbols, met_constraints));
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapsNotTightExtremities) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 7, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {-1, -1, 2, 3, 4, 5, 6};
+  vector<int> source_high = {-1, -1, 3, 4, 5, 6, 7};
+  vector<int> target_low = {-1, -1, 2, 3, 4, 5, 6};
+  vector<int> target_high = {-1, -1, 3, 4, 5, 6, 7};
+  int source_phrase_low = 1, source_phrase_high = 6;
+  int source_back_low = 1, source_back_high = 6;
+  vector<int> matching = {11, 13, 15};
+  vector<int> chunklen = {1, 1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 5;
+  EXPECT_TRUE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                              source_low, source_high, target_low, target_high,
+                              source_phrase_low, source_phrase_high,
+                              source_back_low, source_back_high, 5, 10,
+                              num_symbols, met_constraints));
+  EXPECT_FALSE(met_constraints);
+  vector<pair<int, int> > expected_gaps = {make_pair(2, 3), make_pair(4, 5)};
+  EXPECT_EQ(expected_gaps, source_gaps);
+  EXPECT_EQ(expected_gaps, target_gaps);
+
+  source_low = {-1, 1, 2, 3, 4, -1, 6};
+  source_high = {-1, 2, 3, 4, 5, -1, 7};
+  target_low = {-1, 1, 2, 3, 4, -1, 6};
+  target_high = {-1, 2, 3, 4, 5, -1, 7};
+  met_constraints = true;
+  source_gaps.clear();
+  target_gaps.clear();
+  EXPECT_TRUE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                              source_low, source_high, target_low, target_high,
+                              source_phrase_low, source_phrase_high,
+                              source_back_low, source_back_high, 5, 10,
+                              num_symbols, met_constraints));
+  EXPECT_FALSE(met_constraints);
+  EXPECT_EQ(expected_gaps, source_gaps);
+  EXPECT_EQ(expected_gaps, target_gaps);
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapsWithExtensions) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {-1, 5, 2, 3, 4, 1, -1};
+  vector<int> source_high = {-1, 6, 3, 4, 5, 2, -1};
+  vector<int> target_low = {-1, 5, 2, 3, 4, 1, -1};
+  vector<int> target_high = {-1, 6, 3, 4, 5, 2, -1};
+  int source_phrase_low = 2, source_phrase_high = 5;
+  int source_back_low = 1, source_back_high = 6;
+  vector<int> matching = {12, 14};
+  vector<int> chunklen = {1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 3;
+  EXPECT_TRUE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                              source_low, source_high, target_low, target_high,
+                              source_phrase_low, source_phrase_high,
+                              source_back_low, source_back_high, 5, 10,
+                              num_symbols, met_constraints));
+  vector<pair<int, int> > expected_source_gaps = {
+    make_pair(1, 2), make_pair(3, 4), make_pair(5, 6)
+  };
+  EXPECT_EQ(expected_source_gaps, source_gaps);
+  vector<pair<int, int> > expected_target_gaps = {
+    make_pair(5, 6), make_pair(3, 4), make_pair(1, 2)
+  };
+  EXPECT_EQ(expected_target_gaps, target_gaps);
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGaps) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {-1, 1, 4, 3, 2, 5, -1};
+  vector<int> source_high = {-1, 2, 5, 4, 3, 6, -1};
+  vector<int> target_low = {-1, 1, 4, 3, 2, 5, -1};
+  vector<int> target_high = {-1, 2, 5, 4, 3, 6, -1};
+  int source_phrase_low = 1, source_phrase_high = 6;
+  int source_back_low = 1, source_back_high = 6;
+  vector<int> matching = {11, 13, 15};
+  vector<int> chunklen = {1, 1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 5;
+  EXPECT_TRUE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                              source_low, source_high, target_low, target_high,
+                              source_phrase_low, source_phrase_high,
+                              source_back_low, source_back_high, 5, 10,
+                              num_symbols, met_constraints));
+  vector<pair<int, int> > expected_source_gaps = {
+    make_pair(2, 3), make_pair(4, 5)
+  };
+  EXPECT_EQ(expected_source_gaps, source_gaps);
+  vector<pair<int, int> > expected_target_gaps = {
+    make_pair(4, 5), make_pair(2, 3)
+  };
+  EXPECT_EQ(expected_target_gaps, target_gaps);
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetGapIntegrityChecksFailed) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+  EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+  EXPECT_CALL(*target_data_array, GetSentenceLength(_))
+      .WillRepeatedly(Return(7));
+
+  bool met_constraints = true;
+  vector<int> source_low = {-1, 3, 2, 3, 4, 3, -1};
+  vector<int> source_high = {-1, 4, 3, 4, 5, 4, -1};
+  vector<int> target_low = {-1, -1, 2, 1, 4, -1, -1};
+  vector<int> target_high = {-1, -1, 3, 6, 5, -1, -1};
+  int source_phrase_low = 2, source_phrase_high = 5;
+  int source_back_low = 2, source_back_high = 5;
+  vector<int> matching = {12, 14};
+  vector<int> chunklen = {1, 1};
+  vector<pair<int, int> > source_gaps, target_gaps;
+  int num_symbols = 3;
+  EXPECT_FALSE(helper->GetGaps(source_gaps, target_gaps, matching, chunklen,
+                               source_low, source_high, target_low, target_high,
+                               source_phrase_low, source_phrase_high,
+                               source_back_low, source_back_high, 5, 10,
+                               num_symbols, met_constraints));
+}
+
+TEST_F(RuleExtractorHelperTest, TestGetSourceIndexes) {
+  helper = make_shared<RuleExtractorHelper>(source_data_array,
+      target_data_array, alignment, 10, 5, true, true, true);
+
+  vector<int> matching = {13, 18, 21};
+  vector<int> chunklen = {3, 2, 1};
+  unordered_map<int, int> expected_indexes = {
+      {3, 1}, {4, 2}, {5, 3}, {8, 5}, {9, 6}, {11, 8}
+  };
+  EXPECT_EQ(expected_indexes, helper->GetSourceIndexes(matching, chunklen,
+                                                       1, 10));
+
+  matching = {12, 17};
+  chunklen = {2, 4};
+  expected_indexes = {{2, 0}, {3, 1}, {7, 3}, {8, 4}, {9, 5}, {10, 6}};
+  EXPECT_EQ(expected_indexes, helper->GetSourceIndexes(matching, chunklen,
+                                                       0, 10));
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/rule_extractor_test.cc b/extractor/rule_extractor_test.cc
new file mode 100644
index 00000000..5c1501c7
--- /dev/null
+++ b/extractor/rule_extractor_test.cc
@@ -0,0 +1,168 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "mocks/mock_alignment.h"
+#include "mocks/mock_data_array.h"
+#include "mocks/mock_rule_extractor_helper.h"
+#include "mocks/mock_scorer.h"
+#include "mocks/mock_target_phrase_extractor.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase.h"
+#include "phrase_builder.h"
+#include "phrase_location.h"
+#include "rule_extractor.h"
+#include "rule.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class RuleExtractorTest : public Test {
+ protected:
+  virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*source_data_array, GetSentenceId(_))
+        .WillRepeatedly(Return(0));
+    EXPECT_CALL(*source_data_array, GetSentenceStart(_))
+        .WillRepeatedly(Return(0));
+    EXPECT_CALL(*source_data_array, GetSentenceLength(_))
+        .WillRepeatedly(Return(10));
+
+    helper = make_shared<MockRuleExtractorHelper>();
+    EXPECT_CALL(*helper, CheckAlignedTerminals(_, _, _, _))
+        .WillRepeatedly(Return(true));
+    EXPECT_CALL(*helper, CheckTightPhrases(_, _, _, _))
+        .WillRepeatedly(Return(true));
+    unordered_map<int, int> source_indexes;
+    EXPECT_CALL(*helper, GetSourceIndexes(_, _, _, _))
+        .WillRepeatedly(Return(source_indexes));
+
+    vocabulary = make_shared<MockVocabulary>();
+    EXPECT_CALL(*vocabulary, GetTerminalValue(87))
+        .WillRepeatedly(Return("a"));
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+    vector<int> symbols = {87};
+    Phrase target_phrase = phrase_builder->Build(symbols);
+    PhraseAlignment phrase_alignment = {make_pair(0, 0)};
+
+    target_phrase_extractor = make_shared<MockTargetPhraseExtractor>();
+    vector<pair<Phrase, PhraseAlignment> > target_phrases = {
+      make_pair(target_phrase, phrase_alignment)
+    };
+    EXPECT_CALL(*target_phrase_extractor, ExtractPhrases(_, _, _, _, _, _))
+        .WillRepeatedly(Return(target_phrases));
+
+    scorer = make_shared<MockScorer>();
+    vector<double> scores = {0.3, 7.2};
+    EXPECT_CALL(*scorer, Score(_)).WillRepeatedly(Return(scores));
+
+    extractor = make_shared<RuleExtractor>(source_data_array, phrase_builder,
+        scorer, target_phrase_extractor, helper, 10, 1, 3, 5, false);
+  }
+
+  shared_ptr<MockDataArray> source_data_array;
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<MockRuleExtractorHelper> helper;
+  shared_ptr<MockScorer> scorer;
+  shared_ptr<MockTargetPhraseExtractor> target_phrase_extractor;
+  shared_ptr<RuleExtractor> extractor;
+};
+
+TEST_F(RuleExtractorTest, TestExtractRulesAlignedTerminalsFail) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).Times(1);
+  EXPECT_CALL(*helper, CheckAlignedTerminals(_, _, _, _))
+      .WillRepeatedly(Return(false));
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(0, rules.size());
+}
+
+TEST_F(RuleExtractorTest, TestExtractRulesTightPhrasesFail) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).Times(1);
+  EXPECT_CALL(*helper, CheckTightPhrases(_, _, _, _))
+      .WillRepeatedly(Return(false));
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(0, rules.size());
+}
+
+TEST_F(RuleExtractorTest, TestExtractRulesNoFixPoint) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).Times(1);
+  // Set FindFixPoint to return false.
+  vector<pair<int, int> > gaps;
+  helper->SetUp(0, 0, 0, 0, false, gaps, gaps, 0, true, true);
+
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(0, rules.size());
+}
+
+TEST_F(RuleExtractorTest, TestExtractRulesGapsFail) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).Times(1);
+  // Set CheckGaps to return false.
+  vector<pair<int, int> > gaps;
+  helper->SetUp(0, 0, 0, 0, true, gaps, gaps, 0, true, false);
+
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(0, rules.size());
+}
+
+TEST_F(RuleExtractorTest, TestExtractRulesNoExtremities) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).Times(1);
+  vector<pair<int, int> > gaps(3);
+  // Set FindFixPoint to return true. The number of gaps equals the number of
+  // nonterminals, so we won't add any extremities.
+  helper->SetUp(0, 0, 0, 0, true, gaps, gaps, 0, true, true);
+
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(1, rules.size());
+}
+
+TEST_F(RuleExtractorTest, TestExtractRulesAddExtremities) {
+  vector<int> symbols = {87};
+  Phrase phrase = phrase_builder->Build(symbols);
+  vector<int> matching = {2};
+  PhraseLocation phrase_location(matching, 1);
+
+  vector<int> links(10, -1);
+  EXPECT_CALL(*helper, GetLinksSpans(_, _, _, _, _)).WillOnce(DoAll(
+      SetArgReferee<0>(links),
+      SetArgReferee<1>(links),
+      SetArgReferee<2>(links),
+      SetArgReferee<3>(links)));
+
+  vector<pair<int, int> > gaps;
+  // Set FindFixPoint to return true. The number of gaps equals the number of
+  // nonterminals, so we won't add any extremities.
+  helper->SetUp(0, 0, 2, 3, true, gaps, gaps, 0, true, true);
+
+  vector<Rule> rules = extractor->ExtractRules(phrase, phrase_location);
+  EXPECT_EQ(4, rules.size());
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/rule_factory.cc b/extractor/rule_factory.cc
new file mode 100644
index 00000000..8c30fb9e
--- /dev/null
+++ b/extractor/rule_factory.cc
@@ -0,0 +1,303 @@
+#include "rule_factory.h"
+
+#include <chrono>
+#include <memory>
+#include <queue>
+#include <vector>
+
+#include "grammar.h"
+#include "fast_intersector.h"
+#include "matchings_finder.h"
+#include "phrase.h"
+#include "phrase_builder.h"
+#include "rule.h"
+#include "rule_extractor.h"
+#include "sampler.h"
+#include "scorer.h"
+#include "suffix_array.h"
+#include "time_util.h"
+#include "vocabulary.h"
+
+using namespace std;
+using namespace chrono;
+
+namespace extractor {
+
+typedef high_resolution_clock Clock;
+
+struct State {
+  State(int start, int end, const vector<int>& phrase,
+      const vector<int>& subpatterns_start, shared_ptr<TrieNode> node,
+      bool starts_with_x) :
+      start(start), end(end), phrase(phrase),
+      subpatterns_start(subpatterns_start), node(node),
+      starts_with_x(starts_with_x) {}
+
+  int start, end;
+  vector<int> phrase, subpatterns_start;
+  shared_ptr<TrieNode> node;
+  bool starts_with_x;
+};
+
+HieroCachingRuleFactory::HieroCachingRuleFactory(
+    shared_ptr<SuffixArray> source_suffix_array,
+    shared_ptr<DataArray> target_data_array,
+    shared_ptr<Alignment> alignment,
+    const shared_ptr<Vocabulary>& vocabulary,
+    shared_ptr<Precomputation> precomputation,
+    shared_ptr<Scorer> scorer,
+    int min_gap_size,
+    int max_rule_span,
+    int max_nonterminals,
+    int max_rule_symbols,
+    int max_samples,
+    bool require_tight_phrases) :
+    vocabulary(vocabulary),
+    scorer(scorer),
+    min_gap_size(min_gap_size),
+    max_rule_span(max_rule_span),
+    max_nonterminals(max_nonterminals),
+    max_chunks(max_nonterminals + 1),
+    max_rule_symbols(max_rule_symbols) {
+  matchings_finder = make_shared<MatchingsFinder>(source_suffix_array);
+  fast_intersector = make_shared<FastIntersector>(source_suffix_array,
+      precomputation, vocabulary, max_rule_span, min_gap_size);
+  phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+  rule_extractor = make_shared<RuleExtractor>(source_suffix_array->GetData(),
+      target_data_array, alignment, phrase_builder, scorer, vocabulary,
+      max_rule_span, min_gap_size, max_nonterminals, max_rule_symbols, true,
+      false, require_tight_phrases);
+  sampler = make_shared<Sampler>(source_suffix_array, max_samples);
+}
+
+HieroCachingRuleFactory::HieroCachingRuleFactory(
+    shared_ptr<MatchingsFinder> finder,
+    shared_ptr<FastIntersector> fast_intersector,
+    shared_ptr<PhraseBuilder> phrase_builder,
+    shared_ptr<RuleExtractor> rule_extractor,
+    shared_ptr<Vocabulary> vocabulary,
+    shared_ptr<Sampler> sampler,
+    shared_ptr<Scorer> scorer,
+    int min_gap_size,
+    int max_rule_span,
+    int max_nonterminals,
+    int max_chunks,
+    int max_rule_symbols) :
+    matchings_finder(finder),
+    fast_intersector(fast_intersector),
+    phrase_builder(phrase_builder),
+    rule_extractor(rule_extractor),
+    vocabulary(vocabulary),
+    sampler(sampler),
+    scorer(scorer),
+    min_gap_size(min_gap_size),
+    max_rule_span(max_rule_span),
+    max_nonterminals(max_nonterminals),
+    max_chunks(max_chunks),
+    max_rule_symbols(max_rule_symbols) {}
+
+HieroCachingRuleFactory::HieroCachingRuleFactory() {}
+
+HieroCachingRuleFactory::~HieroCachingRuleFactory() {}
+
+Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids) {
+  Clock::time_point start_time = Clock::now();
+  double total_extract_time = 0;
+  double total_intersect_time = 0;
+  double total_lookup_time = 0;
+
+  MatchingsTrie trie;
+  shared_ptr<TrieNode> root = trie.GetRoot();
+
+  int first_x = vocabulary->GetNonterminalIndex(1);
+  shared_ptr<TrieNode> x_root(new TrieNode(root));
+  root->AddChild(first_x, x_root);
+
+  queue<State> states;
+  for (size_t i = 0; i < word_ids.size(); ++i) {
+    states.push(State(i, i, vector<int>(), vector<int>(1, i), root, false));
+  }
+  for (size_t i = min_gap_size; i < word_ids.size(); ++i) {
+    states.push(State(i - min_gap_size, i, vector<int>(1, first_x),
+        vector<int>(1, i), x_root, true));
+  }
+
+  vector<Rule> rules;
+  while (!states.empty()) {
+    State state = states.front();
+    states.pop();
+
+    shared_ptr<TrieNode> node = state.node;
+    vector<int> phrase = state.phrase;
+    int word_id = word_ids[state.end];
+    phrase.push_back(word_id);
+    Phrase next_phrase = phrase_builder->Build(phrase);
+    shared_ptr<TrieNode> next_node;
+
+    if (CannotHaveMatchings(node, word_id)) {
+      if (!node->HasChild(word_id)) {
+        node->AddChild(word_id, shared_ptr<TrieNode>());
+      }
+      continue;
+    }
+
+    if (RequiresLookup(node, word_id)) {
+      shared_ptr<TrieNode> next_suffix_link = node->suffix_link == NULL ?
+          trie.GetRoot() : node->suffix_link->GetChild(word_id);
+      if (state.starts_with_x) {
+        // If the phrase starts with a non terminal, we simply use the matchings
+        // from the suffix link.
+        next_node = make_shared<TrieNode>(
+            next_suffix_link, next_phrase, next_suffix_link->matchings);
+      } else {
+        PhraseLocation phrase_location;
+        if (next_phrase.Arity() > 0) {
+          // For phrases containing a nonterminal, we use either the occurrences
+          // of the prefix or the suffix to determine the occurrences of the
+          // phrase.
+          Clock::time_point intersect_start = Clock::now();
+          phrase_location = fast_intersector->Intersect(
+              node->matchings, next_suffix_link->matchings, next_phrase);
+          Clock::time_point intersect_stop = Clock::now();
+          total_intersect_time += GetDuration(intersect_start, intersect_stop);
+        } else {
+          // For phrases not containing any nonterminals, we simply query the
+          // suffix array using the suffix array range of the prefix as a
+          // starting point.
+          Clock::time_point lookup_start = Clock::now();
+          phrase_location = matchings_finder->Find(
+              node->matchings,
+              vocabulary->GetTerminalValue(word_id),
+              state.phrase.size());
+          Clock::time_point lookup_stop = Clock::now();
+          total_lookup_time += GetDuration(lookup_start, lookup_stop);
+        }
+
+        if (phrase_location.IsEmpty()) {
+          continue;
+        }
+
+        // Create new trie node to store data about the current phrase.
+        next_node = make_shared<TrieNode>(
+            next_suffix_link, next_phrase, phrase_location);
+      }
+      // Add the new trie node to the trie cache.
+      node->AddChild(word_id, next_node);
+
+      // Automatically adds a trailing non terminal if allowed. Simply copy the
+      // matchings from the prefix node.
+      AddTrailingNonterminal(phrase, next_phrase, next_node,
+                             state.starts_with_x);
+
+      Clock::time_point extract_start = Clock::now();
+      if (!state.starts_with_x) {
+        // Extract rules for the sampled set of occurrences.
+        PhraseLocation sample = sampler->Sample(next_node->matchings);
+        vector<Rule> new_rules =
+            rule_extractor->ExtractRules(next_phrase, sample);
+        rules.insert(rules.end(), new_rules.begin(), new_rules.end());
+      }
+      Clock::time_point extract_stop = Clock::now();
+      total_extract_time += GetDuration(extract_start, extract_stop);
+    } else {
+      next_node = node->GetChild(word_id);
+    }
+
+    // Create more states (phrases) to be analyzed.
+    vector<State> new_states = ExtendState(word_ids, state, phrase, next_phrase,
+                                           next_node);
+    for (State new_state: new_states) {
+      states.push(new_state);
+    }
+  }
+
+  Clock::time_point stop_time = Clock::now();
+  #pragma omp critical (stderr_write)
+  {
+    cerr << "Total time for rule lookup, extraction, and scoring = "
+         << GetDuration(start_time, stop_time) << " seconds" << endl;
+    cerr << "Extract time = " << total_extract_time << " seconds" << endl;
+    cerr << "Intersect time = " << total_intersect_time << " seconds" << endl;
+    cerr << "Lookup time = " << total_lookup_time << " seconds" << endl;
+  }
+  return Grammar(rules, scorer->GetFeatureNames());
+}
+
+bool HieroCachingRuleFactory::CannotHaveMatchings(
+    shared_ptr<TrieNode> node, int word_id) {
+  if (node->HasChild(word_id) && node->GetChild(word_id) == NULL) {
+    return true;
+  }
+
+  shared_ptr<TrieNode> suffix_link = node->suffix_link;
+  return suffix_link != NULL && suffix_link->GetChild(word_id) == NULL;
+}
+
+bool HieroCachingRuleFactory::RequiresLookup(
+    shared_ptr<TrieNode> node, int word_id) {
+  return !node->HasChild(word_id);
+}
+
+void HieroCachingRuleFactory::AddTrailingNonterminal(
+    vector<int> symbols,
+    const Phrase& prefix,
+    const shared_ptr<TrieNode>& prefix_node,
+    bool starts_with_x) {
+  if (prefix.Arity() >= max_nonterminals) {
+    return;
+  }
+
+  int var_id = vocabulary->GetNonterminalIndex(prefix.Arity() + 1);
+  symbols.push_back(var_id);
+  Phrase var_phrase = phrase_builder->Build(symbols);
+
+  int suffix_var_id = vocabulary->GetNonterminalIndex(
+      prefix.Arity() + (starts_with_x == 0));
+  shared_ptr<TrieNode> var_suffix_link =
+      prefix_node->suffix_link->GetChild(suffix_var_id);
+
+  prefix_node->AddChild(var_id, make_shared<TrieNode>(
+      var_suffix_link, var_phrase, prefix_node->matchings));
+}
+
+vector<State> HieroCachingRuleFactory::ExtendState(
+    const vector<int>& word_ids,
+    const State& state,
+    vector<int> symbols,
+    const Phrase& phrase,
+    const shared_ptr<TrieNode>& node) {
+  int span = state.end - state.start;
+  vector<State> new_states;
+  if (symbols.size() >= max_rule_symbols || state.end + 1 >= word_ids.size() ||
+      span >= max_rule_span) {
+    return new_states;
+  }
+
+  // New state for adding the next symbol.
+  new_states.push_back(State(state.start, state.end + 1, symbols,
+      state.subpatterns_start, node, state.starts_with_x));
+
+  int num_subpatterns = phrase.Arity() + (state.starts_with_x == 0);
+  if (symbols.size() + 1 >= max_rule_symbols ||
+      phrase.Arity() >= max_nonterminals ||
+      num_subpatterns >= max_chunks) {
+    return new_states;
+  }
+
+  // New states for adding a nonterminal followed by a new symbol.
+  int var_id = vocabulary->GetNonterminalIndex(phrase.Arity() + 1);
+  symbols.push_back(var_id);
+  vector<int> subpatterns_start = state.subpatterns_start;
+  size_t i = state.end + 1 + min_gap_size;
+  while (i < word_ids.size() && i - state.start <= max_rule_span) {
+    subpatterns_start.push_back(i);
+    new_states.push_back(State(state.start, i, symbols, subpatterns_start,
+        node->GetChild(var_id), state.starts_with_x));
+    subpatterns_start.pop_back();
+    ++i;
+  }
+
+  return new_states;
+}
+
+} // namespace extractor
diff --git a/extractor/rule_factory.h b/extractor/rule_factory.h
new file mode 100644
index 00000000..52e8712a
--- /dev/null
+++ b/extractor/rule_factory.h
@@ -0,0 +1,118 @@
+#ifndef _RULE_FACTORY_H_
+#define _RULE_FACTORY_H_
+
+#include <memory>
+#include <vector>
+
+#include "matchings_trie.h"
+
+using namespace std;
+
+namespace extractor {
+
+class Alignment;
+class DataArray;
+class FastIntersector;
+class Grammar;
+class MatchingsFinder;
+class PhraseBuilder;
+class Precomputation;
+class Rule;
+class RuleExtractor;
+class Sampler;
+class Scorer;
+class State;
+class SuffixArray;
+class Vocabulary;
+
+/**
+ * Component containing most of the logic for extracting SCFG rules for a given
+ * sentence.
+ *
+ * Given a sentence (as a vector of word ids), this class constructs all the
+ * possible source phrases starting from this sentence. For each source phrase,
+ * it finds all its occurrences in the source data and samples some of these
+ * occurrences to extract aligned source-target phrase pairs. A trie cache is
+ * used to avoid unnecessary computations if a source phrase can be constructed
+ * more than once (e.g. some words occur more than once in the sentence).
+ */
+class HieroCachingRuleFactory {
+ public:
+  HieroCachingRuleFactory(
+      shared_ptr<SuffixArray> source_suffix_array,
+      shared_ptr<DataArray> target_data_array,
+      shared_ptr<Alignment> alignment,
+      const shared_ptr<Vocabulary>& vocabulary,
+      shared_ptr<Precomputation> precomputation,
+      shared_ptr<Scorer> scorer,
+      int min_gap_size,
+      int max_rule_span,
+      int max_nonterminals,
+      int max_rule_symbols,
+      int max_samples,
+      bool require_tight_phrases);
+
+  // For testing only.
+  HieroCachingRuleFactory(
+      shared_ptr<MatchingsFinder> finder,
+      shared_ptr<FastIntersector> fast_intersector,
+      shared_ptr<PhraseBuilder> phrase_builder,
+      shared_ptr<RuleExtractor> rule_extractor,
+      shared_ptr<Vocabulary> vocabulary,
+      shared_ptr<Sampler> sampler,
+      shared_ptr<Scorer> scorer,
+      int min_gap_size,
+      int max_rule_span,
+      int max_nonterminals,
+      int max_chunks,
+      int max_rule_symbols);
+
+  virtual ~HieroCachingRuleFactory();
+
+  // Constructs SCFG rules for a given sentence.
+  // (See class description for more details.)
+  virtual Grammar GetGrammar(const vector<int>& word_ids);
+
+ protected:
+  HieroCachingRuleFactory();
+
+ private:
+  // Checks if the phrase (if previously encountered) or its prefix have any
+  // occurrences in the source data.
+  bool CannotHaveMatchings(shared_ptr<TrieNode> node, int word_id);
+
+  // Checks if the phrase has previously been analyzed.
+  bool RequiresLookup(shared_ptr<TrieNode> node, int word_id);
+
+  // Creates a new state in the trie that corresponds to adding a trailing
+  // nonterminal to the current phrase.
+  void AddTrailingNonterminal(vector<int> symbols,
+                              const Phrase& prefix,
+                              const shared_ptr<TrieNode>& prefix_node,
+                              bool starts_with_x);
+
+  // Extends the current state by possibly adding a nonterminal followed by a
+  // terminal.
+  vector<State> ExtendState(const vector<int>& word_ids,
+                            const State& state,
+                            vector<int> symbols,
+                            const Phrase& phrase,
+                            const shared_ptr<TrieNode>& node);
+
+  shared_ptr<MatchingsFinder> matchings_finder;
+  shared_ptr<FastIntersector> fast_intersector;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<RuleExtractor> rule_extractor;
+  shared_ptr<Vocabulary> vocabulary;
+  shared_ptr<Sampler> sampler;
+  shared_ptr<Scorer> scorer;
+  int min_gap_size;
+  int max_rule_span;
+  int max_nonterminals;
+  int max_chunks;
+  int max_rule_symbols;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/rule_factory_test.cc b/extractor/rule_factory_test.cc
new file mode 100644
index 00000000..2129dfa0
--- /dev/null
+++ b/extractor/rule_factory_test.cc
@@ -0,0 +1,103 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "grammar.h"
+#include "mocks/mock_fast_intersector.h"
+#include "mocks/mock_matchings_finder.h"
+#include "mocks/mock_rule_extractor.h"
+#include "mocks/mock_sampler.h"
+#include "mocks/mock_scorer.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase_builder.h"
+#include "phrase_location.h"
+#include "rule_factory.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class RuleFactoryTest : public Test {
+ protected:
+  virtual void SetUp() {
+    finder = make_shared<MockMatchingsFinder>();
+    fast_intersector = make_shared<MockFastIntersector>();
+
+    vocabulary = make_shared<MockVocabulary>();
+    EXPECT_CALL(*vocabulary, GetTerminalValue(2)).WillRepeatedly(Return("a"));
+    EXPECT_CALL(*vocabulary, GetTerminalValue(3)).WillRepeatedly(Return("b"));
+    EXPECT_CALL(*vocabulary, GetTerminalValue(4)).WillRepeatedly(Return("c"));
+
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+
+    scorer = make_shared<MockScorer>();
+    feature_names = {"f1"};
+    EXPECT_CALL(*scorer, GetFeatureNames())
+        .WillRepeatedly(Return(feature_names));
+
+    sampler = make_shared<MockSampler>();
+    EXPECT_CALL(*sampler, Sample(_))
+        .WillRepeatedly(Return(PhraseLocation(0, 1)));
+
+    Phrase phrase;
+    vector<double> scores = {0.5};
+    vector<pair<int, int> > phrase_alignment = {make_pair(0, 0)};
+    vector<Rule> rules = {Rule(phrase, phrase, scores, phrase_alignment)};
+    extractor = make_shared<MockRuleExtractor>();
+    EXPECT_CALL(*extractor, ExtractRules(_, _))
+        .WillRepeatedly(Return(rules));
+  }
+
+  vector<string> feature_names;
+  shared_ptr<MockMatchingsFinder> finder;
+  shared_ptr<MockFastIntersector> fast_intersector;
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<MockScorer> scorer;
+  shared_ptr<MockSampler> sampler;
+  shared_ptr<MockRuleExtractor> extractor;
+  shared_ptr<HieroCachingRuleFactory> factory;
+};
+
+TEST_F(RuleFactoryTest, TestGetGrammarDifferentWords) {
+  factory = make_shared<HieroCachingRuleFactory>(finder, fast_intersector,
+      phrase_builder, extractor, vocabulary, sampler, scorer, 1, 10, 2, 3, 5);
+
+  EXPECT_CALL(*finder, Find(_, _, _))
+      .Times(6)
+      .WillRepeatedly(Return(PhraseLocation(0, 1)));
+
+  EXPECT_CALL(*fast_intersector, Intersect(_, _, _))
+      .Times(1)
+      .WillRepeatedly(Return(PhraseLocation(0, 1)));
+
+  vector<int> word_ids = {2, 3, 4};
+  Grammar grammar = factory->GetGrammar(word_ids);
+  EXPECT_EQ(feature_names, grammar.GetFeatureNames());
+  EXPECT_EQ(7, grammar.GetRules().size());
+}
+
+TEST_F(RuleFactoryTest, TestGetGrammarRepeatingWords) {
+  factory = make_shared<HieroCachingRuleFactory>(finder, fast_intersector,
+      phrase_builder, extractor, vocabulary, sampler, scorer, 1, 10, 2, 3, 5);
+
+  EXPECT_CALL(*finder, Find(_, _, _))
+      .Times(12)
+      .WillRepeatedly(Return(PhraseLocation(0, 1)));
+
+  EXPECT_CALL(*fast_intersector, Intersect(_, _, _))
+      .Times(16)
+      .WillRepeatedly(Return(PhraseLocation(0, 1)));
+
+  vector<int> word_ids = {2, 3, 4, 2, 3};
+  Grammar grammar = factory->GetGrammar(word_ids);
+  EXPECT_EQ(feature_names, grammar.GetFeatureNames());
+  EXPECT_EQ(28, grammar.GetRules().size());
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/run_extractor.cc b/extractor/run_extractor.cc
new file mode 100644
index 00000000..aec83e3b
--- /dev/null
+++ b/extractor/run_extractor.cc
@@ -0,0 +1,242 @@
+#include <chrono>
+#include <fstream>
+#include <iostream>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include <omp.h>
+#include <boost/filesystem.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "alignment.h"
+#include "data_array.h"
+#include "features/count_source_target.h"
+#include "features/feature.h"
+#include "features/is_source_singleton.h"
+#include "features/is_source_target_singleton.h"
+#include "features/max_lex_source_given_target.h"
+#include "features/max_lex_target_given_source.h"
+#include "features/sample_source_count.h"
+#include "features/target_given_source_coherent.h"
+#include "grammar.h"
+#include "grammar_extractor.h"
+#include "precomputation.h"
+#include "rule.h"
+#include "scorer.h"
+#include "suffix_array.h"
+#include "time_util.h"
+#include "translation_table.h"
+
+namespace fs = boost::filesystem;
+namespace po = boost::program_options;
+using namespace std;
+using namespace extractor;
+using namespace features;
+
+// Returns the file path in which a given grammar should be written.
+fs::path GetGrammarFilePath(const fs::path& grammar_path, int file_number) {
+  string file_name = "grammar." + to_string(file_number);
+  return grammar_path / file_name;
+}
+
+int main(int argc, char** argv) {
+  int num_threads_default = 1;
+  #pragma omp parallel
+  num_threads_default = omp_get_num_threads();
+
+  // Sets up the command line arguments map.
+  po::options_description desc("Command line options");
+  desc.add_options()
+    ("help,h", "Show available options")
+    ("source,f", po::value<string>(), "Source language corpus")
+    ("target,e", po::value<string>(), "Target language corpus")
+    ("bitext,b", po::value<string>(), "Parallel text (source ||| target)")
+    ("alignment,a", po::value<string>()->required(), "Bitext word alignment")
+    ("grammars,g", po::value<string>()->required(), "Grammars output path")
+    ("threads,t", po::value<int>()->default_value(num_threads_default),
+        "Number of parallel extractors")
+    ("frequent", po::value<int>()->default_value(100),
+        "Number of precomputed frequent patterns")
+    ("super_frequent", po::value<int>()->default_value(10),
+        "Number of precomputed super frequent patterns")
+    ("max_rule_span", po::value<int>()->default_value(15),
+        "Maximum rule span")
+    ("max_rule_symbols", po::value<int>()->default_value(5),
+        "Maximum number of symbols (terminals + nontermals) in a rule")
+    ("min_gap_size", po::value<int>()->default_value(1), "Minimum gap size")
+    ("max_phrase_len", po::value<int>()->default_value(4),
+        "Maximum frequent phrase length")
+    ("max_nonterminals", po::value<int>()->default_value(2),
+        "Maximum number of nonterminals in a rule")
+    ("min_frequency", po::value<int>()->default_value(1000),
+        "Minimum number of occurrences for a pharse to be considered frequent")
+    ("max_samples", po::value<int>()->default_value(300),
+        "Maximum number of samples")
+    ("tight_phrases", po::value<bool>()->default_value(true),
+        "False if phrases may be loose (better, but slower)");
+
+  po::variables_map vm;
+  po::store(po::parse_command_line(argc, argv, desc), vm);
+
+  // Checks for the help option before calling notify, so the we don't get an
+  // exception for missing required arguments.
+  if (vm.count("help")) {
+    cout << desc << endl;
+    return 0;
+  }
+
+  po::notify(vm);
+
+  if (!((vm.count("source") && vm.count("target")) || vm.count("bitext"))) {
+    cerr << "A paralel corpus is required. "
+         << "Use -f (source) with -e (target) or -b (bitext)."
+         << endl;
+    return 1;
+  }
+
+  int num_threads = vm["threads"].as<int>();
+  cout << "Grammar extraction will use " << num_threads << " threads." << endl;
+
+  // Reads the parallel corpus.
+  Clock::time_point preprocess_start_time = Clock::now();
+  cerr << "Reading source and target data..." << endl;
+  Clock::time_point start_time = Clock::now();
+  shared_ptr<DataArray> source_data_array, target_data_array;
+  if (vm.count("bitext")) {
+    source_data_array = make_shared<DataArray>(
+        vm["bitext"].as<string>(), SOURCE);
+    target_data_array = make_shared<DataArray>(
+        vm["bitext"].as<string>(), TARGET);
+  } else {
+    source_data_array = make_shared<DataArray>(vm["source"].as<string>());
+    target_data_array = make_shared<DataArray>(vm["target"].as<string>());
+  }
+  Clock::time_point stop_time = Clock::now();
+  cerr << "Reading data took " << GetDuration(start_time, stop_time)
+       << " seconds" << endl;
+
+  // Constructs the suffix array for the source data.
+  cerr << "Creating source suffix array..." << endl;
+  start_time = Clock::now();
+  shared_ptr<SuffixArray> source_suffix_array =
+      make_shared<SuffixArray>(source_data_array);
+  stop_time = Clock::now();
+  cerr << "Creating suffix array took "
+       << GetDuration(start_time, stop_time) << " seconds" << endl;
+
+  // Reads the alignment.
+  cerr << "Reading alignment..." << endl;
+  start_time = Clock::now();
+  shared_ptr<Alignment> alignment =
+      make_shared<Alignment>(vm["alignment"].as<string>());
+  stop_time = Clock::now();
+  cerr << "Reading alignment took "
+       << GetDuration(start_time, stop_time) << " seconds" << endl;
+
+  // Constructs an index storing the occurrences in the source data for each
+  // frequent collocation.
+  cerr << "Precomputing collocations..." << endl;
+  start_time = Clock::now();
+  shared_ptr<Precomputation> precomputation = make_shared<Precomputation>(
+      source_suffix_array,
+      vm["frequent"].as<int>(),
+      vm["super_frequent"].as<int>(),
+      vm["max_rule_span"].as<int>(),
+      vm["max_rule_symbols"].as<int>(),
+      vm["min_gap_size"].as<int>(),
+      vm["max_phrase_len"].as<int>(),
+      vm["min_frequency"].as<int>());
+  stop_time = Clock::now();
+  cerr << "Precomputing collocations took "
+       << GetDuration(start_time, stop_time) << " seconds" << endl;
+
+  // Constructs a table storing p(e | f) and p(f | e) for every pair of source
+  // and target words.
+  cerr << "Precomputing conditional probabilities..." << endl;
+  start_time = Clock::now();
+  shared_ptr<TranslationTable> table = make_shared<TranslationTable>(
+      source_data_array, target_data_array, alignment);
+  stop_time = Clock::now();
+  cerr << "Precomputing conditional probabilities took "
+       << GetDuration(start_time, stop_time) << " seconds" << endl;
+
+  Clock::time_point preprocess_stop_time = Clock::now();
+  cerr << "Overall preprocessing step took "
+       << GetDuration(preprocess_start_time, preprocess_stop_time)
+       << " seconds" << endl;
+
+  // Features used to score each grammar rule.
+  Clock::time_point extraction_start_time = Clock::now();
+  vector<shared_ptr<Feature> > features = {
+      make_shared<TargetGivenSourceCoherent>(),
+      make_shared<SampleSourceCount>(),
+      make_shared<CountSourceTarget>(),
+      make_shared<MaxLexSourceGivenTarget>(table),
+      make_shared<MaxLexTargetGivenSource>(table),
+      make_shared<IsSourceSingleton>(),
+      make_shared<IsSourceTargetSingleton>()
+  };
+  shared_ptr<Scorer> scorer = make_shared<Scorer>(features);
+
+  // Sets up the grammar extractor.
+  GrammarExtractor extractor(
+      source_suffix_array,
+      target_data_array,
+      alignment,
+      precomputation,
+      scorer,
+      vm["min_gap_size"].as<int>(),
+      vm["max_rule_span"].as<int>(),
+      vm["max_nonterminals"].as<int>(),
+      vm["max_rule_symbols"].as<int>(),
+      vm["max_samples"].as<int>(),
+      vm["tight_phrases"].as<bool>());
+
+  // Releases extra memory used by the initial precomputation.
+  precomputation.reset();
+
+  // Creates the grammars directory if it doesn't exist.
+  fs::path grammar_path = vm["grammars"].as<string>();
+  if (!fs::is_directory(grammar_path)) {
+    fs::create_directory(grammar_path);
+  }
+
+  // Reads all sentences for which we extract grammar rules (the paralellization
+  // is simplified if we read all sentences upfront).
+  string sentence;
+  vector<string> sentences;
+  while (getline(cin, sentence)) {
+    sentences.push_back(sentence);
+  }
+
+  // Extracts the grammar for each sentence and saves it to a file.
+  vector<string> suffixes(sentences.size());
+  #pragma omp parallel for schedule(dynamic) num_threads(num_threads)
+  for (size_t i = 0; i < sentences.size(); ++i) {
+    string suffix;
+    int position = sentences[i].find("|||");
+    if (position != sentences[i].npos) {
+      suffix = sentences[i].substr(position);
+      sentences[i] = sentences[i].substr(0, position);
+    }
+    suffixes[i] = suffix;
+
+    Grammar grammar = extractor.GetGrammar(sentences[i]);
+    ofstream output(GetGrammarFilePath(grammar_path, i).c_str());
+    output << grammar;
+  }
+
+  for (size_t i = 0; i < sentences.size(); ++i) {
+    cout << "<seg grammar=\"" << GetGrammarFilePath(grammar_path, i) << "\" id=\""
+         << i << "\"> " << sentences[i] << " </seg> " << suffixes[i] << endl;
+  }
+
+  Clock::time_point extraction_stop_time = Clock::now();
+  cerr << "Overall extraction step took "
+       << GetDuration(extraction_start_time, extraction_stop_time)
+       << " seconds" << endl;
+
+  return 0;
+}
diff --git a/extractor/sample_alignment.txt b/extractor/sample_alignment.txt
new file mode 100644
index 00000000..80b446a4
--- /dev/null
+++ b/extractor/sample_alignment.txt
@@ -0,0 +1,2 @@
+0-0 1-1 2-2
+1-0 2-1
diff --git a/extractor/sample_bitext.txt b/extractor/sample_bitext.txt
new file mode 100644
index 00000000..93d6b39d
--- /dev/null
+++ b/extractor/sample_bitext.txt
@@ -0,0 +1,2 @@
+ana are mere . ||| anna has apples .
+ana bea mult lapte . ||| anna drinks a lot of milk .
diff --git a/extractor/sampler.cc b/extractor/sampler.cc
new file mode 100644
index 00000000..d81956b5
--- /dev/null
+++ b/extractor/sampler.cc
@@ -0,0 +1,46 @@
+#include "sampler.h"
+
+#include "phrase_location.h"
+#include "suffix_array.h"
+
+namespace extractor {
+
+Sampler::Sampler(shared_ptr<SuffixArray> suffix_array, int max_samples) :
+    suffix_array(suffix_array), max_samples(max_samples) {}
+
+Sampler::Sampler() {}
+
+Sampler::~Sampler() {}
+
+PhraseLocation Sampler::Sample(const PhraseLocation& location) const {
+  vector<int> sample;
+  int num_subpatterns;
+  if (location.matchings == NULL) {
+    // Sample suffix array range.
+    num_subpatterns = 1;
+    int low = location.sa_low, high = location.sa_high;
+    double step = max(1.0, (double) (high - low) / max_samples);
+    for (double i = low; i < high && sample.size() < max_samples; i += step) {
+      sample.push_back(suffix_array->GetSuffix(Round(i)));
+    }
+  } else {
+    // Sample vector of occurrences.
+    num_subpatterns = location.num_subpatterns;
+    int num_matchings = location.matchings->size() / num_subpatterns;
+    double step = max(1.0, (double) num_matchings / max_samples);
+    for (double i = 0, num_samples = 0;
+         i < num_matchings && num_samples < max_samples;
+         i += step, ++num_samples) {
+      int start = Round(i) * num_subpatterns;
+      sample.insert(sample.end(), location.matchings->begin() + start,
+          location.matchings->begin() + start + num_subpatterns);
+    }
+  }
+  return PhraseLocation(sample, num_subpatterns);
+}
+
+int Sampler::Round(double x) const {
+  return x + 0.5;
+}
+
+} // namespace extractor
diff --git a/extractor/sampler.h b/extractor/sampler.h
new file mode 100644
index 00000000..be4aa1bb
--- /dev/null
+++ b/extractor/sampler.h
@@ -0,0 +1,38 @@
+#ifndef _SAMPLER_H_
+#define _SAMPLER_H_
+
+#include <memory>
+
+using namespace std;
+
+namespace extractor {
+
+class PhraseLocation;
+class SuffixArray;
+
+/**
+ * Provides uniform sampling for a PhraseLocation.
+ */
+class Sampler {
+ public:
+  Sampler(shared_ptr<SuffixArray> suffix_array, int max_samples);
+
+  virtual ~Sampler();
+
+  // Samples uniformly at most max_samples phrase occurrences.
+  virtual PhraseLocation Sample(const PhraseLocation& location) const;
+
+ protected:
+  Sampler();
+
+ private:
+  // Round floating point number to the nearest integer.
+  int Round(double x) const;
+
+  shared_ptr<SuffixArray> suffix_array;
+  int max_samples;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/sampler_test.cc b/extractor/sampler_test.cc
new file mode 100644
index 00000000..e9abebfa
--- /dev/null
+++ b/extractor/sampler_test.cc
@@ -0,0 +1,74 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "mocks/mock_suffix_array.h"
+#include "phrase_location.h"
+#include "sampler.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class SamplerTest : public Test {
+ protected:
+  virtual void SetUp() {
+    suffix_array = make_shared<MockSuffixArray>();
+    for (int i = 0; i < 10; ++i) {
+      EXPECT_CALL(*suffix_array, GetSuffix(i)).WillRepeatedly(Return(i));
+    }
+  }
+
+  shared_ptr<MockSuffixArray> suffix_array;
+  shared_ptr<Sampler> sampler;
+};
+
+TEST_F(SamplerTest, TestSuffixArrayRange) {
+  PhraseLocation location(0, 10);
+
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  vector<int> expected_locations = {0};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {0, 5};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 3);
+  expected_locations = {0, 3, 7};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 4);
+  expected_locations = {0, 3, 5, 8};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 100);
+  expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+}
+
+TEST_F(SamplerTest, TestSubstringsSample) {
+  vector<int> locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+  PhraseLocation location(locations, 2);
+
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  vector<int> expected_locations = {0, 1};
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {0, 1, 6, 7};
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 3);
+  expected_locations = {0, 1, 4, 5, 6, 7};
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+
+  sampler = make_shared<Sampler>(suffix_array, 7);
+  expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/scorer.cc b/extractor/scorer.cc
new file mode 100644
index 00000000..d3ebf1c9
--- /dev/null
+++ b/extractor/scorer.cc
@@ -0,0 +1,30 @@
+#include "scorer.h"
+
+#include "features/feature.h"
+
+namespace extractor {
+
+Scorer::Scorer(const vector<shared_ptr<features::Feature> >& features) :
+    features(features) {}
+
+Scorer::Scorer() {}
+
+Scorer::~Scorer() {}
+
+vector<double> Scorer::Score(const features::FeatureContext& context) const {
+  vector<double> scores;
+  for (auto feature: features) {
+    scores.push_back(feature->Score(context));
+  }
+  return scores;
+}
+
+vector<string> Scorer::GetFeatureNames() const {
+  vector<string> feature_names;
+  for (auto feature: features) {
+    feature_names.push_back(feature->GetName());
+  }
+  return feature_names;
+}
+
+} // namespace extractor
diff --git a/extractor/scorer.h b/extractor/scorer.h
new file mode 100644
index 00000000..af8a3b10
--- /dev/null
+++ b/extractor/scorer.h
@@ -0,0 +1,41 @@
+#ifndef _SCORER_H_
+#define _SCORER_H_
+
+#include <memory>
+#include <string>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+namespace features {
+  class Feature;
+  class FeatureContext;
+} // namespace features
+
+/**
+ * Computes the feature scores for a source-target phrase pair.
+ */
+class Scorer {
+ public:
+  Scorer(const vector<shared_ptr<features::Feature> >& features);
+
+  virtual ~Scorer();
+
+  // Computes the feature score for the given context.
+  virtual vector<double> Score(const features::FeatureContext& context) const;
+
+  // Returns the set of feature names used to score any context.
+  virtual vector<string> GetFeatureNames() const;
+
+ protected:
+  Scorer();
+
+ private:
+  vector<shared_ptr<features::Feature> > features;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/scorer_test.cc b/extractor/scorer_test.cc
new file mode 100644
index 00000000..3a09c9cc
--- /dev/null
+++ b/extractor/scorer_test.cc
@@ -0,0 +1,49 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "mocks/mock_feature.h"
+#include "scorer.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class ScorerTest : public Test {
+ protected:
+  virtual void SetUp() {
+    feature1 = make_shared<features::MockFeature>();
+    EXPECT_CALL(*feature1, Score(_)).WillRepeatedly(Return(0.5));
+    EXPECT_CALL(*feature1, GetName()).WillRepeatedly(Return("f1"));
+
+    feature2 = make_shared<features::MockFeature>();
+    EXPECT_CALL(*feature2, Score(_)).WillRepeatedly(Return(-1.3));
+    EXPECT_CALL(*feature2, GetName()).WillRepeatedly(Return("f2"));
+
+    vector<shared_ptr<features::Feature> > features = {feature1, feature2};
+    scorer = make_shared<Scorer>(features);
+  }
+
+  shared_ptr<features::MockFeature> feature1;
+  shared_ptr<features::MockFeature> feature2;
+  shared_ptr<Scorer> scorer;
+};
+
+TEST_F(ScorerTest, TestScore) {
+  vector<double> expected_scores = {0.5, -1.3};
+  Phrase phrase;
+  features::FeatureContext context(phrase, phrase, 0.3, 2, 11);
+  EXPECT_EQ(expected_scores, scorer->Score(context));
+}
+
+TEST_F(ScorerTest, TestGetNames) {
+  vector<string> expected_names = {"f1", "f2"};
+  EXPECT_EQ(expected_names, scorer->GetFeatureNames());
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/suffix_array.cc b/extractor/suffix_array.cc
new file mode 100644
index 00000000..65b2d581
--- /dev/null
+++ b/extractor/suffix_array.cc
@@ -0,0 +1,235 @@
+#include "suffix_array.h"
+
+#include <cassert>
+#include <chrono>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "data_array.h"
+#include "phrase_location.h"
+#include "time_util.h"
+
+namespace fs = boost::filesystem;
+using namespace std;
+using namespace chrono;
+
+namespace extractor {
+
+SuffixArray::SuffixArray(shared_ptr<DataArray> data_array) :
+    data_array(data_array) {
+  BuildSuffixArray();
+}
+
+SuffixArray::SuffixArray() {}
+
+SuffixArray::~SuffixArray() {}
+
+void SuffixArray::BuildSuffixArray() {
+  vector<int> groups = data_array->GetData();
+  groups.reserve(groups.size() + 1);
+  groups.push_back(DataArray::NULL_WORD);
+  suffix_array.resize(groups.size());
+  word_start.resize(data_array->GetVocabularySize() + 1);
+
+  InitialBucketSort(groups);
+
+  int combined_group_size = 0;
+  for (size_t i = 1; i < word_start.size(); ++i) {
+    if (word_start[i] - word_start[i - 1] == 1) {
+      ++combined_group_size;
+      suffix_array[word_start[i] - combined_group_size] = -combined_group_size;
+    } else {
+      combined_group_size = 0;
+    }
+  }
+
+  PrefixDoublingSort(groups);
+  cerr << "\tFinalizing sort..." << endl;
+
+  for (size_t i = 0; i < groups.size(); ++i) {
+    suffix_array[groups[i]] = i;
+  }
+}
+
+void SuffixArray::InitialBucketSort(vector<int>& groups) {
+  Clock::time_point start_time = Clock::now();
+  for (size_t i = 0; i < groups.size(); ++i) {
+    ++word_start[groups[i]];
+  }
+
+  for (size_t i = 1; i < word_start.size(); ++i) {
+    word_start[i] += word_start[i - 1];
+  }
+
+  for (size_t i = 0; i < groups.size(); ++i) {
+    --word_start[groups[i]];
+    suffix_array[word_start[groups[i]]] = i;
+  }
+
+  for (size_t i = 0; i < suffix_array.size(); ++i) {
+    groups[i] = word_start[groups[i] + 1] - 1;
+  }
+  Clock::time_point stop_time = Clock::now();
+  cerr << "\tBucket sort took " << GetDuration(start_time, stop_time)
+       << " seconds" << endl;
+}
+
+void SuffixArray::PrefixDoublingSort(vector<int>& groups) {
+  int step = 1;
+  while (suffix_array[0] != -suffix_array.size()) {
+    int combined_group_size = 0;
+    int i = 0;
+    while (i < suffix_array.size()) {
+      if (suffix_array[i] < 0) {
+        int skip = -suffix_array[i];
+        combined_group_size += skip;
+        i += skip;
+        suffix_array[i - combined_group_size] = -combined_group_size;
+      } else {
+        combined_group_size = 0;
+        int j = groups[suffix_array[i]];
+        TernaryQuicksort(i, j, step, groups);
+        i = j + 1;
+      }
+    }
+    step *= 2;
+  }
+}
+
+void SuffixArray::TernaryQuicksort(int left, int right, int step,
+    vector<int>& groups) {
+  if (left > right) {
+    return;
+  }
+
+  int pivot = left + rand() % (right - left + 1);
+  int pivot_value = groups[suffix_array[pivot] + step];
+  swap(suffix_array[pivot], suffix_array[left]);
+  int mid_left = left, mid_right = left;
+  for (int i = left + 1; i <= right; ++i) {
+    if (groups[suffix_array[i] + step] < pivot_value) {
+      ++mid_right;
+      int temp = suffix_array[i];
+      suffix_array[i] = suffix_array[mid_right];
+      suffix_array[mid_right] = suffix_array[mid_left];
+      suffix_array[mid_left] = temp;
+      ++mid_left;
+    } else if (groups[suffix_array[i] + step] == pivot_value) {
+      ++mid_right;
+      int temp = suffix_array[i];
+      suffix_array[i] = suffix_array[mid_right];
+      suffix_array[mid_right] = temp;
+    }
+  }
+
+  TernaryQuicksort(left, mid_left - 1, step, groups);
+
+  if (mid_left == mid_right) {
+    groups[suffix_array[mid_left]] = mid_left;
+    suffix_array[mid_left] = -1;
+  } else {
+    for (int i = mid_left; i <= mid_right; ++i) {
+      groups[suffix_array[i]] = mid_right;
+    }
+  }
+
+  TernaryQuicksort(mid_right + 1, right, step, groups);
+}
+
+vector<int> SuffixArray::BuildLCPArray() const {
+  Clock::time_point start_time = Clock::now();
+  cerr << "\tConstructing LCP array..." << endl;
+
+  vector<int> lcp(suffix_array.size());
+  vector<int> rank(suffix_array.size());
+  const vector<int>& data = data_array->GetData();
+
+  for (size_t i = 0; i < suffix_array.size(); ++i) {
+    rank[suffix_array[i]] = i;
+  }
+
+  int prefix_len = 0;
+  for (size_t i = 0; i < suffix_array.size(); ++i) {
+    if (rank[i] == 0) {
+      lcp[rank[i]] = -1;
+    } else {
+      int j = suffix_array[rank[i] - 1];
+      while (i + prefix_len < data.size() && j + prefix_len < data.size()
+          && data[i + prefix_len] == data[j + prefix_len]) {
+        ++prefix_len;
+      }
+      lcp[rank[i]] = prefix_len;
+    }
+
+    if (prefix_len > 0) {
+      --prefix_len;
+    }
+  }
+
+  Clock::time_point stop_time = Clock::now();
+  cerr << "\tConstructing LCP took "
+       << GetDuration(start_time, stop_time) << " seconds" << endl;
+
+  return lcp;
+}
+
+int SuffixArray::GetSuffix(int rank) const {
+  return suffix_array[rank];
+}
+
+int SuffixArray::GetSize() const {
+  return suffix_array.size();
+}
+
+shared_ptr<DataArray> SuffixArray::GetData() const {
+  return data_array;
+}
+
+void SuffixArray::WriteBinary(const fs::path& filepath) const {
+  FILE* file = fopen(filepath.string().c_str(), "w");
+  assert(file);
+  data_array->WriteBinary(file);
+
+  int size = suffix_array.size();
+  fwrite(&size, sizeof(int), 1, file);
+  fwrite(suffix_array.data(), sizeof(int), size, file);
+
+  size = word_start.size();
+  fwrite(&size, sizeof(int), 1, file);
+  fwrite(word_start.data(), sizeof(int), size, file);
+}
+
+PhraseLocation SuffixArray::Lookup(int low, int high, const string& word,
+                                   int offset) const {
+  if (!data_array->HasWord(word)) {
+    // Return empty phrase location.
+    return PhraseLocation(0, 0);
+  }
+
+  int word_id = data_array->GetWordId(word);
+  if (offset == 0) {
+    return PhraseLocation(word_start[word_id], word_start[word_id + 1]);
+  }
+
+  return PhraseLocation(LookupRangeStart(low, high, word_id, offset),
+      LookupRangeStart(low, high, word_id + 1, offset));
+}
+
+int SuffixArray::LookupRangeStart(int low, int high, int word_id,
+                                  int offset) const {
+  int result = high;
+  while (low < high) {
+    int middle = low + (high - low) / 2;
+    if (suffix_array[middle] + offset >= data_array->GetSize() ||
+        data_array->AtIndex(suffix_array[middle] + offset) < word_id) {
+      low = middle + 1;
+    } else {
+      result = middle;
+      high = middle;
+    }
+  }
+  return result;
+}
+
+} // namespace extractor
diff --git a/extractor/suffix_array.h b/extractor/suffix_array.h
new file mode 100644
index 00000000..bf731d79
--- /dev/null
+++ b/extractor/suffix_array.h
@@ -0,0 +1,75 @@
+#ifndef _SUFFIX_ARRAY_H_
+#define _SUFFIX_ARRAY_H_
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include <boost/filesystem.hpp>
+
+namespace fs = boost::filesystem;
+using namespace std;
+
+namespace extractor {
+
+class DataArray;
+class PhraseLocation;
+
+class SuffixArray {
+ public:
+  // Creates a suffix array from a data array.
+  SuffixArray(shared_ptr<DataArray> data_array);
+
+  virtual ~SuffixArray();
+
+  // Returns the size of the suffix array.
+  virtual int GetSize() const;
+
+  // Returns the data array on top of which the suffix array is constructed.
+  virtual shared_ptr<DataArray> GetData() const;
+
+  // Constructs the longest-common-prefix array using the algorithm of Kasai et
+  // al. (2001).
+  virtual vector<int> BuildLCPArray() const;
+
+  // Returns the i-th suffix.
+  virtual int GetSuffix(int rank) const;
+
+  // Given the range in which a phrase is located and the next word, returns the
+  // range corresponding to the phrase extended with the next word.
+  virtual PhraseLocation Lookup(int low, int high, const string& word,
+                                int offset) const;
+
+  void WriteBinary(const fs::path& filepath) const;
+
+ protected:
+  SuffixArray();
+
+ private:
+  // Constructs the suffix array using the algorithm of Larsson and Sadakane
+  // (1999).
+  void BuildSuffixArray();
+
+  // Bucket sort on the data array (used for initializing the construction of
+  // the suffix array.)
+  void InitialBucketSort(vector<int>& groups);
+
+  void TernaryQuicksort(int left, int right, int step, vector<int>& groups);
+
+  // Constructs the suffix array in log(n) steps by doubling the length of the
+  // suffixes at each step.
+  void PrefixDoublingSort(vector<int>& groups);
+
+  // Given a [low, high) range in the suffix array in which all elements have
+  // the first offset-1 values the same, it returns the first position where the
+  // offset value is greater or equal to word_id.
+  int LookupRangeStart(int low, int high, int word_id, int offset) const;
+
+  shared_ptr<DataArray> data_array;
+  vector<int> suffix_array;
+  vector<int> word_start;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/suffix_array_test.cc b/extractor/suffix_array_test.cc
new file mode 100644
index 00000000..8431a16e
--- /dev/null
+++ b/extractor/suffix_array_test.cc
@@ -0,0 +1,78 @@
+#include <gtest/gtest.h>
+
+#include "mocks/mock_data_array.h"
+#include "phrase_location.h"
+#include "suffix_array.h"
+
+#include <vector>
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class SuffixArrayTest : public Test {
+ protected:
+  virtual void SetUp() {
+    data = {6, 4, 1, 2, 4, 5, 3, 4, 6, 6, 4, 1, 2};
+    data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*data_array, GetData()).WillRepeatedly(ReturnRef(data));
+    EXPECT_CALL(*data_array, GetVocabularySize()).WillRepeatedly(Return(7));
+    EXPECT_CALL(*data_array, GetSize()).WillRepeatedly(Return(13));
+    suffix_array = make_shared<SuffixArray>(data_array);
+  }
+
+  vector<int> data;
+  shared_ptr<SuffixArray> suffix_array;
+  shared_ptr<MockDataArray> data_array;
+};
+
+TEST_F(SuffixArrayTest, TestData) {
+  EXPECT_EQ(data_array, suffix_array->GetData());
+  EXPECT_EQ(14, suffix_array->GetSize());
+}
+
+TEST_F(SuffixArrayTest, TestBuildSuffixArray) {
+  vector<int> expected_suffix_array =
+      {13, 11, 2, 12, 3, 6, 10, 1, 4, 7, 5, 9, 0, 8};
+  for (size_t i = 0; i < expected_suffix_array.size(); ++i) {
+    EXPECT_EQ(expected_suffix_array[i], suffix_array->GetSuffix(i));
+  }
+}
+
+TEST_F(SuffixArrayTest, TestBuildLCP) {
+  vector<int> expected_lcp = {-1, 0, 2, 0, 1, 0, 0, 3, 1, 1, 0, 0, 4, 1};
+  EXPECT_EQ(expected_lcp, suffix_array->BuildLCPArray());
+}
+
+TEST_F(SuffixArrayTest, TestLookup) {
+  for (size_t i = 0; i < data.size(); ++i) {
+    EXPECT_CALL(*data_array, AtIndex(i)).WillRepeatedly(Return(data[i]));
+  }
+
+  EXPECT_CALL(*data_array, HasWord("word1")).WillRepeatedly(Return(true));
+  EXPECT_CALL(*data_array, GetWordId("word1")).WillRepeatedly(Return(6));
+  EXPECT_EQ(PhraseLocation(11, 14), suffix_array->Lookup(0, 14, "word1", 0));
+
+  EXPECT_CALL(*data_array, HasWord("word2")).WillRepeatedly(Return(false));
+  EXPECT_EQ(PhraseLocation(0, 0), suffix_array->Lookup(0, 14, "word2", 0));
+
+  EXPECT_CALL(*data_array, HasWord("word3")).WillRepeatedly(Return(true));
+  EXPECT_CALL(*data_array, GetWordId("word3")).WillRepeatedly(Return(4));
+  EXPECT_EQ(PhraseLocation(11, 13), suffix_array->Lookup(11, 14, "word3", 1));
+
+  EXPECT_CALL(*data_array, HasWord("word4")).WillRepeatedly(Return(true));
+  EXPECT_CALL(*data_array, GetWordId("word4")).WillRepeatedly(Return(1));
+  EXPECT_EQ(PhraseLocation(11, 13), suffix_array->Lookup(11, 13, "word4", 2));
+
+  EXPECT_CALL(*data_array, HasWord("word5")).WillRepeatedly(Return(true));
+  EXPECT_CALL(*data_array, GetWordId("word5")).WillRepeatedly(Return(2));
+  EXPECT_EQ(PhraseLocation(11, 13), suffix_array->Lookup(11, 13, "word5", 3));
+
+  EXPECT_EQ(PhraseLocation(12, 13), suffix_array->Lookup(11, 13, "word3", 4));
+  EXPECT_EQ(PhraseLocation(11, 11), suffix_array->Lookup(11, 13, "word5", 1));
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/target_phrase_extractor.cc b/extractor/target_phrase_extractor.cc
new file mode 100644
index 00000000..2b8a2e4a
--- /dev/null
+++ b/extractor/target_phrase_extractor.cc
@@ -0,0 +1,158 @@
+#include "target_phrase_extractor.h"
+
+#include <unordered_set>
+
+#include "alignment.h"
+#include "data_array.h"
+#include "phrase.h"
+#include "phrase_builder.h"
+#include "rule_extractor_helper.h"
+#include "vocabulary.h"
+
+using namespace std;
+
+namespace extractor {
+
+TargetPhraseExtractor::TargetPhraseExtractor(
+    shared_ptr<DataArray> target_data_array,
+    shared_ptr<Alignment> alignment,
+    shared_ptr<PhraseBuilder> phrase_builder,
+    shared_ptr<RuleExtractorHelper> helper,
+    shared_ptr<Vocabulary> vocabulary,
+    int max_rule_span,
+    bool require_tight_phrases) :
+    target_data_array(target_data_array),
+    alignment(alignment),
+    phrase_builder(phrase_builder),
+    helper(helper),
+    vocabulary(vocabulary),
+    max_rule_span(max_rule_span),
+    require_tight_phrases(require_tight_phrases) {}
+
+TargetPhraseExtractor::TargetPhraseExtractor() {}
+
+TargetPhraseExtractor::~TargetPhraseExtractor() {}
+
+vector<pair<Phrase, PhraseAlignment> > TargetPhraseExtractor::ExtractPhrases(
+    const vector<pair<int, int> >& target_gaps, const vector<int>& target_low,
+    int target_phrase_low, int target_phrase_high,
+    const unordered_map<int, int>& source_indexes, int sentence_id) const {
+  int target_sent_len = target_data_array->GetSentenceLength(sentence_id);
+
+  vector<int> target_gap_order = helper->GetGapOrder(target_gaps);
+
+  int target_x_low = target_phrase_low, target_x_high = target_phrase_high;
+  if (!require_tight_phrases) {
+    // Extend loose target phrase to the left.
+    while (target_x_low > 0 &&
+           target_phrase_high - target_x_low < max_rule_span &&
+           target_low[target_x_low - 1] == -1) {
+      --target_x_low;
+    }
+    // Extend loose target phrase to the right.
+    while (target_x_high < target_sent_len &&
+           target_x_high - target_phrase_low < max_rule_span &&
+           target_low[target_x_high] == -1) {
+      ++target_x_high;
+    }
+  }
+
+  vector<pair<int, int> > gaps(target_gaps.size());
+  for (size_t i = 0; i < gaps.size(); ++i) {
+    gaps[i] = target_gaps[target_gap_order[i]];
+    if (!require_tight_phrases) {
+      // Extend gap to the left.
+      while (gaps[i].first > target_x_low &&
+             target_low[gaps[i].first - 1] == -1) {
+        --gaps[i].first;
+      }
+      // Extend gap to the right.
+      while (gaps[i].second < target_x_high &&
+             target_low[gaps[i].second] == -1) {
+        ++gaps[i].second;
+      }
+    }
+  }
+
+  // Compute the range in which each chunk may start or end. (Even indexes
+  // represent the range in which the chunk may start, odd indexes represent the
+  // range in which the chunk may end.)
+  vector<pair<int, int> > ranges(2 * gaps.size() + 2);
+  ranges.front() = make_pair(target_x_low, target_phrase_low);
+  ranges.back() = make_pair(target_phrase_high, target_x_high);
+  for (size_t i = 0; i < gaps.size(); ++i) {
+    int j = target_gap_order[i];
+    ranges[i * 2 + 1] = make_pair(gaps[i].first, target_gaps[j].first);
+    ranges[i * 2 + 2] = make_pair(target_gaps[j].second, gaps[i].second);
+  }
+
+  vector<pair<Phrase, PhraseAlignment> > target_phrases;
+  vector<int> subpatterns(ranges.size());
+  GeneratePhrases(target_phrases, ranges, 0, subpatterns, target_gap_order,
+                  target_phrase_low, target_phrase_high, source_indexes,
+                  sentence_id);
+  return target_phrases;
+}
+
+void TargetPhraseExtractor::GeneratePhrases(
+    vector<pair<Phrase, PhraseAlignment> >& target_phrases,
+    const vector<pair<int, int> >& ranges, int index, vector<int>& subpatterns,
+    const vector<int>& target_gap_order, int target_phrase_low,
+    int target_phrase_high, const unordered_map<int, int>& source_indexes,
+    int sentence_id) const {
+  if (index >= ranges.size()) {
+    if (subpatterns.back() - subpatterns.front() > max_rule_span) {
+      return;
+    }
+
+    vector<int> symbols;
+    unordered_map<int, int> target_indexes;
+
+    // Construct target phrase chunk by chunk.
+    int target_sent_start = target_data_array->GetSentenceStart(sentence_id);
+    for (size_t i = 0; i * 2 < subpatterns.size(); ++i) {
+      for (size_t j = subpatterns[i * 2]; j < subpatterns[i * 2 + 1]; ++j) {
+        target_indexes[j] = symbols.size();
+        string target_word = target_data_array->GetWordAtIndex(
+            target_sent_start + j);
+        symbols.push_back(vocabulary->GetTerminalIndex(target_word));
+      }
+      if (i < target_gap_order.size()) {
+        symbols.push_back(vocabulary->GetNonterminalIndex(
+            target_gap_order[i] + 1));
+      }
+    }
+
+    // Construct the alignment between the source and the target phrase.
+    vector<pair<int, int> > links = alignment->GetLinks(sentence_id);
+    vector<pair<int, int> > alignment;
+    for (pair<int, int> link: links) {
+      if (target_indexes.count(link.second)) {
+        alignment.push_back(make_pair(source_indexes.find(link.first)->second,
+                                      target_indexes[link.second]));
+      }
+    }
+
+    Phrase target_phrase = phrase_builder->Build(symbols);
+    target_phrases.push_back(make_pair(target_phrase, alignment));
+    return;
+  }
+
+  subpatterns[index] = ranges[index].first;
+  if (index > 0) {
+    subpatterns[index] = max(subpatterns[index], subpatterns[index - 1]);
+  }
+  // Choose every possible combination of [start, end) for the current chunk.
+  while (subpatterns[index] <= ranges[index].second) {
+    subpatterns[index + 1] = max(subpatterns[index], ranges[index + 1].first);
+    while (subpatterns[index + 1] <= ranges[index + 1].second) {
+      GeneratePhrases(target_phrases, ranges, index + 2, subpatterns,
+                      target_gap_order, target_phrase_low, target_phrase_high,
+                      source_indexes, sentence_id);
+      ++subpatterns[index + 1];
+    }
+    ++subpatterns[index];
+  }
+}
+
+} // namespace extractor
diff --git a/extractor/target_phrase_extractor.h b/extractor/target_phrase_extractor.h
new file mode 100644
index 00000000..289bae2f
--- /dev/null
+++ b/extractor/target_phrase_extractor.h
@@ -0,0 +1,64 @@
+#ifndef _TARGET_PHRASE_EXTRACTOR_H_
+#define _TARGET_PHRASE_EXTRACTOR_H_
+
+#include <memory>
+#include <unordered_map>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+typedef vector<pair<int, int> > PhraseAlignment;
+
+class Alignment;
+class DataArray;
+class Phrase;
+class PhraseBuilder;
+class RuleExtractorHelper;
+class Vocabulary;
+
+class TargetPhraseExtractor {
+ public:
+  TargetPhraseExtractor(shared_ptr<DataArray> target_data_array,
+                        shared_ptr<Alignment> alignment,
+                        shared_ptr<PhraseBuilder> phrase_builder,
+                        shared_ptr<RuleExtractorHelper> helper,
+                        shared_ptr<Vocabulary> vocabulary,
+                        int max_rule_span,
+                        bool require_tight_phrases);
+
+  virtual ~TargetPhraseExtractor();
+
+  // Finds all the target phrases that can extracted from a span in the
+  // target sentence (matching the given set of target phrase gaps).
+  virtual vector<pair<Phrase, PhraseAlignment> > ExtractPhrases(
+      const vector<pair<int, int> >& target_gaps, const vector<int>& target_low,
+      int target_phrase_low, int target_phrase_high,
+      const unordered_map<int, int>& source_indexes, int sentence_id) const;
+
+ protected:
+  TargetPhraseExtractor();
+
+ private:
+  // Computes the cartesian product over the sets of possible target phrase
+  // chunks.
+  void GeneratePhrases(
+      vector<pair<Phrase, PhraseAlignment> >& target_phrases,
+      const vector<pair<int, int> >& ranges, int index,
+      vector<int>& subpatterns, const vector<int>& target_gap_order,
+      int target_phrase_low, int target_phrase_high,
+      const unordered_map<int, int>& source_indexes, int sentence_id) const;
+
+  shared_ptr<DataArray> target_data_array;
+  shared_ptr<Alignment> alignment;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<RuleExtractorHelper> helper;
+  shared_ptr<Vocabulary> vocabulary;
+  int max_rule_span;
+  bool require_tight_phrases;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/target_phrase_extractor_test.cc b/extractor/target_phrase_extractor_test.cc
new file mode 100644
index 00000000..80927dee
--- /dev/null
+++ b/extractor/target_phrase_extractor_test.cc
@@ -0,0 +1,143 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <vector>
+
+#include "mocks/mock_alignment.h"
+#include "mocks/mock_data_array.h"
+#include "mocks/mock_rule_extractor_helper.h"
+#include "mocks/mock_vocabulary.h"
+#include "phrase.h"
+#include "phrase_builder.h"
+#include "target_phrase_extractor.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class TargetPhraseExtractorTest : public Test {
+ protected:
+  virtual void SetUp() {
+    data_array = make_shared<MockDataArray>();
+    alignment = make_shared<MockAlignment>();
+    vocabulary = make_shared<MockVocabulary>();
+    phrase_builder = make_shared<PhraseBuilder>(vocabulary);
+    helper = make_shared<MockRuleExtractorHelper>();
+  }
+
+  shared_ptr<MockDataArray> data_array;
+  shared_ptr<MockAlignment> alignment;
+  shared_ptr<MockVocabulary> vocabulary;
+  shared_ptr<PhraseBuilder> phrase_builder;
+  shared_ptr<MockRuleExtractorHelper> helper;
+  shared_ptr<TargetPhraseExtractor> extractor;
+};
+
+TEST_F(TargetPhraseExtractorTest, TestExtractTightPhrasesTrue) {
+  EXPECT_CALL(*data_array, GetSentenceLength(1)).WillRepeatedly(Return(5));
+  EXPECT_CALL(*data_array, GetSentenceStart(1)).WillRepeatedly(Return(3));
+
+  vector<string> target_words = {"a", "b", "c", "d", "e"};
+  vector<int> target_symbols = {20, 21, 22, 23, 24};
+  for (size_t i = 0; i < target_words.size(); ++i) {
+    EXPECT_CALL(*data_array, GetWordAtIndex(i + 3))
+        .WillRepeatedly(Return(target_words[i]));
+    EXPECT_CALL(*vocabulary, GetTerminalIndex(target_words[i]))
+        .WillRepeatedly(Return(target_symbols[i]));
+    EXPECT_CALL(*vocabulary, GetTerminalValue(target_symbols[i]))
+        .WillRepeatedly(Return(target_words[i]));
+  }
+
+  vector<pair<int, int> > links = {
+    make_pair(0, 0), make_pair(1, 3), make_pair(2, 2), make_pair(3, 1),
+    make_pair(4, 4)
+  };
+  EXPECT_CALL(*alignment, GetLinks(1)).WillRepeatedly(Return(links));
+
+  vector<int> gap_order = {1, 0};
+  EXPECT_CALL(*helper, GetGapOrder(_)).WillRepeatedly(Return(gap_order));
+
+  extractor = make_shared<TargetPhraseExtractor>(
+      data_array, alignment, phrase_builder, helper, vocabulary, 10, true);
+
+  vector<pair<int, int> > target_gaps = {make_pair(3, 4), make_pair(1, 2)};
+  vector<int> target_low = {0, 3, 2, 1, 4};
+  unordered_map<int, int> source_indexes = {{0, 0}, {2, 2}, {4, 4}};
+
+  vector<pair<Phrase, PhraseAlignment> > results =  extractor->ExtractPhrases(
+      target_gaps, target_low, 0, 5, source_indexes, 1);
+  EXPECT_EQ(1, results.size());
+  vector<int> expected_symbols = {20, -2, 22, -1, 24};
+  EXPECT_EQ(expected_symbols, results[0].first.Get());
+  vector<string> expected_words = {"a", "c", "e"};
+  EXPECT_EQ(expected_words, results[0].first.GetWords());
+  vector<pair<int, int> > expected_alignment = {
+    make_pair(0, 0), make_pair(2, 2), make_pair(4, 4)
+  };
+  EXPECT_EQ(expected_alignment, results[0].second);
+}
+
+TEST_F(TargetPhraseExtractorTest, TestExtractPhrasesTightPhrasesFalse) {
+  vector<string> target_words = {"a", "b", "c", "d", "e", "f", "END_OF_LINE"};
+  vector<int> target_symbols = {20, 21, 22, 23, 24, 25, 1};
+  EXPECT_CALL(*data_array, GetSentenceLength(0)).WillRepeatedly(Return(6));
+  EXPECT_CALL(*data_array, GetSentenceStart(0)).WillRepeatedly(Return(0));
+
+  for (size_t i = 0; i < target_words.size(); ++i) {
+    EXPECT_CALL(*data_array, GetWordAtIndex(i))
+        .WillRepeatedly(Return(target_words[i]));
+    EXPECT_CALL(*vocabulary, GetTerminalIndex(target_words[i]))
+        .WillRepeatedly(Return(target_symbols[i]));
+    EXPECT_CALL(*vocabulary, GetTerminalValue(target_symbols[i]))
+        .WillRepeatedly(Return(target_words[i]));
+  }
+
+  vector<pair<int, int> > links = {make_pair(1, 1)};
+  EXPECT_CALL(*alignment, GetLinks(0)).WillRepeatedly(Return(links));
+
+  vector<int> gap_order = {0};
+  EXPECT_CALL(*helper, GetGapOrder(_)).WillRepeatedly(Return(gap_order));
+
+  extractor = make_shared<TargetPhraseExtractor>(
+      data_array, alignment, phrase_builder, helper, vocabulary, 10, false);
+
+  vector<pair<int, int> > target_gaps = {make_pair(2, 4)};
+  vector<int> target_low = {-1, 1, -1, -1, -1, -1};
+  unordered_map<int, int> source_indexes = {{1, 1}};
+
+  vector<pair<Phrase, PhraseAlignment> > results = extractor->ExtractPhrases(
+      target_gaps, target_low, 1, 5, source_indexes, 0);
+  EXPECT_EQ(10, results.size());
+
+  for (int i = 0; i < 2; ++i) {
+    for (int j = 4; j <= 6; ++j) {
+      for (int k = 4; k <= j; ++k) {
+        vector<string> expected_words;
+        for (int l = i; l < 2; ++l) {
+          expected_words.push_back(target_words[l]);
+        }
+        for (int l = k; l < j; ++l) {
+          expected_words.push_back(target_words[l]);
+        }
+
+        PhraseAlignment expected_alignment;
+        expected_alignment.push_back(make_pair(1, 1 - i));
+
+        bool found_expected_pair = false;
+        for (auto result: results) {
+          if (result.first.GetWords() == expected_words &&
+              result.second == expected_alignment) {
+            found_expected_pair = true;
+          }
+        }
+
+        EXPECT_TRUE(found_expected_pair);
+      }
+    }
+  }
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/time_util.cc b/extractor/time_util.cc
new file mode 100644
index 00000000..e46a0c3d
--- /dev/null
+++ b/extractor/time_util.cc
@@ -0,0 +1,10 @@
+#include "time_util.h"
+
+namespace extractor {
+
+double GetDuration(const Clock::time_point& start_time,
+                   const Clock::time_point& stop_time) {
+  return duration_cast<milliseconds>(stop_time - start_time).count() / 1000.0;
+}
+
+} // namespace extractor
diff --git a/extractor/time_util.h b/extractor/time_util.h
new file mode 100644
index 00000000..f7fd51d3
--- /dev/null
+++ b/extractor/time_util.h
@@ -0,0 +1,19 @@
+#ifndef _TIME_UTIL_H_
+#define _TIME_UTIL_H_
+
+#include <chrono>
+
+using namespace std;
+using namespace chrono;
+
+namespace extractor {
+
+typedef high_resolution_clock Clock;
+
+// Computes the duration in seconds of the specified time interval.
+double GetDuration(const Clock::time_point& start_time,
+                   const Clock::time_point& stop_time);
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/translation_table.cc b/extractor/translation_table.cc
new file mode 100644
index 00000000..45da707a
--- /dev/null
+++ b/extractor/translation_table.cc
@@ -0,0 +1,126 @@
+#include "translation_table.h"
+
+#include <string>
+#include <vector>
+
+#include <boost/functional/hash.hpp>
+
+#include "alignment.h"
+#include "data_array.h"
+
+using namespace std;
+
+namespace extractor {
+
+TranslationTable::TranslationTable(shared_ptr<DataArray> source_data_array,
+                                   shared_ptr<DataArray> target_data_array,
+                                   shared_ptr<Alignment> alignment) :
+    source_data_array(source_data_array), target_data_array(target_data_array) {
+  const vector<int>& source_data = source_data_array->GetData();
+  const vector<int>& target_data = target_data_array->GetData();
+
+  unordered_map<int, int> source_links_count;
+  unordered_map<int, int> target_links_count;
+  unordered_map<pair<int, int>, int, PairHash> links_count;
+
+  // For each pair of aligned source target words increment their link count by
+  // 1. Unaligned words are paired with the NULL token.
+  for (size_t i = 0; i < source_data_array->GetNumSentences(); ++i) {
+    vector<pair<int, int> > links = alignment->GetLinks(i);
+    int source_start = source_data_array->GetSentenceStart(i);
+    int target_start = target_data_array->GetSentenceStart(i);
+    // Ignore END_OF_LINE markers.
+    int next_source_start = source_data_array->GetSentenceStart(i + 1) - 1;
+    int next_target_start = target_data_array->GetSentenceStart(i + 1) - 1;
+    vector<int> source_sentence(source_data.begin() + source_start,
+        source_data.begin() + next_source_start);
+    vector<int> target_sentence(target_data.begin() + target_start,
+        target_data.begin() + next_target_start);
+    vector<int> source_linked_words(source_sentence.size());
+    vector<int> target_linked_words(target_sentence.size());
+
+    for (pair<int, int> link: links) {
+      source_linked_words[link.first] = 1;
+      target_linked_words[link.second] = 1;
+      IncrementLinksCount(source_links_count, target_links_count, links_count,
+          source_sentence[link.first], target_sentence[link.second]);
+    }
+
+    for (size_t i = 0; i < source_sentence.size(); ++i) {
+      if (!source_linked_words[i]) {
+        IncrementLinksCount(source_links_count, target_links_count, links_count,
+                            source_sentence[i], DataArray::NULL_WORD);
+      }
+    }
+
+    for (size_t i = 0; i < target_sentence.size(); ++i) {
+      if (!target_linked_words[i]) {
+        IncrementLinksCount(source_links_count, target_links_count, links_count,
+                            DataArray::NULL_WORD, target_sentence[i]);
+      }
+    }
+  }
+
+  // Calculating:
+  //   p(e | f) = count(e, f) / count(f)
+  //   p(f | e) = count(e, f) / count(e)
+  for (pair<pair<int, int>, int> link_count: links_count) {
+    int source_word = link_count.first.first;
+    int target_word = link_count.first.second;
+    double score1 = 1.0 * link_count.second / source_links_count[source_word];
+    double score2 = 1.0 * link_count.second / target_links_count[target_word];
+    translation_probabilities[link_count.first] = make_pair(score1, score2);
+  }
+}
+
+TranslationTable::TranslationTable() {}
+
+TranslationTable::~TranslationTable() {}
+
+void TranslationTable::IncrementLinksCount(
+    unordered_map<int, int>& source_links_count,
+    unordered_map<int, int>& target_links_count,
+    unordered_map<pair<int, int>, int, PairHash>& links_count,
+    int source_word_id,
+    int target_word_id) const {
+  ++source_links_count[source_word_id];
+  ++target_links_count[target_word_id];
+  ++links_count[make_pair(source_word_id, target_word_id)];
+}
+
+double TranslationTable::GetTargetGivenSourceScore(
+    const string& source_word, const string& target_word) {
+  if (!source_data_array->HasWord(source_word) ||
+      !target_data_array->HasWord(target_word)) {
+    return -1;
+  }
+
+  int source_id = source_data_array->GetWordId(source_word);
+  int target_id = target_data_array->GetWordId(target_word);
+  return translation_probabilities[make_pair(source_id, target_id)].first;
+}
+
+double TranslationTable::GetSourceGivenTargetScore(
+    const string& source_word, const string& target_word) {
+  if (!source_data_array->HasWord(source_word) ||
+      !target_data_array->HasWord(target_word)) {
+    return -1;
+  }
+
+  int source_id = source_data_array->GetWordId(source_word);
+  int target_id = target_data_array->GetWordId(target_word);
+  return translation_probabilities[make_pair(source_id, target_id)].second;
+}
+
+void TranslationTable::WriteBinary(const fs::path& filepath) const {
+  FILE* file = fopen(filepath.string().c_str(), "w");
+
+  int size = translation_probabilities.size();
+  fwrite(&size, sizeof(int), 1, file);
+  for (auto entry: translation_probabilities) {
+    fwrite(&entry.first, sizeof(entry.first), 1, file);
+    fwrite(&entry.second, sizeof(entry.second), 1, file);
+  }
+}
+
+} // namespace extractor
diff --git a/extractor/translation_table.h b/extractor/translation_table.h
new file mode 100644
index 00000000..10504d3b
--- /dev/null
+++ b/extractor/translation_table.h
@@ -0,0 +1,63 @@
+#ifndef _TRANSLATION_TABLE_
+#define _TRANSLATION_TABLE_
+
+#include <memory>
+#include <string>
+#include <unordered_map>
+
+#include <boost/filesystem.hpp>
+#include <boost/functional/hash.hpp>
+
+using namespace std;
+namespace fs = boost::filesystem;
+
+namespace extractor {
+
+typedef boost::hash<pair<int, int> > PairHash;
+
+class Alignment;
+class DataArray;
+
+/**
+ * Bilexical table with conditional probabilities.
+ */
+class TranslationTable {
+ public:
+  TranslationTable(
+      shared_ptr<DataArray> source_data_array,
+      shared_ptr<DataArray> target_data_array,
+      shared_ptr<Alignment> alignment);
+
+  virtual ~TranslationTable();
+
+  // Returns p(e | f).
+  virtual double GetTargetGivenSourceScore(const string& source_word,
+                                           const string& target_word);
+
+  // Returns p(f | e).
+  virtual double GetSourceGivenTargetScore(const string& source_word,
+                                           const string& target_word);
+
+  void WriteBinary(const fs::path& filepath) const;
+
+ protected:
+  TranslationTable();
+
+ private:
+  // Increment links count for the given (f, e) word pair.
+  void IncrementLinksCount(
+      unordered_map<int, int>& source_links_count,
+      unordered_map<int, int>& target_links_count,
+      unordered_map<pair<int, int>, int, PairHash>& links_count,
+      int source_word_id,
+      int target_word_id) const;
+
+  shared_ptr<DataArray> source_data_array;
+  shared_ptr<DataArray> target_data_array;
+  unordered_map<pair<int, int>, pair<double, double>, PairHash>
+      translation_probabilities;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/extractor/translation_table_test.cc b/extractor/translation_table_test.cc
new file mode 100644
index 00000000..051b5715
--- /dev/null
+++ b/extractor/translation_table_test.cc
@@ -0,0 +1,84 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "mocks/mock_alignment.h"
+#include "mocks/mock_data_array.h"
+#include "translation_table.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+TEST(TranslationTableTest, TestScores) {
+  vector<string> words = {"a", "b", "c"};
+
+  vector<int> source_data = {2, 3, 2, 3, 4, 0, 2, 3, 6, 0, 2, 3, 6, 0};
+  vector<int> source_sentence_start = {0, 6, 10, 14};
+  shared_ptr<MockDataArray> source_data_array = make_shared<MockDataArray>();
+  EXPECT_CALL(*source_data_array, GetData())
+      .WillRepeatedly(ReturnRef(source_data));
+  EXPECT_CALL(*source_data_array, GetNumSentences())
+      .WillRepeatedly(Return(3));
+  for (size_t i = 0; i < source_sentence_start.size(); ++i) {
+    EXPECT_CALL(*source_data_array, GetSentenceStart(i))
+        .WillRepeatedly(Return(source_sentence_start[i]));
+  }
+  for (size_t i = 0; i < words.size(); ++i) {
+    EXPECT_CALL(*source_data_array, HasWord(words[i]))
+        .WillRepeatedly(Return(true));
+    EXPECT_CALL(*source_data_array, GetWordId(words[i]))
+        .WillRepeatedly(Return(i + 2));
+  }
+  EXPECT_CALL(*source_data_array, HasWord("d"))
+      .WillRepeatedly(Return(false));
+
+  vector<int> target_data = {2, 3, 2, 3, 4, 5, 0, 3, 6, 0, 2, 7, 0};
+  vector<int> target_sentence_start = {0, 7, 10, 13};
+  shared_ptr<MockDataArray> target_data_array = make_shared<MockDataArray>();
+  EXPECT_CALL(*target_data_array, GetData())
+      .WillRepeatedly(ReturnRef(target_data));
+  for (size_t i = 0; i < target_sentence_start.size(); ++i) {
+    EXPECT_CALL(*target_data_array, GetSentenceStart(i))
+        .WillRepeatedly(Return(target_sentence_start[i]));
+  }
+  for (size_t i = 0; i < words.size(); ++i) {
+    EXPECT_CALL(*target_data_array, HasWord(words[i]))
+        .WillRepeatedly(Return(true));
+    EXPECT_CALL(*target_data_array, GetWordId(words[i]))
+        .WillRepeatedly(Return(i + 2));
+  }
+  EXPECT_CALL(*target_data_array, HasWord("d"))
+      .WillRepeatedly(Return(false));
+
+  vector<pair<int, int> > links1 = {
+    make_pair(0, 0), make_pair(1, 1), make_pair(2, 2), make_pair(3, 3),
+    make_pair(4, 4), make_pair(4, 5)
+  };
+  vector<pair<int, int> > links2 = {make_pair(1, 0), make_pair(2, 1)};
+  vector<pair<int, int> > links3 = {make_pair(0, 0), make_pair(2, 1)};
+  shared_ptr<MockAlignment> alignment = make_shared<MockAlignment>();
+  EXPECT_CALL(*alignment, GetLinks(0)).WillRepeatedly(Return(links1));
+  EXPECT_CALL(*alignment, GetLinks(1)).WillRepeatedly(Return(links2));
+  EXPECT_CALL(*alignment, GetLinks(2)).WillRepeatedly(Return(links3));
+
+  shared_ptr<TranslationTable> table = make_shared<TranslationTable>(
+      source_data_array, target_data_array, alignment);
+
+  EXPECT_EQ(0.75, table->GetTargetGivenSourceScore("a", "a"));
+  EXPECT_EQ(0, table->GetTargetGivenSourceScore("a", "b"));
+  EXPECT_EQ(0.5, table->GetTargetGivenSourceScore("c", "c"));
+  EXPECT_EQ(-1, table->GetTargetGivenSourceScore("c", "d"));
+
+  EXPECT_EQ(1, table->GetSourceGivenTargetScore("a", "a"));
+  EXPECT_EQ(0, table->GetSourceGivenTargetScore("a", "b"));
+  EXPECT_EQ(1, table->GetSourceGivenTargetScore("c", "c"));
+  EXPECT_EQ(-1, table->GetSourceGivenTargetScore("c", "d"));
+}
+
+} // namespace
+} // namespace extractor
diff --git a/extractor/vocabulary.cc b/extractor/vocabulary.cc
new file mode 100644
index 00000000..15795d1e
--- /dev/null
+++ b/extractor/vocabulary.cc
@@ -0,0 +1,37 @@
+#include "vocabulary.h"
+
+namespace extractor {
+
+Vocabulary::~Vocabulary() {}
+
+int Vocabulary::GetTerminalIndex(const string& word) {
+  int word_id = -1;
+  #pragma omp critical (vocabulary)
+  {
+    if (!dictionary.count(word)) {
+      word_id = words.size();
+      dictionary[word] = word_id;
+      words.push_back(word);
+    } else {
+      word_id = dictionary[word];
+    }
+  }
+  return word_id;
+}
+
+int Vocabulary::GetNonterminalIndex(int position) {
+  return -position;
+}
+
+bool Vocabulary::IsTerminal(int symbol) {
+  return symbol >= 0;
+}
+
+string Vocabulary::GetTerminalValue(int symbol) {
+  string word;
+  #pragma omp critical (vocabulary)
+  word = words[symbol];
+  return word;
+}
+
+} // namespace extractor
diff --git a/extractor/vocabulary.h b/extractor/vocabulary.h
new file mode 100644
index 00000000..c8fd9411
--- /dev/null
+++ b/extractor/vocabulary.h
@@ -0,0 +1,48 @@
+#ifndef _VOCABULARY_H_
+#define _VOCABULARY_H_
+
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+using namespace std;
+
+namespace extractor {
+
+/**
+ * Data structure for mapping words to word ids.
+ *
+ * This strucure contains words located in the frequent collocations and words
+ * encountered during the grammar extraction time. This dictionary is
+ * considerably smaller than the dictionaries in the data arrays (and so is the
+ * query time). Note that this is the single data structure that changes state
+ * and needs to have thread safe read/write operations.
+ *
+ * Note: For an experiment using different vocabulary instances for each thread,
+ * the running time did not improve implying that the critical regions do not
+ * cause bottlenecks.
+ */
+class Vocabulary {
+ public:
+  virtual ~Vocabulary();
+
+  // Returns the word id for the given word.
+  virtual int GetTerminalIndex(const string& word);
+
+  // Returns the id for a nonterminal located at the given position in a phrase.
+  int GetNonterminalIndex(int position);
+
+  // Checks if a symbol is a nonterminal.
+  bool IsTerminal(int symbol);
+
+  // Returns the word corresponding to the given word id.
+  virtual string GetTerminalValue(int symbol);
+
+ private:
+  unordered_map<string, int> dictionary;
+  vector<string> words;
+};
+
+} // namespace extractor
+
+#endif
diff --git a/klm/lm/builder/corpus_count.cc b/klm/lm/builder/corpus_count.cc
index abea4ed0..aea93ad1 100644
--- a/klm/lm/builder/corpus_count.cc
+++ b/klm/lm/builder/corpus_count.cc
@@ -3,6 +3,7 @@
 #include "lm/builder/ngram.hh"
 #include "lm/lm_exception.hh"
 #include "lm/word_index.hh"
+#include "util/fake_ofstream.hh"
 #include "util/file.hh"
 #include "util/file_piece.hh"
 #include "util/murmur_hash.hh"
@@ -23,39 +24,71 @@ namespace lm {
 namespace builder {
 namespace {
 
+#pragma pack(push)
+#pragma pack(4)
+struct VocabEntry {
+  typedef uint64_t Key;
+
+  uint64_t GetKey() const { return key; }
+  void SetKey(uint64_t to) { key = to; }
+
+  uint64_t key;
+  lm::WordIndex value;
+};
+#pragma pack(pop)
+
+const float kProbingMultiplier = 1.5;
+
 class VocabHandout {
   public:
-    explicit VocabHandout(int fd) {
-      util::scoped_fd duped(util::DupOrThrow(fd));
-      word_list_.reset(util::FDOpenOrThrow(duped));
-      
+    static std::size_t MemUsage(WordIndex initial_guess) {
+      if (initial_guess < 2) initial_guess = 2;
+      return util::CheckOverflow(Table::Size(initial_guess, kProbingMultiplier));
+    }
+
+    explicit VocabHandout(int fd, WordIndex initial_guess) :
+        table_backing_(util::CallocOrThrow(MemUsage(initial_guess))),
+        table_(table_backing_.get(), MemUsage(initial_guess)),
+        double_cutoff_(std::max<std::size_t>(initial_guess * 1.1, 1)),
+        word_list_(fd) {
       Lookup("<unk>"); // Force 0
       Lookup("<s>"); // Force 1
       Lookup("</s>"); // Force 2
     }
 
     WordIndex Lookup(const StringPiece &word) {
-      uint64_t hashed = util::MurmurHashNative(word.data(), word.size());
-      std::pair<Seen::iterator, bool> ret(seen_.insert(std::pair<uint64_t, lm::WordIndex>(hashed, seen_.size())));
-      if (ret.second) {
-        char null_delimit = 0;
-        util::WriteOrThrow(word_list_.get(), word.data(), word.size());
-        util::WriteOrThrow(word_list_.get(), &null_delimit, 1);
-        UTIL_THROW_IF(seen_.size() >= std::numeric_limits<lm::WordIndex>::max(), VocabLoadException, "Too many vocabulary words.  Change WordIndex to uint64_t in lm/word_index.hh.");
+      VocabEntry entry;
+      entry.key = util::MurmurHashNative(word.data(), word.size());
+      entry.value = table_.SizeNoSerialization();
+
+      Table::MutableIterator it;
+      if (table_.FindOrInsert(entry, it))
+        return it->value;
+      word_list_ << word << '\0';
+      UTIL_THROW_IF(Size() >= std::numeric_limits<lm::WordIndex>::max(), VocabLoadException, "Too many vocabulary words.  Change WordIndex to uint64_t in lm/word_index.hh.");
+      if (Size() >= double_cutoff_) {
+        table_backing_.call_realloc(table_.DoubleTo());
+        table_.Double(table_backing_.get());
+        double_cutoff_ *= 2;
       }
-      return ret.first->second;
+      return entry.value;
     }
 
     WordIndex Size() const {
-      return seen_.size();
+      return table_.SizeNoSerialization();
     }
 
   private:
-    typedef boost::unordered_map<uint64_t, lm::WordIndex> Seen;
+    // TODO: factor out a resizable probing hash table.
+    // TODO: use mremap on linux to get all zeros on resizes.
+    util::scoped_malloc table_backing_;
 
-    Seen seen_;
+    typedef util::ProbingHashTable<VocabEntry, util::IdentityHash> Table;
+    Table table_;
 
-    util::scoped_FILE word_list_;
+    std::size_t double_cutoff_;
+    
+    util::FakeOFStream word_list_;
 };
 
 class DedupeHash : public std::unary_function<const WordIndex *, bool> {
@@ -85,6 +118,7 @@ class DedupeEquals : public std::binary_function<const WordIndex *, const WordIn
 struct DedupeEntry {
   typedef WordIndex *Key;
   Key GetKey() const { return key; }
+  void SetKey(WordIndex *to) { key = to; }
   Key key;
   static DedupeEntry Construct(WordIndex *at) {
     DedupeEntry ret;
@@ -95,8 +129,6 @@ struct DedupeEntry {
 
 typedef util::ProbingHashTable<DedupeEntry, DedupeHash, DedupeEquals> Dedupe;
 
-const float kProbingMultiplier = 1.5;
-
 class Writer {
   public:
     Writer(std::size_t order, const util::stream::ChainPosition &position, void *dedupe_mem, std::size_t dedupe_mem_size) 
@@ -105,7 +137,7 @@ class Writer {
         dedupe_(dedupe_mem, dedupe_mem_size, &dedupe_invalid_[0], DedupeHash(order), DedupeEquals(order)),
         buffer_(new WordIndex[order - 1]),
         block_size_(position.GetChain().BlockSize()) {
-      dedupe_.Clear(DedupeEntry::Construct(&dedupe_invalid_[0]));
+      dedupe_.Clear();
       assert(Dedupe::Size(position.GetChain().BlockSize() / position.GetChain().EntrySize(), kProbingMultiplier) == dedupe_mem_size);
       if (order == 1) {
         // Add special words.  AdjustCounts is responsible if order != 1.    
@@ -149,7 +181,7 @@ class Writer {
       }
       // Block end.  Need to store the context in a temporary buffer.  
       std::copy(gram_.begin() + 1, gram_.end(), buffer_.get());
-      dedupe_.Clear(DedupeEntry::Construct(&dedupe_invalid_[0]));
+      dedupe_.Clear();
       block_->SetValidSize(block_size_);
       gram_.ReBase((++block_)->Get());
       std::copy(buffer_.get(), buffer_.get() + gram_.Order() - 1, gram_.begin());
@@ -187,18 +219,22 @@ float CorpusCount::DedupeMultiplier(std::size_t order) {
   return kProbingMultiplier * static_cast<float>(sizeof(DedupeEntry)) / static_cast<float>(NGram::TotalSize(order));
 }
 
+std::size_t CorpusCount::VocabUsage(std::size_t vocab_estimate) {
+  return VocabHandout::MemUsage(vocab_estimate);
+}
+
 CorpusCount::CorpusCount(util::FilePiece &from, int vocab_write, uint64_t &token_count, WordIndex &type_count, std::size_t entries_per_block) 
   : from_(from), vocab_write_(vocab_write), token_count_(token_count), type_count_(type_count),
     dedupe_mem_size_(Dedupe::Size(entries_per_block, kProbingMultiplier)),
     dedupe_mem_(util::MallocOrThrow(dedupe_mem_size_)) {
-  token_count_ = 0;
-  type_count_ = 0;
 }
 
 void CorpusCount::Run(const util::stream::ChainPosition &position) {
   UTIL_TIMER("(%w s) Counted n-grams\n");
 
-  VocabHandout vocab(vocab_write_);
+  VocabHandout vocab(vocab_write_, type_count_);
+  token_count_ = 0;
+  type_count_ = 0;
   const WordIndex end_sentence = vocab.Lookup("</s>");
   Writer writer(NGram::OrderFromSize(position.GetChain().EntrySize()), position, dedupe_mem_.get(), dedupe_mem_size_);
   uint64_t count = 0;
diff --git a/klm/lm/builder/corpus_count.hh b/klm/lm/builder/corpus_count.hh
index e255bad1..aa0ed8ed 100644
--- a/klm/lm/builder/corpus_count.hh
+++ b/klm/lm/builder/corpus_count.hh
@@ -23,6 +23,11 @@ class CorpusCount {
     // Memory usage will be DedupeMultipler(order) * block_size + total_chain_size + unknown vocab_hash_size
     static float DedupeMultiplier(std::size_t order);
 
+    // How much memory vocabulary will use based on estimated size of the vocab.
+    static std::size_t VocabUsage(std::size_t vocab_estimate);
+
+    // token_count: out.
+    // type_count aka vocabulary size.  Initialize to an estimate.  It is set to the exact value.
     CorpusCount(util::FilePiece &from, int vocab_write, uint64_t &token_count, WordIndex &type_count, std::size_t entries_per_block);
 
     void Run(const util::stream::ChainPosition &position);
diff --git a/klm/lm/builder/corpus_count_test.cc b/klm/lm/builder/corpus_count_test.cc
index 8d53ca9d..6d325ef5 100644
--- a/klm/lm/builder/corpus_count_test.cc
+++ b/klm/lm/builder/corpus_count_test.cc
@@ -44,7 +44,7 @@ BOOST_AUTO_TEST_CASE(Short) {
   util::stream::Chain chain(config);
   NGramStream stream;
   uint64_t token_count;
-  WordIndex type_count;
+  WordIndex type_count = 10;
   CorpusCount counter(input_piece, vocab.get(), token_count, type_count, chain.BlockSize() / chain.EntrySize());
   chain >> boost::ref(counter) >> stream >> util::stream::kRecycle;
 
diff --git a/klm/lm/builder/lmplz_main.cc b/klm/lm/builder/lmplz_main.cc
index 90b9dca2..1e086dcc 100644
--- a/klm/lm/builder/lmplz_main.cc
+++ b/klm/lm/builder/lmplz_main.cc
@@ -6,6 +6,7 @@
 #include <iostream>
 
 #include <boost/program_options.hpp>
+#include <boost/version.hpp>
 
 namespace {
 class SizeNotify {
@@ -33,13 +34,17 @@ int main(int argc, char *argv[]) {
     lm::builder::PipelineConfig pipeline;
 
     options.add_options()
-      ("order,o", po::value<std::size_t>(&pipeline.order)->required(), "Order of the model")
+      ("order,o", po::value<std::size_t>(&pipeline.order)
+#if BOOST_VERSION >= 104200
+         ->required()
+#endif
+         , "Order of the model")
       ("interpolate_unigrams", po::bool_switch(&pipeline.initial_probs.interpolate_unigrams), "Interpolate the unigrams (default: emulate SRILM by not interpolating)")
       ("temp_prefix,T", po::value<std::string>(&pipeline.sort.temp_prefix)->default_value("/tmp/lm"), "Temporary file prefix")
       ("memory,S", SizeOption(pipeline.sort.total_memory, util::GuessPhysicalMemory() ? "80%" : "1G"), "Sorting memory")
-      ("vocab_memory", SizeOption(pipeline.assume_vocab_hash_size, "50M"), "Assume that the vocabulary hash table will use this much memory for purposes of calculating total memory in the count step")
       ("minimum_block", SizeOption(pipeline.minimum_block, "8K"), "Minimum block size to allow")
       ("sort_block", SizeOption(pipeline.sort.buffer_size, "64M"), "Size of IO operations for sort (determines arity)")
+      ("vocab_estimate", po::value<lm::WordIndex>(&pipeline.vocab_estimate)->default_value(1000000), "Assume this vocabulary size for purposes of calculating memory in step 1 (corpus count) and pre-sizing the hash table")
       ("block_count", po::value<std::size_t>(&pipeline.block_count)->default_value(2), "Block count (per order)")
       ("vocab_file", po::value<std::string>(&pipeline.vocab_file)->default_value(""), "Location to write vocabulary file")
       ("verbose_header", po::bool_switch(&pipeline.verbose_header), "Add a verbose header to the ARPA file that includes information such as token count, smoothing type, etc.");
@@ -68,6 +73,14 @@ int main(int argc, char *argv[]) {
     po::store(po::parse_command_line(argc, argv, options), vm);
     po::notify(vm);
 
+    // required() appeared in Boost 1.42.0.
+#if BOOST_VERSION < 104200
+    if (!vm.count("order")) {
+      std::cerr << "the option '--order' is required but missing" << std::endl;
+      return 1;
+    }
+#endif
+
     util::NormalizeTempPrefix(pipeline.sort.temp_prefix);
 
     lm::builder::InitialProbabilitiesConfig &initial = pipeline.initial_probs;
diff --git a/klm/lm/builder/pipeline.cc b/klm/lm/builder/pipeline.cc
index 14a1f721..b89ea6ba 100644
--- a/klm/lm/builder/pipeline.cc
+++ b/klm/lm/builder/pipeline.cc
@@ -207,17 +207,18 @@ void CountText(int text_file /* input */, int vocab_file /* output */, Master &m
   const PipelineConfig &config = master.Config();
   std::cerr << "=== 1/5 Counting and sorting n-grams ===" << std::endl;
 
-  UTIL_THROW_IF(config.TotalMemory() < config.assume_vocab_hash_size, util::Exception, "Vocab hash size estimate " << config.assume_vocab_hash_size << " exceeds total memory " << config.TotalMemory());
+  const std::size_t vocab_usage = CorpusCount::VocabUsage(config.vocab_estimate);
+  UTIL_THROW_IF(config.TotalMemory() < vocab_usage, util::Exception, "Vocab hash size estimate " << vocab_usage << " exceeds total memory " << config.TotalMemory());
   std::size_t memory_for_chain = 
     // This much memory to work with after vocab hash table.
-    static_cast<float>(config.TotalMemory() - config.assume_vocab_hash_size) /
+    static_cast<float>(config.TotalMemory() - vocab_usage) /
     // Solve for block size including the dedupe multiplier for one block.
     (static_cast<float>(config.block_count) + CorpusCount::DedupeMultiplier(config.order)) *
     // Chain likes memory expressed in terms of total memory.
     static_cast<float>(config.block_count);
   util::stream::Chain chain(util::stream::ChainConfig(NGram::TotalSize(config.order), config.block_count, memory_for_chain));
 
-  WordIndex type_count;
+  WordIndex type_count = config.vocab_estimate;
   util::FilePiece text(text_file, NULL, &std::cerr);
   text_file_name = text.FileName();
   CorpusCount counter(text, vocab_file, token_count, type_count, chain.BlockSize() / chain.EntrySize());
diff --git a/klm/lm/builder/pipeline.hh b/klm/lm/builder/pipeline.hh
index f1d6c5f6..845e5481 100644
--- a/klm/lm/builder/pipeline.hh
+++ b/klm/lm/builder/pipeline.hh
@@ -3,6 +3,7 @@
 
 #include "lm/builder/initial_probabilities.hh"
 #include "lm/builder/header_info.hh"
+#include "lm/word_index.hh"
 #include "util/stream/config.hh"
 #include "util/file_piece.hh"
 
@@ -19,9 +20,9 @@ struct PipelineConfig {
   util::stream::ChainConfig read_backoffs;
   bool verbose_header;
 
-  // Amount of memory to assume that the vocabulary hash table will use.  This
-  // is subtracted from total memory for CorpusCount.
-  std::size_t assume_vocab_hash_size;
+  // Estimated vocabulary size.  Used for sizing CorpusCount memory and
+  // initial probing hash table sizing, also in CorpusCount.
+  lm::WordIndex vocab_estimate;
 
   // Minimum block size to tolerate.
   std::size_t minimum_block;
@@ -33,7 +34,7 @@ struct PipelineConfig {
   std::size_t TotalMemory() const { return sort.total_memory; }
 };
 
-// Takes ownership of text_file.
+// Takes ownership of text_file and out_arpa.
 void Pipeline(PipelineConfig config, int text_file, int out_arpa);
 
 }} // namespaces
diff --git a/klm/lm/builder/print.cc b/klm/lm/builder/print.cc
index b0323221..84bd81ca 100644
--- a/klm/lm/builder/print.cc
+++ b/klm/lm/builder/print.cc
@@ -1,15 +1,11 @@
 #include "lm/builder/print.hh"
 
-#include "util/double-conversion/double-conversion.h"
-#include "util/double-conversion/utils.h"
+#include "util/fake_ofstream.hh"
 #include "util/file.hh"
 #include "util/mmap.hh"
 #include "util/scoped.hh"
 #include "util/stream/timer.hh"
 
-#define BOOST_LEXICAL_CAST_ASSUME_C_LOCALE
-#include <boost/lexical_cast.hpp>
-
 #include <sstream>
 
 #include <string.h>
@@ -28,71 +24,6 @@ VocabReconstitute::VocabReconstitute(int fd) {
   map_.push_back(i);
 }
 
-namespace {
-class OutputManager {
-  public:
-    static const std::size_t kOutBuf = 1048576;
-
-    // Does not take ownership of out.
-    explicit OutputManager(int out)
-      : buf_(util::MallocOrThrow(kOutBuf)),
-        builder_(static_cast<char*>(buf_.get()), kOutBuf),
-        // Mostly the default but with inf instead.  And no flags.
-        convert_(double_conversion::DoubleToStringConverter::NO_FLAGS, "inf", "NaN", 'e', -6, 21, 6, 0),
-        fd_(out) {}
-
-    ~OutputManager() {
-      Flush();
-    }
-
-    OutputManager &operator<<(float value) {
-      // Odd, but this is the largest number found in the comments.
-      EnsureRemaining(double_conversion::DoubleToStringConverter::kMaxPrecisionDigits + 8);
-      convert_.ToShortestSingle(value, &builder_);
-      return *this;
-    }
-
-    OutputManager &operator<<(StringPiece str) {
-      if (str.size() > kOutBuf) {
-        Flush();
-        util::WriteOrThrow(fd_, str.data(), str.size());
-      } else {
-        EnsureRemaining(str.size());
-        builder_.AddSubstring(str.data(), str.size());
-      }
-      return *this;
-    }
-
-    // Inefficient!
-    OutputManager &operator<<(unsigned val) {
-      return *this << boost::lexical_cast<std::string>(val);
-    }
-
-    OutputManager &operator<<(char c) {
-      EnsureRemaining(1);
-      builder_.AddCharacter(c);
-      return *this;
-    }
-
-    void Flush() {
-      util::WriteOrThrow(fd_, buf_.get(), builder_.position());
-      builder_.Reset();
-    }
-
-  private:
-    void EnsureRemaining(std::size_t amount) {
-      if (static_cast<std::size_t>(builder_.size() - builder_.position()) < amount) {
-        Flush();
-      }
-    }
-
-    util::scoped_malloc buf_;
-    double_conversion::StringBuilder builder_;
-    double_conversion::DoubleToStringConverter convert_;
-    int fd_;
-};
-} // namespace
-
 PrintARPA::PrintARPA(const VocabReconstitute &vocab, const std::vector<uint64_t> &counts, const HeaderInfo* header_info, int out_fd) 
   : vocab_(vocab), out_fd_(out_fd) {
   std::stringstream stream;
@@ -112,8 +43,9 @@ PrintARPA::PrintARPA(const VocabReconstitute &vocab, const std::vector<uint64_t>
 }
 
 void PrintARPA::Run(const ChainPositions &positions) {
+  util::scoped_fd closer(out_fd_);
   UTIL_TIMER("(%w s) Wrote ARPA file\n");
-  OutputManager out(out_fd_);
+  util::FakeOFStream out(out_fd_);
   for (unsigned order = 1; order <= positions.size(); ++order) {
     out << "\\" << order << "-grams:" << '\n';
     for (NGramStream stream(positions[order - 1]); stream; ++stream) {
diff --git a/klm/lm/builder/print.hh b/klm/lm/builder/print.hh
index aa932e75..adbbb94a 100644
--- a/klm/lm/builder/print.hh
+++ b/klm/lm/builder/print.hh
@@ -88,7 +88,8 @@ template <class V> class Print {
 
 class PrintARPA {
   public:
-    // header_info may be NULL to disable the header
+    // header_info may be NULL to disable the header.
+    // Takes ownership of out_fd upon Run().
     explicit PrintARPA(const VocabReconstitute &vocab, const std::vector<uint64_t> &counts, const HeaderInfo* header_info, int out_fd);
 
     void Run(const ChainPositions &positions);
diff --git a/klm/lm/filter/filter_main.cc b/klm/lm/filter/filter_main.cc
index 1a4ba84f..1736bc40 100644
--- a/klm/lm/filter/filter_main.cc
+++ b/klm/lm/filter/filter_main.cc
@@ -25,8 +25,8 @@ void DisplayHelp(const char *name) {
     "    parser.\n"
     "single mode treats the entire input as a single sentence.\n"
     "multiple mode filters to multiple sentences in parallel.  Each sentence is on\n"
-    "    a separate line.  A separate file is created for each file by appending the\n"
-    "    0-indexed line number to the output file name.\n"
+    "    a separate line.  A separate file is created for each sentence by appending\n"
+    "    the 0-indexed line number to the output file name.\n"
     "union mode produces one filtered model that is the union of models created by\n"
     "    multiple mode.\n\n"
     "context means only the context (all but last word) has to pass the filter, but\n"
diff --git a/klm/lm/kenlm_max_order_main.cc b/klm/lm/kenlm_max_order_main.cc
deleted file mode 100644
index 94221201..00000000
--- a/klm/lm/kenlm_max_order_main.cc
+++ /dev/null
@@ -1,6 +0,0 @@
-#include "lm/max_order.hh"
-#include <iostream>
-
-int main(int argc, char *argv[]) {
-  std::cerr << "KenLM was compiled with a maximum supported n-gram order set to " << KENLM_MAX_ORDER << "." << std::endl;
-}
diff --git a/klm/lm/query_main.cc b/klm/lm/query_main.cc
index 49757d9a..27d3a1a5 100644
--- a/klm/lm/query_main.cc
+++ b/klm/lm/query_main.cc
@@ -2,6 +2,7 @@
 
 int main(int argc, char *argv[]) {
   if (!(argc == 2 || (argc == 3 && !strcmp(argv[2], "null")))) {
+    std::cerr << "KenLM was compiled with maximum order " << KENLM_MAX_ORDER << "." << std::endl;
     std::cerr << "Usage: " << argv[0] << " lm_file [null]" << std::endl;
     std::cerr << "Input is wrapped in <s> and </s> unless null is passed." << std::endl;
     return 1;
diff --git a/klm/util/fake_ofstream.hh b/klm/util/fake_ofstream.hh
new file mode 100644
index 00000000..bcdebe45
--- /dev/null
+++ b/klm/util/fake_ofstream.hh
@@ -0,0 +1,94 @@
+/* Like std::ofstream but without being incredibly slow.  Backed by a raw fd.
+ * Does not support many data types.  Currently, it's targeted at writing ARPA
+ * files quickly.
+ */
+#include "util/double-conversion/double-conversion.h"
+#include "util/double-conversion/utils.h"
+#include "util/file.hh"
+#include "util/scoped.hh"
+#include "util/string_piece.hh"
+
+#define BOOST_LEXICAL_CAST_ASSUME_C_LOCALE
+#include <boost/lexical_cast.hpp>
+
+namespace util {
+class FakeOFStream {
+  public:
+    static const std::size_t kOutBuf = 1048576;
+
+    // Does not take ownership of out.
+    explicit FakeOFStream(int out)
+      : buf_(util::MallocOrThrow(kOutBuf)),
+        builder_(static_cast<char*>(buf_.get()), kOutBuf),
+        // Mostly the default but with inf instead.  And no flags.
+        convert_(double_conversion::DoubleToStringConverter::NO_FLAGS, "inf", "NaN", 'e', -6, 21, 6, 0),
+        fd_(out) {}
+
+    ~FakeOFStream() {
+      if (buf_.get()) Flush();
+    }
+
+    FakeOFStream &operator<<(float value) {
+      // Odd, but this is the largest number found in the comments.
+      EnsureRemaining(double_conversion::DoubleToStringConverter::kMaxPrecisionDigits + 8);
+      convert_.ToShortestSingle(value, &builder_);
+      return *this;
+    }
+
+    FakeOFStream &operator<<(double value) {
+      EnsureRemaining(double_conversion::DoubleToStringConverter::kMaxPrecisionDigits + 8);
+      convert_.ToShortest(value, &builder_);
+      return *this;
+    }
+
+    FakeOFStream &operator<<(StringPiece str) {
+      if (str.size() > kOutBuf) {
+        Flush();
+        util::WriteOrThrow(fd_, str.data(), str.size());
+      } else {
+        EnsureRemaining(str.size());
+        builder_.AddSubstring(str.data(), str.size());
+      }
+      return *this;
+    }
+
+    // Inefficient!  TODO: more efficient implementation
+    FakeOFStream &operator<<(unsigned value) {
+      return *this << boost::lexical_cast<std::string>(value);
+    }
+
+    FakeOFStream &operator<<(char c) {
+      EnsureRemaining(1);
+      builder_.AddCharacter(c);
+      return *this;
+    }
+
+    // Note this does not sync.
+    void Flush() {
+      util::WriteOrThrow(fd_, buf_.get(), builder_.position());
+      builder_.Reset();
+    }
+
+    // Not necessary, but does assure the data is cleared.
+    void Finish() {
+      Flush();
+      // It will segfault trying to null terminate otherwise.
+      builder_.Finalize();
+      buf_.reset();
+      util::FSyncOrThrow(fd_);
+    }
+
+  private:
+    void EnsureRemaining(std::size_t amount) {
+      if (static_cast<std::size_t>(builder_.size() - builder_.position()) <= amount) {
+        Flush();
+      }
+    }
+
+    util::scoped_malloc buf_;
+    double_conversion::StringBuilder builder_;
+    double_conversion::DoubleToStringConverter convert_;
+    int fd_;
+};
+
+} // namespace
diff --git a/klm/util/file.cc b/klm/util/file.cc
index 86d9b12d..c7d8e23b 100644
--- a/klm/util/file.cc
+++ b/klm/util/file.cc
@@ -111,15 +111,26 @@ void ResizeOrThrow(int fd, uint64_t to) {
   UTIL_THROW_IF_ARG(ret, FDException, (fd), "while resizing to " << to << " bytes");
 }
 
+namespace {
+std::size_t GuardLarge(std::size_t size) {
+  // The following operating systems have broken read/write/pread/pwrite that
+  // only supports up to 2^31.
+#if defined(_WIN32) || defined(_WIN64) || defined(__APPLE__) || defined(OS_ANDROID)
+  return std::min(static_cast<std::size_t>(INT_MAX), size);
+#else
+  return size;
+#endif
+}
+}
+
 std::size_t PartialRead(int fd, void *to, std::size_t amount) {
 #if defined(_WIN32) || defined(_WIN64)
-  amount = min(static_cast<std::size_t>(INT_MAX), amount);
-  int ret = _read(fd, to, amount); 
+  int ret = _read(fd, to, GuardLarge(amount));
 #else
   errno = 0;
   ssize_t ret;
   do {
-    ret = read(fd, to, amount);
+    ret = read(fd, to, GuardLarge(amount));
   } while (ret == -1 && errno == EINTR);
 #endif
   UTIL_THROW_IF_ARG(ret < 0, FDException, (fd), "while reading " << amount << " bytes");
@@ -169,11 +180,13 @@ void PReadOrThrow(int fd, void *to_void, std::size_t size, uint64_t off) {
     ssize_t ret;
     errno = 0;
     do {
+      ret =
 #ifdef OS_ANDROID
-      ret = pread64(fd, to, size, off);
+        pread64
 #else
-      ret = pread(fd, to, size, off);
+        pread
 #endif
+        (fd, to, GuardLarge(size), off);
     } while (ret == -1 && errno == EINTR);
     if (ret <= 0) {
       UTIL_THROW_IF(ret == 0, EndOfFileException, " for reading " << size << " bytes at " << off << " from " << NameFromFD(fd));
@@ -190,14 +203,20 @@ void WriteOrThrow(int fd, const void *data_void, std::size_t size) {
   const uint8_t *data = static_cast<const uint8_t*>(data_void);
   while (size) {
 #if defined(_WIN32) || defined(_WIN64)
-    int ret = write(fd, data, min(static_cast<std::size_t>(INT_MAX), size));
+    int ret;
 #else
-    errno = 0;
     ssize_t ret;
+#endif
+    errno = 0;
     do {
-      ret = write(fd, data, size);
-    } while (ret == -1 && errno == EINTR);
+      ret = 
+#if defined(_WIN32) || defined(_WIN64)
+        _write
+#else
+        write
 #endif
+        (fd, data, GuardLarge(size));
+    } while (ret == -1 && errno == EINTR);
     UTIL_THROW_IF_ARG(ret < 1, FDException, (fd), "while writing " << size << " bytes");
     data += ret;
     size -= ret;
diff --git a/klm/util/file_piece.cc b/klm/util/file_piece.cc
index 9de30fc4..b5961bea 100644
--- a/klm/util/file_piece.cc
+++ b/klm/util/file_piece.cc
@@ -51,7 +51,7 @@ FilePiece::FilePiece(int fd, const char *name, std::ostream *show_progress, std:
 
 FilePiece::FilePiece(std::istream &stream, const char *name, std::size_t min_buffer) :
   total_size_(kBadSize), page_(SizePage()) {
-  InitializeNoRead(name ? name : "istream", min_buffer);
+  InitializeNoRead("istream", min_buffer);
 
   fallback_to_read_ = true;
   data_.reset(MallocOrThrow(default_map_size_), default_map_size_, scoped_memory::MALLOC_ALLOCATED);
@@ -95,32 +95,6 @@ unsigned long int FilePiece::ReadULong() {
   return ReadNumber<unsigned long int>();
 }
 
-std::size_t FilePiece::Raw(void *to, std::size_t limit) {
-  if (!limit) return 0;
-  std::size_t in_buf = static_cast<std::size_t>(position_end_ - position_);
-  if (in_buf) {
-    std::size_t amount = std::min(in_buf, limit);
-    memcpy(to, position_, amount);
-    position_ += amount;
-    return amount;
-  }
-
-  std::size_t read_return;
-  if (fallback_to_read_) {
-    read_return = fell_back_.Read(to, limit);
-    progress_.Set(fell_back_.RawAmount());
-  } else {
-    uint64_t desired_begin = mapped_offset_ + static_cast<uint64_t>(position_ - data_.begin());
-    SeekOrThrow(file_.get(), desired_begin);
-    read_return = ReadOrEOF(file_.get(), to, limit);
-    // Good thing we never rewind.  This makes desired_begin calculate the right way the next time.
-    mapped_offset_ += static_cast<uint64_t>(read_return);
-    progress_ += read_return;
-  }
-  at_end_ |= (read_return == 0);
-  return read_return;
-}
-
 // Factored out so that istream can call this.
 void FilePiece::InitializeNoRead(const char *name, std::size_t min_buffer) {
   file_name_ = name;
@@ -146,7 +120,7 @@ void FilePiece::Initialize(const char *name, std::ostream *show_progress, std::s
   }
   Shift();
   // gzip detect.
-  if ((position_end_ - position_) >= ReadCompressed::kMagicSize && ReadCompressed::DetectCompressedMagic(position_)) {
+  if ((position_end_ >= position_ + ReadCompressed::kMagicSize) && ReadCompressed::DetectCompressedMagic(position_)) {
     if (!fallback_to_read_) {
       at_end_ = false;
       TransitionToRead();
@@ -244,7 +218,7 @@ void FilePiece::MMapShift(uint64_t desired_begin) {
   // Use mmap.  
   uint64_t ignore = desired_begin % page_;
   // Duplicate request for Shift means give more data.  
-  if (position_ == data_.begin() + ignore) {
+  if (position_ == data_.begin() + ignore && position_) {
     default_map_size_ *= 2;
   }
   // Local version so that in case of failure it doesn't overwrite the class variable.  
diff --git a/klm/util/file_piece.hh b/klm/util/file_piece.hh
index 1b110287..c07c6011 100644
--- a/klm/util/file_piece.hh
+++ b/klm/util/file_piece.hh
@@ -64,10 +64,7 @@ class FilePiece {
     long int ReadLong();
     unsigned long int ReadULong();
 
-    // Fake read() function.  Reads up to limit bytes, returning the amount read.  Returns 0 on EOF || limit == 0. 
-    std::size_t Raw(void *to, std::size_t limit);
-
-    // Skip spaces defined by being in delim.
+    // Skip spaces defined by isspace.
     void SkipSpaces(const bool *delim = kSpaces) {
       for (; ; ++position_) {
         if (position_ == position_end_) Shift();
diff --git a/klm/util/mmap.cc b/klm/util/mmap.cc
index bc9e3f81..6f79f26f 100644
--- a/klm/util/mmap.cc
+++ b/klm/util/mmap.cc
@@ -6,6 +6,7 @@
 
 #include "util/exception.hh"
 #include "util/file.hh"
+#include "util/scoped.hh"
 
 #include <iostream>
 
@@ -110,8 +111,14 @@ void *MapOrThrow(std::size_t size, bool for_write, int flags, bool prefault, int
   UTIL_THROW_IF(!ret, ErrnoException, "MapViewOfFile failed");
 #else
   int protect = for_write ? (PROT_READ | PROT_WRITE) : PROT_READ;
-  void *ret = mmap(NULL, size, protect, flags, fd, offset);
-  UTIL_THROW_IF(ret == MAP_FAILED, ErrnoException, "mmap failed for size " << size << " at offset " << offset);
+  void *ret;
+  UTIL_THROW_IF((ret = mmap(NULL, size, protect, flags, fd, offset)) == MAP_FAILED, ErrnoException, "mmap failed for size " << size << " at offset " << offset);
+#  ifdef MADV_HUGEPAGE
+  /* We like huge pages but it's fine if we can't have them.  Note that huge
+   * pages are not supported for file-backed mmap on linux.
+   */
+  madvise(ret, size, MADV_HUGEPAGE);
+#  endif
 #endif
   return ret;
 }
@@ -141,8 +148,7 @@ void MapRead(LoadMethod method, int fd, uint64_t offset, std::size_t size, scope
     case POPULATE_OR_READ:
 #endif
     case READ:
-      out.reset(malloc(size), size, scoped_memory::MALLOC_ALLOCATED);
-      if (!out.get()) UTIL_THROW(util::ErrnoException, "Allocating " << size << " bytes with malloc");
+      out.reset(MallocOrThrow(size), size, scoped_memory::MALLOC_ALLOCATED);
       SeekOrThrow(fd, offset);
       ReadOrThrow(fd, out.get(), size);
       break;
diff --git a/klm/util/probing_hash_table.hh b/klm/util/probing_hash_table.hh
index 6780489d..57866ff9 100644
--- a/klm/util/probing_hash_table.hh
+++ b/klm/util/probing_hash_table.hh
@@ -6,6 +6,7 @@
 #include <algorithm>
 #include <cstddef>
 #include <functional>
+#include <vector>
 
 #include <assert.h>
 #include <stdint.h>
@@ -73,10 +74,7 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
       assert(initialized_);
 #endif
       UTIL_THROW_IF(++entries_ >= buckets_, ProbingSizeException, "Hash table with " << buckets_ << " buckets is full.");
-      for (MutableIterator i(begin_ + (hash_(t.GetKey()) % buckets_));;) {
-        if (equal_(i->GetKey(), invalid_)) { *i = t; return i; }
-        if (++i == end_) { i = begin_; }
-      }
+      return UncheckedInsert(t);
     }
 
     // Return true if the value was found (and not inserted).  This is consistent with Find but the opposite if hash_map!
@@ -126,12 +124,96 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
       }    
     }
 
-    void Clear(Entry invalid) {
+    void Clear() {
+      Entry invalid;
+      invalid.SetKey(invalid_);
       std::fill(begin_, end_, invalid);
       entries_ = 0;
     }
 
+    // Return number of entries assuming no serialization went on.
+    std::size_t SizeNoSerialization() const {
+      return entries_;
+    }
+
+    // Return memory size expected by Double.
+    std::size_t DoubleTo() const {
+      return buckets_ * 2 * sizeof(Entry);
+    }
+
+    // Inform the table that it has double the amount of memory.
+    // Pass clear_new = false if you are sure the new memory is initialized
+    // properly (to invalid_) i.e. by mremap.
+    void Double(void *new_base, bool clear_new = true) {
+      begin_ = static_cast<MutableIterator>(new_base);
+      MutableIterator old_end = begin_ + buckets_;
+      buckets_ *= 2;
+      end_ = begin_ + buckets_;
+      if (clear_new) {
+        Entry invalid;
+        invalid.SetKey(invalid_);
+        std::fill(old_end, end_, invalid);
+      }
+      std::vector<Entry> rolled_over;
+      // Move roll-over entries to a buffer because they might not roll over anymore.  This should be small.
+      for (MutableIterator i = begin_; i != old_end && !equal_(i->GetKey(), invalid_); ++i) {
+        rolled_over.push_back(*i);
+        i->SetKey(invalid_);
+      }
+      /* Re-insert everything.  Entries might go backwards to take over a
+       * recently opened gap, stay, move to new territory, or wrap around.   If
+       * an entry wraps around, it might go to a pointer greater than i (which
+       * can happen at the beginning) and it will be revisited to possibly fill
+       * in a gap created later.
+       */
+      Entry temp;
+      for (MutableIterator i = begin_; i != old_end; ++i) {
+        if (!equal_(i->GetKey(), invalid_)) {
+          temp = *i;
+          i->SetKey(invalid_);
+          UncheckedInsert(temp);
+        }
+      }
+      // Put the roll-over entries back in.
+      for (typename std::vector<Entry>::const_iterator i(rolled_over.begin()); i != rolled_over.end(); ++i) {
+        UncheckedInsert(*i);
+      }
+    }
+
+    // Mostly for tests, check consistency of every entry.
+    void CheckConsistency() {
+      MutableIterator last;
+      for (last = end_ - 1; last >= begin_ && !equal_(last->GetKey(), invalid_); --last) {}
+      UTIL_THROW_IF(last == begin_, ProbingSizeException, "Completely full");
+      MutableIterator i;
+      // Beginning can be wrap-arounds.
+      for (i = begin_; !equal_(i->GetKey(), invalid_); ++i) {
+        MutableIterator ideal = Ideal(*i);
+        UTIL_THROW_IF(ideal > i && ideal <= last, Exception, "Inconsistency at position " << (i - begin_) << " should be at " << (ideal - begin_));
+      }
+      MutableIterator pre_gap = i;
+      for (; i != end_; ++i) {
+        if (equal_(i->GetKey(), invalid_)) {
+          pre_gap = i;
+          continue;
+        }
+        MutableIterator ideal = Ideal(*i);
+        UTIL_THROW_IF(ideal > i || ideal <= pre_gap, Exception, "Inconsistency at position " << (i - begin_) << " with ideal " << (ideal - begin_));
+      }
+    }
+
   private:
+    template <class T> MutableIterator Ideal(const T &t) {
+      return begin_ + (hash_(t.GetKey()) % buckets_);
+    }
+
+    template <class T> MutableIterator UncheckedInsert(const T &t) {
+      for (MutableIterator i(Ideal(t));;) {
+        if (equal_(i->GetKey(), invalid_)) { *i = t; return i; }
+        if (++i == end_) { i = begin_; }
+      }
+    }
+
     MutableIterator begin_;
     std::size_t buckets_;
     MutableIterator end_;
diff --git a/klm/util/probing_hash_table_test.cc b/klm/util/probing_hash_table_test.cc
index be0fa859..9f7948ce 100644
--- a/klm/util/probing_hash_table_test.cc
+++ b/klm/util/probing_hash_table_test.cc
@@ -1,10 +1,14 @@
 #include "util/probing_hash_table.hh"
 
+#include "util/murmur_hash.hh"
+#include "util/scoped.hh"
+
 #define BOOST_TEST_MODULE ProbingHashTableTest
 #include <boost/test/unit_test.hpp>
 #include <boost/scoped_array.hpp>
 #include <boost/functional/hash.hpp>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
 #include <stdint.h>
 
@@ -19,6 +23,10 @@ struct Entry {
     return key;
   }
 
+  void SetKey(unsigned char to) {
+    key = to;
+  }
+
   uint64_t GetValue() const {
     return value;
   }
@@ -46,5 +54,49 @@ BOOST_AUTO_TEST_CASE(simple) {
   BOOST_CHECK(!table.Find(2, i));
 }
 
+struct Entry64 {
+  uint64_t key;
+  typedef uint64_t Key;
+
+  Entry64() {}
+
+  explicit Entry64(uint64_t key_in) {
+    key = key_in;
+  }
+
+  Key GetKey() const { return key; }
+  void SetKey(uint64_t to) { key = to; }
+};
+
+struct MurmurHashEntry64 {
+  std::size_t operator()(uint64_t value) const {
+    return util::MurmurHash64A(&value, 8);
+  }
+};
+
+typedef ProbingHashTable<Entry64, MurmurHashEntry64> Table64;
+
+BOOST_AUTO_TEST_CASE(Double) {
+  for (std::size_t initial = 19; initial < 30; ++initial) {
+    size_t size = Table64::Size(initial, 1.2);
+    scoped_malloc mem(MallocOrThrow(size));
+    Table64 table(mem.get(), size, std::numeric_limits<uint64_t>::max());
+    table.Clear();
+    for (uint64_t i = 0; i < 19; ++i) {
+      table.Insert(Entry64(i));
+    }
+    table.CheckConsistency();
+    mem.call_realloc(table.DoubleTo());
+    table.Double(mem.get());
+    table.CheckConsistency();
+    for (uint64_t i = 20; i < 40 ; ++i) {
+      table.Insert(Entry64(i));
+    }
+    mem.call_realloc(table.DoubleTo());
+    table.Double(mem.get());
+    table.CheckConsistency();
+  }
+}
+
 } // namespace
 } // namespace util
diff --git a/klm/util/read_compressed.cc b/klm/util/read_compressed.cc
index b81549e4..b62a6e83 100644
--- a/klm/util/read_compressed.cc
+++ b/klm/util/read_compressed.cc
@@ -180,12 +180,73 @@ class GZip : public ReadBase {
 };
 #endif // HAVE_ZLIB
 
+const uint8_t kBZMagic[3] = {'B', 'Z', 'h'};
+
 #ifdef HAVE_BZLIB
 class BZip : public ReadBase {
   public:
-    explicit BZip(int fd, void *already_data, std::size_t already_size) {
+    BZip(int fd, void *already_data, std::size_t already_size) {
       scoped_fd hold(fd);
       closer_.reset(FDOpenReadOrThrow(hold));
+      file_ = NULL;
+      Open(already_data, already_size);
+    }
+
+    BZip(FILE *file, void *already_data, std::size_t already_size) {
+      closer_.reset(file);
+      file_ = NULL;
+      Open(already_data, already_size);
+    }
+
+    ~BZip() {
+      Close(file_);
+    }
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      assert(file_);
+      int bzerror = BZ_OK;
+      int ret = BZ2_bzRead(&bzerror, file_, to, std::min<std::size_t>(static_cast<std::size_t>(INT_MAX), amount));
+      long pos = ftell(closer_.get());
+      if (pos != -1) ReadCount(thunk) = pos;
+      switch (bzerror) {
+        case BZ_STREAM_END:
+          /* bzip2 files can be concatenated by e.g. pbzip2.  Annoyingly, the
+           * library doesn't handle this internally.  This gets the trailing
+           * data, grows it up to magic as needed, validates the magic, and
+           * reopens.
+           */
+          {
+            bzerror = BZ_OK;
+            void *trailing_data;
+            int trailing_size;
+            BZ2_bzReadGetUnused(&bzerror, file_, &trailing_data, &trailing_size);
+            UTIL_THROW_IF(bzerror != BZ_OK, BZException, "bzip2 error in BZ2_bzReadGetUnused " << BZ2_bzerror(file_, &bzerror) << " code " << bzerror);
+            std::string trailing(static_cast<const char*>(trailing_data), trailing_size);
+            Close(file_);
+
+            if (trailing_size < (int)sizeof(kBZMagic)) {
+              trailing.resize(sizeof(kBZMagic));
+              if (1 != fread(&trailing[trailing_size], sizeof(kBZMagic) - trailing_size, 1, closer_.get())) {
+                UTIL_THROW_IF(trailing_size, BZException, "File has trailing cruft");
+                // Legitimate end of file.
+                ReplaceThis(new Complete(), thunk);
+                return ret;
+              }
+            }
+            UTIL_THROW_IF(memcmp(trailing.data(), kBZMagic, sizeof(kBZMagic)), BZException, "Trailing cruft is not another bzip2 stream");
+            Open(&trailing[0], trailing.size());
+          }
+          return ret;
+        case BZ_OK:
+          return ret;
+        default:
+          UTIL_THROW(BZException, "bzip2 error " << BZ2_bzerror(file_, &bzerror) << " code " << bzerror);
+      }
+    }
+
+  private:
+    void Open(void *already_data, std::size_t already_size) {
+      assert(!file_);
       int bzerror = BZ_OK;
       file_ = BZ2_bzReadOpen(&bzerror, closer_.get(), 0, 0, already_data, already_size);
       switch (bzerror) {
@@ -199,38 +260,23 @@ class BZip : public ReadBase {
           UTIL_THROW(BZException, "IO error reading file");
         case BZ_MEM_ERROR:
           throw std::bad_alloc();
+        default:
+          UTIL_THROW(BZException, "Unknown bzip2 error code " << bzerror);
       }
+      assert(file_);
     }
 
-    ~BZip() {
+    static void Close(BZFILE *&file) {
+      if (file == NULL) return;
       int bzerror = BZ_OK;
-      BZ2_bzReadClose(&bzerror, file_);
+      BZ2_bzReadClose(&bzerror, file);
       if (bzerror != BZ_OK) {
-        std::cerr << "bz2 readclose error" << std::endl;
+        std::cerr << "bz2 readclose error number " << bzerror << std::endl;
         abort();
       }
+      file = NULL;
     }
 
-    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
-      int bzerror = BZ_OK;
-      int ret = BZ2_bzRead(&bzerror, file_, to, std::min<std::size_t>(static_cast<std::size_t>(INT_MAX), amount));
-      long pos;
-      switch (bzerror) {
-        case BZ_STREAM_END:
-          pos = ftell(closer_.get());
-          if (pos != -1) ReadCount(thunk) = pos;
-          ReplaceThis(new Complete(), thunk);
-          return ret;
-        case BZ_OK:
-          pos = ftell(closer_.get());
-          if (pos != -1) ReadCount(thunk) = pos;
-          return ret;
-        default:
-          UTIL_THROW(BZException, "bzip2 error " << BZ2_bzerror(file_, &bzerror) << " code " << bzerror);
-      }
-    }
-
-  private:
     scoped_FILE closer_;
     BZFILE *file_;
 };
@@ -346,11 +392,11 @@ MagicResult DetectMagic(const void *from_void) {
   if (header[0] == 0x1f && header[1] == 0x8b) {
     return GZIP;
   }
-  if (header[0] == 'B' && header[1] == 'Z' && header[2] == 'h') {
+  if (!memcmp(header, kBZMagic, sizeof(kBZMagic))) {
     return BZIP;
   }
-  const uint8_t xzmagic[6] = { 0xFD, '7', 'z', 'X', 'Z', 0x00 };
-  if (!memcmp(header, xzmagic, 6)) {
+  const uint8_t kXZMagic[6] = { 0xFD, '7', 'z', 'X', 'Z', 0x00 };
+  if (!memcmp(header, kXZMagic, sizeof(kXZMagic))) {
     return XZIP;
   }
   return UNKNOWN;
diff --git a/klm/util/scoped.cc b/klm/util/scoped.cc
index e7066ee4..6c5b0c2d 100644
--- a/klm/util/scoped.cc
+++ b/klm/util/scoped.cc
@@ -1,6 +1,9 @@
 #include "util/scoped.hh"
 
 #include <cstdlib>
+#if !defined(_WIN32) && !defined(_WIN64)
+#include <sys/mman.h>
+#endif
 
 namespace util {
 
@@ -10,20 +13,31 @@ MallocException::MallocException(std::size_t requested) throw() {
 
 MallocException::~MallocException() throw() {}
 
+namespace {
+void *InspectAddr(void *addr, std::size_t requested, const char *func_name) {
+  UTIL_THROW_IF_ARG(!addr && requested, MallocException, (requested), "in " << func_name);
+  // These routines are often used for large chunks of memory where huge pages help.
+#if MADV_HUGEPAGE
+  madvise(addr, requested, MADV_HUGEPAGE);
+#endif
+  return addr;
+}
+} // namespace
+
 void *MallocOrThrow(std::size_t requested) {
-  void *ret;
-  UTIL_THROW_IF_ARG(!(ret = std::malloc(requested)), MallocException, (requested), "in malloc");
-  return ret;
+  return InspectAddr(std::malloc(requested), requested, "malloc");
+}
+
+void *CallocOrThrow(std::size_t requested) {
+  return InspectAddr(std::calloc(1, requested), requested, "calloc");
 }
 
 scoped_malloc::~scoped_malloc() {
   std::free(p_);
 }
 
-void scoped_malloc::call_realloc(std::size_t to) {
-  void *ret;
-  UTIL_THROW_IF_ARG(!(ret = std::realloc(p_, to)) && to, MallocException, (to), "in realloc");
-  p_ = ret;
+void scoped_malloc::call_realloc(std::size_t requested) {
+  p_ = InspectAddr(std::realloc(p_, requested), requested, "realloc");
 }
 
 } // namespace util
diff --git a/klm/util/scoped.hh b/klm/util/scoped.hh
index d0a5aabd..b642d064 100644
--- a/klm/util/scoped.hh
+++ b/klm/util/scoped.hh
@@ -14,6 +14,7 @@ class MallocException : public ErrnoException {
 };
 
 void *MallocOrThrow(std::size_t requested);
+void *CallocOrThrow(std::size_t requested);
 
 class scoped_malloc {
   public:
diff --git a/klm/util/sized_iterator.hh b/klm/util/sized_iterator.hh
index aabcc531..cf998953 100644
--- a/klm/util/sized_iterator.hh
+++ b/klm/util/sized_iterator.hh
@@ -3,6 +3,7 @@
 
 #include "util/proxy_iterator.hh"
 
+#include <algorithm>
 #include <functional>
 #include <string>
 
@@ -63,6 +64,13 @@ class SizedProxy {
     const void *Data() const { return inner_.Data(); }
     void *Data() { return inner_.Data(); }
 
+    friend void swap(SizedProxy &first, SizedProxy &second) {
+      std::swap_ranges(
+          static_cast<char*>(first.inner_.Data()), 
+          static_cast<char*>(first.inner_.Data()) + first.inner_.EntrySize(),
+          static_cast<char*>(second.inner_.Data()));
+    }
+
   private:
     friend class util::ProxyIterator<SizedProxy>;
 
diff --git a/klm/util/usage.cc b/klm/util/usage.cc
index b8e125d0..ad4dc7b4 100644
--- a/klm/util/usage.cc
+++ b/klm/util/usage.cc
@@ -22,6 +22,11 @@ float FloatSec(const struct timeval &tv) {
   return static_cast<float>(tv.tv_sec) + (static_cast<float>(tv.tv_usec) / 1000000.0);
 }
 #endif
+
+const char *SkipSpaces(const char *at) {
+  for (; *at == ' '; ++at) {}
+  return at;
+}
 } // namespace
 
 void PrintUsage(std::ostream &out) {
@@ -32,18 +37,19 @@ void PrintUsage(std::ostream &out) {
     return;
   }
   out << "user\t" << FloatSec(usage.ru_utime) << "\nsys\t" << FloatSec(usage.ru_stime) << '\n';
-
+  out << "CPU\t" << (FloatSec(usage.ru_utime) + FloatSec(usage.ru_stime)) << '\n';
   // Linux doesn't set memory usage :-(.  
   std::ifstream status("/proc/self/status", std::ios::in);
   std::string line;
   while (getline(status, line)) {
     if (!strncmp(line.c_str(), "VmRSS:\t", 7)) {
-      out << "VmRSS:  " << (line.c_str() + 7) << '\n';
+      out << "RSSCur\t" << SkipSpaces(line.c_str() + 7) << '\n';
       break;
     } else if (!strncmp(line.c_str(), "VmPeak:\t", 8)) {
-      out << "VmPeak: " << (line.c_str() + 8) << '\n';
+      out << "VmPeak\t" << SkipSpaces(line.c_str() + 8) << '\n';
     }
   }
+  out << "RSSMax\t" << usage.ru_maxrss << " kB" << '\n';
 #endif
 }
 
diff --git a/m4/ax_cxx_compile_stdcxx_11.m4 b/m4/ax_cxx_compile_stdcxx_11.m4
new file mode 100644
index 00000000..f6cf4a15
--- /dev/null
+++ b/m4/ax_cxx_compile_stdcxx_11.m4
@@ -0,0 +1,140 @@
+# ============================================================================
+#  http://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html
+# ============================================================================
+#
+# SYNOPSIS
+#
+#   AX_CXX_COMPILE_STDCXX_11([ext|noext],[mandatory|optional])
+#
+# DESCRIPTION
+#
+#   Check for baseline language coverage in the compiler for the C++11
+#   standard; if necessary, add switches to CXXFLAGS to enable support.
+#
+#   The first argument, if specified, indicates whether you insist on an
+#   extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
+#   -std=c++11).  If neither is specified, you get whatever works, with
+#   preference for an extended mode.
+#
+#   The second argument, if specified 'mandatory' or if left unspecified,
+#   indicates that baseline C++11 support is required and that the macro
+#   should error out if no mode with that support is found.  If specified
+#   'optional', then configuration proceeds regardless, after defining
+#   HAVE_CXX11 if and only if a supporting mode is found.
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
+#   Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
+#   Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 3
+
+m4_define([_AX_CXX_COMPILE_STDCXX_11_testbody], [
+  template <typename T>
+    struct check
+    {
+      static_assert(sizeof(int) <= sizeof(T), "not big enough");
+    };
+
+    typedef check<check<bool>> right_angle_brackets;
+
+    int a;
+    decltype(a) b;
+
+    typedef check<int> check_type;
+    check_type c;
+    check_type&& cr = static_cast<check_type&&>(c);
+
+    auto d = a;
+])
+
+AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [dnl
+  m4_if([$1], [], [],
+        [$1], [ext], [],
+        [$1], [noext], [],
+        [m4_fatal([invalid argument `$1' to AX_CXX_COMPILE_STDCXX_11])])dnl
+  m4_if([$2], [], [ax_cxx_compile_cxx11_required=true],
+        [$2], [mandatory], [ax_cxx_compile_cxx11_required=true],
+        [$2], [optional], [ax_cxx_compile_cxx11_required=false],
+        [m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX_11])])dnl
+  AC_LANG_PUSH([C++])dnl
+  ac_success=no
+  AC_CACHE_CHECK(whether $CXX supports C++11 features by default,
+  ax_cv_cxx_compile_cxx11,
+  [AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])],
+    [ax_cv_cxx_compile_cxx11=yes],
+    [ax_cv_cxx_compile_cxx11=no])])
+  if test x$ax_cv_cxx_compile_cxx11 = xyes; then
+    ac_success=yes
+  fi
+
+  restore_it="$CXXFLAGS"
+  m4_if([$1], [noext], [], [dnl
+  if test x$ac_success = xno; then
+    for switch in -std=gnu++11 -std=gnu++0x; do
+      cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch])
+      AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch,
+                     $cachevar,
+        [ac_save_CXXFLAGS="$CXXFLAGS"
+         CXXFLAGS="$CXXFLAGS $switch"
+         AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])],
+          [eval $cachevar=yes],
+          [eval $cachevar=no])
+         CXXFLAGS="$ac_save_CXXFLAGS"])
+      if eval test x\$$cachevar = xyes; then
+        CXXFLAGS="$CXXFLAGS"
+        c11switch="$switch"
+        ac_success=yes
+        break
+      fi
+    done
+  fi])
+
+  m4_if([$1], [ext], [], [dnl
+  if test x$ac_success = xno; then
+    for switch in -std=c++11 -std=c++0x; do
+      cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch])
+      AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch,
+                     $cachevar,
+        [ac_save_CXXFLAGS="$CXXFLAGS"
+         CXXFLAGS="$CXXFLAGS $switch"
+         AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])],
+          [eval $cachevar=yes],
+          [eval $cachevar=no])
+         CXXFLAGS="$ac_save_CXXFLAGS"])
+      if eval test x\$$cachevar = xyes; then
+        CXXFLAGS="$CXXFLAGS"
+        c11switch="$switch"
+        ac_success=yes
+        break
+      fi
+    done
+  fi])
+  CXXFLAGS="$restore_it"
+  AC_SUBST([CXX11_SWITCH], ["$c11switch"])
+  AC_LANG_POP([C++])
+  if test x$ax_cxx_compile_cxx11_required = xtrue; then
+    if test x$ac_success = xno; then
+      AC_MSG_ERROR([*** A compiler with support for C++11 language features is required.])
+    fi
+  else
+    if test x$ac_success = xno; then
+      HAVE_CXX11=0
+      AC_MSG_NOTICE([No compiler with C++11 support was found])
+    else
+      HAVE_CXX11=1
+      AC_DEFINE(HAVE_CXX11,1,
+                [define if the compiler supports basic C++11 syntax])
+    fi
+    AM_CONDITIONAL([HAVE_CXX11],[test "x$HAVE_CXX11" = "x1"])
+
+    AC_SUBST(HAVE_CXX11)
+  fi
+])
+
diff --git a/m4/misc.m4 b/m4/misc.m4
new file mode 100644
index 00000000..d4aab47b
--- /dev/null
+++ b/m4/misc.m4
@@ -0,0 +1,110 @@
+dnl @synopsis AX_CXX_CHECK_LIB(libname, functioname, action-if, action-if-not)
+dnl
+dnl The standard AC_CHECK_LIB can not test functions in namespaces.
+dnl Therefore AC_CHECK_LIB(cgicc, cgicc::Cgicc::getVersion) will always
+dnl fail. We need to decompose the functionname into a series of namespaces
+dnl where it gets declared so that it can be used for a link test.
+dnl
+dnl In the first version I did allow namespace::functionname to be a
+dnl reference to a void-argument global functionname (just wrapped in a
+dnl namespace) like its C counterparts would be - but in reality such
+dnl thing does not exist. The only global / static functions are always
+dnl made const-functions which is an attribute mangled along into the
+dnl library function export name. 
+dnl
+dnl The normal usage will ask for a test of a class-member function which
+dnl should be presented with a full function spec with arguments given in 
+dnl parentheses following the function name - if the function to test for 
+dnl does expect arguments then you should add default initial values in the 
+dnl prototype (even if they do not exist originally, these are used only 
+dnl locally to build a correct function call in the configure test script).
+dnl
+dnl In the current version if you do omit the parenthesis from the macro
+dnl argument then the macro will assume that you want to check for the
+dnl class name - which is really to check for default constructor being
+dnl exported from the given library name. 
+dnl
+dnl   EXAMPLE:
+dnl AX_CXX_CHECK_LIB(cgicc, [cgicc::HTTPCookie])
+dnl AX_CXX_CHECK_LIB(cgicc, [cgicc::Cgicc::getVersion () const],
+dnl AX_CXX_CHECK_LIB(boost_regex, [boost::RegEx::Position (int i = 0) const])
+dnl
+dnl Result:
+dnl Just as the usual AX_CXX_CHECK_LIB - defines HAVE_LIBCGICC 
+dnl and adds the libraries to the default library path (and
+dnl uses internally the normal ac_check_lib cache symbol
+dnl like ac_cv_lib_cgicc_cgicc__Cgicc)
+dnl
+dnl Footnote: The C++ language is not good at creating stable library
+dnl interfaces at the binary level - a lot of functionality is usually being 
+dnl given as inline functions plus there is hardly a chance to create opaque 
+dnl types. Therefore most C++ library tests will only do compile tests using
+dnl the header files. Doing a check_lib is however good to check the link
+dnl dependency before hitting it as an error in the build later.
+dnl
+dnl @category C++
+dnl @author Guido U. Draheim
+dnl @vesion 2006-12-18
+
+AC_DEFUN([AX_CXX_CHECK_LIB],
+[m4_ifval([$3], , [AH_CHECK_LIB([$1])])dnl
+AS_LITERAL_IF([$1],
+	      [AS_VAR_PUSHDEF([ac_Lib], [ac_cv_lib_$1_$2])],
+	      [AS_VAR_PUSHDEF([ac_Lib], [ac_cv_lib_$1''_$2])])dnl
+AC_CACHE_CHECK([for $2 in -l$1], ac_Lib,
+[ac_check_lib_save_LIBS=$LIBS
+LIBS="-l$1 $5 $LIBS"
+case "$2" 
+in *::*::*\(*)
+AC_LINK_IFELSE([AC_LANG_PROGRAM([
+ namespace `echo "$2" | sed -e "s/::.*//"` 
+ { class `echo "$2" | sed -e "s/.*::\\(.*\\)::.*/\\1/" -e "s/(.*//"` 
+   { public: int `echo "$2" | sed -e "s/.*:://" -e "/(/!s/..*/&()/"`;
+   };
+ }
+],[`echo "$2" | sed  -e "s/(.*//" -e "s/\\(.*\\)::\\(.*\\)/((\\1*)(0))->\\2/g"`()])],
+	       [AS_VAR_SET(ac_Lib, yes)],
+	       [AS_VAR_SET(ac_Lib, no)])
+;; *::*::*)
+AC_LINK_IFELSE([AC_LANG_PROGRAM([
+ namespace `echo "$2" | sed -e "s/::.*//"` 
+ { namespace `echo "$2" | sed -e "s/.*::\\(.*\\)::.*/\\1/"` 
+   { class `echo "$2" | sed -e "s/.*:://"` 
+      { public: `echo "$2" | sed -e "s/.*:://"` ();
+      };
+   }
+ }
+],[new $2()])],
+	       [AS_VAR_SET(ac_Lib, yes)],
+	       [AS_VAR_SET(ac_Lib, no)])
+;; *::*\(*)
+AC_LINK_IFELSE([AC_LANG_PROGRAM([
+ class `echo "$2" | sed -e "s/\\(.*\\)::.*/\\1/" -e "s/(.*//"` 
+   { public: int `echo "$2" | sed -e "s/.*:://" -e "/(/!s/..*/&()/"`;
+   };
+],[`echo "$2" | sed  -e "s/(.*//" -e "s/\\(.*\\)::\\(.*\\)/((\\1*)(0))->\\2/g"`()])],
+	       [AS_VAR_SET(ac_Lib, yes)],
+	       [AS_VAR_SET(ac_Lib, no)])
+;; *::*)
+AC_LINK_IFELSE([AC_LANG_PROGRAM([
+ namespace `echo "$2" | sed -e "s/::.*//"` 
+ { class `echo "$2" | sed -e "s/.*:://"`
+   { public: `echo "$2" | sed -e "s/.*:://"` ();
+   };
+ }
+],[new $2()])],
+	       [AS_VAR_SET(ac_Lib, yes)],
+	       [AS_VAR_SET(ac_Lib, no)])
+;; *)
+AC_LINK_IFELSE([AC_LANG_CALL([], [$2])],
+	       [AS_VAR_SET(ac_Lib, yes)],
+	       [AS_VAR_SET(ac_Lib, no)])
+;; esac
+LIBS=$ac_check_lib_save_LIBS])
+AS_IF([test AS_VAR_GET(ac_Lib) = yes],
+      [m4_default([$3], [AC_DEFINE_UNQUOTED(AS_TR_CPP(HAVE_LIB$1))
+  LIBS="-l$1 $LIBS"
+])],
+      [$4])dnl
+AS_VAR_POPDEF([ac_Lib])dnl
+])# AC_CHECK_LIB
diff --git a/python/pkg/cdec/sa/compile.py b/python/pkg/cdec/sa/compile.py
index ce249c0f..d4cd8387 100644
--- a/python/pkg/cdec/sa/compile.py
+++ b/python/pkg/cdec/sa/compile.py
@@ -4,6 +4,7 @@ import os
 import logging
 import cdec.configobj
 import cdec.sa
+from cdec.sa._sa import monitor_cpu
 import sys
 
 MAX_PHRASE_LENGTH = 4
@@ -21,6 +22,7 @@ def precompute(f_sa, max_len, max_nt, max_size, min_gap, rank1, rank2, tight_phr
     return precomp
 
 def main():
+    preprocess_start_time = monitor_cpu()
     sys.setrecursionlimit(sys.getrecursionlimit() * 100)
 
     logging.basicConfig(level=logging.INFO)
@@ -73,31 +75,46 @@ def main():
     a_bin = os.path.join(args.output, 'a.bin')
     lex_bin = os.path.join(args.output, 'lex.bin')
 
+    start_time = monitor_cpu()
     logger.info('Compiling source suffix array')
     if args.bitext:
         f_sa = cdec.sa.SuffixArray(from_text=args.bitext, side='source')
     else:
         f_sa = cdec.sa.SuffixArray(from_text=args.source)
     f_sa.write_binary(f_sa_bin)
+    stop_time = monitor_cpu()
+    logger.info('Compiling source suffix array took %f seconds', stop_time - start_time)
 
+    start_time = monitor_cpu()
     logger.info('Compiling target data array')
     if args.bitext:
         e = cdec.sa.DataArray(from_text=args.bitext, side='target')
     else:
         e = cdec.sa.DataArray(from_text=args.target)
     e.write_binary(e_bin)
+    stop_time = monitor_cpu()
+    logger.info('Compiling target data array took %f seconds', stop_time - start_time)
 
+    start_time = monitor_cpu()
     logger.info('Precomputing frequent phrases')
     precompute(f_sa, *params).write_binary(precomp_bin)
+    stop_time = monitor_cpu()
+    logger.info('Compiling precomputations took %f seconds', stop_time - start_time)
 
+    start_time = monitor_cpu()
     logger.info('Compiling alignment')
     a = cdec.sa.Alignment(from_text=args.alignment)
     a.write_binary(a_bin)
+    stop_time = monitor_cpu()
+    logger.info('Compiling alignment took %f seonds', stop_time - start_time)
 
+    start_time = monitor_cpu()
     logger.info('Compiling bilexical dictionary')
     lex = cdec.sa.BiLex(from_data=True, alignment=a, earray=e, fsarray=f_sa)
     lex.write_binary(lex_bin)
-    
+    stop_time = monitor_cpu()
+    logger.info('Compiling bilexical dictionary took %f seconds', stop_time - start_time)
+
     # Write configuration
     config = cdec.configobj.ConfigObj(args.config, unrepr=True)
     config['f_sa_file'] = os.path.abspath(f_sa_bin)
@@ -108,6 +125,8 @@ def main():
     for name, value in zip(param_names, params):
         config[name] = value
     config.write()
+    preprocess_stop_time = monitor_cpu()
+    logger.info('Overall preprocessing step took %f seconds', preprocess_stop_time - preprocess_start_time)
 
 if __name__ == '__main__':
     main()
diff --git a/python/pkg/cdec/sa/extract.py b/python/pkg/cdec/sa/extract.py
index 782bed8b..b6502c52 100644
--- a/python/pkg/cdec/sa/extract.py
+++ b/python/pkg/cdec/sa/extract.py
@@ -8,6 +8,7 @@ import logging
 import signal
 import multiprocessing as mp
 import cdec.sa
+from cdec.sa._sa import monitor_cpu
 
 extractor, prefix = None, None
 online, compress = False, False
@@ -62,6 +63,7 @@ def extract(inp):
     return '<seg grammar="{}" id="{}">{}</seg>{}'.format(grammar_file, i, sentence, suffix)
 
 def main():
+    global online
     logging.basicConfig(level=logging.INFO)
     parser = argparse.ArgumentParser(description='Extract grammars from a compiled corpus.')
     parser.add_argument('-c', '--config', required=True,
@@ -87,7 +89,10 @@ def main():
             sys.stderr.write('Error: feature definition file <{}>'
                     ' should be a python module\n'.format(featdef))
             sys.exit(1)
-    
+
+    online = args.online
+
+    start_time = monitor_cpu()
     if args.jobs > 1:
         logging.info('Starting %d workers; chunk size: %d', args.jobs, args.chunksize)
         pool = mp.Pool(args.jobs, make_extractor, (args,))
@@ -101,5 +106,8 @@ def main():
         for output in map(extract, enumerate(sys.stdin)):
             print(output)
 
+    stop_time = monitor_cpu()
+    logging.info("Overall extraction step took %f seconds", stop_time - start_time)
+
 if __name__ == '__main__':
     main()
diff --git a/python/pkg/cdec/sa/features.py b/python/pkg/cdec/sa/features.py
index 46412cd5..c8fc1cca 100644
--- a/python/pkg/cdec/sa/features.py
+++ b/python/pkg/cdec/sa/features.py
@@ -105,7 +105,7 @@ def IsSingletonF(ctx):
         count = ctx.fcount
     else:
         count = ctx.fcount + ctx.online.fcount  
-    return (count == 1)
+    return math.fabs(count - 1) < 1e-6
 
 def IsSingletonFE(ctx):
     if not ctx.online:
@@ -139,4 +139,4 @@ def IsSupportedOnline(ctx): # Occurs in online data?
     if ctx.online:
         return (ctx.online.paircount > 0.01)
     else:
-        return False
\ No newline at end of file
+        return False
diff --git a/python/src/_cdec.cpp b/python/src/_cdec.cpp
index 770b422c..4b950f01 100644
--- a/python/src/_cdec.cpp
+++ b/python/src/_cdec.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Thu Feb 21 19:39:13 2013 */
+/* Generated by Cython 0.18 on Tue Apr 23 18:41:37 2013 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -441,7 +441,7 @@ struct __pyx_opt_args_5_cdec_as_str {
   char *error_msg;
 };
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":25
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":25
  *     cdef void read_handle(self, FILE* f)
  * 
  * cdef class FeatureVector:             # <<<<<<<<<<<<<<
@@ -468,7 +468,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":21
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":21
  *         return '[%s]' % self.cat
  * 
  * cdef class NTRef:             # <<<<<<<<<<<<<<
@@ -481,7 +481,7 @@ struct __pyx_obj_5_cdec_NTRef {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":121
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":121
  *         return CandidateSet(self)
  * 
  * cdef class Scorer:             # <<<<<<<<<<<<<<
@@ -495,7 +495,7 @@ struct __pyx_obj_5_cdec_Scorer {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":12
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":12
  *     cdef void read_handle(self, FILE* f)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -512,7 +512,7 @@ struct __pyx_obj_4cdec_2sa_3_sa_IntList {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":29
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":29
  *     cdef FloatList values
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -529,7 +529,7 @@ struct __pyx_obj_4cdec_2sa_3_sa_Phrase {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":90
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":90
  *         return candidate
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -545,7 +545,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":193
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":193
  *         super(MRule, self).__init__(lhs, rhs, e, scores, None)
  * 
  * cdef class Grammar:             # <<<<<<<<<<<<<<
@@ -558,7 +558,7 @@ struct __pyx_obj_5_cdec_Grammar {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":63
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":63
  *     def todot(self):
  *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():             # <<<<<<<<<<<<<<
@@ -581,7 +581,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":108
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":108
  *             del hypos
  * 
  *     def sample_trees(self, unsigned n):             # <<<<<<<<<<<<<<
@@ -599,7 +599,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":161
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":161
  * 
  *     property edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -615,7 +615,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":5
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -628,7 +628,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_2__phrase {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":65
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":65
  *         return result
  * 
  * cdef class CandidateSet:             # <<<<<<<<<<<<<<
@@ -643,7 +643,7 @@ struct __pyx_obj_5_cdec_CandidateSet {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":167
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":167
  * 
  *     property nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -659,7 +659,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":49
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":49
  *     return TRule(lhs, f, e, scores, a)
  * 
  * cdef class TRule:             # <<<<<<<<<<<<<<
@@ -672,7 +672,7 @@ struct __pyx_obj_5_cdec_TRule {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":35
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":35
  *     cdef public int chunklen(self, int k)
  * 
  * cdef class Rule:             # <<<<<<<<<<<<<<
@@ -690,7 +690,7 @@ struct __pyx_obj_4cdec_2sa_3_sa_Rule {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":177
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":177
  *                 _phrase(self.f), _phrase(self.e), scores)
  * 
  * cdef class MRule(TRule):             # <<<<<<<<<<<<<<
@@ -702,7 +702,7 @@ struct __pyx_obj_5_cdec_MRule {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":100
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":100
  *         self.cs.AddKBestCandidates(hypergraph.hg[0], k, self.scorer.get())
  * 
  * cdef class SegmentEvaluator:             # <<<<<<<<<<<<<<
@@ -733,7 +733,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":61
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":61
  *             yield self[i]
  * 
  *     def todot(self):             # <<<<<<<<<<<<<<
@@ -746,7 +746,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":12
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":12
  *         return stats
  * 
  * cdef class Candidate:             # <<<<<<<<<<<<<<
@@ -760,7 +760,7 @@ struct __pyx_obj_5_cdec_Candidate {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":173
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":173
  * 
  *     def __str__(self):
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)             # <<<<<<<<<<<<<<
@@ -777,7 +777,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_6_genexpr {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":8
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":8
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)
  * 
  * cdef class NT:             # <<<<<<<<<<<<<<
@@ -791,7 +791,7 @@ struct __pyx_obj_5_cdec_NT {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":3
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":3
  * from libc.stdio cimport FILE
  * 
  * cdef class FloatList:             # <<<<<<<<<<<<<<
@@ -808,7 +808,7 @@ struct __pyx_obj_4cdec_2sa_3_sa_FloatList {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":196
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":196
  *         return vector
  * 
  * cdef class HypergraphEdge:             # <<<<<<<<<<<<<<
@@ -824,7 +824,7 @@ struct __pyx_obj_5_cdec_HypergraphEdge {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":72
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":72
  *         self.vector.set_value(fid, value)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -841,7 +841,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_1___iter__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":256
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":256
  * 
  *     property in_edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -857,7 +857,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":131
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":131
  * 
  *     property a:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -874,7 +874,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_4___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":56
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":56
  *         return unicode(str(self), 'utf8')
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -904,7 +904,7 @@ struct __pyx_obj_5_cdec_Decoder {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":246
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":246
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')
  * 
  * cdef class HypergraphNode:             # <<<<<<<<<<<<<<
@@ -919,7 +919,7 @@ struct __pyx_obj_5_cdec_HypergraphNode {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":48
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":48
  *         return sparse
  * 
  * cdef class SparseVector:             # <<<<<<<<<<<<<<
@@ -932,7 +932,7 @@ struct __pyx_obj_5_cdec_SparseVector {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":262
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":262
  * 
  *     property out_edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -948,7 +948,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":32
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":32
  *         self.vector[0][fid] = value
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -964,7 +964,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct____iter__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":44
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":44
  *         return self.stats.size()
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -981,7 +981,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":3
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":3
  * from cython.operator cimport preincrement as pinc
  * 
  * cdef class DenseVector:             # <<<<<<<<<<<<<<
@@ -995,7 +995,7 @@ struct __pyx_obj_5_cdec_DenseVector {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":199
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":199
  *         del self.grammar
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -1014,7 +1014,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_7___iter__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":176
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":176
  *         out.fields[i] = ss[i]
  * 
  * cdef class Metric:             # <<<<<<<<<<<<<<
@@ -1027,7 +1027,7 @@ struct __pyx_obj_5_cdec_Metric {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":26
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":26
  *             return fmap
  * 
  * cdef class SufficientStats:             # <<<<<<<<<<<<<<
@@ -1041,7 +1041,7 @@ struct __pyx_obj_5_cdec_SufficientStats {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":49
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":49
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
  * 
  *     def kbest(self, size):             # <<<<<<<<<<<<<<
@@ -1060,7 +1060,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_8_kbest {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":81
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":81
  *             del e_derivations
  * 
  *     def kbest_features(self, size):             # <<<<<<<<<<<<<<
@@ -1080,7 +1080,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_10_kbest_features {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":216
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":216
  * 
  *     property tail_nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -1096,7 +1096,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":172
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":172
  *             self.rule.get().lhs_ = -TDConvert((<NT> lhs).cat)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -1109,7 +1109,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_5___str__ {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":6
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -1126,7 +1126,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_3_genexpr {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":62
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":62
  *             del derivations
  * 
  *     def kbest_trees(self, size):             # <<<<<<<<<<<<<<
@@ -1149,7 +1149,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":4
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":4
  * cimport kbest
  * 
  * cdef class Hypergraph:             # <<<<<<<<<<<<<<
@@ -1164,7 +1164,7 @@ struct __pyx_obj_5_cdec_Hypergraph {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":3
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":3
  * cimport lattice
  * 
  * cdef class Lattice:             # <<<<<<<<<<<<<<
@@ -1177,7 +1177,7 @@ struct __pyx_obj_5_cdec_Lattice {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":97
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":97
  *             del derivations
  * 
  *     def sample(self, unsigned n):             # <<<<<<<<<<<<<<
@@ -1218,7 +1218,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config {
 };
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":217
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":217
  *             self.grammar.get().SetGrammarName(name)
  * 
  * cdef class TextGrammar(Grammar):             # <<<<<<<<<<<<<<
@@ -1231,7 +1231,7 @@ struct __pyx_obj_5_cdec_TextGrammar {
 
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":4
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":4
  * cimport kbest
  * 
  * cdef class Hypergraph:             # <<<<<<<<<<<<<<
@@ -1245,7 +1245,7 @@ struct __pyx_vtabstruct_5_cdec_Hypergraph {
 static struct __pyx_vtabstruct_5_cdec_Hypergraph *__pyx_vtabptr_5_cdec_Hypergraph;
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":196
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":196
  *         return vector
  * 
  * cdef class HypergraphEdge:             # <<<<<<<<<<<<<<
@@ -1259,7 +1259,7 @@ struct __pyx_vtabstruct_5_cdec_HypergraphEdge {
 static struct __pyx_vtabstruct_5_cdec_HypergraphEdge *__pyx_vtabptr_5_cdec_HypergraphEdge;
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":12
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":12
  *     cdef void read_handle(self, FILE* f)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -1279,7 +1279,7 @@ struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList {
 static struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList *__pyx_vtabptr_4cdec_2sa_3_sa_IntList;
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":3
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":3
  * from libc.stdio cimport FILE
  * 
  * cdef class FloatList:             # <<<<<<<<<<<<<<
@@ -1295,7 +1295,7 @@ struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList {
 static struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList *__pyx_vtabptr_4cdec_2sa_3_sa_FloatList;
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/cdec.sa._sa.pxd":29
+/* "/usr0/home/cdyer/cdec-merge/python/src/cdec.sa._sa.pxd":29
  *     cdef FloatList values
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -1310,7 +1310,7 @@ struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase {
 static struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase *__pyx_vtabptr_4cdec_2sa_3_sa_Phrase;
 
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":246
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":246
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')
  * 
  * cdef class HypergraphNode:             # <<<<<<<<<<<<<<
@@ -2049,7 +2049,7 @@ static char __pyx_k_26[] = "digraph lattice {";
   static char __pyx_k_31[] = "\\\"";
   static char __pyx_k_33[] = "%d [shape=doublecircle]";
 static char __pyx_k_34[] = "}";
-static char __pyx_k_37[] = "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi";
+static char __pyx_k_37[] = "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi";
 static char __pyx_k_38[] = "Lattice.todot.<locals>.lines";
 static char __pyx_k_39[] = "\n";
 static char __pyx_k_41[] = "sufficient stats vector index out of range";
@@ -2062,8 +2062,8 @@ static char __pyx_k_49[] = "#";
 static char __pyx_k_52[] = "Cannot translate input type %s";
 static char __pyx_k_53[] = "cdec.sa._sa";
 static char __pyx_k_54[] = "*";
-static char __pyx_k_57[] = "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi";
-static char __pyx_k_65[] = "/home/jmflanig/tools/cdec-jflanig/python/src/_cdec.pyx";
+static char __pyx_k_57[] = "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi";
+static char __pyx_k_65[] = "/usr0/home/cdyer/cdec-merge/python/src/_cdec.pyx";
 static char __pyx_k__a[] = "a";
 static char __pyx_k__e[] = "e";
 static char __pyx_k__f[] = "f";
@@ -2476,7 +2476,7 @@ static int __pyx_pw_5_cdec_11DenseVector_1__init__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":7
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":7
  *     cdef bint owned # if True, do not manage memory
  * 
  *     def __init__(self):             # <<<<<<<<<<<<<<
@@ -2493,7 +2493,7 @@ static int __pyx_pf_5_cdec_11DenseVector___init__(struct __pyx_obj_5_cdec_DenseV
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":9
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":9
  *     def __init__(self):
  *         """DenseVector() -> Dense weight/feature vector."""
  *         self.vector = new vector[weight_t]()             # <<<<<<<<<<<<<<
@@ -2508,7 +2508,7 @@ static int __pyx_pf_5_cdec_11DenseVector___init__(struct __pyx_obj_5_cdec_DenseV
   }
   __pyx_v_self->vector = __pyx_t_1;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":10
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":10
  *         """DenseVector() -> Dense weight/feature vector."""
  *         self.vector = new vector[weight_t]()
  *         self.owned = False             # <<<<<<<<<<<<<<
@@ -2536,7 +2536,7 @@ static void __pyx_pw_5_cdec_11DenseVector_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":12
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":12
  *         self.owned = False
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -2549,7 +2549,7 @@ static void __pyx_pf_5_cdec_11DenseVector_2__dealloc__(struct __pyx_obj_5_cdec_D
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":13
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":13
  * 
  *     def __dealloc__(self):
  *         if not self.owned:             # <<<<<<<<<<<<<<
@@ -2559,7 +2559,7 @@ static void __pyx_pf_5_cdec_11DenseVector_2__dealloc__(struct __pyx_obj_5_cdec_D
   __pyx_t_1 = (!__pyx_v_self->owned);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":14
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":14
  *     def __dealloc__(self):
  *         if not self.owned:
  *             del self.vector             # <<<<<<<<<<<<<<
@@ -2585,7 +2585,7 @@ static Py_ssize_t __pyx_pw_5_cdec_11DenseVector_5__len__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":16
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":16
  *             del self.vector
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -2598,7 +2598,7 @@ static Py_ssize_t __pyx_pf_5_cdec_11DenseVector_4__len__(struct __pyx_obj_5_cdec
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":17
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":17
  * 
  *     def __len__(self):
  *         return self.vector.size()             # <<<<<<<<<<<<<<
@@ -2635,7 +2635,7 @@ static PyObject *__pyx_pw_5_cdec_11DenseVector_7__getitem__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":19
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":19
  *         return self.vector.size()
  * 
  *     def __getitem__(self, char* fname):             # <<<<<<<<<<<<<<
@@ -2655,7 +2655,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_6__getitem__(struct __pyx_obj_5_c
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":20
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":20
  * 
  *     def __getitem__(self, char* fname):
  *         cdef int fid = FDConvert(fname)             # <<<<<<<<<<<<<<
@@ -2664,7 +2664,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_6__getitem__(struct __pyx_obj_5_c
  */
   __pyx_v_fid = FD::Convert(__pyx_v_fname);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":21
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":21
  *     def __getitem__(self, char* fname):
  *         cdef int fid = FDConvert(fname)
  *         if 0 <= fid < self.vector.size():             # <<<<<<<<<<<<<<
@@ -2677,7 +2677,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_6__getitem__(struct __pyx_obj_5_c
   }
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":22
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":22
  *         cdef int fid = FDConvert(fname)
  *         if 0 <= fid < self.vector.size():
  *             return self.vector[0][fid]             # <<<<<<<<<<<<<<
@@ -2694,7 +2694,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_6__getitem__(struct __pyx_obj_5_c
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":23
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":23
  *         if 0 <= fid < self.vector.size():
  *             return self.vector[0][fid]
  *         raise KeyError(fname)             # <<<<<<<<<<<<<<
@@ -2753,7 +2753,7 @@ static int __pyx_pw_5_cdec_11DenseVector_9__setitem__(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":25
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":25
  *         raise KeyError(fname)
  * 
  *     def __setitem__(self, char* fname, float value):             # <<<<<<<<<<<<<<
@@ -2773,7 +2773,7 @@ static int __pyx_pf_5_cdec_11DenseVector_8__setitem__(struct __pyx_obj_5_cdec_De
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__setitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":26
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":26
  * 
  *     def __setitem__(self, char* fname, float value):
  *         cdef int fid = FDConvert(fname)             # <<<<<<<<<<<<<<
@@ -2782,7 +2782,7 @@ static int __pyx_pf_5_cdec_11DenseVector_8__setitem__(struct __pyx_obj_5_cdec_De
  */
   __pyx_v_fid = FD::Convert(__pyx_v_fname);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":27
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":27
  *     def __setitem__(self, char* fname, float value):
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)             # <<<<<<<<<<<<<<
@@ -2808,7 +2808,7 @@ static int __pyx_pf_5_cdec_11DenseVector_8__setitem__(struct __pyx_obj_5_cdec_De
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":28
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":28
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)
  *         if self.vector.size() <= fid:             # <<<<<<<<<<<<<<
@@ -2818,7 +2818,7 @@ static int __pyx_pf_5_cdec_11DenseVector_8__setitem__(struct __pyx_obj_5_cdec_De
   __pyx_t_1 = (__pyx_v_self->vector->size() <= __pyx_v_fid);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":29
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":29
  *         if fid < 0: raise KeyError(fname)
  *         if self.vector.size() <= fid:
  *             self.vector.resize(fid + 1)             # <<<<<<<<<<<<<<
@@ -2830,7 +2830,7 @@ static int __pyx_pf_5_cdec_11DenseVector_8__setitem__(struct __pyx_obj_5_cdec_De
   }
   __pyx_L4:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":30
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":30
  *         if self.vector.size() <= fid:
  *             self.vector.resize(fid + 1)
  *         self.vector[0][fid] = value             # <<<<<<<<<<<<<<
@@ -2863,7 +2863,7 @@ static PyObject *__pyx_pw_5_cdec_11DenseVector_11__iter__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":32
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":32
  *         self.vector[0][fid] = value
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -2928,7 +2928,7 @@ static PyObject *__pyx_gb_5_cdec_11DenseVector_12generator(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":34
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":34
  *     def __iter__(self):
  *         cdef unsigned fid
  *         for fid in range(1, self.vector.size()):             # <<<<<<<<<<<<<<
@@ -2939,7 +2939,7 @@ static PyObject *__pyx_gb_5_cdec_11DenseVector_12generator(__pyx_GeneratorObject
   for (__pyx_t_2 = 1; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_fid = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":35
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":35
  *         cdef unsigned fid
  *         for fid in range(1, self.vector.size()):
  *             yield str(FDConvert(fid).c_str()), self.vector[0][fid]             # <<<<<<<<<<<<<<
@@ -3012,7 +3012,7 @@ static PyObject *__pyx_pw_5_cdec_11DenseVector_14dot(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":37
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":37
  *             yield str(FDConvert(fid).c_str()), self.vector[0][fid]
  * 
  *     def dot(self, SparseVector other):             # <<<<<<<<<<<<<<
@@ -3031,7 +3031,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_13dot(struct __pyx_obj_5_cdec_Den
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("dot", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":39
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":39
  *     def dot(self, SparseVector other):
  *         """vector.dot(SparseVector other) -> Dot product of the two vectors."""
  *         return other.dot(self)             # <<<<<<<<<<<<<<
@@ -3080,7 +3080,7 @@ static PyObject *__pyx_pw_5_cdec_11DenseVector_16tosparse(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":41
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":41
  *         return other.dot(self)
  * 
  *     def tosparse(self):             # <<<<<<<<<<<<<<
@@ -3098,7 +3098,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_15tosparse(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("tosparse", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":43
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":43
  *     def tosparse(self):
  *         """vector.tosparse() -> Equivalent SparseVector."""
  *         cdef SparseVector sparse = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -3111,7 +3111,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_15tosparse(struct __pyx_obj_5_cde
   __pyx_v_sparse = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":44
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":44
  *         """vector.tosparse() -> Equivalent SparseVector."""
  *         cdef SparseVector sparse = SparseVector.__new__(SparseVector)
  *         sparse.vector = new FastSparseVector[weight_t]()             # <<<<<<<<<<<<<<
@@ -3120,7 +3120,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_15tosparse(struct __pyx_obj_5_cde
  */
   __pyx_v_sparse->vector = new FastSparseVector<weight_t>();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":45
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":45
  *         cdef SparseVector sparse = SparseVector.__new__(SparseVector)
  *         sparse.vector = new FastSparseVector[weight_t]()
  *         InitSparseVector(self.vector[0], sparse.vector)             # <<<<<<<<<<<<<<
@@ -3129,7 +3129,7 @@ static PyObject *__pyx_pf_5_cdec_11DenseVector_15tosparse(struct __pyx_obj_5_cde
  */
   Weights::InitSparseVector((__pyx_v_self->vector[0]), __pyx_v_sparse->vector);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":46
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":46
  *         sparse.vector = new FastSparseVector[weight_t]()
  *         InitSparseVector(self.vector[0], sparse.vector)
  *         return sparse             # <<<<<<<<<<<<<<
@@ -3172,7 +3172,7 @@ static int __pyx_pw_5_cdec_12SparseVector_1__init__(PyObject *__pyx_v_self, PyOb
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":51
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":51
  *     cdef FastSparseVector[weight_t]* vector
  * 
  *     def __init__(self):             # <<<<<<<<<<<<<<
@@ -3185,7 +3185,7 @@ static int __pyx_pf_5_cdec_12SparseVector___init__(struct __pyx_obj_5_cdec_Spars
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":53
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":53
  *     def __init__(self):
  *         """SparseVector() -> Sparse feature/weight vector."""
  *         self.vector = new FastSparseVector[weight_t]()             # <<<<<<<<<<<<<<
@@ -3208,7 +3208,7 @@ static void __pyx_pw_5_cdec_12SparseVector_3__dealloc__(PyObject *__pyx_v_self)
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":55
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":55
  *         self.vector = new FastSparseVector[weight_t]()
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -3220,7 +3220,7 @@ static void __pyx_pf_5_cdec_12SparseVector_2__dealloc__(CYTHON_UNUSED struct __p
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":56
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":56
  * 
  *     def __dealloc__(self):
  *         del self.vector             # <<<<<<<<<<<<<<
@@ -3244,7 +3244,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_5copy(PyObject *__pyx_v_self, CY
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":58
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":58
  *         del self.vector
  * 
  *     def copy(self):             # <<<<<<<<<<<<<<
@@ -3261,7 +3261,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_4copy(struct __pyx_obj_5_cdec_Sp
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("copy", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":60
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":60
  *     def copy(self):
  *         """vector.copy() -> SparseVector copy."""
  *         return self * 1             # <<<<<<<<<<<<<<
@@ -3308,7 +3308,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_7__getitem__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":62
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":62
  *         return self * 1
  * 
  *     def __getitem__(self, char* fname):             # <<<<<<<<<<<<<<
@@ -3328,7 +3328,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_6__getitem__(struct __pyx_obj_5_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":63
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":63
  * 
  *     def __getitem__(self, char* fname):
  *         cdef int fid = FDConvert(fname)             # <<<<<<<<<<<<<<
@@ -3337,7 +3337,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_6__getitem__(struct __pyx_obj_5_
  */
   __pyx_v_fid = FD::Convert(__pyx_v_fname);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":64
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":64
  *     def __getitem__(self, char* fname):
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)             # <<<<<<<<<<<<<<
@@ -3363,7 +3363,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_6__getitem__(struct __pyx_obj_5_
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":65
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":65
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)
  *         return self.vector.value(fid)             # <<<<<<<<<<<<<<
@@ -3415,7 +3415,7 @@ static int __pyx_pw_5_cdec_12SparseVector_9__setitem__(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":67
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":67
  *         return self.vector.value(fid)
  * 
  *     def __setitem__(self, char* fname, float value):             # <<<<<<<<<<<<<<
@@ -3435,7 +3435,7 @@ static int __pyx_pf_5_cdec_12SparseVector_8__setitem__(struct __pyx_obj_5_cdec_S
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__setitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":68
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":68
  * 
  *     def __setitem__(self, char* fname, float value):
  *         cdef int fid = FDConvert(fname)             # <<<<<<<<<<<<<<
@@ -3444,7 +3444,7 @@ static int __pyx_pf_5_cdec_12SparseVector_8__setitem__(struct __pyx_obj_5_cdec_S
  */
   __pyx_v_fid = FD::Convert(__pyx_v_fname);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":69
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":69
  *     def __setitem__(self, char* fname, float value):
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)             # <<<<<<<<<<<<<<
@@ -3470,7 +3470,7 @@ static int __pyx_pf_5_cdec_12SparseVector_8__setitem__(struct __pyx_obj_5_cdec_S
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":70
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":70
  *         cdef int fid = FDConvert(fname)
  *         if fid < 0: raise KeyError(fname)
  *         self.vector.set_value(fid, value)             # <<<<<<<<<<<<<<
@@ -3503,7 +3503,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_11__iter__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":72
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":72
  *         self.vector.set_value(fid, value)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -3568,7 +3568,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":73
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":73
  * 
  *     def __iter__(self):
  *         cdef FastSparseVector[weight_t].const_iterator* it = new FastSparseVector[weight_t].const_iterator(self.vector[0], False)             # <<<<<<<<<<<<<<
@@ -3577,7 +3577,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
  */
   __pyx_cur_scope->__pyx_v_it = new FastSparseVector<weight_t>::const_iterator((__pyx_cur_scope->__pyx_v_self->vector[0]), 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":75
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":75
  *         cdef FastSparseVector[weight_t].const_iterator* it = new FastSparseVector[weight_t].const_iterator(self.vector[0], False)
  *         cdef unsigned i
  *         try:             # <<<<<<<<<<<<<<
@@ -3586,7 +3586,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":76
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":76
  *         cdef unsigned i
  *         try:
  *             for i in range(self.vector.size()):             # <<<<<<<<<<<<<<
@@ -3597,7 +3597,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
     for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
       __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":77
+      /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":77
  *         try:
  *             for i in range(self.vector.size()):
  *                 yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)             # <<<<<<<<<<<<<<
@@ -3638,7 +3638,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
       __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
       if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L5;}
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":78
+      /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":78
  *             for i in range(self.vector.size()):
  *                 yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)
  *                 pinc(it[0]) # ++it             # <<<<<<<<<<<<<<
@@ -3649,7 +3649,7 @@ static PyObject *__pyx_gb_5_cdec_12SparseVector_12generator1(__pyx_GeneratorObje
     }
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":80
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":80
  *                 pinc(it[0]) # ++it
  *         finally:
  *             del it             # <<<<<<<<<<<<<<
@@ -3711,7 +3711,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_14dot(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":82
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":82
  *             del it
  * 
  *     def dot(self, other):             # <<<<<<<<<<<<<<
@@ -3730,7 +3730,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("dot", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":84
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":84
  *     def dot(self, other):
  *         """vector.dot(SparseVector/DenseVector other) -> Dot product of the two vectors."""
  *         if isinstance(other, DenseVector):             # <<<<<<<<<<<<<<
@@ -3740,7 +3740,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_other, ((PyObject*)__pyx_ptype_5_cdec_DenseVector)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":85
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":85
  *         """vector.dot(SparseVector/DenseVector other) -> Dot product of the two vectors."""
  *         if isinstance(other, DenseVector):
  *             return self.vector.dot((<DenseVector> other).vector[0])             # <<<<<<<<<<<<<<
@@ -3756,7 +3756,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
     goto __pyx_L3;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":86
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":86
  *         if isinstance(other, DenseVector):
  *             return self.vector.dot((<DenseVector> other).vector[0])
  *         elif isinstance(other, SparseVector):             # <<<<<<<<<<<<<<
@@ -3766,7 +3766,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_other, ((PyObject*)__pyx_ptype_5_cdec_SparseVector)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":87
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":87
  *             return self.vector.dot((<DenseVector> other).vector[0])
  *         elif isinstance(other, SparseVector):
  *             return self.vector.dot((<SparseVector> other).vector[0])             # <<<<<<<<<<<<<<
@@ -3783,7 +3783,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":88
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":88
  *         elif isinstance(other, SparseVector):
  *             return self.vector.dot((<SparseVector> other).vector[0])
  *         raise TypeError('cannot take the dot product of %s and SparseVector' % type(other))             # <<<<<<<<<<<<<<
@@ -3834,7 +3834,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_16__richcmp__(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":90
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":90
  *         raise TypeError('cannot take the dot product of %s and SparseVector' % type(other))
  * 
  *     def __richcmp__(SparseVector x, SparseVector y, int op):             # <<<<<<<<<<<<<<
@@ -3852,7 +3852,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__richcmp__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":93
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":93
  *         if op == 2: # ==
  *             return x.vector[0] == y.vector[0]
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -3861,7 +3861,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
  */
   switch (__pyx_v_op) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":91
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":91
  * 
  *     def __richcmp__(SparseVector x, SparseVector y, int op):
  *         if op == 2: # ==             # <<<<<<<<<<<<<<
@@ -3870,7 +3870,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
  */
     case 2:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":92
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":92
  *     def __richcmp__(SparseVector x, SparseVector y, int op):
  *         if op == 2: # ==
  *             return x.vector[0] == y.vector[0]             # <<<<<<<<<<<<<<
@@ -3885,7 +3885,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
     goto __pyx_L0;
     break;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":93
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":93
  *         if op == 2: # ==
  *             return x.vector[0] == y.vector[0]
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -3894,7 +3894,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
  */
     case 3:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":94
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":94
  *             return x.vector[0] == y.vector[0]
  *         elif op == 3: # !=
  *             return not (x == y)             # <<<<<<<<<<<<<<
@@ -3913,7 +3913,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
     break;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":95
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":95
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for SparseVector')             # <<<<<<<<<<<<<<
@@ -3949,7 +3949,7 @@ static Py_ssize_t __pyx_pw_5_cdec_12SparseVector_18__len__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":97
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":97
  *         raise NotImplemented('comparison not implemented for SparseVector')
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -3962,7 +3962,7 @@ static Py_ssize_t __pyx_pf_5_cdec_12SparseVector_17__len__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":98
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":98
  * 
  *     def __len__(self):
  *         return self.vector.size()             # <<<<<<<<<<<<<<
@@ -3999,7 +3999,7 @@ static int __pyx_pw_5_cdec_12SparseVector_20__contains__(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":100
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":100
  *         return self.vector.size()
  * 
  *     def __contains__(self, char* fname):             # <<<<<<<<<<<<<<
@@ -4012,7 +4012,7 @@ static int __pyx_pf_5_cdec_12SparseVector_19__contains__(struct __pyx_obj_5_cdec
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__contains__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":101
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":101
  * 
  *     def __contains__(self, char* fname):
  *         return self.vector.nonzero(FDConvert(fname))             # <<<<<<<<<<<<<<
@@ -4039,7 +4039,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_22__neg__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":103
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":103
  *         return self.vector.nonzero(FDConvert(fname))
  * 
  *     def __neg__(self):             # <<<<<<<<<<<<<<
@@ -4057,7 +4057,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_21__neg__(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__neg__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":104
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":104
  * 
  *     def __neg__(self):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -4070,7 +4070,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_21__neg__(struct __pyx_obj_5_cde
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":105
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":105
  *     def __neg__(self):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](self.vector[0])             # <<<<<<<<<<<<<<
@@ -4079,7 +4079,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_21__neg__(struct __pyx_obj_5_cde
  */
   __pyx_v_result->vector = new FastSparseVector<weight_t>((__pyx_v_self->vector[0]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":106
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":106
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](self.vector[0])
  *         result.vector[0] *= -1.0             # <<<<<<<<<<<<<<
@@ -4088,7 +4088,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_21__neg__(struct __pyx_obj_5_cde
  */
   (__pyx_v_result->vector[0]) *= -1.0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":107
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":107
  *         result.vector = new FastSparseVector[weight_t](self.vector[0])
  *         result.vector[0] *= -1.0
  *         return result             # <<<<<<<<<<<<<<
@@ -4129,7 +4129,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_24__iadd__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":109
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":109
  *         return result
  * 
  *     def __iadd__(SparseVector self, SparseVector other):             # <<<<<<<<<<<<<<
@@ -4142,7 +4142,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_23__iadd__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__iadd__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":110
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":110
  * 
  *     def __iadd__(SparseVector self, SparseVector other):
  *         self.vector[0] += other.vector[0]             # <<<<<<<<<<<<<<
@@ -4151,7 +4151,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_23__iadd__(struct __pyx_obj_5_cd
  */
   (__pyx_v_self->vector[0]) += (__pyx_v_other->vector[0]);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":111
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":111
  *     def __iadd__(SparseVector self, SparseVector other):
  *         self.vector[0] += other.vector[0]
  *         return self             # <<<<<<<<<<<<<<
@@ -4186,7 +4186,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_26__isub__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":113
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":113
  *         return self
  * 
  *     def __isub__(SparseVector self, SparseVector other):             # <<<<<<<<<<<<<<
@@ -4199,7 +4199,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_25__isub__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__isub__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":114
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":114
  * 
  *     def __isub__(SparseVector self, SparseVector other):
  *         self.vector[0] -= other.vector[0]             # <<<<<<<<<<<<<<
@@ -4208,7 +4208,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_25__isub__(struct __pyx_obj_5_cd
  */
   (__pyx_v_self->vector[0]) -= (__pyx_v_other->vector[0]);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":115
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":115
  *     def __isub__(SparseVector self, SparseVector other):
  *         self.vector[0] -= other.vector[0]
  *         return self             # <<<<<<<<<<<<<<
@@ -4248,7 +4248,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_28__imul__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":117
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":117
  *         return self
  * 
  *     def __imul__(SparseVector self, float scalar):             # <<<<<<<<<<<<<<
@@ -4261,7 +4261,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_27__imul__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__imul__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":118
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":118
  * 
  *     def __imul__(SparseVector self, float scalar):
  *         self.vector[0] *= scalar             # <<<<<<<<<<<<<<
@@ -4270,7 +4270,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_27__imul__(struct __pyx_obj_5_cd
  */
   (__pyx_v_self->vector[0]) *= __pyx_v_scalar;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":119
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":119
  *     def __imul__(SparseVector self, float scalar):
  *         self.vector[0] *= scalar
  *         return self             # <<<<<<<<<<<<<<
@@ -4312,7 +4312,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_30__idiv__(PyObject *__pyx_v_sel
 }
 #endif /*!(#if PY_MAJOR_VERSION < 3)*/
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":121
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":121
  *         return self
  * 
  *     def __idiv__(SparseVector self, float scalar):             # <<<<<<<<<<<<<<
@@ -4326,7 +4326,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_29__idiv__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__idiv__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":122
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":122
  * 
  *     def __idiv__(SparseVector self, float scalar):
  *         self.vector[0] /= scalar             # <<<<<<<<<<<<<<
@@ -4335,7 +4335,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_29__idiv__(struct __pyx_obj_5_cd
  */
   (__pyx_v_self->vector[0]) /= __pyx_v_scalar;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":123
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":123
  *     def __idiv__(SparseVector self, float scalar):
  *         self.vector[0] /= scalar
  *         return self             # <<<<<<<<<<<<<<
@@ -4372,7 +4372,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_32__add__(PyObject *__pyx_v_x, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":125
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":125
  *         return self
  * 
  *     def __add__(SparseVector x, SparseVector y):             # <<<<<<<<<<<<<<
@@ -4390,7 +4390,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_31__add__(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__add__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":126
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":126
  * 
  *     def __add__(SparseVector x, SparseVector y):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -4403,7 +4403,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_31__add__(struct __pyx_obj_5_cde
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":127
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":127
  *     def __add__(SparseVector x, SparseVector y):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](x.vector[0] + y.vector[0])             # <<<<<<<<<<<<<<
@@ -4412,7 +4412,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_31__add__(struct __pyx_obj_5_cde
  */
   __pyx_v_result->vector = new FastSparseVector<weight_t>(((__pyx_v_x->vector[0]) + (__pyx_v_y->vector[0])));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":128
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":128
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](x.vector[0] + y.vector[0])
  *         return result             # <<<<<<<<<<<<<<
@@ -4454,7 +4454,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_34__sub__(PyObject *__pyx_v_x, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":130
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":130
  *         return result
  * 
  *     def __sub__(SparseVector x, SparseVector y):             # <<<<<<<<<<<<<<
@@ -4472,7 +4472,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_33__sub__(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__sub__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":131
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":131
  * 
  *     def __sub__(SparseVector x, SparseVector y):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -4485,7 +4485,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_33__sub__(struct __pyx_obj_5_cde
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":132
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":132
  *     def __sub__(SparseVector x, SparseVector y):
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](x.vector[0] - y.vector[0])             # <<<<<<<<<<<<<<
@@ -4494,7 +4494,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_33__sub__(struct __pyx_obj_5_cde
  */
   __pyx_v_result->vector = new FastSparseVector<weight_t>(((__pyx_v_x->vector[0]) - (__pyx_v_y->vector[0])));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":133
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":133
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](x.vector[0] - y.vector[0])
  *         return result             # <<<<<<<<<<<<<<
@@ -4530,7 +4530,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_36__mul__(PyObject *__pyx_v_x, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":135
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":135
  *         return result
  * 
  *     def __mul__(x, y):             # <<<<<<<<<<<<<<
@@ -4552,7 +4552,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_35__mul__(PyObject *__pyx_v_x, P
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__mul__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":138
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":138
  *         cdef SparseVector vector
  *         cdef float scalar
  *         if isinstance(x, SparseVector): vector, scalar = x, y             # <<<<<<<<<<<<<<
@@ -4572,7 +4572,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_35__mul__(PyObject *__pyx_v_x, P
   }
   /*else*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":139
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":139
  *         cdef float scalar
  *         if isinstance(x, SparseVector): vector, scalar = x, y
  *         else: vector, scalar = y, x             # <<<<<<<<<<<<<<
@@ -4589,7 +4589,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_35__mul__(PyObject *__pyx_v_x, P
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":140
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":140
  *         if isinstance(x, SparseVector): vector, scalar = x, y
  *         else: vector, scalar = y, x
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -4602,7 +4602,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_35__mul__(PyObject *__pyx_v_x, P
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":141
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":141
  *         else: vector, scalar = y, x
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](vector.vector[0] * scalar)             # <<<<<<<<<<<<<<
@@ -4611,7 +4611,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_35__mul__(PyObject *__pyx_v_x, P
  */
   __pyx_v_result->vector = new FastSparseVector<weight_t>(((__pyx_v_vector->vector[0]) * __pyx_v_scalar));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":142
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":142
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](vector.vector[0] * scalar)
  *         return result             # <<<<<<<<<<<<<<
@@ -4650,7 +4650,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_38__div__(PyObject *__pyx_v_x, P
 }
 #endif /*!(#if PY_MAJOR_VERSION < 3)*/
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":144
+/* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":144
  *         return result
  * 
  *     def __div__(x, y):             # <<<<<<<<<<<<<<
@@ -4673,7 +4673,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
   int __pyx_clineno = 0;
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-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":147
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":147
  *         cdef SparseVector vector
  *         cdef float scalar
  *         if isinstance(x, SparseVector): vector, scalar = x, y             # <<<<<<<<<<<<<<
@@ -4693,7 +4693,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
   }
   /*else*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":148
+    /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":148
  *         cdef float scalar
  *         if isinstance(x, SparseVector): vector, scalar = x, y
  *         else: vector, scalar = y, x             # <<<<<<<<<<<<<<
@@ -4710,7 +4710,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":149
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":149
  *         if isinstance(x, SparseVector): vector, scalar = x, y
  *         else: vector, scalar = y, x
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -4723,7 +4723,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":150
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":150
  *         else: vector, scalar = y, x
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](vector.vector[0] / scalar)             # <<<<<<<<<<<<<<
@@ -4731,7 +4731,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
  */
   __pyx_v_result->vector = new FastSparseVector<weight_t>(((__pyx_v_vector->vector[0]) / __pyx_v_scalar));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":151
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":151
  *         cdef SparseVector result = SparseVector.__new__(SparseVector)
  *         result.vector = new FastSparseVector[weight_t](vector.vector[0] / scalar)
  *         return result             # <<<<<<<<<<<<<<
@@ -4769,7 +4769,7 @@ static PyObject *__pyx_pw_5_cdec_1_phrase(PyObject *__pyx_self, PyObject *__pyx_
 }
 static PyObject *__pyx_gb_5_cdec_7_phrase_2generator18(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":6
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -4932,7 +4932,7 @@ static PyObject *__pyx_gb_5_cdec_7_phrase_2generator18(__pyx_GeneratorObject *__
   return NULL;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":5
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -4961,7 +4961,7 @@ static PyObject *__pyx_pf_5_cdec__phrase(CYTHON_UNUSED PyObject *__pyx_self, PyO
   __Pyx_INCREF(__pyx_cur_scope->__pyx_v_phrase);
   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_phrase);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":6
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -5072,7 +5072,7 @@ static int __pyx_pw_5_cdec_2NT_1__init__(PyObject *__pyx_v_self, PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":11
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":11
  *     cdef public bytes cat
  *     cdef public unsigned ref
  *     def __init__(self, bytes cat, unsigned ref=0):             # <<<<<<<<<<<<<<
@@ -5085,7 +5085,7 @@ static int __pyx_pf_5_cdec_2NT___init__(struct __pyx_obj_5_cdec_NT *__pyx_v_self
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":13
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":13
  *     def __init__(self, bytes cat, unsigned ref=0):
  *         """NT(bytes cat, int ref=0) -> Non-terminal from category `cat`."""
  *         self.cat = cat             # <<<<<<<<<<<<<<
@@ -5098,7 +5098,7 @@ static int __pyx_pf_5_cdec_2NT___init__(struct __pyx_obj_5_cdec_NT *__pyx_v_self
   __Pyx_DECREF(((PyObject *)__pyx_v_self->cat));
   __pyx_v_self->cat = __pyx_v_cat;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":14
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":14
  *         """NT(bytes cat, int ref=0) -> Non-terminal from category `cat`."""
  *         self.cat = cat
  *         self.ref = ref             # <<<<<<<<<<<<<<
@@ -5123,7 +5123,7 @@ static PyObject *__pyx_pw_5_cdec_2NT_3__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":16
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":16
  *         self.ref = ref
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -5142,7 +5142,7 @@ static PyObject *__pyx_pf_5_cdec_2NT_2__str__(struct __pyx_obj_5_cdec_NT *__pyx_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":17
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":17
  * 
  *     def __str__(self):
  *         if self.ref > 0:             # <<<<<<<<<<<<<<
@@ -5152,7 +5152,7 @@ static PyObject *__pyx_pf_5_cdec_2NT_2__str__(struct __pyx_obj_5_cdec_NT *__pyx_
   __pyx_t_1 = (__pyx_v_self->ref > 0);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":18
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":18
  *     def __str__(self):
  *         if self.ref > 0:
  *             return '[%s,%d]' % (self.cat, self.ref)             # <<<<<<<<<<<<<<
@@ -5180,7 +5180,7 @@ static PyObject *__pyx_pf_5_cdec_2NT_2__str__(struct __pyx_obj_5_cdec_NT *__pyx_
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":19
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":19
  *         if self.ref > 0:
  *             return '[%s,%d]' % (self.cat, self.ref)
  *         return '[%s]' % self.cat             # <<<<<<<<<<<<<<
@@ -5218,7 +5218,7 @@ static PyObject *__pyx_pw_5_cdec_2NT_3cat_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":9
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":9
  * 
  * cdef class NT:
  *     cdef public bytes cat             # <<<<<<<<<<<<<<
@@ -5314,7 +5314,7 @@ static PyObject *__pyx_pw_5_cdec_2NT_3ref_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":10
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":10
  * cdef class NT:
  *     cdef public bytes cat
  *     cdef public unsigned ref             # <<<<<<<<<<<<<<
@@ -5432,7 +5432,7 @@ static int __pyx_pw_5_cdec_5NTRef_1__init__(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":23
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":23
  * cdef class NTRef:
  *     cdef public unsigned ref
  *     def __init__(self, unsigned ref):             # <<<<<<<<<<<<<<
@@ -5445,7 +5445,7 @@ static int __pyx_pf_5_cdec_5NTRef___init__(struct __pyx_obj_5_cdec_NTRef *__pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":25
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":25
  *     def __init__(self, unsigned ref):
  *         """NTRef(int ref) -> Non-terminal reference."""
  *         self.ref = ref             # <<<<<<<<<<<<<<
@@ -5470,7 +5470,7 @@ static PyObject *__pyx_pw_5_cdec_5NTRef_3__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":27
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":27
  *         self.ref = ref
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -5488,7 +5488,7 @@ static PyObject *__pyx_pf_5_cdec_5NTRef_2__str__(struct __pyx_obj_5_cdec_NTRef *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":28
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":28
  * 
  *     def __str__(self):
  *         return '[%d]' % self.ref             # <<<<<<<<<<<<<<
@@ -5529,7 +5529,7 @@ static PyObject *__pyx_pw_5_cdec_5NTRef_3ref_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":22
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":22
  * 
  * cdef class NTRef:
  *     cdef public unsigned ref             # <<<<<<<<<<<<<<
@@ -5596,7 +5596,7 @@ static int __pyx_pf_5_cdec_5NTRef_3ref_2__set__(struct __pyx_obj_5_cdec_NTRef *_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":30
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":30
  *         return '[%d]' % self.ref
  * 
  * cdef TRule convert_rule(_sa.Rule rule):             # <<<<<<<<<<<<<<
@@ -5627,7 +5627,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("convert_rule", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":31
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":31
  * 
  * cdef TRule convert_rule(_sa.Rule rule):
  *     lhs = _sa.sym_tocat(rule.lhs)             # <<<<<<<<<<<<<<
@@ -5636,7 +5636,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
  */
   __pyx_v_lhs = __pyx_f_4cdec_2sa_3_sa_sym_tocat(__pyx_v_rule->lhs);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":32
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":32
  * cdef TRule convert_rule(_sa.Rule rule):
  *     lhs = _sa.sym_tocat(rule.lhs)
  *     scores = dict(rule.scores)             # <<<<<<<<<<<<<<
@@ -5654,7 +5654,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   __pyx_v_scores = ((PyObject*)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":33
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":33
  *     lhs = _sa.sym_tocat(rule.lhs)
  *     scores = dict(rule.scores)
  *     f, e = [], []             # <<<<<<<<<<<<<<
@@ -5670,7 +5670,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   __pyx_v_e = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":34
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":34
  *     scores = dict(rule.scores)
  *     f, e = [], []
  *     cdef int* fsyms = rule.f.syms             # <<<<<<<<<<<<<<
@@ -5680,7 +5680,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   __pyx_t_3 = __pyx_v_rule->f->syms;
   __pyx_v_fsyms = __pyx_t_3;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":35
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":35
  *     f, e = [], []
  *     cdef int* fsyms = rule.f.syms
  *     for i in range(rule.f.n):             # <<<<<<<<<<<<<<
@@ -5691,7 +5691,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
     __pyx_v_i = __pyx_t_5;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":36
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":36
  *     cdef int* fsyms = rule.f.syms
  *     for i in range(rule.f.n):
  *         if _sa.sym_isvar(fsyms[i]):             # <<<<<<<<<<<<<<
@@ -5701,7 +5701,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     __pyx_t_6 = __pyx_f_4cdec_2sa_3_sa_sym_isvar((__pyx_v_fsyms[__pyx_v_i]));
     if (__pyx_t_6) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":37
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":37
  *     for i in range(rule.f.n):
  *         if _sa.sym_isvar(fsyms[i]):
  *             f.append(NT(_sa.sym_tocat(fsyms[i])))             # <<<<<<<<<<<<<<
@@ -5724,7 +5724,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":39
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":39
  *             f.append(NT(_sa.sym_tocat(fsyms[i])))
  *         else:
  *             f.append(_sa.sym_tostring(fsyms[i]))             # <<<<<<<<<<<<<<
@@ -5739,7 +5739,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     __pyx_L5:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":40
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":40
  *         else:
  *             f.append(_sa.sym_tostring(fsyms[i]))
  *     cdef int* esyms = rule.e.syms             # <<<<<<<<<<<<<<
@@ -5749,7 +5749,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   __pyx_t_3 = __pyx_v_rule->e->syms;
   __pyx_v_esyms = __pyx_t_3;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":41
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":41
  *             f.append(_sa.sym_tostring(fsyms[i]))
  *     cdef int* esyms = rule.e.syms
  *     for i in range(rule.e.n):             # <<<<<<<<<<<<<<
@@ -5760,7 +5760,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
     __pyx_v_i = __pyx_t_5;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":42
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":42
  *     cdef int* esyms = rule.e.syms
  *     for i in range(rule.e.n):
  *         if _sa.sym_isvar(esyms[i]):             # <<<<<<<<<<<<<<
@@ -5770,7 +5770,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     __pyx_t_6 = __pyx_f_4cdec_2sa_3_sa_sym_isvar((__pyx_v_esyms[__pyx_v_i]));
     if (__pyx_t_6) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":43
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":43
  *     for i in range(rule.e.n):
  *         if _sa.sym_isvar(esyms[i]):
  *             e.append(NTRef(_sa.sym_getindex(esyms[i])))             # <<<<<<<<<<<<<<
@@ -5793,7 +5793,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":45
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":45
  *             e.append(NTRef(_sa.sym_getindex(esyms[i])))
  *         else:
  *             e.append(_sa.sym_tostring(esyms[i]))             # <<<<<<<<<<<<<<
@@ -5808,7 +5808,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
     __pyx_L8:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":46
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":46
  *         else:
  *             e.append(_sa.sym_tostring(esyms[i]))
  *     a = list(rule.alignments())             # <<<<<<<<<<<<<<
@@ -5831,7 +5831,7 @@ static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_o
   __pyx_v_a = ((PyObject*)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":47
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":47
  *             e.append(_sa.sym_tostring(esyms[i]))
  *     a = list(rule.alignments())
  *     return TRule(lhs, f, e, scores, a)             # <<<<<<<<<<<<<<
@@ -5901,7 +5901,7 @@ static int __pyx_pw_5_cdec_5TRule_1__init__(PyObject *__pyx_v_self, PyObject *__
     static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__lhs,&__pyx_n_s__f,&__pyx_n_s__e,&__pyx_n_s__scores,&__pyx_n_s__a,0};
     PyObject* values[5] = {0,0,0,0,0};
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":52
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":52
  *     cdef shared_ptr[grammar.TRule]* rule
  * 
  *     def __init__(self, lhs, f, e, scores, a=None):             # <<<<<<<<<<<<<<
@@ -5990,7 +5990,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":59
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":59
  *         scores: dictionary of feature scores
  *         a: optional list of alignment points"""
  *         self.rule = new shared_ptr[grammar.TRule](new grammar.TRule())             # <<<<<<<<<<<<<<
@@ -6005,7 +6005,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
   }
   __pyx_v_self->rule = new boost::shared_ptr<TRule>(__pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":60
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":60
  *         a: optional list of alignment points"""
  *         self.rule = new shared_ptr[grammar.TRule](new grammar.TRule())
  *         self.lhs = lhs             # <<<<<<<<<<<<<<
@@ -6014,7 +6014,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
  */
   if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lhs, __pyx_v_lhs) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":61
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":61
  *         self.rule = new shared_ptr[grammar.TRule](new grammar.TRule())
  *         self.lhs = lhs
  *         self.e = e             # <<<<<<<<<<<<<<
@@ -6023,7 +6023,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
  */
   if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__e, __pyx_v_e) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":62
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":62
  *         self.lhs = lhs
  *         self.e = e
  *         self.f = f             # <<<<<<<<<<<<<<
@@ -6032,7 +6032,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
  */
   if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__f, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":63
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":63
  *         self.e = e
  *         self.f = f
  *         self.scores = scores             # <<<<<<<<<<<<<<
@@ -6041,7 +6041,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
  */
   if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__scores, __pyx_v_scores) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":64
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":64
  *         self.f = f
  *         self.scores = scores
  *         if a:             # <<<<<<<<<<<<<<
@@ -6051,7 +6051,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_a); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":65
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":65
  *         self.scores = scores
  *         if a:
  *             self.a = a             # <<<<<<<<<<<<<<
@@ -6063,7 +6063,7 @@ static int __pyx_pf_5_cdec_5TRule___init__(struct __pyx_obj_5_cdec_TRule *__pyx_
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":66
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":66
  *         if a:
  *             self.a = a
  *         self.rule.get().ComputeArity()             # <<<<<<<<<<<<<<
@@ -6091,7 +6091,7 @@ static void __pyx_pw_5_cdec_5TRule_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":68
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":68
  *         self.rule.get().ComputeArity()
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -6103,7 +6103,7 @@ static void __pyx_pf_5_cdec_5TRule_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_5
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":69
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":69
  * 
  *     def __dealloc__(self):
  *         del self.rule             # <<<<<<<<<<<<<<
@@ -6126,7 +6126,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_5arity_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":72
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":72
  * 
  *     property arity:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -6143,7 +6143,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_5arity___get__(struct __pyx_obj_5_cdec_T
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":73
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":73
  *     property arity:
  *         def __get__(self):
  *             return self.rule.get().arity_             # <<<<<<<<<<<<<<
@@ -6180,7 +6180,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_1f_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":76
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":76
  * 
  *     property f:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -6207,7 +6207,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":77
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":77
  *     property f:
  *         def __get__(self):
  *             cdef vector[WordID]* f_ = &self.rule.get().f_             # <<<<<<<<<<<<<<
@@ -6216,7 +6216,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_f_ = (&__pyx_v_self->rule->get()->f_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":79
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":79
  *             cdef vector[WordID]* f_ = &self.rule.get().f_
  *             cdef WordID w
  *             cdef f = []             # <<<<<<<<<<<<<<
@@ -6228,7 +6228,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
   __pyx_v_f = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":81
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":81
  *             cdef f = []
  *             cdef unsigned i
  *             cdef int idx = 0             # <<<<<<<<<<<<<<
@@ -6237,7 +6237,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_idx = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":82
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":82
  *             cdef unsigned i
  *             cdef int idx = 0
  *             for i in range(f_.size()):             # <<<<<<<<<<<<<<
@@ -6248,7 +6248,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":83
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":83
  *             cdef int idx = 0
  *             for i in range(f_.size()):
  *                 w = f_[0][i]             # <<<<<<<<<<<<<<
@@ -6257,7 +6257,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
  */
     __pyx_v_w = ((__pyx_v_f_[0])[__pyx_v_i]);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":84
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":84
  *             for i in range(f_.size()):
  *                 w = f_[0][i]
  *                 if w < 0:             # <<<<<<<<<<<<<<
@@ -6267,7 +6267,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
     __pyx_t_4 = (__pyx_v_w < 0);
     if (__pyx_t_4) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":85
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":85
  *                 w = f_[0][i]
  *                 if w < 0:
  *                     idx += 1             # <<<<<<<<<<<<<<
@@ -6276,7 +6276,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
  */
       __pyx_v_idx = (__pyx_v_idx + 1);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":86
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":86
  *                 if w < 0:
  *                     idx += 1
  *                     f.append(NT(TDConvert(-w).c_str(), idx))             # <<<<<<<<<<<<<<
@@ -6306,7 +6306,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":88
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":88
  *                     f.append(NT(TDConvert(-w).c_str(), idx))
  *                 else:
  *                     f.append(unicode(TDConvert(w).c_str(), encoding='utf8'))             # <<<<<<<<<<<<<<
@@ -6335,7 +6335,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
     __pyx_L5:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":89
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":89
  *                 else:
  *                     f.append(unicode(TDConvert(w).c_str(), encoding='utf8'))
  *             return f             # <<<<<<<<<<<<<<
@@ -6373,7 +6373,7 @@ static int __pyx_pw_5_cdec_5TRule_1f_3__set__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":91
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":91
  *             return f
  * 
  *         def __set__(self, f):             # <<<<<<<<<<<<<<
@@ -6399,7 +6399,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__set__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":92
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":92
  * 
  *         def __set__(self, f):
  *             cdef vector[WordID]* f_ = &self.rule.get().f_             # <<<<<<<<<<<<<<
@@ -6408,7 +6408,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
  */
   __pyx_v_f_ = (&__pyx_v_self->rule->get()->f_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":93
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":93
  *         def __set__(self, f):
  *             cdef vector[WordID]* f_ = &self.rule.get().f_
  *             f_.resize(len(f))             # <<<<<<<<<<<<<<
@@ -6418,7 +6418,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   __pyx_t_1 = PyObject_Length(__pyx_v_f); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_f_->resize(__pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":95
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":95
  *             f_.resize(len(f))
  *             cdef unsigned i
  *             cdef int idx = 0             # <<<<<<<<<<<<<<
@@ -6427,7 +6427,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
  */
   __pyx_v_idx = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":96
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":96
  *             cdef unsigned i
  *             cdef int idx = 0
  *             for i in range(len(f)):             # <<<<<<<<<<<<<<
@@ -6438,7 +6438,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":97
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":97
  *             cdef int idx = 0
  *             for i in range(len(f)):
  *                 if isinstance(f[i], NT):             # <<<<<<<<<<<<<<
@@ -6451,7 +6451,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     if (__pyx_t_4) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":98
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":98
  *             for i in range(len(f)):
  *                 if isinstance(f[i], NT):
  *                     f_[0][i] = -TDConvert((<NT> f[i]).cat)             # <<<<<<<<<<<<<<
@@ -6467,7 +6467,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":100
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":100
  *                     f_[0][i] = -TDConvert((<NT> f[i]).cat)
  *                 else:
  *                     fi = as_str(f[i])             # <<<<<<<<<<<<<<
@@ -6483,7 +6483,7 @@ static int __pyx_pf_5_cdec_5TRule_1f_2__set__(struct __pyx_obj_5_cdec_TRule *__p
       __pyx_v_fi = ((PyObject*)__pyx_t_6);
       __pyx_t_6 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":101
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":101
  *                 else:
  *                     fi = as_str(f[i])
  *                     f_[0][i] = TDConvert(fi)             # <<<<<<<<<<<<<<
@@ -6520,7 +6520,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_1e_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":104
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":104
  * 
  *     property e:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -6547,7 +6547,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":105
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":105
  *     property e:
  *         def __get__(self):
  *             cdef vector[WordID]* e_ = &self.rule.get().e_             # <<<<<<<<<<<<<<
@@ -6556,7 +6556,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_e_ = (&__pyx_v_self->rule->get()->e_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":107
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":107
  *             cdef vector[WordID]* e_ = &self.rule.get().e_
  *             cdef WordID w
  *             cdef e = []             # <<<<<<<<<<<<<<
@@ -6568,7 +6568,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
   __pyx_v_e = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":109
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":109
  *             cdef e = []
  *             cdef unsigned i
  *             cdef int idx = 0             # <<<<<<<<<<<<<<
@@ -6577,7 +6577,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_idx = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":110
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":110
  *             cdef unsigned i
  *             cdef int idx = 0
  *             for i in range(e_.size()):             # <<<<<<<<<<<<<<
@@ -6588,7 +6588,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":111
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":111
  *             cdef int idx = 0
  *             for i in range(e_.size()):
  *                 w = e_[0][i]             # <<<<<<<<<<<<<<
@@ -6597,7 +6597,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
  */
     __pyx_v_w = ((__pyx_v_e_[0])[__pyx_v_i]);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":112
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":112
  *             for i in range(e_.size()):
  *                 w = e_[0][i]
  *                 if w < 1:             # <<<<<<<<<<<<<<
@@ -6607,7 +6607,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
     __pyx_t_4 = (__pyx_v_w < 1);
     if (__pyx_t_4) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":113
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":113
  *                 w = e_[0][i]
  *                 if w < 1:
  *                     idx += 1             # <<<<<<<<<<<<<<
@@ -6616,7 +6616,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
  */
       __pyx_v_idx = (__pyx_v_idx + 1);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":114
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":114
  *                 if w < 1:
  *                     idx += 1
  *                     e.append(NTRef(1-w))             # <<<<<<<<<<<<<<
@@ -6641,7 +6641,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":116
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":116
  *                     e.append(NTRef(1-w))
  *                 else:
  *                     e.append(unicode(TDConvert(w).c_str(), encoding='utf8'))             # <<<<<<<<<<<<<<
@@ -6670,7 +6670,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1e___get__(struct __pyx_obj_5_cdec_TRule
     __pyx_L5:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":117
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":117
  *                 else:
  *                     e.append(unicode(TDConvert(w).c_str(), encoding='utf8'))
  *             return e             # <<<<<<<<<<<<<<
@@ -6708,7 +6708,7 @@ static int __pyx_pw_5_cdec_5TRule_1e_3__set__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":119
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":119
  *             return e
  * 
  *         def __set__(self, e):             # <<<<<<<<<<<<<<
@@ -6734,7 +6734,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__set__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":120
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":120
  * 
  *         def __set__(self, e):
  *             cdef vector[WordID]* e_ = &self.rule.get().e_             # <<<<<<<<<<<<<<
@@ -6743,7 +6743,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
  */
   __pyx_v_e_ = (&__pyx_v_self->rule->get()->e_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":121
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":121
  *         def __set__(self, e):
  *             cdef vector[WordID]* e_ = &self.rule.get().e_
  *             e_.resize(len(e))             # <<<<<<<<<<<<<<
@@ -6753,7 +6753,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   __pyx_t_1 = PyObject_Length(__pyx_v_e); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_e_->resize(__pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":123
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":123
  *             e_.resize(len(e))
  *             cdef unsigned i
  *             for i in range(len(e)):             # <<<<<<<<<<<<<<
@@ -6764,7 +6764,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":124
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":124
  *             cdef unsigned i
  *             for i in range(len(e)):
  *                 if isinstance(e[i], NTRef):             # <<<<<<<<<<<<<<
@@ -6777,7 +6777,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     if (__pyx_t_4) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":125
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":125
  *             for i in range(len(e)):
  *                 if isinstance(e[i], NTRef):
  *                     e_[0][i] = 1-e[i].ref             # <<<<<<<<<<<<<<
@@ -6799,7 +6799,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":127
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":127
  *                     e_[0][i] = 1-e[i].ref
  *                 else:
  *                     ei = as_str(e[i])             # <<<<<<<<<<<<<<
@@ -6815,7 +6815,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
       __pyx_v_ei = ((PyObject*)__pyx_t_5);
       __pyx_t_5 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":128
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":128
  *                 else:
  *                     ei = as_str(e[i])
  *                     e_[0][i] = TDConvert(ei)             # <<<<<<<<<<<<<<
@@ -6853,7 +6853,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_1a_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":131
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":131
  * 
  *     property a:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -6918,7 +6918,7 @@ static PyObject *__pyx_gb_5_cdec_5TRule_1a_2generator2(__pyx_GeneratorObject *__
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":133
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":133
  *         def __get__(self):
  *             cdef unsigned i
  *             cdef vector[grammar.AlignmentPoint]* a = &self.rule.get().a_             # <<<<<<<<<<<<<<
@@ -6927,7 +6927,7 @@ static PyObject *__pyx_gb_5_cdec_5TRule_1a_2generator2(__pyx_GeneratorObject *__
  */
   __pyx_cur_scope->__pyx_v_a = (&__pyx_cur_scope->__pyx_v_self->rule->get()->a_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":134
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":134
  *             cdef unsigned i
  *             cdef vector[grammar.AlignmentPoint]* a = &self.rule.get().a_
  *             for i in range(a.size()):             # <<<<<<<<<<<<<<
@@ -6938,7 +6938,7 @@ static PyObject *__pyx_gb_5_cdec_5TRule_1a_2generator2(__pyx_GeneratorObject *__
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":135
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":135
  *             cdef vector[grammar.AlignmentPoint]* a = &self.rule.get().a_
  *             for i in range(a.size()):
  *                 yield (a[0][i].s_, a[0][i].t_)             # <<<<<<<<<<<<<<
@@ -6997,7 +6997,7 @@ static int __pyx_pw_5_cdec_5TRule_1a_4__set__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":137
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":137
  *                 yield (a[0][i].s_, a[0][i].t_)
  * 
  *         def __set__(self, a):             # <<<<<<<<<<<<<<
@@ -7026,7 +7026,7 @@ static int __pyx_pf_5_cdec_5TRule_1a_3__set__(struct __pyx_obj_5_cdec_TRule *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__set__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":138
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":138
  * 
  *         def __set__(self, a):
  *             cdef vector[grammar.AlignmentPoint]* a_ = &self.rule.get().a_             # <<<<<<<<<<<<<<
@@ -7035,7 +7035,7 @@ static int __pyx_pf_5_cdec_5TRule_1a_3__set__(struct __pyx_obj_5_cdec_TRule *__p
  */
   __pyx_v_a_ = (&__pyx_v_self->rule->get()->a_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":139
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":139
  *         def __set__(self, a):
  *             cdef vector[grammar.AlignmentPoint]* a_ = &self.rule.get().a_
  *             a_.resize(len(a))             # <<<<<<<<<<<<<<
@@ -7045,7 +7045,7 @@ static int __pyx_pf_5_cdec_5TRule_1a_3__set__(struct __pyx_obj_5_cdec_TRule *__p
   __pyx_t_1 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_a_->resize(__pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":142
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":142
  *             cdef unsigned i
  *             cdef int s, t
  *             for i in range(len(a)):             # <<<<<<<<<<<<<<
@@ -7056,7 +7056,7 @@ static int __pyx_pf_5_cdec_5TRule_1a_3__set__(struct __pyx_obj_5_cdec_TRule *__p
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":143
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":143
  *             cdef int s, t
  *             for i in range(len(a)):
  *                 s, t = a[i]             # <<<<<<<<<<<<<<
@@ -7123,7 +7123,7 @@ static int __pyx_pf_5_cdec_5TRule_1a_3__set__(struct __pyx_obj_5_cdec_TRule *__p
     __pyx_v_s = __pyx_t_8;
     __pyx_v_t = __pyx_t_9;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":144
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":144
  *             for i in range(len(a)):
  *                 s, t = a[i]
  *                 a_[0][i] = grammar.AlignmentPoint(s, t)             # <<<<<<<<<<<<<<
@@ -7158,7 +7158,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_6scores_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":147
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":147
  * 
  *     property scores:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -7176,7 +7176,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_6scores___get__(struct __pyx_obj_5_cdec_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":148
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":148
  *     property scores:
  *         def __get__(self):
  *             cdef SparseVector scores = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -7189,7 +7189,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_6scores___get__(struct __pyx_obj_5_cdec_
   __pyx_v_scores = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":149
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":149
  *         def __get__(self):
  *             cdef SparseVector scores = SparseVector.__new__(SparseVector)
  *             scores.vector = new FastSparseVector[double](self.rule.get().scores_)             # <<<<<<<<<<<<<<
@@ -7198,7 +7198,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_6scores___get__(struct __pyx_obj_5_cdec_
  */
   __pyx_v_scores->vector = new FastSparseVector<double>(__pyx_v_self->rule->get()->scores_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":150
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":150
  *             cdef SparseVector scores = SparseVector.__new__(SparseVector)
  *             scores.vector = new FastSparseVector[double](self.rule.get().scores_)
  *             return scores             # <<<<<<<<<<<<<<
@@ -7234,7 +7234,7 @@ static int __pyx_pw_5_cdec_5TRule_6scores_3__set__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":152
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":152
  *             return scores
  * 
  *         def __set__(self, scores):             # <<<<<<<<<<<<<<
@@ -7266,7 +7266,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__set__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":153
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":153
  * 
  *         def __set__(self, scores):
  *             cdef FastSparseVector[double]* scores_ = &self.rule.get().scores_             # <<<<<<<<<<<<<<
@@ -7275,7 +7275,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_scores_ = (&__pyx_v_self->rule->get()->scores_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":154
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":154
  *         def __set__(self, scores):
  *             cdef FastSparseVector[double]* scores_ = &self.rule.get().scores_
  *             scores_.clear()             # <<<<<<<<<<<<<<
@@ -7284,7 +7284,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
  */
   __pyx_v_scores_->clear();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":157
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":157
  *             cdef int fid
  *             cdef float fval
  *             for fname, fval in scores.items():             # <<<<<<<<<<<<<<
@@ -7389,7 +7389,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
     __pyx_t_5 = 0;
     __pyx_v_fval = __pyx_t_9;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":158
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":158
  *             cdef float fval
  *             for fname, fval in scores.items():
  *                 fn = as_str(fname)             # <<<<<<<<<<<<<<
@@ -7402,7 +7402,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
     __pyx_v_fn = ((PyObject*)__pyx_t_2);
     __pyx_t_2 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":159
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":159
  *             for fname, fval in scores.items():
  *                 fn = as_str(fname)
  *                 fid = FDConvert(fn)             # <<<<<<<<<<<<<<
@@ -7412,7 +7412,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
     __pyx_t_10 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_fid = FD::Convert(__pyx_t_10);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":160
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":160
  *                 fn = as_str(fname)
  *                 fid = FDConvert(fn)
  *                 if fid < 0: raise KeyError(fname)             # <<<<<<<<<<<<<<
@@ -7436,7 +7436,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
     }
     __pyx_L7:;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":161
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":161
  *                 fid = FDConvert(fn)
  *                 if fid < 0: raise KeyError(fname)
  *                 scores_.set_value(fid, fval)             # <<<<<<<<<<<<<<
@@ -7475,7 +7475,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_3lhs_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":164
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":164
  * 
  *     property lhs:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -7493,7 +7493,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_3lhs___get__(struct __pyx_obj_5_cdec_TRu
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":165
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":165
  *     property lhs:
  *         def __get__(self):
  *             return NT(TDConvert(-self.rule.get().lhs_).c_str())             # <<<<<<<<<<<<<<
@@ -7539,7 +7539,7 @@ static int __pyx_pw_5_cdec_5TRule_3lhs_3__set__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":167
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":167
  *             return NT(TDConvert(-self.rule.get().lhs_).c_str())
  * 
  *         def __set__(self, lhs):             # <<<<<<<<<<<<<<
@@ -7561,7 +7561,7 @@ static int __pyx_pf_5_cdec_5TRule_3lhs_2__set__(struct __pyx_obj_5_cdec_TRule *_
   __Pyx_RefNannySetupContext("__set__", 0);
   __Pyx_INCREF(__pyx_v_lhs);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":168
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":168
  * 
  *         def __set__(self, lhs):
  *             if not isinstance(lhs, NT):             # <<<<<<<<<<<<<<
@@ -7572,7 +7572,7 @@ static int __pyx_pf_5_cdec_5TRule_3lhs_2__set__(struct __pyx_obj_5_cdec_TRule *_
   __pyx_t_2 = (!__pyx_t_1);
   if (__pyx_t_2) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":169
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":169
  *         def __set__(self, lhs):
  *             if not isinstance(lhs, NT):
  *                 lhs = NT(lhs)             # <<<<<<<<<<<<<<
@@ -7594,7 +7594,7 @@ static int __pyx_pf_5_cdec_5TRule_3lhs_2__set__(struct __pyx_obj_5_cdec_TRule *_
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":170
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":170
  *             if not isinstance(lhs, NT):
  *                 lhs = NT(lhs)
  *             self.rule.get().lhs_ = -TDConvert((<NT> lhs).cat)             # <<<<<<<<<<<<<<
@@ -7629,7 +7629,7 @@ static PyObject *__pyx_pw_5_cdec_5TRule_5__str__(PyObject *__pyx_v_self) {
 }
 static PyObject *__pyx_gb_5_cdec_5TRule_7__str___2generator19(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":173
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":173
  * 
  *     def __str__(self):
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)             # <<<<<<<<<<<<<<
@@ -7771,7 +7771,7 @@ static PyObject *__pyx_gb_5_cdec_5TRule_7__str___2generator19(__pyx_GeneratorObj
   return NULL;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":172
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":172
  *             self.rule.get().lhs_ = -TDConvert((<NT> lhs).cat)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -7803,7 +7803,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_4__str__(struct __pyx_obj_5_cdec_TRule *
   __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
   __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":173
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":173
  * 
  *     def __str__(self):
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)             # <<<<<<<<<<<<<<
@@ -7826,7 +7826,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_4__str__(struct __pyx_obj_5_cdec_TRule *
   __pyx_v_scores = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":174
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":174
  *     def __str__(self):
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)
  *         return '%s ||| %s ||| %s ||| %s' % (self.lhs,             # <<<<<<<<<<<<<<
@@ -7837,7 +7837,7 @@ static PyObject *__pyx_pf_5_cdec_5TRule_4__str__(struct __pyx_obj_5_cdec_TRule *
   __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_cur_scope->__pyx_v_self), __pyx_n_s__lhs); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":175
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":175
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)
  *         return '%s ||| %s ||| %s ||| %s' % (self.lhs,
  *                 _phrase(self.f), _phrase(self.e), scores)             # <<<<<<<<<<<<<<
@@ -7978,7 +7978,7 @@ static int __pyx_pw_5_cdec_5MRule_1__init__(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":178
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":178
  * 
  * cdef class MRule(TRule):
  *     def __init__(self, lhs, rhs, scores):             # <<<<<<<<<<<<<<
@@ -8004,7 +8004,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":183
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":183
  *         rhs: right hand side phrase (list of words/NT)
  *         scores: dictionary of feature scores"""
  *         cdef unsigned i = 1             # <<<<<<<<<<<<<<
@@ -8013,7 +8013,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
  */
   __pyx_v_i = 1;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":184
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":184
  *         scores: dictionary of feature scores"""
  *         cdef unsigned i = 1
  *         e = []             # <<<<<<<<<<<<<<
@@ -8025,7 +8025,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
   __pyx_v_e = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":185
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":185
  *         cdef unsigned i = 1
  *         e = []
  *         for s in rhs:             # <<<<<<<<<<<<<<
@@ -8070,7 +8070,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
     __pyx_v_s = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":186
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":186
  *         e = []
  *         for s in rhs:
  *             if isinstance(s, NT):             # <<<<<<<<<<<<<<
@@ -8080,7 +8080,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
     __pyx_t_5 = __Pyx_TypeCheck(__pyx_v_s, ((PyObject*)__pyx_ptype_5_cdec_NT)); 
     if (__pyx_t_5) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":187
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":187
  *         for s in rhs:
  *             if isinstance(s, NT):
  *                 e.append(NTRef(i))             # <<<<<<<<<<<<<<
@@ -8100,7 +8100,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
       __pyx_t_7 = PyList_Append(__pyx_v_e, __pyx_t_4); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":188
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":188
  *             if isinstance(s, NT):
  *                 e.append(NTRef(i))
  *                 i += 1             # <<<<<<<<<<<<<<
@@ -8112,7 +8112,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
     }
     /*else*/ {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":190
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":190
  *                 i += 1
  *             else:
  *                 e.append(s)             # <<<<<<<<<<<<<<
@@ -8125,7 +8125,7 @@ static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":191
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":191
  *             else:
  *                 e.append(s)
  *         super(MRule, self).__init__(lhs, rhs, e, scores, None)             # <<<<<<<<<<<<<<
@@ -8193,7 +8193,7 @@ static void __pyx_pw_5_cdec_7Grammar_1__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":196
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":196
  *     cdef shared_ptr[grammar.Grammar]* grammar
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -8205,7 +8205,7 @@ static void __pyx_pf_5_cdec_7Grammar___dealloc__(CYTHON_UNUSED struct __pyx_obj_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":197
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":197
  * 
  *     def __dealloc__(self):
  *         del self.grammar             # <<<<<<<<<<<<<<
@@ -8229,7 +8229,7 @@ static PyObject *__pyx_pw_5_cdec_7Grammar_3__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":199
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":199
  *         del self.grammar
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -8292,7 +8292,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":200
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":200
  * 
  *     def __iter__(self):
  *         cdef grammar.const_GrammarIter* root = self.grammar.get().GetRoot()             # <<<<<<<<<<<<<<
@@ -8301,7 +8301,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
  */
   __pyx_cur_scope->__pyx_v_root = __pyx_cur_scope->__pyx_v_self->grammar->get()->GetRoot();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":201
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":201
  *     def __iter__(self):
  *         cdef grammar.const_GrammarIter* root = self.grammar.get().GetRoot()
  *         cdef grammar.const_RuleBin* rbin = root.GetRules()             # <<<<<<<<<<<<<<
@@ -8310,7 +8310,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
  */
   __pyx_cur_scope->__pyx_v_rbin = __pyx_cur_scope->__pyx_v_root->GetRules();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":204
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":204
  *         cdef TRule trule
  *         cdef unsigned i
  *         for i in range(rbin.GetNumRules()):             # <<<<<<<<<<<<<<
@@ -8321,7 +8321,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":205
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":205
  *         cdef unsigned i
  *         for i in range(rbin.GetNumRules()):
  *             trule = TRule.__new__(TRule)             # <<<<<<<<<<<<<<
@@ -8337,7 +8337,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
     __pyx_cur_scope->__pyx_v_trule = ((struct __pyx_obj_5_cdec_TRule *)__pyx_t_3);
     __pyx_t_3 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":206
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":206
  *         for i in range(rbin.GetNumRules()):
  *             trule = TRule.__new__(TRule)
  *             trule.rule = new shared_ptr[grammar.TRule](rbin.GetIthRule(i))             # <<<<<<<<<<<<<<
@@ -8346,7 +8346,7 @@ static PyObject *__pyx_gb_5_cdec_7Grammar_4generator3(__pyx_GeneratorObject *__p
  */
     __pyx_cur_scope->__pyx_v_trule->rule = new boost::shared_ptr<TRule>(__pyx_cur_scope->__pyx_v_rbin->GetIthRule(__pyx_cur_scope->__pyx_v_i));
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":207
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":207
  *             trule = TRule.__new__(TRule)
  *             trule.rule = new shared_ptr[grammar.TRule](rbin.GetIthRule(i))
  *             yield trule             # <<<<<<<<<<<<<<
@@ -8391,7 +8391,7 @@ static PyObject *__pyx_pw_5_cdec_7Grammar_4name_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":210
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":210
  * 
  *     property name:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -8409,7 +8409,7 @@ static PyObject *__pyx_pf_5_cdec_7Grammar_4name___get__(struct __pyx_obj_5_cdec_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":211
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":211
  *     property name:
  *         def __get__(self):
  *             str(self.grammar.get().GetGrammarName().c_str())             # <<<<<<<<<<<<<<
@@ -8452,7 +8452,7 @@ static int __pyx_pw_5_cdec_7Grammar_4name_3__set__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":213
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":213
  *             str(self.grammar.get().GetGrammarName().c_str())
  * 
  *         def __set__(self, name):             # <<<<<<<<<<<<<<
@@ -8471,7 +8471,7 @@ static int __pyx_pf_5_cdec_7Grammar_4name_2__set__(struct __pyx_obj_5_cdec_Gramm
   __Pyx_RefNannySetupContext("__set__", 0);
   __Pyx_INCREF(__pyx_v_name);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":214
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":214
  * 
  *         def __set__(self, name):
  *             name = as_str(name)             # <<<<<<<<<<<<<<
@@ -8484,7 +8484,7 @@ static int __pyx_pf_5_cdec_7Grammar_4name_2__set__(struct __pyx_obj_5_cdec_Gramm
   __pyx_v_name = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":215
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":215
  *         def __set__(self, name):
  *             name = as_str(name)
  *             self.grammar.get().SetGrammarName(name)             # <<<<<<<<<<<<<<
@@ -8557,7 +8557,7 @@ static int __pyx_pw_5_cdec_11TextGrammar_1__init__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":218
+/* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":218
  * 
  * cdef class TextGrammar(Grammar):
  *     def __init__(self, rules):             # <<<<<<<<<<<<<<
@@ -8581,7 +8581,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":220
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":220
  *     def __init__(self, rules):
  *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())             # <<<<<<<<<<<<<<
@@ -8590,7 +8590,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
  */
   __pyx_v_self->__pyx_base.grammar = new boost::shared_ptr<Grammar>(new TextGrammar());
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":221
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":221
  *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()             # <<<<<<<<<<<<<<
@@ -8599,7 +8599,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
  */
   __pyx_v__g = ((TextGrammar *)__pyx_v_self->__pyx_base.grammar->get());
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":222
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":222
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
  *         for trule in rules:             # <<<<<<<<<<<<<<
@@ -8644,7 +8644,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
     __pyx_v_trule = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":223
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":223
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
  *         for trule in rules:
  *             if isinstance(trule, _sa.Rule):             # <<<<<<<<<<<<<<
@@ -8654,7 +8654,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
     __pyx_t_5 = __Pyx_TypeCheck(__pyx_v_trule, ((PyObject*)__pyx_ptype_4cdec_2sa_3_sa_Rule)); 
     if (__pyx_t_5) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":224
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":224
  *         for trule in rules:
  *             if isinstance(trule, _sa.Rule):
  *                 trule = convert_rule(trule)             # <<<<<<<<<<<<<<
@@ -8670,7 +8670,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
       goto __pyx_L5;
     }
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":225
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":225
  *             if isinstance(trule, _sa.Rule):
  *                 trule = convert_rule(trule)
  *             elif not isinstance(trule, TRule):             # <<<<<<<<<<<<<<
@@ -8681,7 +8681,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
     __pyx_t_6 = (!__pyx_t_5);
     if (__pyx_t_6) {
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":226
+      /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":226
  *                 trule = convert_rule(trule)
  *             elif not isinstance(trule, TRule):
  *                 raise ValueError('the grammar should contain TRule objects')             # <<<<<<<<<<<<<<
@@ -8696,7 +8696,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGr
     }
     __pyx_L5:;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":227
+    /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":227
  *             elif not isinstance(trule, TRule):
  *                 raise ValueError('the grammar should contain TRule objects')
  *             _g.AddRule((<TRule> trule).rule[0])             # <<<<<<<<<<<<<<
@@ -8727,7 +8727,7 @@ static void __pyx_pw_5_cdec_10Hypergraph_1__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":8
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":8
  *     cdef MT19937* rng
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -8740,7 +8740,7 @@ static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hyp
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":9
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":9
  * 
  *     def __dealloc__(self):
  *         del self.hg             # <<<<<<<<<<<<<<
@@ -8749,7 +8749,7 @@ static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hyp
  */
   delete __pyx_v_self->hg;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":10
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":10
  *     def __dealloc__(self):
  *         del self.hg
  *         if self.rng != NULL:             # <<<<<<<<<<<<<<
@@ -8759,7 +8759,7 @@ static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hyp
   __pyx_t_1 = (__pyx_v_self->rng != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":11
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":11
  *         del self.hg
  *         if self.rng != NULL:
  *             del self.rng             # <<<<<<<<<<<<<<
@@ -8774,7 +8774,7 @@ static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hyp
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":13
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":13
  *             del self.rng
  * 
  *     cdef MT19937* _rng(self):             # <<<<<<<<<<<<<<
@@ -8792,7 +8792,7 @@ static MT19937 *__pyx_f_5_cdec_10Hypergraph__rng(struct __pyx_obj_5_cdec_Hypergr
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("_rng", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":14
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":14
  * 
  *     cdef MT19937* _rng(self):
  *         if self.rng == NULL:             # <<<<<<<<<<<<<<
@@ -8802,7 +8802,7 @@ static MT19937 *__pyx_f_5_cdec_10Hypergraph__rng(struct __pyx_obj_5_cdec_Hypergr
   __pyx_t_1 = (__pyx_v_self->rng == NULL);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":15
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":15
  *     cdef MT19937* _rng(self):
  *         if self.rng == NULL:
  *             self.rng = new MT19937()             # <<<<<<<<<<<<<<
@@ -8820,7 +8820,7 @@ static MT19937 *__pyx_f_5_cdec_10Hypergraph__rng(struct __pyx_obj_5_cdec_Hypergr
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":16
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":16
  *         if self.rng == NULL:
  *             self.rng = new MT19937()
  *         return self.rng             # <<<<<<<<<<<<<<
@@ -8852,7 +8852,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_3viterbi(PyObject *__pyx_v_self, C
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":18
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":18
  *         return self.rng
  * 
  *     def viterbi(self):             # <<<<<<<<<<<<<<
@@ -8871,7 +8871,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_2viterbi(struct __pyx_obj_5_cdec_H
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":21
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":21
  *         """hg.viterbi() -> String for the best hypothesis in the hypergraph."""
  *         cdef vector[WordID] trans
  *         hypergraph.ViterbiESentence(self.hg[0], &trans)             # <<<<<<<<<<<<<<
@@ -8880,7 +8880,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_2viterbi(struct __pyx_obj_5_cdec_H
  */
   ViterbiESentence((__pyx_v_self->hg[0]), (&__pyx_v_trans));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":22
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":22
  *         cdef vector[WordID] trans
  *         hypergraph.ViterbiESentence(self.hg[0], &trans)
  *         return unicode(GetString(trans).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -8930,7 +8930,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_5viterbi_trees(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":24
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":24
  *         return unicode(GetString(trans).c_str(), 'utf8')
  * 
  *     def viterbi_trees(self):             # <<<<<<<<<<<<<<
@@ -8950,7 +8950,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_trees", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":29
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":29
  *         e_tree: Target tree for the best hypothesis in the hypergraph.
  *         """
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -8973,7 +8973,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_
   __pyx_v_f_tree = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":30
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":30
  *         """
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
  *         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -8996,7 +8996,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_
   __pyx_v_e_tree = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":31
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":31
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
  *         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')
  *         return (f_tree, e_tree)             # <<<<<<<<<<<<<<
@@ -9043,7 +9043,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_7viterbi_features(PyObject *__pyx_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":33
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":33
  *         return (f_tree, e_tree)
  * 
  *     def viterbi_features(self):             # <<<<<<<<<<<<<<
@@ -9061,7 +9061,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_features", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":36
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":36
  *         """hg.viterbi_features() -> SparseVector with the features corresponding
  *         to the best derivation in the hypergraph."""
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -9074,7 +9074,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
   __pyx_v_fmap = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":37
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":37
  *         to the best derivation in the hypergraph."""
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))             # <<<<<<<<<<<<<<
@@ -9083,7 +9083,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
  */
   __pyx_v_fmap->vector = new FastSparseVector<weight_t>(ViterbiFeatures((__pyx_v_self->hg[0])));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":38
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":38
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))
  *         return fmap             # <<<<<<<<<<<<<<
@@ -9119,7 +9119,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_9viterbi_forest(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":40
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":40
  *         return fmap
  * 
  *     def viterbi_forest(self):             # <<<<<<<<<<<<<<
@@ -9137,7 +9137,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_forest(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_forest", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":41
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":41
  * 
  *     def viterbi_forest(self):
  *         cdef Hypergraph hg = Hypergraph()             # <<<<<<<<<<<<<<
@@ -9149,7 +9149,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_forest(struct __pyx_obj_5
   __pyx_v_hg = ((struct __pyx_obj_5_cdec_Hypergraph *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":42
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":42
  *     def viterbi_forest(self):
  *         cdef Hypergraph hg = Hypergraph()
  *         hg.hg = new hypergraph.Hypergraph(self.hg[0].CreateViterbiHypergraph(NULL).get()[0])             # <<<<<<<<<<<<<<
@@ -9158,7 +9158,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_forest(struct __pyx_obj_5
  */
   __pyx_v_hg->hg = new Hypergraph(((__pyx_v_self->hg[0]).CreateViterbiHypergraph(NULL).get()[0]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":43
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":43
  *         cdef Hypergraph hg = Hypergraph()
  *         hg.hg = new hypergraph.Hypergraph(self.hg[0].CreateViterbiHypergraph(NULL).get()[0])
  *         return hg             # <<<<<<<<<<<<<<
@@ -9195,7 +9195,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_11viterbi_joshua(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":45
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":45
  *         return hg
  * 
  *     def viterbi_joshua(self):             # <<<<<<<<<<<<<<
@@ -9213,7 +9213,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_10viterbi_joshua(struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_joshua", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":47
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":47
  *     def viterbi_joshua(self):
  *         """hg.viterbi_joshua() -> Joshua representation of the best derivation."""
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -9264,7 +9264,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_13kbest(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":49
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":49
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
  * 
  *     def kbest(self, size):             # <<<<<<<<<<<<<<
@@ -9332,7 +9332,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":51
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":51
  *     def kbest(self, size):
  *         """hg.kbest(size) -> List of k-best hypotheses in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal]* derivations = new kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
@@ -9342,7 +9342,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
   __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_derivations = new KBest::KBestDerivations<std::vector<WordID>,ESentenceTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":54
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":54
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9351,7 +9351,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":55
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":55
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
@@ -9362,7 +9362,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
     for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_2; __pyx_t_1+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":56
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":56
  *         try:
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9371,7 +9371,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_derivation = __pyx_cur_scope->__pyx_v_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":57
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":57
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break             # <<<<<<<<<<<<<<
@@ -9385,7 +9385,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":58
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":58
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  *                 yield unicode(GetString(derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -9422,7 +9422,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_14generator4(__pyx_GeneratorObject
     __pyx_L8_break:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":60
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":60
  *                 yield unicode(GetString(derivation._yield).c_str(), 'utf8')
  *         finally:
  *             del derivations             # <<<<<<<<<<<<<<
@@ -9483,7 +9483,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_16kbest_trees(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":62
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":62
  *             del derivations
  * 
  *     def kbest_trees(self, size):             # <<<<<<<<<<<<<<
@@ -9553,7 +9553,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":64
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":64
  *     def kbest_trees(self, size):
  *         """hg.kbest_trees(size) -> List of k-best trees in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
@@ -9563,7 +9563,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
   __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_f_derivations = new KBest::KBestDerivations<std::vector<WordID>,FTreeTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":66
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":66
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal]* e_derivations = new kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
@@ -9573,7 +9573,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
   __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_e_derivations = new KBest::KBestDerivations<std::vector<WordID>,ETreeTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":69
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":69
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal].Derivation* e_derivation
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9582,7 +9582,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":70
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":70
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
@@ -9593,7 +9593,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
     for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_2; __pyx_t_1+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":71
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":71
  *         try:
  *             for k in range(size):
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9602,7 +9602,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_f_derivation = __pyx_cur_scope->__pyx_v_f_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":72
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":72
  *             for k in range(size):
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9611,7 +9611,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_e_derivation = __pyx_cur_scope->__pyx_v_e_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":73
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":73
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not f_derivation or not e_derivation: break             # <<<<<<<<<<<<<<
@@ -9631,7 +9631,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":74
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":74
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not f_derivation or not e_derivation: break
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -9657,7 +9657,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
       __pyx_cur_scope->__pyx_v_f_tree = ((PyObject*)__pyx_t_6);
       __pyx_t_6 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":75
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":75
  *                 if not f_derivation or not e_derivation: break
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')
  *                 e_tree = unicode(GetString(e_derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -9683,7 +9683,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
       __pyx_cur_scope->__pyx_v_e_tree = ((PyObject*)__pyx_t_6);
       __pyx_t_6 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":76
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":76
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')
  *                 e_tree = unicode(GetString(e_derivation._yield).c_str(), 'utf8')
  *                 yield (f_tree, e_tree)             # <<<<<<<<<<<<<<
@@ -9715,7 +9715,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
     __pyx_L8_break:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":78
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":78
  *                 yield (f_tree, e_tree)
  *         finally:
  *             del f_derivations             # <<<<<<<<<<<<<<
@@ -9739,7 +9739,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_17generator5(__pyx_GeneratorObject
     __pyx_L6:;
     delete __pyx_cur_scope->__pyx_v_f_derivations;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":79
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":79
  *         finally:
  *             del f_derivations
  *             del e_derivations             # <<<<<<<<<<<<<<
@@ -9785,7 +9785,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_19kbest_features(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":81
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":81
  *             del e_derivations
  * 
  *     def kbest_features(self, size):             # <<<<<<<<<<<<<<
@@ -9852,7 +9852,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":83
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":83
  *     def kbest_features(self, size):
  *         """hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph."""
  *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal]* derivations = new kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
@@ -9862,7 +9862,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
   __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_derivations = new KBest::KBestDerivations<FastSparseVector<weight_t>,FeatureVectorTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":87
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":87
  *         cdef SparseVector fmap
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9871,7 +9871,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":88
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":88
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
@@ -9882,7 +9882,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
     for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_2; __pyx_t_1+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":89
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":89
  *         try:
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9891,7 +9891,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_derivation = __pyx_cur_scope->__pyx_v_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":90
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":90
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break             # <<<<<<<<<<<<<<
@@ -9905,7 +9905,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":91
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":91
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  *                 fmap = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -9921,7 +9921,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
       __pyx_cur_scope->__pyx_v_fmap = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_4);
       __pyx_t_4 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":92
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":92
  *                 if not derivation: break
  *                 fmap = SparseVector.__new__(SparseVector)
  *                 fmap.vector = new FastSparseVector[weight_t](derivation._yield)             # <<<<<<<<<<<<<<
@@ -9930,7 +9930,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_fmap->vector = new FastSparseVector<weight_t>(__pyx_cur_scope->__pyx_v_derivation->yield);
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":93
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":93
  *                 fmap = SparseVector.__new__(SparseVector)
  *                 fmap.vector = new FastSparseVector[weight_t](derivation._yield)
  *                 yield fmap             # <<<<<<<<<<<<<<
@@ -9954,7 +9954,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_20generator6(__pyx_GeneratorObject
     __pyx_L8_break:;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":95
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":95
  *                 yield fmap
  *         finally:
  *             del derivations             # <<<<<<<<<<<<<<
@@ -10023,7 +10023,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_22sample(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":97
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":97
  *             del derivations
  * 
  *     def sample(self, unsigned n):             # <<<<<<<<<<<<<<
@@ -10089,7 +10089,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":99
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":99
  *     def sample(self, unsigned n):
  *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
  *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()             # <<<<<<<<<<<<<<
@@ -10104,7 +10104,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
   }
   __pyx_cur_scope->__pyx_v_hypos = __pyx_t_1;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":100
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":100
  *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
  *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()
  *         hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)             # <<<<<<<<<<<<<<
@@ -10113,7 +10113,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
  */
   HypergraphSampler::sample_hypotheses((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_cur_scope->__pyx_v_n, ((struct __pyx_vtabstruct_5_cdec_Hypergraph *)__pyx_cur_scope->__pyx_v_self->__pyx_vtab)->_rng(__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_hypos);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":102
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":102
  *         hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -10122,7 +10122,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":103
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":103
  *         cdef unsigned k
  *         try:
  *             for k in range(hypos.size()):             # <<<<<<<<<<<<<<
@@ -10133,7 +10133,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
     for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_3;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":104
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":104
  *         try:
  *             for k in range(hypos.size()):
  *                 yield unicode(GetString(hypos[0][k].words).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -10169,7 +10169,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_23generator7(__pyx_GeneratorObject
     }
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":106
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":106
  *                 yield unicode(GetString(hypos[0][k].words).c_str(), 'utf8')
  *         finally:
  *             del hypos             # <<<<<<<<<<<<<<
@@ -10240,7 +10240,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_25sample_trees(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":108
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":108
  *             del hypos
  * 
  *     def sample_trees(self, unsigned n):             # <<<<<<<<<<<<<<
@@ -10306,7 +10306,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":110
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":110
  *     def sample_trees(self, unsigned n):
  *        """hg.sample_trees(n) -> Sample of n trees from the hypergraph."""
  *        cdef vector[string]* trees = new vector[string]()             # <<<<<<<<<<<<<<
@@ -10321,7 +10321,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
   }
   __pyx_cur_scope->__pyx_v_trees = __pyx_t_1;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":111
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":111
  *        """hg.sample_trees(n) -> Sample of n trees from the hypergraph."""
  *        cdef vector[string]* trees = new vector[string]()
  *        hypergraph.sample_trees(self.hg[0], n, self._rng(), trees)             # <<<<<<<<<<<<<<
@@ -10330,7 +10330,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
  */
   HypergraphSampler::sample_trees((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_cur_scope->__pyx_v_n, ((struct __pyx_vtabstruct_5_cdec_Hypergraph *)__pyx_cur_scope->__pyx_v_self->__pyx_vtab)->_rng(__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_trees);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":113
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":113
  *        hypergraph.sample_trees(self.hg[0], n, self._rng(), trees)
  *        cdef unsigned k
  *        try:             # <<<<<<<<<<<<<<
@@ -10339,7 +10339,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":114
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":114
  *        cdef unsigned k
  *        try:
  *            for k in range(trees.size()):             # <<<<<<<<<<<<<<
@@ -10350,7 +10350,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
     for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_3;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":115
+      /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":115
  *        try:
  *            for k in range(trees.size()):
  *                yield unicode(trees[0][k].c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -10386,7 +10386,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_26generator8(__pyx_GeneratorObject
     }
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":117
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":117
  *                yield unicode(trees[0][k].c_str(), 'utf8')
  *        finally:
  *            del trees             # <<<<<<<<<<<<<<
@@ -10446,7 +10446,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_28intersect(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":119
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":119
  *            del trees
  * 
  *     def intersect(self, inp):             # <<<<<<<<<<<<<<
@@ -10466,7 +10466,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("intersect", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":122
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":122
  *         """hg.intersect(Lattice/string): Intersect the hypergraph with the provided reference."""
  *         cdef Lattice lat
  *         if isinstance(inp, Lattice):             # <<<<<<<<<<<<<<
@@ -10476,7 +10476,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_inp, ((PyObject*)__pyx_ptype_5_cdec_Lattice)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":123
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":123
  *         cdef Lattice lat
  *         if isinstance(inp, Lattice):
  *             lat = <Lattice> inp             # <<<<<<<<<<<<<<
@@ -10488,7 +10488,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
     goto __pyx_L3;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":124
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":124
  *         if isinstance(inp, Lattice):
  *             lat = <Lattice> inp
  *         elif isinstance(inp, basestring):             # <<<<<<<<<<<<<<
@@ -10498,7 +10498,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
   __pyx_t_1 = PyObject_IsInstance(__pyx_v_inp, __pyx_builtin_basestring); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":125
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":125
  *             lat = <Lattice> inp
  *         elif isinstance(inp, basestring):
  *             lat = Lattice(inp)             # <<<<<<<<<<<<<<
@@ -10519,7 +10519,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
   }
   /*else*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":127
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":127
  *             lat = Lattice(inp)
  *         else:
  *             raise TypeError('cannot intersect hypergraph with %s' % type(inp))             # <<<<<<<<<<<<<<
@@ -10542,7 +10542,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_27intersect(struct __pyx_obj_5_cde
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":128
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":128
  *         else:
  *             raise TypeError('cannot intersect hypergraph with %s' % type(inp))
  *         return hypergraph.Intersect(lat.lattice[0], self.hg)             # <<<<<<<<<<<<<<
@@ -10638,7 +10638,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_30prune(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":130
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":130
  *         return hypergraph.Intersect(lat.lattice[0], self.hg)
  * 
  *     def prune(self, beam_alpha=0, density=0, **kwargs):             # <<<<<<<<<<<<<<
@@ -10658,7 +10658,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("prune", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":134
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":134
  *         beam_alpha: use beam pruning
  *         density: use density pruning"""
  *         cdef hypergraph.EdgeMask* preserve_mask = NULL             # <<<<<<<<<<<<<<
@@ -10667,7 +10667,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_preserve_mask = NULL;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":135
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":135
  *         density: use density pruning"""
  *         cdef hypergraph.EdgeMask* preserve_mask = NULL
  *         if 'csplit_preserve_full_word' in kwargs:             # <<<<<<<<<<<<<<
@@ -10677,7 +10677,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
   __pyx_t_1 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s_16), ((PyObject *)__pyx_v_kwargs), Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":136
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":136
  *         cdef hypergraph.EdgeMask* preserve_mask = NULL
  *         if 'csplit_preserve_full_word' in kwargs:
  *              preserve_mask = new hypergraph.EdgeMask(self.hg.edges_.size())             # <<<<<<<<<<<<<<
@@ -10686,7 +10686,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
  */
     __pyx_v_preserve_mask = new std::vector<bool>(__pyx_v_self->hg->edges_.size());
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":137
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":137
  *         if 'csplit_preserve_full_word' in kwargs:
  *              preserve_mask = new hypergraph.EdgeMask(self.hg.edges_.size())
  *              preserve_mask[0][hypergraph.GetFullWordEdgeIndex(self.hg[0])] = True             # <<<<<<<<<<<<<<
@@ -10698,7 +10698,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":138
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":138
  *              preserve_mask = new hypergraph.EdgeMask(self.hg.edges_.size())
  *              preserve_mask[0][hypergraph.GetFullWordEdgeIndex(self.hg[0])] = True
  *         self.hg.PruneInsideOutside(beam_alpha, density, preserve_mask, False, 1, False)             # <<<<<<<<<<<<<<
@@ -10709,7 +10709,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
   __pyx_t_3 = __pyx_PyFloat_AsDouble(__pyx_v_density); if (unlikely((__pyx_t_3 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->hg->PruneInsideOutside(__pyx_t_2, __pyx_t_3, __pyx_v_preserve_mask, 0, 1.0, 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":139
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":139
  *              preserve_mask[0][hypergraph.GetFullWordEdgeIndex(self.hg[0])] = True
  *         self.hg.PruneInsideOutside(beam_alpha, density, preserve_mask, False, 1, False)
  *         if preserve_mask:             # <<<<<<<<<<<<<<
@@ -10719,7 +10719,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_29prune(struct __pyx_obj_5_cdec_Hy
   __pyx_t_1 = (__pyx_v_preserve_mask != 0);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":140
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":140
  *         self.hg.PruneInsideOutside(beam_alpha, density, preserve_mask, False, 1, False)
  *         if preserve_mask:
  *             del preserve_mask             # <<<<<<<<<<<<<<
@@ -10754,7 +10754,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_32lattice(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":142
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":142
  *             del preserve_mask
  * 
  *     def lattice(self): # TODO direct hg -> lattice conversion in cdec             # <<<<<<<<<<<<<<
@@ -10774,7 +10774,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_31lattice(struct __pyx_obj_5_cdec_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("lattice", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":144
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":144
  *     def lattice(self): # TODO direct hg -> lattice conversion in cdec
  *         """hg.lattice() -> Lattice corresponding to the hypergraph."""
  *         cdef bytes plf = hypergraph.AsPLF(self.hg[0], True).c_str()             # <<<<<<<<<<<<<<
@@ -10786,7 +10786,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_31lattice(struct __pyx_obj_5_cdec_
   __pyx_v_plf = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":145
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":145
  *         """hg.lattice() -> Lattice corresponding to the hypergraph."""
  *         cdef bytes plf = hypergraph.AsPLF(self.hg[0], True).c_str()
  *         return Lattice(eval(plf))             # <<<<<<<<<<<<<<
@@ -10857,7 +10857,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_34plf(PyObject *__pyx_v_self, CYTH
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":147
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":147
  *         return Lattice(eval(plf))
  * 
  *     def plf(self):             # <<<<<<<<<<<<<<
@@ -10875,7 +10875,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_33plf(struct __pyx_obj_5_cdec_Hype
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("plf", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":149
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":149
  *     def plf(self):
  *         """hg.plf() -> Lattice PLF representation corresponding to the hypergraph."""
  *         return bytes(hypergraph.AsPLF(self.hg[0], True).c_str())             # <<<<<<<<<<<<<<
@@ -10922,7 +10922,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_36reweight(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":151
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":151
  *         return bytes(hypergraph.AsPLF(self.hg[0], True).c_str())
  * 
  *     def reweight(self, weights):             # <<<<<<<<<<<<<<
@@ -10941,7 +10941,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_35reweight(struct __pyx_obj_5_cdec
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("reweight", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":153
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":153
  *     def reweight(self, weights):
  *         """hg.reweight(SparseVector/DenseVector): Reweight the hypergraph with a new vector."""
  *         if isinstance(weights, SparseVector):             # <<<<<<<<<<<<<<
@@ -10951,7 +10951,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_35reweight(struct __pyx_obj_5_cdec
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_weights, ((PyObject*)__pyx_ptype_5_cdec_SparseVector)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":154
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":154
  *         """hg.reweight(SparseVector/DenseVector): Reweight the hypergraph with a new vector."""
  *         if isinstance(weights, SparseVector):
  *             self.hg.Reweight((<SparseVector> weights).vector[0])             # <<<<<<<<<<<<<<
@@ -10962,7 +10962,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_35reweight(struct __pyx_obj_5_cdec
     goto __pyx_L3;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":155
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":155
  *         if isinstance(weights, SparseVector):
  *             self.hg.Reweight((<SparseVector> weights).vector[0])
  *         elif isinstance(weights, DenseVector):             # <<<<<<<<<<<<<<
@@ -10972,7 +10972,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_35reweight(struct __pyx_obj_5_cdec
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_weights, ((PyObject*)__pyx_ptype_5_cdec_DenseVector)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":156
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":156
  *             self.hg.Reweight((<SparseVector> weights).vector[0])
  *         elif isinstance(weights, DenseVector):
  *             self.hg.Reweight((<DenseVector> weights).vector[0])             # <<<<<<<<<<<<<<
@@ -10984,7 +10984,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_35reweight(struct __pyx_obj_5_cdec
   }
   /*else*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":158
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":158
  *             self.hg.Reweight((<DenseVector> weights).vector[0])
  *         else:
  *             raise TypeError('cannot reweight hypergraph with %s' % type(weights))             # <<<<<<<<<<<<<<
@@ -11032,7 +11032,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_5edges_1__get__(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":161
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":161
  * 
  *     property edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11096,7 +11096,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5edges_2generator9(__pyx_Generator
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":163
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":163
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.hg.edges_.size()):             # <<<<<<<<<<<<<<
@@ -11107,7 +11107,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5edges_2generator9(__pyx_Generator
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":164
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":164
  *             cdef unsigned i
  *             for i in range(self.hg.edges_.size()):
  *                 yield HypergraphEdge().init(self.hg, i)             # <<<<<<<<<<<<<<
@@ -11159,7 +11159,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_5nodes_1__get__(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":167
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":167
  * 
  *     property nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11223,7 +11223,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5nodes_2generator10(__pyx_Generato
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":169
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":169
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.hg.nodes_.size()):             # <<<<<<<<<<<<<<
@@ -11234,7 +11234,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5nodes_2generator10(__pyx_Generato
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":170
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":170
  *             cdef unsigned i
  *             for i in range(self.hg.nodes_.size()):
  *                 yield HypergraphNode().init(self.hg, i)             # <<<<<<<<<<<<<<
@@ -11285,7 +11285,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_4goal_1__get__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":173
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":173
  * 
  *     property goal:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11303,7 +11303,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4goal___get__(struct __pyx_obj_5_c
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":174
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":174
  *     property goal:
  *         def __get__(self):
  *             return HypergraphNode().init(self.hg, self.hg.GoalNode())             # <<<<<<<<<<<<<<
@@ -11344,7 +11344,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_6npaths_1__get__(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":177
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":177
  * 
  *     property npaths:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11361,7 +11361,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6npaths___get__(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":178
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":178
  *     property npaths:
  *         def __get__(self):
  *             return self.hg.NumberOfPaths()             # <<<<<<<<<<<<<<
@@ -11399,7 +11399,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_38inside_outside(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":180
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":180
  *             return self.hg.NumberOfPaths()
  * 
  *     def inside_outside(self):             # <<<<<<<<<<<<<<
@@ -11423,7 +11423,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("inside_outside", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":182
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":182
  *     def inside_outside(self):
  *         """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()             # <<<<<<<<<<<<<<
@@ -11432,7 +11432,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   __pyx_v_result = new FastSparseVector<prob_t>();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":183
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":183
  *         """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)             # <<<<<<<<<<<<<<
@@ -11441,7 +11441,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   __pyx_v_z = InsideOutside<prob_t, EdgeProb, SparseVector<prob_t>, EdgeFeaturesAndProbWeightFunction>((__pyx_v_self->hg[0]), __pyx_v_result);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":184
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":184
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  *         result[0] /= z             # <<<<<<<<<<<<<<
@@ -11450,7 +11450,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   (__pyx_v_result[0]) /= __pyx_v_z;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":185
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":185
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  *         result[0] /= z
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -11463,7 +11463,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
   __pyx_v_vector = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":186
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":186
  *         result[0] /= z
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *         vector.vector = new FastSparseVector[double]()             # <<<<<<<<<<<<<<
@@ -11472,7 +11472,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   __pyx_v_vector->vector = new FastSparseVector<double>();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":187
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":187
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *         vector.vector = new FastSparseVector[double]()
  *         cdef FastSparseVector[prob_t].const_iterator* it = new FastSparseVector[prob_t].const_iterator(result[0], False)             # <<<<<<<<<<<<<<
@@ -11481,7 +11481,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   __pyx_v_it = new FastSparseVector<prob_t>::const_iterator((__pyx_v_result[0]), 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":189
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":189
  *         cdef FastSparseVector[prob_t].const_iterator* it = new FastSparseVector[prob_t].const_iterator(result[0], False)
  *         cdef unsigned i
  *         for i in range(result.size()):             # <<<<<<<<<<<<<<
@@ -11492,7 +11492,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":190
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":190
  *         cdef unsigned i
  *         for i in range(result.size()):
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))             # <<<<<<<<<<<<<<
@@ -11501,7 +11501,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
     __pyx_v_vector->vector->set_value((__pyx_v_it[0]).operator->()->first, log((__pyx_v_it[0]).operator->()->second));
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":191
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":191
  *         for i in range(result.size()):
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))
  *             pinc(it[0]) # ++it             # <<<<<<<<<<<<<<
@@ -11511,7 +11511,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
     (++(__pyx_v_it[0]));
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":192
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":192
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))
  *             pinc(it[0]) # ++it
  *         del it             # <<<<<<<<<<<<<<
@@ -11520,7 +11520,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   delete __pyx_v_it;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":193
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":193
  *             pinc(it[0]) # ++it
  *         del it
  *         del result             # <<<<<<<<<<<<<<
@@ -11529,7 +11529,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
  */
   delete __pyx_v_result;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":194
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":194
  *         del it
  *         del result
  *         return vector             # <<<<<<<<<<<<<<
@@ -11554,7 +11554,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_37inside_outside(struct __pyx_obj_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":201
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":201
  *     cdef public TRule trule
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):             # <<<<<<<<<<<<<<
@@ -11571,7 +11571,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("init", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":202
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":202
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg             # <<<<<<<<<<<<<<
@@ -11580,7 +11580,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->hg = __pyx_v_hg;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":203
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":203
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg
  *         self.edge = &hg.edges_[i]             # <<<<<<<<<<<<<<
@@ -11589,7 +11589,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->edge = (&(__pyx_v_hg->edges_[__pyx_v_i]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":204
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":204
  *         self.hg = hg
  *         self.edge = &hg.edges_[i]
  *         self.trule = TRule.__new__(TRule)             # <<<<<<<<<<<<<<
@@ -11605,7 +11605,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
   __pyx_v_self->trule = ((struct __pyx_obj_5_cdec_TRule *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":205
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":205
  *         self.edge = &hg.edges_[i]
  *         self.trule = TRule.__new__(TRule)
  *         self.trule.rule = new shared_ptr[grammar.TRule](self.edge.rule_)             # <<<<<<<<<<<<<<
@@ -11614,7 +11614,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->trule->rule = new boost::shared_ptr<TRule>(__pyx_v_self->edge->rule_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":206
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":206
  *         self.trule = TRule.__new__(TRule)
  *         self.trule.rule = new shared_ptr[grammar.TRule](self.edge.rule_)
  *         return self             # <<<<<<<<<<<<<<
@@ -11649,7 +11649,7 @@ static Py_ssize_t __pyx_pw_5_cdec_14HypergraphEdge_1__len__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":208
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":208
  *         return self
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -11662,7 +11662,7 @@ static Py_ssize_t __pyx_pf_5_cdec_14HypergraphEdge___len__(struct __pyx_obj_5_cd
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":209
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":209
  * 
  *     def __len__(self):
  *         return self.edge.tail_nodes_.size()             # <<<<<<<<<<<<<<
@@ -11689,7 +11689,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_9head_node_1__get__(PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":212
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":212
  * 
  *     property head_node:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11707,7 +11707,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_9head_node___get__(struct __py
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":213
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":213
  *     property head_node:
  *         def __get__(self):
  *             return HypergraphNode().init(self.hg, self.edge.head_node_)             # <<<<<<<<<<<<<<
@@ -11749,7 +11749,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_10tail_nodes_1__get__(PyObject
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":216
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":216
  * 
  *     property tail_nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11813,7 +11813,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator11(__py
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":218
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":218
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.edge.tail_nodes_.size()):             # <<<<<<<<<<<<<<
@@ -11824,7 +11824,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator11(__py
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":219
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":219
  *             cdef unsigned i
  *             for i in range(self.edge.tail_nodes_.size()):
  *                 yield HypergraphNode().init(self.hg, self.edge.tail_nodes_[i])             # <<<<<<<<<<<<<<
@@ -11875,7 +11875,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_4span_1__get__(PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":222
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":222
  * 
  *     property span:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11894,7 +11894,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_4span___get__(struct __pyx_obj
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":223
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":223
  *     property span:
  *         def __get__(self):
  *             return (self.edge.i_, self.edge.j_)             # <<<<<<<<<<<<<<
@@ -11943,7 +11943,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_8src_span_1__get__(PyObject *_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":226
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":226
  * 
  *     property src_span:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -11962,7 +11962,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_8src_span___get__(struct __pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":227
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":227
  *     property src_span:
  *         def __get__(self):
  *             return (self.edge.prev_i_, self.edge.prev_j_)             # <<<<<<<<<<<<<<
@@ -12011,7 +12011,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_14feature_values_1__get__(PyOb
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":230
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":230
  * 
  *     property feature_values:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12029,7 +12029,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_14feature_values___get__(struc
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":231
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":231
  *     property feature_values:
  *         def __get__(self):
  *             cdef SparseVector vector = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -12042,7 +12042,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_14feature_values___get__(struc
   __pyx_v_vector = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":232
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":232
  *         def __get__(self):
  *             cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *             vector.vector = new FastSparseVector[double](self.edge.feature_values_)             # <<<<<<<<<<<<<<
@@ -12051,7 +12051,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_14feature_values___get__(struc
  */
   __pyx_v_vector->vector = new FastSparseVector<double>(__pyx_v_self->edge->feature_values_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":233
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":233
  *             cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *             vector.vector = new FastSparseVector[double](self.edge.feature_values_)
  *             return vector             # <<<<<<<<<<<<<<
@@ -12087,7 +12087,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_4prob_1__get__(PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":236
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":236
  * 
  *     property prob:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12104,7 +12104,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_4prob___get__(struct __pyx_obj
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":237
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":237
  *     property prob:
  *         def __get__(self):
  *             return self.edge.edge_prob_.as_float()             # <<<<<<<<<<<<<<
@@ -12147,7 +12147,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_3__richcmp__(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":239
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":239
  *             return self.edge.edge_prob_.as_float()
  * 
  *     def __richcmp__(HypergraphEdge x, HypergraphEdge y, int op):             # <<<<<<<<<<<<<<
@@ -12165,7 +12165,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__richcmp__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":242
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":242
  *         if op == 2: # ==
  *             return x.edge == y.edge
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -12174,7 +12174,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
  */
   switch (__pyx_v_op) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":240
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":240
  * 
  *     def __richcmp__(HypergraphEdge x, HypergraphEdge y, int op):
  *         if op == 2: # ==             # <<<<<<<<<<<<<<
@@ -12183,7 +12183,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
  */
     case 2:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":241
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":241
  *     def __richcmp__(HypergraphEdge x, HypergraphEdge y, int op):
  *         if op == 2: # ==
  *             return x.edge == y.edge             # <<<<<<<<<<<<<<
@@ -12198,7 +12198,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
     goto __pyx_L0;
     break;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":242
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":242
  *         if op == 2: # ==
  *             return x.edge == y.edge
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -12207,7 +12207,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
  */
     case 3:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":243
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":243
  *             return x.edge == y.edge
  *         elif op == 3: # !=
  *             return not (x == y)             # <<<<<<<<<<<<<<
@@ -12226,7 +12226,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
     break;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":244
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":244
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')             # <<<<<<<<<<<<<<
@@ -12262,7 +12262,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_5trule_1__get__(PyObject *__py
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":199
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":199
  *     cdef hypergraph.Hypergraph* hg
  *     cdef hypergraph.HypergraphEdge* edge
  *     cdef public TRule trule             # <<<<<<<<<<<<<<
@@ -12347,7 +12347,7 @@ static int __pyx_pf_5_cdec_14HypergraphEdge_5trule_4__del__(struct __pyx_obj_5_c
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":250
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":250
  *     cdef hypergraph.HypergraphNode* node
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):             # <<<<<<<<<<<<<<
@@ -12360,7 +12360,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphNode_init(struct __pyx_obj_5_cdec_Hy
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("init", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":251
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":251
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg             # <<<<<<<<<<<<<<
@@ -12369,7 +12369,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphNode_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->hg = __pyx_v_hg;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":252
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":252
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg
  *         self.node = &hg.nodes_[i]             # <<<<<<<<<<<<<<
@@ -12378,7 +12378,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphNode_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->node = (&(__pyx_v_hg->nodes_[__pyx_v_i]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":253
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":253
  *         self.hg = hg
  *         self.node = &hg.nodes_[i]
  *         return self             # <<<<<<<<<<<<<<
@@ -12409,7 +12409,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphNode_8in_edges_1__get__(PyObject *_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":256
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":256
  * 
  *     property in_edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12473,7 +12473,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphNode_8in_edges_2generator12(__pyx_G
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":258
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":258
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.node.in_edges_.size()):             # <<<<<<<<<<<<<<
@@ -12484,7 +12484,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphNode_8in_edges_2generator12(__pyx_G
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":259
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":259
  *             cdef unsigned i
  *             for i in range(self.node.in_edges_.size()):
  *                 yield HypergraphEdge().init(self.hg, self.node.in_edges_[i])             # <<<<<<<<<<<<<<
@@ -12536,7 +12536,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphNode_9out_edges_1__get__(PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":262
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":262
  * 
  *     property out_edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12600,7 +12600,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator13(__pyx_
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":264
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":264
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.node.out_edges_.size()):             # <<<<<<<<<<<<<<
@@ -12611,7 +12611,7 @@ static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator13(__pyx_
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":265
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":265
  *             cdef unsigned i
  *             for i in range(self.node.out_edges_.size()):
  *                 yield HypergraphEdge().init(self.hg, self.node.out_edges_[i])             # <<<<<<<<<<<<<<
@@ -12662,7 +12662,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphNode_4span_1__get__(PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":268
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":268
  * 
  *     property span:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12680,7 +12680,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode_4span___get__(struct __pyx_obj
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":269
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":269
  *     property span:
  *         def __get__(self):
  *             return next(self.in_edges).span             # <<<<<<<<<<<<<<
@@ -12724,7 +12724,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphNode_3cat_1__get__(PyObject *__pyx_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":272
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":272
  * 
  *     property cat:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -12742,7 +12742,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode_3cat___get__(struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":273
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":273
  *     property cat:
  *         def __get__(self):
  *             if self.node.cat_:             # <<<<<<<<<<<<<<
@@ -12751,7 +12751,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode_3cat___get__(struct __pyx_obj_
  */
   if (__pyx_v_self->node->cat_) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":274
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":274
  *         def __get__(self):
  *             if self.node.cat_:
  *                 return str(TDConvert(-self.node.cat_).c_str())             # <<<<<<<<<<<<<<
@@ -12806,7 +12806,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphNode_1__richcmp__(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":276
+/* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":276
  *                 return str(TDConvert(-self.node.cat_).c_str())
  * 
  *     def __richcmp__(HypergraphNode x, HypergraphNode y, int op):             # <<<<<<<<<<<<<<
@@ -12824,7 +12824,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__richcmp__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":279
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":279
  *         if op == 2: # ==
  *             return x.node == y.node
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -12833,7 +12833,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
  */
   switch (__pyx_v_op) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":277
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":277
  * 
  *     def __richcmp__(HypergraphNode x, HypergraphNode y, int op):
  *         if op == 2: # ==             # <<<<<<<<<<<<<<
@@ -12842,7 +12842,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
  */
     case 2:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":278
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":278
  *     def __richcmp__(HypergraphNode x, HypergraphNode y, int op):
  *         if op == 2: # ==
  *             return x.node == y.node             # <<<<<<<<<<<<<<
@@ -12857,7 +12857,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
     goto __pyx_L0;
     break;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":279
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":279
  *         if op == 2: # ==
  *             return x.node == y.node
  *         elif op == 3: # !=             # <<<<<<<<<<<<<<
@@ -12866,7 +12866,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
  */
     case 3:
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":280
+    /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":280
  *             return x.node == y.node
  *         elif op == 3: # !=
  *             return not (x == y)             # <<<<<<<<<<<<<<
@@ -12884,7 +12884,7 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
     break;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":281
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":281
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphNode')             # <<<<<<<<<<<<<<
@@ -12921,7 +12921,7 @@ static int __pyx_pw_5_cdec_7Lattice_1__cinit__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":6
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":6
  *     cdef lattice.Lattice* lattice
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -12934,7 +12934,7 @@ static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":7
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":7
  * 
  *     def __cinit__(self):
  *         self.lattice = new lattice.Lattice()             # <<<<<<<<<<<<<<
@@ -12999,7 +12999,7 @@ static int __pyx_pw_5_cdec_7Lattice_3__init__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":9
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":9
  *         self.lattice = new lattice.Lattice()
  * 
  *     def __init__(self, inp):             # <<<<<<<<<<<<<<
@@ -13024,7 +13024,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":12
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":12
  *         """Lattice(tuple) -> Lattice from node list.
  *         Lattice(string) -> Lattice from PLF representation."""
  *         if isinstance(inp, tuple):             # <<<<<<<<<<<<<<
@@ -13034,7 +13034,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
   __pyx_t_1 = PyTuple_Check(__pyx_v_inp); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":13
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":13
  *         Lattice(string) -> Lattice from PLF representation."""
  *         if isinstance(inp, tuple):
  *             self.lattice.resize(len(inp))             # <<<<<<<<<<<<<<
@@ -13044,7 +13044,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
     __pyx_t_2 = PyObject_Length(__pyx_v_inp); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_self->lattice->resize(__pyx_t_2);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":14
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":14
  *         if isinstance(inp, tuple):
  *             self.lattice.resize(len(inp))
  *             for i, arcs in enumerate(inp):             # <<<<<<<<<<<<<<
@@ -13099,7 +13099,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
       __pyx_t_3 = __pyx_t_6;
       __pyx_t_6 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":15
+      /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":15
  *             self.lattice.resize(len(inp))
  *             for i, arcs in enumerate(inp):
  *                 self[i] = arcs             # <<<<<<<<<<<<<<
@@ -13113,7 +13113,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
     goto __pyx_L3;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":16
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":16
  *             for i, arcs in enumerate(inp):
  *                 self[i] = arcs
  *         elif isinstance(inp, basestring):             # <<<<<<<<<<<<<<
@@ -13123,7 +13123,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
   __pyx_t_1 = PyObject_IsInstance(__pyx_v_inp, __pyx_builtin_basestring); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":17
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":17
  *                 self[i] = arcs
  *         elif isinstance(inp, basestring):
  *             lattice.ConvertTextOrPLF(as_str(inp), self.lattice)             # <<<<<<<<<<<<<<
@@ -13139,7 +13139,7 @@ static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *_
   }
   /*else*/ {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":19
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":19
  *             lattice.ConvertTextOrPLF(as_str(inp), self.lattice)
  *         else:
  *             raise TypeError('cannot create lattice from %s' % type(inp))             # <<<<<<<<<<<<<<
@@ -13186,7 +13186,7 @@ static void __pyx_pw_5_cdec_7Lattice_5__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":21
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":21
  *             raise TypeError('cannot create lattice from %s' % type(inp))
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -13198,7 +13198,7 @@ static void __pyx_pf_5_cdec_7Lattice_4__dealloc__(CYTHON_UNUSED struct __pyx_obj
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":22
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":22
  * 
  *     def __dealloc__(self):
  *         del self.lattice             # <<<<<<<<<<<<<<
@@ -13231,7 +13231,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_7__getitem__(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":24
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":24
  *         del self.lattice
  * 
  *     def __getitem__(self, int index):             # <<<<<<<<<<<<<<
@@ -13261,7 +13261,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":25
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":25
  * 
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):             # <<<<<<<<<<<<<<
@@ -13276,7 +13276,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
   __pyx_t_3 = (!__pyx_t_1);
   if (__pyx_t_3) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":26
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":26
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
@@ -13292,7 +13292,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":27
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":27
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')
  *         arcs = []             # <<<<<<<<<<<<<<
@@ -13304,7 +13304,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
   __pyx_v_arcs = ((PyObject*)__pyx_t_4);
   __pyx_t_4 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":28
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":28
  *             raise IndexError('lattice index out of range')
  *         arcs = []
  *         cdef vector[lattice.LatticeArc] arc_vector = self.lattice[0][index]             # <<<<<<<<<<<<<<
@@ -13313,7 +13313,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
  */
   __pyx_v_arc_vector = ((__pyx_v_self->lattice[0])[__pyx_v_index]);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":31
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":31
  *         cdef lattice.LatticeArc* arc
  *         cdef unsigned i
  *         for i in range(arc_vector.size()):             # <<<<<<<<<<<<<<
@@ -13324,7 +13324,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
   for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
     __pyx_v_i = __pyx_t_6;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":32
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":32
  *         cdef unsigned i
  *         for i in range(arc_vector.size()):
  *             arc = &arc_vector[i]             # <<<<<<<<<<<<<<
@@ -13333,7 +13333,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
  */
     __pyx_v_arc = (&(__pyx_v_arc_vector[__pyx_v_i]));
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":33
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":33
  *         for i in range(arc_vector.size()):
  *             arc = &arc_vector[i]
  *             label = unicode(TDConvert(arc.label).c_str(), 'utf8')             # <<<<<<<<<<<<<<
@@ -13357,7 +13357,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
     __pyx_v_label = ((PyObject*)__pyx_t_4);
     __pyx_t_4 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":34
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":34
  *             arc = &arc_vector[i]
  *             label = unicode(TDConvert(arc.label).c_str(), 'utf8')
  *             arcs.append((label, arc.cost, arc.dist2next))             # <<<<<<<<<<<<<<
@@ -13383,7 +13383,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_L
     __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":35
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":35
  *             label = unicode(TDConvert(arc.label).c_str(), 'utf8')
  *             arcs.append((label, arc.cost, arc.dist2next))
  *         return tuple(arcs)             # <<<<<<<<<<<<<<
@@ -13439,7 +13439,7 @@ static int __pyx_pw_5_cdec_7Lattice_9__setitem__(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":37
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":37
  *         return tuple(arcs)
  * 
  *     def __setitem__(self, int index, tuple arcs):             # <<<<<<<<<<<<<<
@@ -13473,7 +13473,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__setitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":38
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":38
  * 
  *     def __setitem__(self, int index, tuple arcs):
  *         if not 0 <= index < len(self):             # <<<<<<<<<<<<<<
@@ -13488,7 +13488,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
   __pyx_t_3 = (!__pyx_t_1);
   if (__pyx_t_3) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":39
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":39
  *     def __setitem__(self, int index, tuple arcs):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
@@ -13504,7 +13504,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":41
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":41
  *             raise IndexError('lattice index out of range')
  *         cdef lattice.LatticeArc* arc
  *         for (label, cost, dist2next) in arcs:             # <<<<<<<<<<<<<<
@@ -13591,7 +13591,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
     __pyx_v_dist2next = __pyx_t_8;
     __pyx_t_8 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":42
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":42
  *         cdef lattice.LatticeArc* arc
  *         for (label, cost, dist2next) in arcs:
  *             label_str = as_str(label)             # <<<<<<<<<<<<<<
@@ -13604,7 +13604,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
     __pyx_v_label_str = ((PyObject*)__pyx_t_5);
     __pyx_t_5 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":43
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":43
  *         for (label, cost, dist2next) in arcs:
  *             label_str = as_str(label)
  *             arc = new lattice.LatticeArc(TDConvert(label_str), cost, dist2next)             # <<<<<<<<<<<<<<
@@ -13616,7 +13616,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
     __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_v_dist2next); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_arc = new LatticeArc(TD::Convert(__pyx_t_11), __pyx_t_12, __pyx_t_13);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":44
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":44
  *             label_str = as_str(label)
  *             arc = new lattice.LatticeArc(TDConvert(label_str), cost, dist2next)
  *             self.lattice[0][index].push_back(arc[0])             # <<<<<<<<<<<<<<
@@ -13625,7 +13625,7 @@ static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice
  */
     ((__pyx_v_self->lattice[0])[__pyx_v_index]).push_back((__pyx_v_arc[0]));
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":45
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":45
  *             arc = new lattice.LatticeArc(TDConvert(label_str), cost, dist2next)
  *             self.lattice[0][index].push_back(arc[0])
  *             del arc             # <<<<<<<<<<<<<<
@@ -13667,7 +13667,7 @@ static Py_ssize_t __pyx_pw_5_cdec_7Lattice_11__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":47
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":47
  *             del arc
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -13680,7 +13680,7 @@ static Py_ssize_t __pyx_pf_5_cdec_7Lattice_10__len__(struct __pyx_obj_5_cdec_Lat
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":48
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":48
  * 
  *     def __len__(self):
  *         return self.lattice.size()             # <<<<<<<<<<<<<<
@@ -13707,7 +13707,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_13__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":50
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":50
  *         return self.lattice.size()
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -13725,7 +13725,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_12__str__(struct __pyx_obj_5_cdec_Latt
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":51
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":51
  * 
  *     def __str__(self):
  *         return str(hypergraph.AsPLF(self.lattice[0], True).c_str())             # <<<<<<<<<<<<<<
@@ -13771,7 +13771,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_15__unicode__(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":53
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":53
  *         return str(hypergraph.AsPLF(self.lattice[0], True).c_str())
  * 
  *     def __unicode__(self):             # <<<<<<<<<<<<<<
@@ -13789,7 +13789,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_14__unicode__(struct __pyx_obj_5_cdec_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__unicode__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":54
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":54
  * 
  *     def __unicode__(self):
  *         return unicode(str(self), 'utf8')             # <<<<<<<<<<<<<<
@@ -13845,7 +13845,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_17__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":56
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":56
  *         return unicode(str(self), 'utf8')
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -13908,7 +13908,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_18generator14(__pyx_GeneratorObject *_
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":58
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":58
  *     def __iter__(self):
  *         cdef unsigned i
  *         for i in range(len(self)):             # <<<<<<<<<<<<<<
@@ -13919,7 +13919,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_18generator14(__pyx_GeneratorObject *_
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":59
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":59
  *         cdef unsigned i
  *         for i in range(len(self)):
  *             yield self[i]             # <<<<<<<<<<<<<<
@@ -13980,7 +13980,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_5todot_1lines(PyObject *__pyx_self, CY
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":63
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":63
  *     def todot(self):
  *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():             # <<<<<<<<<<<<<<
@@ -14057,7 +14057,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":64
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":64
  *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():
  *             yield 'digraph lattice {'             # <<<<<<<<<<<<<<
@@ -14074,7 +14074,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   __pyx_L4_resume_from_yield:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":65
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":65
  *         def lines():
  *             yield 'digraph lattice {'
  *             yield 'rankdir = LR;'             # <<<<<<<<<<<<<<
@@ -14091,7 +14091,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   __pyx_L5_resume_from_yield:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":66
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":66
  *             yield 'digraph lattice {'
  *             yield 'rankdir = LR;'
  *             yield 'node [shape=circle];'             # <<<<<<<<<<<<<<
@@ -14108,7 +14108,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   __pyx_L6_resume_from_yield:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":67
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":67
  *             yield 'rankdir = LR;'
  *             yield 'node [shape=circle];'
  *             for i in range(len(self)):             # <<<<<<<<<<<<<<
@@ -14171,7 +14171,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
     __pyx_cur_scope->__pyx_v_i = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":68
+    /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":68
  *             yield 'node [shape=circle];'
  *             for i in range(len(self)):
  *                 for label, weight, delta in self[i]:             # <<<<<<<<<<<<<<
@@ -14289,7 +14289,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
       __pyx_cur_scope->__pyx_v_delta = __pyx_t_10;
       __pyx_t_10 = 0;
 
-      /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":69
+      /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":69
  *             for i in range(len(self)):
  *                 for label, weight, delta in self[i]:
  *                     yield '%d -> %d [label="%s"];' % (i, i+delta, label.replace('"', '\\"'))             # <<<<<<<<<<<<<<
@@ -14349,7 +14349,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   }
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":70
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":70
  *                 for label, weight, delta in self[i]:
  *                     yield '%d -> %d [label="%s"];' % (i, i+delta, label.replace('"', '\\"'))
  *             yield '%d [shape=doublecircle]' % len(self)             # <<<<<<<<<<<<<<
@@ -14375,7 +14375,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   __pyx_L14_resume_from_yield:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":71
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":71
  *                     yield '%d -> %d [label="%s"];' % (i, i+delta, label.replace('"', '\\"'))
  *             yield '%d [shape=doublecircle]' % len(self)
  *             yield '}'             # <<<<<<<<<<<<<<
@@ -14410,7 +14410,7 @@ static PyObject *__pyx_gb_5_cdec_7Lattice_5todot_2generator20(__pyx_GeneratorObj
   return NULL;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":61
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":61
  *             yield self[i]
  * 
  *     def todot(self):             # <<<<<<<<<<<<<<
@@ -14440,7 +14440,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_19todot(struct __pyx_obj_5_cdec_Lattic
   __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
   __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":63
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":63
  *     def todot(self):
  *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():             # <<<<<<<<<<<<<<
@@ -14452,7 +14452,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_19todot(struct __pyx_obj_5_cdec_Lattic
   __pyx_v_lines = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":72
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":72
  *             yield '%d [shape=doublecircle]' % len(self)
  *             yield '}'
  *         return '\n'.join(lines()).encode('utf8')             # <<<<<<<<<<<<<<
@@ -14511,7 +14511,7 @@ static PyObject *__pyx_pw_5_cdec_7Lattice_22as_hypergraph(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":74
+/* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":74
  *         return '\n'.join(lines()).encode('utf8')
  * 
  *     def as_hypergraph(self):             # <<<<<<<<<<<<<<
@@ -14532,7 +14532,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("as_hypergraph", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":76
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":76
  *     def as_hypergraph(self):
  *         """lattice.as_hypergraph() -> Hypergraph representation of the lattice."""
  *         cdef Hypergraph result = Hypergraph.__new__(Hypergraph)             # <<<<<<<<<<<<<<
@@ -14545,7 +14545,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
   __pyx_v_result = ((struct __pyx_obj_5_cdec_Hypergraph *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":77
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":77
  *         """lattice.as_hypergraph() -> Hypergraph representation of the lattice."""
  *         cdef Hypergraph result = Hypergraph.__new__(Hypergraph)
  *         result.hg = new hypergraph.Hypergraph()             # <<<<<<<<<<<<<<
@@ -14554,7 +14554,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
  */
   __pyx_v_result->hg = new Hypergraph();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":78
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":78
  *         cdef Hypergraph result = Hypergraph.__new__(Hypergraph)
  *         result.hg = new hypergraph.Hypergraph()
  *         cdef bytes plf = str(self)             # <<<<<<<<<<<<<<
@@ -14573,7 +14573,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
   __pyx_v_plf = ((PyObject*)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":79
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":79
  *         result.hg = new hypergraph.Hypergraph()
  *         cdef bytes plf = str(self)
  *         hypergraph.ReadFromPLF(plf, result.hg)             # <<<<<<<<<<<<<<
@@ -14582,7 +14582,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
   __pyx_t_3 = __pyx_convert_string_from_py_(((PyObject *)__pyx_v_plf)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   HypergraphIO::ReadFromPLF(__pyx_t_3, __pyx_v_result->hg);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":80
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":80
  *         cdef bytes plf = str(self)
  *         hypergraph.ReadFromPLF(plf, result.hg)
  *         return result             # <<<<<<<<<<<<<<
@@ -14607,7 +14607,7 @@ static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cde
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":3
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":3
  * cimport mteval
  * 
  * cdef SufficientStats as_stats(x, y):             # <<<<<<<<<<<<<<
@@ -14629,7 +14629,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("as_stats", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":4
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":4
  * 
  * cdef SufficientStats as_stats(x, y):
  *     if isinstance(x, SufficientStats):             # <<<<<<<<<<<<<<
@@ -14639,7 +14639,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
   __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_x, ((PyObject*)__pyx_ptype_5_cdec_SufficientStats)); 
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":5
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":5
  * cdef SufficientStats as_stats(x, y):
  *     if isinstance(x, SufficientStats):
  *         return x             # <<<<<<<<<<<<<<
@@ -14654,7 +14654,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
     goto __pyx_L3;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":6
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":6
  *     if isinstance(x, SufficientStats):
  *         return x
  *     elif x == 0 and isinstance(y, SufficientStats):             # <<<<<<<<<<<<<<
@@ -14672,7 +14672,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
   }
   if (__pyx_t_4) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":7
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":7
  *         return x
  *     elif x == 0 and isinstance(y, SufficientStats):
  *         stats = SufficientStats()             # <<<<<<<<<<<<<<
@@ -14684,7 +14684,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
     __pyx_v_stats = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_t_2);
     __pyx_t_2 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":8
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":8
  *     elif x == 0 and isinstance(y, SufficientStats):
  *         stats = SufficientStats()
  *         stats.stats = new mteval.SufficientStats()             # <<<<<<<<<<<<<<
@@ -14693,7 +14693,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
  */
     __pyx_v_stats->stats = new SufficientStats();
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":9
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":9
  *         stats = SufficientStats()
  *         stats.stats = new mteval.SufficientStats()
  *         stats.metric = (<SufficientStats> y).metric             # <<<<<<<<<<<<<<
@@ -14703,7 +14703,7 @@ static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject
     __pyx_t_5 = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_v_y)->metric;
     __pyx_v_stats->metric = __pyx_t_5;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":10
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":10
  *         stats.stats = new mteval.SufficientStats()
  *         stats.metric = (<SufficientStats> y).metric
  *         return stats             # <<<<<<<<<<<<<<
@@ -14742,7 +14742,7 @@ static PyObject *__pyx_pw_5_cdec_9Candidate_5words_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":17
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":17
  * 
  *     property words:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -14761,7 +14761,7 @@ static PyObject *__pyx_pf_5_cdec_9Candidate_5words___get__(struct __pyx_obj_5_cd
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":18
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":18
  *     property words:
  *         def __get__(self):
  *             return unicode(GetString(self.candidate.ewords).c_str(), encoding='utf8')             # <<<<<<<<<<<<<<
@@ -14812,7 +14812,7 @@ static PyObject *__pyx_pw_5_cdec_9Candidate_4fmap_1__get__(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":21
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":21
  * 
  *     property fmap:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -14830,7 +14830,7 @@ static PyObject *__pyx_pf_5_cdec_9Candidate_4fmap___get__(struct __pyx_obj_5_cde
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":22
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":22
  *     property fmap:
  *         def __get__(self):
  *             cdef SparseVector fmap = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
@@ -14843,7 +14843,7 @@ static PyObject *__pyx_pf_5_cdec_9Candidate_4fmap___get__(struct __pyx_obj_5_cde
   __pyx_v_fmap = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":23
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":23
  *         def __get__(self):
  *             cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *             fmap.vector = new FastSparseVector[weight_t](self.candidate.fmap)             # <<<<<<<<<<<<<<
@@ -14852,7 +14852,7 @@ static PyObject *__pyx_pf_5_cdec_9Candidate_4fmap___get__(struct __pyx_obj_5_cde
  */
   __pyx_v_fmap->vector = new FastSparseVector<weight_t>(__pyx_v_self->candidate->fmap);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":24
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":24
  *             cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *             fmap.vector = new FastSparseVector[weight_t](self.candidate.fmap)
  *             return fmap             # <<<<<<<<<<<<<<
@@ -14888,7 +14888,7 @@ static PyObject *__pyx_pw_5_cdec_9Candidate_5score_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":14
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":14
  * cdef class Candidate:
  *     cdef mteval.const_Candidate* candidate
  *     cdef public float score             # <<<<<<<<<<<<<<
@@ -14964,7 +14964,7 @@ static void __pyx_pw_5_cdec_15SufficientStats_1__dealloc__(PyObject *__pyx_v_sel
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":30
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":30
  *     cdef mteval.EvaluationMetric* metric
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -14976,7 +14976,7 @@ static void __pyx_pf_5_cdec_15SufficientStats___dealloc__(CYTHON_UNUSED struct _
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   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":31
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":31
  * 
  *     def __dealloc__(self):
  *         del self.stats             # <<<<<<<<<<<<<<
@@ -14999,7 +14999,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_5score_1__get__(PyObject *__p
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":34
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":34
  * 
  *     property score:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -15016,7 +15016,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_5score___get__(struct __pyx_o
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   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":35
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":35
  *     property score:
  *         def __get__(self):
  *             return self.metric.ComputeScore(self.stats[0])             # <<<<<<<<<<<<<<
@@ -15053,7 +15053,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_6detail_1__get__(PyObject *__
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":38
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":38
  * 
  *     property detail:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -15071,7 +15071,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_6detail___get__(struct __pyx_
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   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":39
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":39
  *     property detail:
  *         def __get__(self):
  *             return str(self.metric.DetailedScore(self.stats[0]).c_str())             # <<<<<<<<<<<<<<
@@ -15117,7 +15117,7 @@ static Py_ssize_t __pyx_pw_5_cdec_15SufficientStats_3__len__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":41
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":41
  *             return str(self.metric.DetailedScore(self.stats[0]).c_str())
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -15130,7 +15130,7 @@ static Py_ssize_t __pyx_pf_5_cdec_15SufficientStats_2__len__(struct __pyx_obj_5_
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   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":42
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":42
  * 
  *     def __len__(self):
  *         return self.stats.size()             # <<<<<<<<<<<<<<
@@ -15158,7 +15158,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_5__iter__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":44
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":44
  *         return self.stats.size()
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -15222,7 +15222,7 @@ static PyObject *__pyx_gb_5_cdec_15SufficientStats_6generator15(__pyx_GeneratorO
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":45
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":45
  * 
  *     def __iter__(self):
  *         for i in range(len(self)):             # <<<<<<<<<<<<<<
@@ -15281,7 +15281,7 @@ static PyObject *__pyx_gb_5_cdec_15SufficientStats_6generator15(__pyx_GeneratorO
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
     __pyx_t_2 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":46
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":46
  *     def __iter__(self):
  *         for i in range(len(self)):
  *             yield self[i]             # <<<<<<<<<<<<<<
@@ -15345,7 +15345,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_8__getitem__(PyObject *__pyx_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":48
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":48
  *             yield self[i]
  * 
  *     def __getitem__(self, int index):             # <<<<<<<<<<<<<<
@@ -15365,7 +15365,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_7__getitem__(struct __pyx_obj
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-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":49
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":49
  * 
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):             # <<<<<<<<<<<<<<
@@ -15380,7 +15380,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_7__getitem__(struct __pyx_obj
   __pyx_t_3 = (!__pyx_t_1);
   if (__pyx_t_3) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":50
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":50
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('sufficient stats vector index out of range')             # <<<<<<<<<<<<<<
@@ -15396,7 +15396,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_7__getitem__(struct __pyx_obj
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":51
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":51
  *         if not 0 <= index < len(self):
  *             raise IndexError('sufficient stats vector index out of range')
  *         return self.stats[0][index]             # <<<<<<<<<<<<<<
@@ -15438,7 +15438,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_10__iadd__(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":53
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":53
  *         return self.stats[0][index]
  * 
  *     def __iadd__(SufficientStats self, SufficientStats other):             # <<<<<<<<<<<<<<
@@ -15451,7 +15451,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_9__iadd__(struct __pyx_obj_5_
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   __Pyx_RefNannySetupContext("__iadd__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":54
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":54
  * 
  *     def __iadd__(SufficientStats self, SufficientStats other):
  *         self.stats[0] += other.stats[0]             # <<<<<<<<<<<<<<
@@ -15460,7 +15460,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_9__iadd__(struct __pyx_obj_5_
  */
   (__pyx_v_self->stats[0]) += (__pyx_v_other->stats[0]);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":55
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":55
  *     def __iadd__(SufficientStats self, SufficientStats other):
  *         self.stats[0] += other.stats[0]
  *         return self             # <<<<<<<<<<<<<<
@@ -15490,7 +15490,7 @@ static PyObject *__pyx_pw_5_cdec_15SufficientStats_12__add__(PyObject *__pyx_v_x
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":57
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":57
  *         return self
  * 
  *     def __add__(x, y):             # <<<<<<<<<<<<<<
@@ -15511,7 +15511,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
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   __Pyx_RefNannySetupContext("__add__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":58
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":58
  * 
  *     def __add__(x, y):
  *         cdef SufficientStats sx = as_stats(x, y)             # <<<<<<<<<<<<<<
@@ -15523,7 +15523,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
   __pyx_v_sx = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":59
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":59
  *     def __add__(x, y):
  *         cdef SufficientStats sx = as_stats(x, y)
  *         cdef SufficientStats sy = as_stats(y, x)             # <<<<<<<<<<<<<<
@@ -15535,7 +15535,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
   __pyx_v_sy = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":60
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":60
  *         cdef SufficientStats sx = as_stats(x, y)
  *         cdef SufficientStats sy = as_stats(y, x)
  *         cdef SufficientStats result = SufficientStats()             # <<<<<<<<<<<<<<
@@ -15547,7 +15547,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
   __pyx_v_result = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":61
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":61
  *         cdef SufficientStats sy = as_stats(y, x)
  *         cdef SufficientStats result = SufficientStats()
  *         result.stats = new mteval.SufficientStats(mteval.add(sx.stats[0], sy.stats[0]))             # <<<<<<<<<<<<<<
@@ -15556,7 +15556,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
  */
   __pyx_v_result->stats = new SufficientStats(operator+((__pyx_v_sx->stats[0]), (__pyx_v_sy->stats[0])));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":62
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":62
  *         cdef SufficientStats result = SufficientStats()
  *         result.stats = new mteval.SufficientStats(mteval.add(sx.stats[0], sy.stats[0]))
  *         result.metric = sx.metric             # <<<<<<<<<<<<<<
@@ -15566,7 +15566,7 @@ static PyObject *__pyx_pf_5_cdec_15SufficientStats_11__add__(PyObject *__pyx_v_x
   __pyx_t_2 = __pyx_v_sx->metric;
   __pyx_v_result->metric = __pyx_t_2;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":63
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":63
  *         result.stats = new mteval.SufficientStats(mteval.add(sx.stats[0], sy.stats[0]))
  *         result.metric = sx.metric
  *         return result             # <<<<<<<<<<<<<<
@@ -15645,7 +15645,7 @@ static int __pyx_pw_5_cdec_12CandidateSet_1__cinit__(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":70
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":70
  *     cdef mteval.CandidateSet* cs
  * 
  *     def __cinit__(self, SegmentEvaluator evaluator):             # <<<<<<<<<<<<<<
@@ -15659,7 +15659,7 @@ static int __pyx_pf_5_cdec_12CandidateSet___cinit__(struct __pyx_obj_5_cdec_Cand
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   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":71
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":71
  * 
  *     def __cinit__(self, SegmentEvaluator evaluator):
  *         self.scorer = new shared_ptr[mteval.SegmentEvaluator](evaluator.scorer[0])             # <<<<<<<<<<<<<<
@@ -15668,7 +15668,7 @@ static int __pyx_pf_5_cdec_12CandidateSet___cinit__(struct __pyx_obj_5_cdec_Cand
  */
   __pyx_v_self->scorer = new boost::shared_ptr<SegmentEvaluator>((__pyx_v_evaluator->scorer[0]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":72
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":72
  *     def __cinit__(self, SegmentEvaluator evaluator):
  *         self.scorer = new shared_ptr[mteval.SegmentEvaluator](evaluator.scorer[0])
  *         self.metric = evaluator.metric             # <<<<<<<<<<<<<<
@@ -15678,7 +15678,7 @@ static int __pyx_pf_5_cdec_12CandidateSet___cinit__(struct __pyx_obj_5_cdec_Cand
   __pyx_t_1 = __pyx_v_evaluator->metric;
   __pyx_v_self->metric = __pyx_t_1;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":73
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":73
  *         self.scorer = new shared_ptr[mteval.SegmentEvaluator](evaluator.scorer[0])
  *         self.metric = evaluator.metric
  *         self.cs = new mteval.CandidateSet()             # <<<<<<<<<<<<<<
@@ -15701,7 +15701,7 @@ static void __pyx_pw_5_cdec_12CandidateSet_3__dealloc__(PyObject *__pyx_v_self)
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":75
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":75
  *         self.cs = new mteval.CandidateSet()
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -15713,7 +15713,7 @@ static void __pyx_pf_5_cdec_12CandidateSet_2__dealloc__(CYTHON_UNUSED struct __p
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   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":76
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":76
  * 
  *     def __dealloc__(self):
  *         del self.scorer             # <<<<<<<<<<<<<<
@@ -15722,7 +15722,7 @@ static void __pyx_pf_5_cdec_12CandidateSet_2__dealloc__(CYTHON_UNUSED struct __p
  */
   delete __pyx_v_self->scorer;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":77
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":77
  *     def __dealloc__(self):
  *         del self.scorer
  *         del self.cs             # <<<<<<<<<<<<<<
@@ -15745,7 +15745,7 @@ static Py_ssize_t __pyx_pw_5_cdec_12CandidateSet_5__len__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":79
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":79
  *         del self.cs
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -15758,7 +15758,7 @@ static Py_ssize_t __pyx_pf_5_cdec_12CandidateSet_4__len__(struct __pyx_obj_5_cde
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   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":80
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":80
  * 
  *     def __len__(self):
  *         return self.cs.size()             # <<<<<<<<<<<<<<
@@ -15795,7 +15795,7 @@ static PyObject *__pyx_pw_5_cdec_12CandidateSet_7__getitem__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":82
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":82
  *         return self.cs.size()
  * 
  *     def __getitem__(self,int k):             # <<<<<<<<<<<<<<
@@ -15815,7 +15815,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_6__getitem__(struct __pyx_obj_5_
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   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":83
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":83
  * 
  *     def __getitem__(self,int k):
  *         if not 0 <= k < self.cs.size():             # <<<<<<<<<<<<<<
@@ -15829,7 +15829,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_6__getitem__(struct __pyx_obj_5_
   __pyx_t_2 = (!__pyx_t_1);
   if (__pyx_t_2) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":84
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":84
  *     def __getitem__(self,int k):
  *         if not 0 <= k < self.cs.size():
  *             raise IndexError('candidate set index out of range')             # <<<<<<<<<<<<<<
@@ -15845,7 +15845,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_6__getitem__(struct __pyx_obj_5_
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":85
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":85
  *         if not 0 <= k < self.cs.size():
  *             raise IndexError('candidate set index out of range')
  *         cdef Candidate candidate = Candidate()             # <<<<<<<<<<<<<<
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   __pyx_v_candidate = ((struct __pyx_obj_5_cdec_Candidate *)__pyx_t_3);
   __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":86
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":86
  *             raise IndexError('candidate set index out of range')
  *         cdef Candidate candidate = Candidate()
  *         candidate.candidate = &self.cs[0][k]             # <<<<<<<<<<<<<<
@@ -15866,7 +15866,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_6__getitem__(struct __pyx_obj_5_
  */
   __pyx_v_candidate->candidate = (&((__pyx_v_self->cs[0])[__pyx_v_k]));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":87
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":87
  *         cdef Candidate candidate = Candidate()
  *         candidate.candidate = &self.cs[0][k]
  *         candidate.score = self.metric.ComputeScore(self.cs[0][k].eval_feats)             # <<<<<<<<<<<<<<
@@ -15875,7 +15875,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_6__getitem__(struct __pyx_obj_5_
  */
   __pyx_v_candidate->score = __pyx_v_self->metric->ComputeScore(((__pyx_v_self->cs[0])[__pyx_v_k]).eval_feats);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":88
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":88
  *         candidate.candidate = &self.cs[0][k]
  *         candidate.score = self.metric.ComputeScore(self.cs[0][k].eval_feats)
  *         return candidate             # <<<<<<<<<<<<<<
@@ -15912,7 +15912,7 @@ static PyObject *__pyx_pw_5_cdec_12CandidateSet_9__iter__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":90
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":90
  *         return candidate
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -15975,7 +15975,7 @@ static PyObject *__pyx_gb_5_cdec_12CandidateSet_10generator16(__pyx_GeneratorObj
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":92
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":92
  *     def __iter__(self):
  *         cdef unsigned i
  *         for i in range(len(self)):             # <<<<<<<<<<<<<<
@@ -15986,7 +15986,7 @@ static PyObject *__pyx_gb_5_cdec_12CandidateSet_10generator16(__pyx_GeneratorObj
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":93
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":93
  *         cdef unsigned i
  *         for i in range(len(self)):
  *             yield self[i]             # <<<<<<<<<<<<<<
@@ -16084,7 +16084,7 @@ static PyObject *__pyx_pw_5_cdec_12CandidateSet_12add_kbest(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":95
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":95
  *             yield self[i]
  * 
  *     def add_kbest(self, Hypergraph hypergraph, unsigned k):             # <<<<<<<<<<<<<<
@@ -16097,7 +16097,7 @@ static PyObject *__pyx_pf_5_cdec_12CandidateSet_11add_kbest(struct __pyx_obj_5_c
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   __Pyx_RefNannySetupContext("add_kbest", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":98
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":98
  *         """cs.add_kbest(Hypergraph hypergraph, int k) -> Extract K-best hypotheses
  *         from the hypergraph and add them to the candidate set."""
  *         self.cs.AddKBestCandidates(hypergraph.hg[0], k, self.scorer.get())             # <<<<<<<<<<<<<<
@@ -16121,7 +16121,7 @@ static void __pyx_pw_5_cdec_16SegmentEvaluator_1__dealloc__(PyObject *__pyx_v_se
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":104
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":104
  *     cdef mteval.EvaluationMetric* metric
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -16133,7 +16133,7 @@ static void __pyx_pf_5_cdec_16SegmentEvaluator___dealloc__(CYTHON_UNUSED struct
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":105
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":105
  * 
  *     def __dealloc__(self):
  *         del self.scorer             # <<<<<<<<<<<<<<
@@ -16157,7 +16157,7 @@ static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_3evaluate(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":107
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":107
  *         del self.scorer
  * 
  *     def evaluate(self, sentence):             # <<<<<<<<<<<<<<
@@ -16179,7 +16179,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
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   __Pyx_RefNannySetupContext("evaluate", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":110
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":110
  *         """se.evaluate(sentence) -> SufficientStats for the given hypothesis."""
  *         cdef vector[WordID] hyp
  *         cdef SufficientStats sf = SufficientStats()             # <<<<<<<<<<<<<<
@@ -16191,7 +16191,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
   __pyx_v_sf = ((struct __pyx_obj_5_cdec_SufficientStats *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":111
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":111
  *         cdef vector[WordID] hyp
  *         cdef SufficientStats sf = SufficientStats()
  *         sf.metric = self.metric             # <<<<<<<<<<<<<<
@@ -16201,7 +16201,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
   __pyx_t_2 = __pyx_v_self->metric;
   __pyx_v_sf->metric = __pyx_t_2;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":112
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":112
  *         cdef SufficientStats sf = SufficientStats()
  *         sf.metric = self.metric
  *         sf.stats = new mteval.SufficientStats()             # <<<<<<<<<<<<<<
@@ -16210,7 +16210,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
  */
   __pyx_v_sf->stats = new SufficientStats();
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":113
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":113
  *         sf.metric = self.metric
  *         sf.stats = new mteval.SufficientStats()
  *         ConvertSentence(as_str(sentence.strip()), &hyp)             # <<<<<<<<<<<<<<
@@ -16229,7 +16229,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   TD::ConvertSentence(__pyx_t_4, (&__pyx_v_hyp));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":114
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":114
  *         sf.stats = new mteval.SufficientStats()
  *         ConvertSentence(as_str(sentence.strip()), &hyp)
  *         self.scorer.get().Evaluate(hyp, sf.stats)             # <<<<<<<<<<<<<<
@@ -16238,7 +16238,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_2evaluate(struct __pyx_obj_5
  */
   __pyx_v_self->scorer->get()->Evaluate(__pyx_v_hyp, __pyx_v_sf->stats);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":115
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":115
  *         ConvertSentence(as_str(sentence.strip()), &hyp)
  *         self.scorer.get().Evaluate(hyp, sf.stats)
  *         return sf             # <<<<<<<<<<<<<<
@@ -16276,7 +16276,7 @@ static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_5candidate_set(PyObject *__p
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":117
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":117
  *         return sf
  * 
  *     def candidate_set(self):             # <<<<<<<<<<<<<<
@@ -16294,7 +16294,7 @@ static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_4candidate_set(struct __pyx_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("candidate_set", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":119
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":119
  *     def candidate_set(self):
  *         """se.candidate_set() -> Candidate set using this segment evaluator for scoring."""
  *         return CandidateSet(self)             # <<<<<<<<<<<<<<
@@ -16338,7 +16338,7 @@ static int __pyx_pw_5_cdec_6Scorer_1__cinit__(PyObject *__pyx_v_self, PyObject *
     static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__name,0};
     PyObject* values[1] = {0};
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":125
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":125
  *     cdef mteval.EvaluationMetric* metric
  * 
  *     def __cinit__(self, bytes name=None):             # <<<<<<<<<<<<<<
@@ -16403,7 +16403,7 @@ static int __pyx_pf_5_cdec_6Scorer___cinit__(struct __pyx_obj_5_cdec_Scorer *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":126
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":126
  * 
  *     def __cinit__(self, bytes name=None):
  *         if name:             # <<<<<<<<<<<<<<
@@ -16413,7 +16413,7 @@ static int __pyx_pf_5_cdec_6Scorer___cinit__(struct __pyx_obj_5_cdec_Scorer *__p
   __pyx_t_1 = (((PyObject *)__pyx_v_name) != Py_None) && (PyBytes_GET_SIZE(((PyObject *)__pyx_v_name)) != 0);
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":127
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":127
  *     def __cinit__(self, bytes name=None):
  *         if name:
  *             self.name = new string(name)             # <<<<<<<<<<<<<<
@@ -16429,7 +16429,7 @@ static int __pyx_pf_5_cdec_6Scorer___cinit__(struct __pyx_obj_5_cdec_Scorer *__p
     }
     __pyx_v_self->name = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":128
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":128
  *         if name:
  *             self.name = new string(name)
  *             self.metric = mteval.MetricInstance(self.name[0])             # <<<<<<<<<<<<<<
@@ -16460,7 +16460,7 @@ static void __pyx_pw_5_cdec_6Scorer_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":130
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":130
  *             self.metric = mteval.MetricInstance(self.name[0])
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -16472,7 +16472,7 @@ static void __pyx_pf_5_cdec_6Scorer_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":131
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":131
  * 
  *     def __dealloc__(self):
  *         del self.name             # <<<<<<<<<<<<<<
@@ -16531,7 +16531,7 @@ static PyObject *__pyx_pw_5_cdec_6Scorer_5__call__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":133
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":133
  *         del self.name
  * 
  *     def __call__(self, refs):             # <<<<<<<<<<<<<<
@@ -16562,7 +16562,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   __Pyx_RefNannySetupContext("__call__", 0);
   __Pyx_INCREF(__pyx_v_refs);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":134
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":134
  * 
  *     def __call__(self, refs):
  *         if isinstance(refs, basestring):             # <<<<<<<<<<<<<<
@@ -16572,7 +16572,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   __pyx_t_1 = PyObject_IsInstance(__pyx_v_refs, __pyx_builtin_basestring); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":135
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":135
  *     def __call__(self, refs):
  *         if isinstance(refs, basestring):
  *             refs = [refs]             # <<<<<<<<<<<<<<
@@ -16591,7 +16591,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   }
   __pyx_L3:;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":136
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":136
  *         if isinstance(refs, basestring):
  *             refs = [refs]
  *         cdef vector[vector[WordID]]* refsv = new vector[vector[WordID]]()             # <<<<<<<<<<<<<<
@@ -16606,7 +16606,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   }
   __pyx_v_refsv = __pyx_t_3;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":138
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":138
  *         cdef vector[vector[WordID]]* refsv = new vector[vector[WordID]]()
  *         cdef vector[WordID]* refv
  *         for ref in refs:             # <<<<<<<<<<<<<<
@@ -16651,7 +16651,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
     __pyx_v_ref = __pyx_t_6;
     __pyx_t_6 = 0;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":139
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":139
  *         cdef vector[WordID]* refv
  *         for ref in refs:
  *             refv = new vector[WordID]()             # <<<<<<<<<<<<<<
@@ -16666,7 +16666,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
     }
     __pyx_v_refv = __pyx_t_7;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":140
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":140
  *         for ref in refs:
  *             refv = new vector[WordID]()
  *             ConvertSentence(as_str(ref.strip()), refv)             # <<<<<<<<<<<<<<
@@ -16685,7 +16685,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     TD::ConvertSentence(__pyx_t_9, __pyx_v_refv);
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":141
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":141
  *             refv = new vector[WordID]()
  *             ConvertSentence(as_str(ref.strip()), refv)
  *             refsv.push_back(refv[0])             # <<<<<<<<<<<<<<
@@ -16694,7 +16694,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
  */
     __pyx_v_refsv->push_back((__pyx_v_refv[0]));
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":142
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":142
  *             ConvertSentence(as_str(ref.strip()), refv)
  *             refsv.push_back(refv[0])
  *             del refv             # <<<<<<<<<<<<<<
@@ -16705,7 +16705,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   }
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":144
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":144
  *             del refv
  *         cdef unsigned i
  *         cdef SegmentEvaluator evaluator = SegmentEvaluator()             # <<<<<<<<<<<<<<
@@ -16717,7 +16717,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   __pyx_v_evaluator = ((struct __pyx_obj_5_cdec_SegmentEvaluator *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":145
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":145
  *         cdef unsigned i
  *         cdef SegmentEvaluator evaluator = SegmentEvaluator()
  *         evaluator.metric = self.metric             # <<<<<<<<<<<<<<
@@ -16727,7 +16727,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
   __pyx_t_10 = __pyx_v_self->metric;
   __pyx_v_evaluator->metric = __pyx_t_10;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":146
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":146
  *         cdef SegmentEvaluator evaluator = SegmentEvaluator()
  *         evaluator.metric = self.metric
  *         evaluator.scorer = new shared_ptr[mteval.SegmentEvaluator](             # <<<<<<<<<<<<<<
@@ -16736,7 +16736,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
  */
   __pyx_v_evaluator->scorer = new boost::shared_ptr<SegmentEvaluator>(__pyx_v_self->metric->CreateSegmentEvaluator((__pyx_v_refsv[0])));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":148
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":148
  *         evaluator.scorer = new shared_ptr[mteval.SegmentEvaluator](
  *                 self.metric.CreateSegmentEvaluator(refsv[0]))
  *         del refsv # in theory should not delete but store in SegmentEvaluator             # <<<<<<<<<<<<<<
@@ -16745,7 +16745,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_4__call__(struct __pyx_obj_5_cdec_Score
  */
   delete __pyx_v_refsv;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":149
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":149
  *                 self.metric.CreateSegmentEvaluator(refsv[0]))
  *         del refsv # in theory should not delete but store in SegmentEvaluator
  *         return evaluator             # <<<<<<<<<<<<<<
@@ -16785,7 +16785,7 @@ static PyObject *__pyx_pw_5_cdec_6Scorer_7__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":151
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":151
  *         return evaluator
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":152
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":152
  * 
  *     def __str__(self):
  *         return str(self.name.c_str())             # <<<<<<<<<<<<<<
@@ -16838,7 +16838,7 @@ static PyObject *__pyx_pf_5_cdec_6Scorer_6__str__(struct __pyx_obj_5_cdec_Scorer
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":154
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":154
  *         return str(self.name.c_str())
  * 
  * cdef float _compute_score(void* metric_, mteval.SufficientStats* stats):             # <<<<<<<<<<<<<<
@@ -16864,7 +16864,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
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   __Pyx_RefNannySetupContext("_compute_score", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":155
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":155
  * 
  * cdef float _compute_score(void* metric_, mteval.SufficientStats* stats):
  *     cdef Metric metric = <Metric> metric_             # <<<<<<<<<<<<<<
@@ -16874,7 +16874,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
   __Pyx_INCREF(((PyObject *)((struct __pyx_obj_5_cdec_Metric *)__pyx_v_metric_)));
   __pyx_v_metric = ((struct __pyx_obj_5_cdec_Metric *)__pyx_v_metric_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":156
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":156
  * cdef float _compute_score(void* metric_, mteval.SufficientStats* stats):
  *     cdef Metric metric = <Metric> metric_
  *     cdef list ss = []             # <<<<<<<<<<<<<<
@@ -16886,7 +16886,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
   __pyx_v_ss = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":158
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":158
  *     cdef list ss = []
  *     cdef unsigned i
  *     for i in range(stats.size()):             # <<<<<<<<<<<<<<
@@ -16897,7 +16897,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":159
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":159
  *     cdef unsigned i
  *     for i in range(stats.size()):
  *         ss.append(stats[0][i])             # <<<<<<<<<<<<<<
@@ -16910,7 +16910,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":160
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":160
  *     for i in range(stats.size()):
  *         ss.append(stats[0][i])
  *     return metric.score(ss)             # <<<<<<<<<<<<<<
@@ -16948,7 +16948,7 @@ static float __pyx_f_5_cdec__compute_score(void *__pyx_v_metric_, SufficientStat
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":162
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":162
  *     return metric.score(ss)
  * 
  * cdef void _compute_sufficient_stats(void* metric_,             # <<<<<<<<<<<<<<
@@ -16975,7 +16975,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("_compute_sufficient_stats", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":166
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":166
  *         vector[string]* refs,
  *         mteval.SufficientStats* out):
  *     cdef Metric metric = <Metric> metric_             # <<<<<<<<<<<<<<
@@ -16985,7 +16985,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   __Pyx_INCREF(((PyObject *)((struct __pyx_obj_5_cdec_Metric *)__pyx_v_metric_)));
   __pyx_v_metric = ((struct __pyx_obj_5_cdec_Metric *)__pyx_v_metric_);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":167
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":167
  *         mteval.SufficientStats* out):
  *     cdef Metric metric = <Metric> metric_
  *     cdef list refs_ = []             # <<<<<<<<<<<<<<
@@ -16997,7 +16997,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   __pyx_v_refs_ = ((PyObject*)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":169
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":169
  *     cdef list refs_ = []
  *     cdef unsigned i
  *     for i in range(refs.size()):             # <<<<<<<<<<<<<<
@@ -17008,7 +17008,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":170
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":170
  *     cdef unsigned i
  *     for i in range(refs.size()):
  *         refs_.append(str(refs[0][i].c_str()))             # <<<<<<<<<<<<<<
@@ -17029,7 +17029,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   }
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":171
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":171
  *     for i in range(refs.size()):
  *         refs_.append(str(refs[0][i].c_str()))
  *     cdef list ss = metric.evaluate(str(hyp.c_str()), refs_)             # <<<<<<<<<<<<<<
@@ -17064,7 +17064,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   __pyx_v_ss = ((PyObject*)__pyx_t_4);
   __pyx_t_4 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":172
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":172
  *         refs_.append(str(refs[0][i].c_str()))
  *     cdef list ss = metric.evaluate(str(hyp.c_str()), refs_)
  *     out.fields.resize(len(ss))             # <<<<<<<<<<<<<<
@@ -17078,7 +17078,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   __pyx_t_7 = PyList_GET_SIZE(((PyObject *)__pyx_v_ss)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_out->fields.resize(__pyx_t_7);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":173
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":173
  *     cdef list ss = metric.evaluate(str(hyp.c_str()), refs_)
  *     out.fields.resize(len(ss))
  *     for i in range(len(ss)):             # <<<<<<<<<<<<<<
@@ -17093,7 +17093,7 @@ static void __pyx_f_5_cdec__compute_sufficient_stats(void *__pyx_v_metric_, std:
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_7; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":174
+    /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":174
  *     out.fields.resize(len(ss))
  *     for i in range(len(ss)):
  *         out.fields[i] = ss[i]             # <<<<<<<<<<<<<<
@@ -17138,7 +17138,7 @@ static int __pyx_pw_5_cdec_6Metric_1__cinit__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":178
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":178
  * cdef class Metric:
  *     cdef Scorer scorer
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -17159,7 +17159,7 @@ static int __pyx_pf_5_cdec_6Metric___cinit__(struct __pyx_obj_5_cdec_Metric *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":179
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":179
  *     cdef Scorer scorer
  *     def __cinit__(self):
  *         self.scorer = Scorer()             # <<<<<<<<<<<<<<
@@ -17174,7 +17174,7 @@ static int __pyx_pf_5_cdec_6Metric___cinit__(struct __pyx_obj_5_cdec_Metric *__p
   __pyx_v_self->scorer = ((struct __pyx_obj_5_cdec_Scorer *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":180
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":180
  *     def __cinit__(self):
  *         self.scorer = Scorer()
  *         cdef bytes class_name = self.__class__.__name__             # <<<<<<<<<<<<<<
@@ -17190,7 +17190,7 @@ static int __pyx_pf_5_cdec_6Metric___cinit__(struct __pyx_obj_5_cdec_Metric *__p
   __pyx_v_class_name = ((PyObject*)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":181
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":181
  *         self.scorer = Scorer()
  *         cdef bytes class_name = self.__class__.__name__
  *         self.scorer.name = new string(class_name)             # <<<<<<<<<<<<<<
@@ -17206,7 +17206,7 @@ static int __pyx_pf_5_cdec_6Metric___cinit__(struct __pyx_obj_5_cdec_Metric *__p
   }
   __pyx_v_self->scorer->name = __pyx_t_4;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":182
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":182
  *         cdef bytes class_name = self.__class__.__name__
  *         self.scorer.name = new string(class_name)
  *         self.scorer.metric = mteval.PyMetricInstance(self.scorer.name[0],             # <<<<<<<<<<<<<<
@@ -17275,7 +17275,7 @@ static PyObject *__pyx_pw_5_cdec_6Metric_3__call__(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":185
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":185
  *                 <void*> self, _compute_sufficient_stats, _compute_score)
  * 
  *     def __call__(self, refs):             # <<<<<<<<<<<<<<
@@ -17293,7 +17293,7 @@ static PyObject *__pyx_pf_5_cdec_6Metric_2__call__(struct __pyx_obj_5_cdec_Metri
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__call__", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":186
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":186
  * 
  *     def __call__(self, refs):
  *         return self.scorer(refs)             # <<<<<<<<<<<<<<
@@ -17337,7 +17337,7 @@ static PyObject *__pyx_pw_5_cdec_6Metric_5score(PyObject *__pyx_v_stats, CYTHON_
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":188
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":188
  *         return self.scorer(refs)
  * 
  *     def score(SufficientStats stats):             # <<<<<<<<<<<<<<
@@ -17350,7 +17350,7 @@ static PyObject *__pyx_pf_5_cdec_6Metric_4score(CYTHON_UNUSED struct __pyx_obj_5
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("score", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":189
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":189
  * 
  *     def score(SufficientStats stats):
  *         return 0             # <<<<<<<<<<<<<<
@@ -17425,7 +17425,7 @@ static PyObject *__pyx_pw_5_cdec_6Metric_7evaluate(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":191
+/* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":191
  *         return 0
  * 
  *     def evaluate(self, hyp, refs):             # <<<<<<<<<<<<<<
@@ -17442,7 +17442,7 @@ static PyObject *__pyx_pf_5_cdec_6Metric_6evaluate(CYTHON_UNUSED struct __pyx_ob
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("evaluate", 0);
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":192
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":192
  * 
  *     def evaluate(self, hyp, refs):
  *         return []             # <<<<<<<<<<<<<<
@@ -28921,7 +28921,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_2);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/vectors.pxi":95
+  /* "/usr0/home/cdyer/cdec-merge/python/src/vectors.pxi":95
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for SparseVector')             # <<<<<<<<<<<<<<
@@ -28932,7 +28932,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_5);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":6
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -28943,7 +28943,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_6);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_6));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":226
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":226
  *                 trule = convert_rule(trule)
  *             elif not isinstance(trule, TRule):
  *                 raise ValueError('the grammar should contain TRule objects')             # <<<<<<<<<<<<<<
@@ -28953,7 +28953,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_14);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":244
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":244
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')             # <<<<<<<<<<<<<<
@@ -28964,7 +28964,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_19);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/hypergraph.pxi":281
+  /* "/usr0/home/cdyer/cdec-merge/python/src/hypergraph.pxi":281
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphNode')             # <<<<<<<<<<<<<<
@@ -28973,7 +28973,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_21);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_21));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":26
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":26
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
@@ -28984,7 +28984,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_24);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":39
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":39
  *     def __setitem__(self, int index, tuple arcs):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
@@ -28995,7 +28995,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_25);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":69
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":69
  *             for i in range(len(self)):
  *                 for label, weight, delta in self[i]:
  *                     yield '%d -> %d [label="%s"];' % (i, i+delta, label.replace('"', '\\"'))             # <<<<<<<<<<<<<<
@@ -29006,7 +29006,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_32);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_32));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":63
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":63
  *     def todot(self):
  *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():             # <<<<<<<<<<<<<<
@@ -29018,7 +29018,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
   __pyx_k_codeobj_36 = (PyObject*)__Pyx_PyCode_New(0, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_35, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_37, __pyx_n_s__lines, 63, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_36)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/lattice.pxi":72
+  /* "/usr0/home/cdyer/cdec-merge/python/src/lattice.pxi":72
  *             yield '%d [shape=doublecircle]' % len(self)
  *             yield '}'
  *         return '\n'.join(lines()).encode('utf8')             # <<<<<<<<<<<<<<
@@ -29029,7 +29029,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_40);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":50
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":50
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('sufficient stats vector index out of range')             # <<<<<<<<<<<<<<
@@ -29040,7 +29040,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_42);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":84
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":84
  *     def __getitem__(self,int k):
  *         if not 0 <= k < self.cs.size():
  *             raise IndexError('candidate set index out of range')             # <<<<<<<<<<<<<<
@@ -29073,7 +29073,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_51);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":5
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -29085,7 +29085,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
   __pyx_k_codeobj_56 = (PyObject*)__Pyx_PyCode_New(1, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_55, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_57, __pyx_n_s___phrase, 5, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_56)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":194
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":194
  *         return []
  * 
  * BLEU = Scorer('IBM_BLEU')             # <<<<<<<<<<<<<<
@@ -29096,7 +29096,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_58);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_58));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":195
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":195
  * 
  * BLEU = Scorer('IBM_BLEU')
  * QCRI = Scorer('QCRI_BLEU')             # <<<<<<<<<<<<<<
@@ -29107,7 +29107,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_59);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":196
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":196
  * BLEU = Scorer('IBM_BLEU')
  * QCRI = Scorer('QCRI_BLEU')
  * TER = Scorer('TER')             # <<<<<<<<<<<<<<
@@ -29118,7 +29118,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_60);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_60));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":197
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":197
  * QCRI = Scorer('QCRI_BLEU')
  * TER = Scorer('TER')
  * CER = Scorer('CER')             # <<<<<<<<<<<<<<
@@ -29128,7 +29128,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_k_tuple_61);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":198
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":198
  * TER = Scorer('TER')
  * CER = Scorer('CER')
  * SSK = Scorer('SSK')             # <<<<<<<<<<<<<<
@@ -29480,7 +29480,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   /*--- Execution code ---*/
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":3
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":3
  * cimport grammar
  * cimport cdec.sa._sa as _sa
  * import cdec.sa._sa as _sa             # <<<<<<<<<<<<<<
@@ -29498,7 +29498,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s___sa, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/grammar.pxi":5
+  /* "/usr0/home/cdyer/cdec-merge/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -29510,7 +29510,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s___phrase, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":194
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":194
  *         return []
  * 
  * BLEU = Scorer('IBM_BLEU')             # <<<<<<<<<<<<<<
@@ -29522,7 +29522,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s__BLEU, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":195
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":195
  * 
  * BLEU = Scorer('IBM_BLEU')
  * QCRI = Scorer('QCRI_BLEU')             # <<<<<<<<<<<<<<
@@ -29534,7 +29534,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s__QCRI, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":196
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":196
  * BLEU = Scorer('IBM_BLEU')
  * QCRI = Scorer('QCRI_BLEU')
  * TER = Scorer('TER')             # <<<<<<<<<<<<<<
@@ -29546,7 +29546,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s__TER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":197
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":197
  * QCRI = Scorer('QCRI_BLEU')
  * TER = Scorer('TER')
  * CER = Scorer('CER')             # <<<<<<<<<<<<<<
@@ -29557,7 +29557,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/jmflanig/tools/cdec-jflanig/python/src/mteval.pxi":198
+  /* "/usr0/home/cdyer/cdec-merge/python/src/mteval.pxi":198
  * TER = Scorer('TER')
  * CER = Scorer('CER')
  * SSK = Scorer('SSK')             # <<<<<<<<<<<<<<
diff --git a/python/src/sa/_sa.c b/python/src/sa/_sa.c
index 89445b45..80f5a440 100644
--- a/python/src/sa/_sa.c
+++ b/python/src/sa/_sa.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.1 on Mon Jan 28 14:28:01 2013 */
+/* Generated by Cython 0.16 on Tue Apr 23 15:15:58 2013 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -11,6 +11,7 @@
 #ifndef offsetof
 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
 #endif
+
 #if !defined(WIN32) && !defined(MS_WINDOWS)
   #ifndef __stdcall
     #define __stdcall
@@ -22,18 +23,22 @@
     #define __fastcall
   #endif
 #endif
+
 #ifndef DL_IMPORT
   #define DL_IMPORT(t) t
 #endif
 #ifndef DL_EXPORT
   #define DL_EXPORT(t) t
 #endif
+
 #ifndef PY_LONG_LONG
   #define PY_LONG_LONG LONG_LONG
 #endif
+
 #ifndef Py_HUGE_VAL
   #define Py_HUGE_VAL HUGE_VAL
 #endif
+
 #ifdef PYPY_VERSION
 #define CYTHON_COMPILING_IN_PYPY 1
 #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -41,25 +46,28 @@
 #define CYTHON_COMPILING_IN_PYPY 0
 #define CYTHON_COMPILING_IN_CPYTHON 1
 #endif
+
+#if CYTHON_COMPILING_IN_PYPY
+  #define __Pyx_PyCFunction_Call PyObject_Call
+#else
+  #define __Pyx_PyCFunction_Call PyCFunction_Call
+#endif
+
 #if PY_VERSION_HEX < 0x02050000
   typedef int Py_ssize_t;
   #define PY_SSIZE_T_MAX INT_MAX
   #define PY_SSIZE_T_MIN INT_MIN
   #define PY_FORMAT_SIZE_T ""
-  #define CYTHON_FORMAT_SSIZE_T ""
   #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
   #define PyInt_AsSsize_t(o)   __Pyx_PyInt_AsInt(o)
-  #define PyNumber_Index(o)    ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
-                                (PyErr_Format(PyExc_TypeError, \
-                                              "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
-                                 (PyObject*)0))
-  #define PyIndex_Check(o)     (PyNumber_Check(o) && !PyFloat_Check(o) && !PyComplex_Check(o))
+  #define PyNumber_Index(o)    PyNumber_Int(o)
+  #define PyIndex_Check(o)     PyNumber_Check(o)
   #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
   #define __PYX_BUILD_PY_SSIZE_T "i"
 #else
   #define __PYX_BUILD_PY_SSIZE_T "n"
-  #define CYTHON_FORMAT_SSIZE_T "z"
 #endif
+
 #if PY_VERSION_HEX < 0x02060000
   #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
   #define Py_TYPE(ob)   (((PyObject*)(ob))->ob_type)
@@ -67,6 +75,7 @@
   #define PyVarObject_HEAD_INIT(type, size) \
           PyObject_HEAD_INIT(type) size,
   #define PyType_Modified(t)
+
   typedef struct {
      void *buf;
      PyObject *obj;
@@ -80,6 +89,7 @@
      Py_ssize_t *suboffsets;
      void *internal;
   } Py_buffer;
+
   #define PyBUF_SIMPLE 0
   #define PyBUF_WRITABLE 0x0001
   #define PyBUF_FORMAT 0x0004
@@ -91,9 +101,11 @@
   #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
   #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
   #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+
   typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
   typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
 #endif
+
 #if PY_MAJOR_VERSION < 3
   #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -103,30 +115,31 @@
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
           PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
 #endif
+
 #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
   #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
 #endif
+
 #if PY_MAJOR_VERSION >= 3
   #define Py_TPFLAGS_CHECKTYPES 0
   #define Py_TPFLAGS_HAVE_INDEX 0
 #endif
+
 #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
   #define Py_TPFLAGS_HAVE_NEWBUFFER 0
 #endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
   #define CYTHON_PEP393_ENABLED 1
-  #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ? \
-                                              0 : _PyUnicode_Ready((PyObject *)(op)))
-  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
+  #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
   #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
-  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
 #else
   #define CYTHON_PEP393_ENABLED 0
-  #define __Pyx_PyUnicode_READY(op)       (0)
-  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
+  #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
   #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
-  #define __Pyx_PyUnicode_READ(k, d, i)   ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
 #endif
+
 #if PY_MAJOR_VERSION >= 3
   #define PyBaseString_Type            PyUnicode_Type
   #define PyStringObject               PyUnicodeObject
@@ -134,6 +147,7 @@
   #define PyString_Check               PyUnicode_Check
   #define PyString_CheckExact          PyUnicode_CheckExact
 #endif
+
 #if PY_VERSION_HEX < 0x02060000
   #define PyBytesObject                PyStringObject
   #define PyBytes_Type                 PyString_Type
@@ -152,6 +166,7 @@
   #define PyBytes_Concat               PyString_Concat
   #define PyBytes_ConcatAndDel         PyString_ConcatAndDel
 #endif
+
 #if PY_VERSION_HEX < 0x02060000
   #define PySet_Check(obj)             PyObject_TypeCheck(obj, &PySet_Type)
   #define PyFrozenSet_Check(obj)       PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -159,7 +174,9 @@
 #ifndef PySet_CheckExact
   #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
 #endif
+
 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
 #if PY_MAJOR_VERSION >= 3
   #define PyIntObject                  PyLongObject
   #define PyInt_Type                   PyLong_Type
@@ -176,9 +193,11 @@
   #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
   #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
 #endif
+
 #if PY_MAJOR_VERSION >= 3
   #define PyBoolObject                 PyLongObject
 #endif
+
 #if PY_VERSION_HEX < 0x03020000
   typedef long Py_hash_t;
   #define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -187,6 +206,7 @@
   #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
   #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
 #endif
+
 #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
   #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
   #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -205,9 +225,11 @@
         (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
             (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
 #endif
+
 #if PY_MAJOR_VERSION >= 3
   #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
 #endif
+
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),((char *)(n)))
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -217,6 +239,7 @@
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
   #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),(n))
 #endif
+
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_NAMESTR(n) ((char *)(n))
   #define __Pyx_DOCSTR(n)  ((char *)(n))
@@ -225,7 +248,6 @@
   #define __Pyx_DOCSTR(n)  (n)
 #endif
 
-
 #if PY_MAJOR_VERSION >= 3
   #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
   #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
@@ -307,11 +329,7 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
 static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
 
-#if CYTHON_COMPILING_IN_CPYTHON
 #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
 #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
 
 #ifdef __GNUC__
@@ -420,7 +438,7 @@ struct __pyx_t_3_sa__Trie_Node;
 struct __pyx_t_3_sa_match_node;
 struct __pyx_t_3_sa_Matching;
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":9
  * from libc.string cimport memset, strcpy
  * 
  * cdef struct _node:             # <<<<<<<<<<<<<<
@@ -434,7 +452,7 @@ struct __pyx_t_3_sa__node {
   int val;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":30
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":30
  * _init_lower_mask()
  * 
  * cdef struct _BitSet:             # <<<<<<<<<<<<<<
@@ -448,7 +466,7 @@ struct __pyx_t_3_sa__BitSet {
   int size;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":168
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":168
  *     return result
  * 
  * cdef struct _VEB:             # <<<<<<<<<<<<<<
@@ -465,7 +483,7 @@ struct __pyx_t_3_sa__VEB {
   void **bottom;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":10
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":10
  * cdef struct _Trie_Node    # forward decl
  * 
  * cdef struct _Trie_Edge:             # <<<<<<<<<<<<<<
@@ -479,7 +497,7 @@ struct __pyx_t_3_sa__Trie_Edge {
   struct __pyx_t_3_sa__Trie_Edge *smaller;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":8
  * from libc.string cimport memset, memcpy
  * 
  * cdef struct _Trie_Node    # forward decl             # <<<<<<<<<<<<<<
@@ -492,7 +510,7 @@ struct __pyx_t_3_sa__Trie_Node {
   int arr_len;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":76
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":76
  * 
  * # linked list structure for storing matches in BaselineRuleFactory
  * cdef struct match_node:             # <<<<<<<<<<<<<<
@@ -504,7 +522,7 @@ struct __pyx_t_3_sa_match_node {
   struct __pyx_t_3_sa_match_node *next;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":172
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":172
  * 
  * # struct used to encapsulate a single matching
  * cdef struct Matching:             # <<<<<<<<<<<<<<
@@ -519,7 +537,7 @@ struct __pyx_t_3_sa_Matching {
   int size;
 };
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":228
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":228
  * 
  * 
  * cdef class HieroCachingRuleFactory:             # <<<<<<<<<<<<<<
@@ -554,6 +572,7 @@ struct __pyx_obj_3_sa_HieroCachingRuleFactory {
   float by_slack_factor;
   PyObject *prev_norm_prefix;
   float extract_time;
+  float intersect_time;
   struct __pyx_obj_3_sa_SuffixArray *fsa;
   struct __pyx_obj_3_sa_DataArray *fda;
   struct __pyx_obj_3_sa_DataArray *eda;
@@ -577,7 +596,7 @@ struct __pyx_obj_3_sa_HieroCachingRuleFactory {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":118
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":118
  *             for arc in node for node in lattice)
  * 
  * def decode_sentence(lattice):             # <<<<<<<<<<<<<<
@@ -590,7 +609,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":187
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":187
  *         fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
  *         if self.word_alignments is not None:
  *             fields.append(' '.join('%d-%d' % a for a in self.alignments()))             # <<<<<<<<<<<<<<
@@ -607,7 +626,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_17_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1182
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1187
  *         # Online rule extraction and scoring
  *         if self.online:
  *             f_syms = tuple(word[0][0] for word in fwords)             # <<<<<<<<<<<<<<
@@ -624,7 +643,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_20_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":36
+/* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":36
  *         logger.info("LCP array completed")
  * 
  *     def compute_stats(self, int max_n):             # <<<<<<<<<<<<<<
@@ -655,7 +674,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":122
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":122
  * 
  * def encode_words(words):
  *     return tuple(sym_fromstring(word, True) for word in words)             # <<<<<<<<<<<<<<
@@ -672,7 +691,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_12_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":21
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":21
  * 
  *     def __str__(self):
  *         return ' '.join('%s=%s' % feat for feat in self)             # <<<<<<<<<<<<<<
@@ -706,7 +725,7 @@ struct __pyx_obj_3_sa_IntList {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":340
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":340
  * 
  * 
  * cdef class VEBIterator:             # <<<<<<<<<<<<<<
@@ -720,7 +739,7 @@ struct __pyx_obj_3_sa_VEBIterator {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":47
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":47
  * 
  * 
  * cdef class BiLex:             # <<<<<<<<<<<<<<
@@ -741,7 +760,7 @@ struct __pyx_obj_3_sa_BiLex {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":354
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":354
  * 
  * 
  * cdef class VEB:             # <<<<<<<<<<<<<<
@@ -755,7 +774,7 @@ struct __pyx_obj_3_sa_VEB {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":121
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":121
  *     return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)
  * 
  * def encode_words(words):             # <<<<<<<<<<<<<<
@@ -768,7 +787,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_11_encode_words {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":5
+/* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":5
  * as k most frequent n-grams"""
  * 
  * cdef class LCP:             # <<<<<<<<<<<<<<
@@ -782,7 +801,7 @@ struct __pyx_obj_3_sa_LCP {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":9
  * from libc.string cimport memset, strcpy
  * 
  * cdef class DataArray:             # <<<<<<<<<<<<<<
@@ -801,7 +820,7 @@ struct __pyx_obj_3_sa_DataArray {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":100
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":100
  * 
  * 
  * cdef class BitSetIterator:             # <<<<<<<<<<<<<<
@@ -815,7 +834,7 @@ struct __pyx_obj_3_sa_BitSetIterator {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2110
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2115
  *         f = Phrase(f_sym)
  *         e = Phrase(e_sym)
  *         a = tuple(self.alignment.link(i, j) for (i, j) in links)             # <<<<<<<<<<<<<<
@@ -833,7 +852,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_23_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":188
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":188
  * 
  * 
  * cdef class Precomputation:             # <<<<<<<<<<<<<<
@@ -854,7 +873,7 @@ struct __pyx_obj_3_sa_Precomputation {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":190
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":190
  *         return ' ||| '.join(fields)
  * 
  *     def alignments(self):             # <<<<<<<<<<<<<<
@@ -871,7 +890,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_18_alignments {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":125
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":125
  * 
  * def decode_words(syms):
  *     return tuple(sym_tostring(sym) for sym in syms)             # <<<<<<<<<<<<<<
@@ -886,7 +905,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_14_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":6
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":6
  * from libc.stdio cimport FILE, fclose, fopen
  * 
  * cdef class SuffixArray:             # <<<<<<<<<<<<<<
@@ -902,7 +921,7 @@ struct __pyx_obj_3_sa_SuffixArray {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":183
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":183
  *         return self.f.arity()
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -915,7 +934,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_16___str__ {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":7
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":7
  * cdef int INDEX_MASK = (1<<INDEX_SHIFT)-1
  * 
  * cdef class Alphabet:             # <<<<<<<<<<<<<<
@@ -951,7 +970,7 @@ struct __pyx_obj_3_sa_Rule {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":112
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":112
  * def make_lattice(words):
  *     word_ids = (sym_fromstring(word, True) for word in words)
  *     return tuple(((word, None, 1), ) for word in word_ids)             # <<<<<<<<<<<<<<
@@ -968,7 +987,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1879
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1884
  *     # Aggregate stats from a training instance
  *     # (Extract rules, update counts)
  *     def add_instance(self, f_words, e_words, alignment):             # <<<<<<<<<<<<<<
@@ -991,7 +1010,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_21_add_instance {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":74
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":74
  *     def read_bitext(self, char* filename, int side):
  *         with gzip_or_text(filename) as fp:
  *             data = (line.split(' ||| ')[side] for line in fp)             # <<<<<<<<<<<<<<
@@ -1008,7 +1027,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":84
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":84
  * # in the suffix array; if discontiguous, it is the set of
  * # actual locations (packed into an array)
  * cdef class PhraseLocation:             # <<<<<<<<<<<<<<
@@ -1027,7 +1046,7 @@ struct __pyx_obj_3_sa_PhraseLocation {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":141
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":141
  *         return self.syms[i]
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -1042,7 +1061,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_15___iter__ {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2049
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2054
  * 
  *     # Create a rule from source, target, non-terminals, and alignments
  *     def form_rule(self, f_i, e_i, f_span, e_span, nt, al):             # <<<<<<<<<<<<<<
@@ -1056,7 +1075,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_22_form_rule {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2115
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2120
  *     # Rule string from rule
  *     def fmt_rule(self, f, e, a):
  *         a_str = ' '.join('{0}-{1}'.format(*self.alignment.unlink(packed)) for packed in a)             # <<<<<<<<<<<<<<
@@ -1073,7 +1092,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_25_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2114
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2119
  * 
  *     # Rule string from rule
  *     def fmt_rule(self, f, e, a):             # <<<<<<<<<<<<<<
@@ -1087,7 +1106,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_24_fmt_rule {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":20
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":20
  *             yield (FD.word(self.names[i]), self.values[i])
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -1100,7 +1119,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_28___str__ {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":72
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":72
  *             self.read_text_data(fp)
  * 
  *     def read_bitext(self, char* filename, int side):             # <<<<<<<<<<<<<<
@@ -1114,7 +1133,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":124
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":124
  *     return tuple(sym_fromstring(word, True) for word in words)
  * 
  * def decode_words(syms):             # <<<<<<<<<<<<<<
@@ -1140,7 +1159,7 @@ struct __pyx_obj_3_sa_FeatureVector {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":114
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":114
  *     return tuple(((word, None, 1), ) for word in word_ids)
  * 
  * def decode_lattice(lattice):             # <<<<<<<<<<<<<<
@@ -1153,7 +1172,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":972
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":973
  *         return sorted(result);
  * 
  *     def input(self, fwords, meta):             # <<<<<<<<<<<<<<
@@ -1189,6 +1208,8 @@ struct __pyx_obj_3_sa___pyx_scope_struct_19_input {
   long __pyx_v_hit;
   int __pyx_v_i;
   PyObject *__pyx_v_input_match;
+  PyObject *__pyx_v_intersect_start_time;
+  PyObject *__pyx_v_intersect_stop_time;
   PyObject *__pyx_v_is_shadow_path;
   int __pyx_v_j;
   int __pyx_v_k;
@@ -1232,21 +1253,17 @@ struct __pyx_obj_3_sa___pyx_scope_struct_19_input {
   PyObject *__pyx_v_xnode;
   PyObject *__pyx_v_xroot;
   Py_ssize_t __pyx_t_0;
-  PyObject *__pyx_t_1;
-  Py_ssize_t __pyx_t_2;
-  int __pyx_t_3;
+  Py_ssize_t __pyx_t_1;
+  PyObject *__pyx_t_2;
+  PyObject *__pyx_t_3;
   PyObject *__pyx_t_4;
-  PyObject *__pyx_t_5;
-  int __pyx_t_6;
-  Py_ssize_t __pyx_t_7;
-  Py_ssize_t __pyx_t_8;
-  Py_ssize_t __pyx_t_9;
-  PyObject *(*__pyx_t_10)(PyObject *);
-  PyObject *(*__pyx_t_11)(PyObject *);
+  PyObject *(*__pyx_t_5)(PyObject *);
+  Py_ssize_t __pyx_t_6;
+  PyObject *(*__pyx_t_7)(PyObject *);
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":23
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":23
  *         return ' '.join('%s=%s' % feat for feat in self)
  * 
  * cdef class Scorer:             # <<<<<<<<<<<<<<
@@ -1260,7 +1277,7 @@ struct __pyx_obj_3_sa_Scorer {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":8
  * # May need to revisit if things get really tight, though.
  * 
  * cdef class Alignment:             # <<<<<<<<<<<<<<
@@ -1275,7 +1292,7 @@ struct __pyx_obj_3_sa_Alignment {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":118
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":118
  * # (entirely C-implemented) _BitSet struct.
  * # Very slow; use only for debugging
  * cdef class BitSet:             # <<<<<<<<<<<<<<
@@ -1288,7 +1305,7 @@ struct __pyx_obj_3_sa_BitSet {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":106
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":106
  * 
  * 
  * cdef class Sampler:             # <<<<<<<<<<<<<<
@@ -1302,7 +1319,7 @@ struct __pyx_obj_3_sa_Sampler {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/str_map.pxi":8
  *     char* stringmap_word(StrMap *vocab, int i)
  * 
  * cdef class StringMap:             # <<<<<<<<<<<<<<
@@ -1316,7 +1333,7 @@ struct __pyx_obj_3_sa_StringMap {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2161
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2166
  *     # (Used for EGivenFCoherent)
  *     # Return set of (fphrase, lex_i, lex_j)
  *     def get_f_phrases(self, f_words):             # <<<<<<<<<<<<<<
@@ -1333,7 +1350,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_26_get_f_phrases {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":46
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":46
  * cdef int EPSILON = sym_fromstring('*EPS*', True)
  * 
  * cdef class TrieNode:             # <<<<<<<<<<<<<<
@@ -1346,7 +1363,7 @@ struct __pyx_obj_3_sa_TrieNode {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":52
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":52
  *         self.children = {}
  * 
  * cdef class ExtendedTrieNode(TrieNode):             # <<<<<<<<<<<<<<
@@ -1361,7 +1378,7 @@ struct __pyx_obj_3_sa_ExtendedTrieNode {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":109
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":109
  *         trie_node_to_map(edge.node, result, prefix, include_zeros)
  * 
  * cdef class TrieMap:             # <<<<<<<<<<<<<<
@@ -1376,7 +1393,7 @@ struct __pyx_obj_3_sa_TrieMap {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":115
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":115
  * 
  * def decode_lattice(lattice):
  *     return tuple((sym_tostring(sym), weight, dist) for (sym, weight, dist) in arc             # <<<<<<<<<<<<<<
@@ -1403,7 +1420,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":110
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":110
  *     return sym_isvar(sym)
  * 
  * def make_lattice(words):             # <<<<<<<<<<<<<<
@@ -1434,7 +1451,7 @@ struct __pyx_obj_3_sa_Phrase {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":15
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":15
  *         self.values.append(value)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -1450,7 +1467,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_27___iter__ {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":81
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":81
  *         free(self.arr)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -1466,7 +1483,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct____iter__ {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":63
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":63
  * 
  * 
  * cdef class TrieTable:             # <<<<<<<<<<<<<<
@@ -1481,7 +1498,7 @@ struct __pyx_obj_3_sa_TrieTable {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":111
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":111
  * 
  * def make_lattice(words):
  *     word_ids = (sym_fromstring(word, True) for word in words)             # <<<<<<<<<<<<<<
@@ -1498,7 +1515,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr {
 };
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":119
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":119
  * 
  * def decode_sentence(lattice):
  *     return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)             # <<<<<<<<<<<<<<
@@ -1534,7 +1551,7 @@ struct __pyx_obj_3_sa_FloatList {
 
 
 
-/* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/str_map.pxi":8
  *     char* stringmap_word(StrMap *vocab, int i)
  * 
  * cdef class StringMap:             # <<<<<<<<<<<<<<
@@ -1549,7 +1566,7 @@ struct __pyx_vtabstruct_3_sa_StringMap {
 static struct __pyx_vtabstruct_3_sa_StringMap *__pyx_vtabptr_3_sa_StringMap;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":9
  * from libc.string cimport memset, strcpy
  * 
  * cdef class DataArray:             # <<<<<<<<<<<<<<
@@ -1564,7 +1581,7 @@ struct __pyx_vtabstruct_3_sa_DataArray {
 static struct __pyx_vtabstruct_3_sa_DataArray *__pyx_vtabptr_3_sa_DataArray;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":109
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":109
  *         trie_node_to_map(edge.node, result, prefix, include_zeros)
  * 
  * cdef class TrieMap:             # <<<<<<<<<<<<<<
@@ -1579,7 +1596,7 @@ struct __pyx_vtabstruct_3_sa_TrieMap {
 static struct __pyx_vtabstruct_3_sa_TrieMap *__pyx_vtabptr_3_sa_TrieMap;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":8
  * # May need to revisit if things get really tight, though.
  * 
  * cdef class Alignment:             # <<<<<<<<<<<<<<
@@ -1595,7 +1612,7 @@ struct __pyx_vtabstruct_3_sa_Alignment {
 static struct __pyx_vtabstruct_3_sa_Alignment *__pyx_vtabptr_3_sa_Alignment;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":47
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":47
  * 
  * 
  * cdef class BiLex:             # <<<<<<<<<<<<<<
@@ -1614,7 +1631,7 @@ struct __pyx_vtabstruct_3_sa_BiLex {
 static struct __pyx_vtabstruct_3_sa_BiLex *__pyx_vtabptr_3_sa_BiLex;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":9
  * from libc.string cimport memset, memcpy
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -1634,7 +1651,7 @@ struct __pyx_vtabstruct_3_sa_IntList {
 static struct __pyx_vtabstruct_3_sa_IntList *__pyx_vtabptr_3_sa_IntList;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":4
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":4
  * from libc.string cimport strsep, strcpy, strlen
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -1649,7 +1666,7 @@ struct __pyx_vtabstruct_3_sa_Phrase {
 static struct __pyx_vtabstruct_3_sa_Phrase *__pyx_vtabptr_3_sa_Phrase;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":84
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":84
  * # in the suffix array; if discontiguous, it is the set of
  * # actual locations (packed into an array)
  * cdef class PhraseLocation:             # <<<<<<<<<<<<<<
@@ -1663,7 +1680,7 @@ struct __pyx_vtabstruct_3_sa_PhraseLocation {
 static struct __pyx_vtabstruct_3_sa_PhraseLocation *__pyx_vtabptr_3_sa_PhraseLocation;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":188
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":188
  * 
  * 
  * cdef class Precomputation:             # <<<<<<<<<<<<<<
@@ -1678,7 +1695,7 @@ struct __pyx_vtabstruct_3_sa_Precomputation {
 static struct __pyx_vtabstruct_3_sa_Precomputation *__pyx_vtabptr_3_sa_Precomputation;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":23
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":23
  *         return ' '.join('%s=%s' % feat for feat in self)
  * 
  * cdef class Scorer:             # <<<<<<<<<<<<<<
@@ -1692,7 +1709,7 @@ struct __pyx_vtabstruct_3_sa_Scorer {
 static struct __pyx_vtabstruct_3_sa_Scorer *__pyx_vtabptr_3_sa_Scorer;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/float_list.pxi":9
  * from libc.string cimport memset, strcpy, strlen
  * 
  * cdef class FloatList:             # <<<<<<<<<<<<<<
@@ -1708,7 +1725,7 @@ struct __pyx_vtabstruct_3_sa_FloatList {
 static struct __pyx_vtabstruct_3_sa_FloatList *__pyx_vtabptr_3_sa_FloatList;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":354
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":354
  * 
  * 
  * cdef class VEB:             # <<<<<<<<<<<<<<
@@ -1724,7 +1741,7 @@ struct __pyx_vtabstruct_3_sa_VEB {
 static struct __pyx_vtabstruct_3_sa_VEB *__pyx_vtabptr_3_sa_VEB;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":7
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":7
  * cdef int INDEX_MASK = (1<<INDEX_SHIFT)-1
  * 
  * cdef class Alphabet:             # <<<<<<<<<<<<<<
@@ -1747,7 +1764,7 @@ struct __pyx_vtabstruct_3_sa_Alphabet {
 static struct __pyx_vtabstruct_3_sa_Alphabet *__pyx_vtabptr_3_sa_Alphabet;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":228
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":228
  * 
  * 
  * cdef class HieroCachingRuleFactory:             # <<<<<<<<<<<<<<
@@ -1775,7 +1792,7 @@ struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory {
 static struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *__pyx_vtabptr_3_sa_HieroCachingRuleFactory;
 
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":6
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":6
  * from libc.stdio cimport FILE, fclose, fopen
  * 
  * cdef class SuffixArray:             # <<<<<<<<<<<<<<
@@ -1906,18 +1923,11 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, Py_ssize_t
                                    Py_ssize_t end, int direction)
 {
     if (unlikely(PyTuple_Check(substr))) {
-        Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
-        for (i = 0; i < count; i++) {
-            int result;
-#if CYTHON_COMPILING_IN_CPYTHON
+        int result;
+        Py_ssize_t i;
+        for (i = 0; i < PyTuple_GET_SIZE(substr); i++) {
             result = __Pyx_PyBytes_SingleTailmatch(self, PyTuple_GET_ITEM(substr, i),
                                                    start, end, direction);
-#else
-            PyObject* sub = PySequence_GetItem(substr, i);
-            if (unlikely(!sub)) return -1;
-            result = __Pyx_PyBytes_SingleTailmatch(self, sub, start, end, direction);
-            Py_DECREF(sub);
-#endif
             if (result) {
                 return result;
             }
@@ -1956,47 +1966,42 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
                                                     __Pyx_GetItemInt_List_Fast(o, i) : \
                                                     __Pyx_GetItemInt_Generic(o, to_py_func(i)))
 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
-    if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
-        PyObject *r = PyList_GET_ITEM(o, i);
-        Py_INCREF(r);
-        return r;
-    }
-    else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
-        PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
-        Py_INCREF(r);
-        return r;
+    if (likely(o != Py_None)) {
+        if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+            PyObject *r = PyList_GET_ITEM(o, i);
+            Py_INCREF(r);
+            return r;
+        }
+        else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+            PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+            Py_INCREF(r);
+            return r;
+        }
     }
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
-    return PySequence_GetItem(o, i);
-#endif
 }
 #define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
                                                     __Pyx_GetItemInt_Tuple_Fast(o, i) : \
                                                     __Pyx_GetItemInt_Generic(o, to_py_func(i)))
 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
-    if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
-        PyObject *r = PyTuple_GET_ITEM(o, i);
-        Py_INCREF(r);
-        return r;
-    }
-    else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
-        PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
-        Py_INCREF(r);
-        return r;
+    if (likely(o != Py_None)) {
+        if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+            PyObject *r = PyTuple_GET_ITEM(o, i);
+            Py_INCREF(r);
+            return r;
+        }
+        else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+            PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+            Py_INCREF(r);
+            return r;
+        }
     }
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
-    return PySequence_GetItem(o, i);
-#endif
 }
 #define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
                                                     __Pyx_GetItemInt_Fast(o, i) : \
                                                     __Pyx_GetItemInt_Generic(o, to_py_func(i)))
 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
     if (PyList_CheckExact(o)) {
         Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
         if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -2012,36 +2017,30 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
             Py_INCREF(r);
             return r;
         }
-    } else {  /* inlined PySequence_GetItem() */
+    }
+    else if (likely(i >= 0)) {
         PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
         if (likely(m && m->sq_item)) {
-            if (unlikely(i < 0) && likely(m->sq_length)) {
-                Py_ssize_t l = m->sq_length(o);
-                if (unlikely(l < 0)) return NULL;
-                i += l;
-            }
             return m->sq_item(o, i);
         }
     }
-#else
-    if (PySequence_Check(o)) {
-        return PySequence_GetItem(o, i);
-    }
-#endif
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
 }
 
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
-    int result = PySequence_Contains(seq, item);
-    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+    return unlikely(b < 0) ? b : !b;
+}
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+    return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
 }
 
 static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
     if (likely(PyList_CheckExact(L))) {
-        if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+        if (PyList_Append(L, x) < 0) return NULL;
         Py_INCREF(Py_None);
         return Py_None; /* this is just to have an accurate signature */
-    } else {
+    }
+    else {
         PyObject *r, *m;
         m = __Pyx_GetAttrString(L, "append");
         if (!m) return NULL;
@@ -2059,11 +2058,9 @@ static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */
 
 static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */
 
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
 
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
 
 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
 
@@ -2078,7 +2075,6 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb
     return r;
 }
 static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
-#if CYTHON_COMPILING_IN_CPYTHON
     if (PyList_CheckExact(o)) {
         Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
         if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -2088,79 +2084,26 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje
             Py_DECREF(old);
             return 1;
         }
-    } else {  /* inlined PySequence_SetItem() */
+    }
+    else if (likely(i >= 0)) {
         PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
         if (likely(m && m->sq_ass_item)) {
-            if (unlikely(i < 0) && likely(m->sq_length)) {
-                Py_ssize_t l = m->sq_length(o);
-                if (unlikely(l < 0)) return -1;
-                i += l;
-            }
             return m->sq_ass_item(o, i, v);
         }
     }
-#else
-#if CYTHON_COMPILING_IN_PYPY
-    if (PySequence_Check(o) && !PyDict_Check(o)) {
-#else
-    if (PySequence_Check(o)) {
-#endif
-        return PySequence_SetItem(o, i, v);
-    }
-#endif
     return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
 }
 
 static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
-#if CYTHON_COMPILING_IN_PYPY
-#define __Pyx_PyObject_AsDouble(obj) \
-(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
- likely(PyInt_CheckExact(obj)) ? \
- PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
-#else
 #define __Pyx_PyObject_AsDouble(obj) \
 ((likely(PyFloat_CheckExact(obj))) ? \
  PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-#endif
 
 static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
 
 static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
     const char *name, int exact); /*proto*/
 
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
-    PyListObject* L = (PyListObject*) list;
-    Py_ssize_t len = Py_SIZE(list);
-    if (likely(L->allocated > len)) {
-        Py_INCREF(x);
-        PyList_SET_ITEM(list, len, x);
-        Py_SIZE(list) = len+1;
-        return 0;
-    }
-    return PyList_Append(list, x);
-}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
-static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
-    int result = PyDict_Contains(dict, item);
-    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
-static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
-                                             int is_tuple, int has_known_size, int decref_tuple);
-
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
-                                                   Py_ssize_t* p_orig_length, int* p_is_dict);
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
-                                              PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
-
 #if PY_VERSION_HEX < 0x02050000
 #ifndef PyAnySet_CheckExact
 #define PyAnySet_CheckExact(ob) \
@@ -2194,9 +2137,15 @@ static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
 #endif /* PyAnySet_CheckExact (<= Py2.4) */
 #endif /* < Py2.5  */
 
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
 #if PY_MAJOR_VERSION >= 3
 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
     PyObject *value;
+    if (unlikely(d == Py_None)) {
+        __Pyx_RaiseNoneIndexingError();
+        return NULL;
+    }
     value = PyDict_GetItemWithError(d, key);
     if (unlikely(!value)) {
         if (!PyErr_Occurred())
@@ -2237,6 +2186,18 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level);
 
 static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
 
+#include <string.h>
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
 #define __Pyx_CyFunction_USED 1
 #include <structmember.h>
 #define __Pyx_CYFUNCTION_STATICMETHOD  0x01
@@ -2318,30 +2279,22 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
 
 #define __Pyx_Generator_USED
 #include <structmember.h>
-#include <frameobject.h>
 typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
 typedef struct {
     PyObject_HEAD
     __pyx_generator_body_t body;
     PyObject *closure;
+    int is_running;
+    int resume_label;
     PyObject *exc_type;
     PyObject *exc_value;
     PyObject *exc_traceback;
     PyObject *gi_weakreflist;
     PyObject *classobj;
-    PyObject *yieldfrom;
-    int resume_label;
-    char is_running;  // using T_BOOL for property below requires char value
 } __pyx_GeneratorObject;
 static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
                                                   PyObject *closure);
 static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
 
 static int __Pyx_check_binary_version(void);
 
@@ -2447,7 +2400,6 @@ static struct __pyx_obj_3_sa_StringMap *__pyx_v_3_sa_FD = 0;
 static char *__pyx_f_3_sa_sym_tostring(int); /*proto*/
 static int __pyx_f_3_sa_sym_isvar(int); /*proto*/
 static int __pyx_f_3_sa_sym_getindex(int); /*proto*/
-static float __pyx_f_3_sa_monitor_cpu(void); /*proto*/
 static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int); /*proto*/
 static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *); /*proto*/
 static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *, int); /*proto*/
@@ -2494,7 +2446,8 @@ static PyObject *__pyx_builtin_StopIteration;
 static PyObject *__pyx_builtin_cmp;
 static PyObject *__pyx_builtin_sorted;
 static PyObject *__pyx_builtin_max;
-static PyObject *__pyx_pf_3_sa_gzip_or_text(CYTHON_UNUSED PyObject *__pyx_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_monitor_cpu(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_2gzip_or_text(CYTHON_UNUSED PyObject *__pyx_self, char *__pyx_v_filename); /* proto */
 static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self, int __pyx_v_size, int __pyx_v_increment, int __pyx_v_initial_len); /* proto */
 static void __pyx_pf_3_sa_9FloatList_2__dealloc__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_9FloatList_4__getitem__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
@@ -2596,18 +2549,18 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
 static void __pyx_pf_3_sa_8Alphabet_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_8Alphabet_9terminals___get__(struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_8Alphabet_12nonterminals___get__(struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_2isvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_sym); /* proto */
+static PyObject *__pyx_pf_3_sa_4isvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_sym); /* proto */
 static PyObject *__pyx_pf_3_sa_12make_lattice_genexpr(PyObject *__pyx_self); /* proto */
 static PyObject *__pyx_pf_3_sa_12make_lattice_3genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_3_sa_4make_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words); /* proto */
+static PyObject *__pyx_pf_3_sa_6make_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words); /* proto */
 static PyObject *__pyx_pf_3_sa_14decode_lattice_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_3_sa_6decode_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
+static PyObject *__pyx_pf_3_sa_8decode_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
 static PyObject *__pyx_pf_3_sa_15decode_sentence_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_3_sa_8decode_sentence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
+static PyObject *__pyx_pf_3_sa_10decode_sentence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
 static PyObject *__pyx_pf_3_sa_12encode_words_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_3_sa_10encode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words); /* proto */
+static PyObject *__pyx_pf_3_sa_12encode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words); /* proto */
 static PyObject *__pyx_pf_3_sa_12decode_words_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_3_sa_12decode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_syms); /* proto */
+static PyObject *__pyx_pf_3_sa_14decode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_syms); /* proto */
 static int __pyx_pf_3_sa_6Phrase___cinit__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, PyObject *__pyx_v_words); /* proto */
 static void __pyx_pf_3_sa_6Phrase_2__dealloc__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self); /* proto */
@@ -2714,9 +2667,9 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_33dump_online_rules(str
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_35online_ctx_lookup(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_f, PyObject *__pyx_v_e); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_13get_f_phrases_extract(PyObject *__pyx_self, PyObject *__pyx_v_f_i, PyObject *__pyx_v_f_j, PyObject *__pyx_v_lex_i, PyObject *__pyx_v_lex_j, PyObject *__pyx_v_wc, PyObject *__pyx_v_ntc, PyObject *__pyx_v_syms); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_37get_f_phrases(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_f_words); /* proto */
-static PyObject *__pyx_pf_3_sa_14span_check(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
-static PyObject *__pyx_pf_3_sa_16span_inc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
-static PyObject *__pyx_pf_3_sa_18span_dec(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
+static PyObject *__pyx_pf_3_sa_16span_check(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
+static PyObject *__pyx_pf_3_sa_18span_inc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
+static PyObject *__pyx_pf_3_sa_20span_dec(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_vec, PyObject *__pyx_v_i, PyObject *__pyx_v_j); /* proto */
 static int __pyx_pf_3_sa_13FeatureVector___cinit__(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_13FeatureVector_2set(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self, unsigned int __pyx_v_name, float __pyx_v_value); /* proto */
 static PyObject *__pyx_pf_3_sa_13FeatureVector_4__iter__(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self); /* proto */
@@ -2813,26 +2766,27 @@ static char __pyx_k_121[] = "Keyword trie error";
 static char __pyx_k_123[] = "get_all_nodes_isteps_away";
 static char __pyx_k_124[] = "Total time for rule lookup, extraction, and scoring = %f seconds";
 static char __pyx_k_125[] = "    Extract time = %f seconds";
-static char __pyx_k_126[] = "No aligned terminals";
-static char __pyx_k_127[] = "Unaligned chunk";
-static char __pyx_k_128[] = "Gaps are not tight phrases";
-static char __pyx_k_129[] = "Inside edges of preceding subphrase are not tight";
-static char __pyx_k_130[] = "Inside edges of following subphrase are not tight";
-static char __pyx_k_131[] = "Subphrase [%d, %d] failed integrity check";
-static char __pyx_k_132[] = "Didn't extract anything from [%d, %d] -> [%d, %d]";
-static char __pyx_k_133[] = "Unable to extract basic phrase";
-static char __pyx_k_136[] = "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi";
-static char __pyx_k_137[] = "{0}-{1}";
-static char __pyx_k_138[] = "[X] ||| {0} ||| {1} ||| {2}";
-static char __pyx_k_139[] = "------------------------------";
-static char __pyx_k_141[] = "         Online Stats         ";
-static char __pyx_k_145[] = " : ";
-static char __pyx_k_151[] = "OnlineFeatureContext";
-static char __pyx_k_154[] = "%s=%s";
-static char __pyx_k_157[] = "/home/m/workspace/cdec/python/src/sa/_sa.pyx";
-static char __pyx_k_158[] = "cdec.sa";
-static char __pyx_k_162[] = "/home/m/workspace/cdec/python/src/sa/sym.pxi";
-static char __pyx_k_173[] = "*EPS*";
+static char __pyx_k_126[] = "    Intersect time = %f seconds";
+static char __pyx_k_127[] = "No aligned terminals";
+static char __pyx_k_128[] = "Unaligned chunk";
+static char __pyx_k_129[] = "Gaps are not tight phrases";
+static char __pyx_k_130[] = "Inside edges of preceding subphrase are not tight";
+static char __pyx_k_131[] = "Inside edges of following subphrase are not tight";
+static char __pyx_k_132[] = "Subphrase [%d, %d] failed integrity check";
+static char __pyx_k_133[] = "Didn't extract anything from [%d, %d] -> [%d, %d]";
+static char __pyx_k_134[] = "Unable to extract basic phrase";
+static char __pyx_k_137[] = "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi";
+static char __pyx_k_138[] = "{0}-{1}";
+static char __pyx_k_139[] = "[X] ||| {0} ||| {1} ||| {2}";
+static char __pyx_k_140[] = "------------------------------";
+static char __pyx_k_142[] = "         Online Stats         ";
+static char __pyx_k_146[] = " : ";
+static char __pyx_k_152[] = "OnlineFeatureContext";
+static char __pyx_k_155[] = "%s=%s";
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+static char __pyx_k_164[] = "/home/paulb/workspace/cdec/python/src/sa/sym.pxi";
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 static char __pyx_k__from_binary[] = "from_binary";
 static char __pyx_k__initial_len[] = "initial_len";
 static char __pyx_k__input_match[] = "input_match";
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 static char __pyx_k__next_states[] = "next_states";
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 static PyObject *__pyx_n_s__min_bound;
 static PyObject *__pyx_n_s__min_dist;
 static PyObject *__pyx_n_s__min_gap_size;
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+    __pyx_t_1 = PyObject_RichCompare(__pyx_v_j, __pyx_t_3, Py_GE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_1);
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-    /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":28
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":29
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-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":31
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":32
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":33
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-    /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":34
+    /* "/home/paulb/workspace/cdec/python/src/sa/float_list.pxi":34
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":35
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-    /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":36
+    /* "/home/paulb/workspace/cdec/python/src/sa/float_list.pxi":36
  *             j = self.len + i
  *         if j<0 or j>=self.len:
  *             raise IndexError("Requested index %d of %d-length FloatList" % (i, self.len))             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":37
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":39
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":40
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":42
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":43
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-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":45
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":46
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-    /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":47
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-    /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":48
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":49
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":50
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-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":52
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":53
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":54
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-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":56
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":58
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":59
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":60
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":62
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":63
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":64
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   fread((&__pyx_v_self->len), (sizeof(float)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":65
+  /* "/home/paulb/workspace/cdec/python/src/sa/float_list.pxi":65
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":66
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   __pyx_v_self->size = __pyx_v_self->len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":67
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":69
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  *     def read(self, char* filename):             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":71
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":72
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-  /* "/home/m/workspace/cdec/python/src/sa/float_list.pxi":73
+  /* "/home/paulb/workspace/cdec/python/src/sa/float_list.pxi":73
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   int __pyx_v_initial_len;
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@@ -4677,6 +4664,18 @@ static int __pyx_pw_3_sa_7IntList_1__cinit__(PyObject *__pyx_v_self, PyObject *_
       if (unlikely(kw_args > 0)) {
         if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
       }
+      if (values[0]) {
+      } else {
+        __pyx_v_size = ((int)0);
+      }
+      if (values[1]) {
+      } else {
+        __pyx_v_increment = ((int)1);
+      }
+      if (values[2]) {
+      } else {
+        __pyx_v_initial_len = ((int)0);
+      }
     } else {
       switch (PyTuple_GET_SIZE(__pyx_args)) {
         case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -4715,7 +4714,7 @@ static int __pyx_pw_3_sa_7IntList_1__cinit__(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":11
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":11
  * cdef class IntList:
  * 
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):             # <<<<<<<<<<<<<<
@@ -4729,7 +4728,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":12
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":12
  * 
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
  *         if initial_len > size:             # <<<<<<<<<<<<<<
@@ -4739,7 +4738,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
   __pyx_t_1 = (__pyx_v_initial_len > __pyx_v_size);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":13
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":13
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
  *         if initial_len > size:
  *             size = initial_len             # <<<<<<<<<<<<<<
@@ -4751,7 +4750,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":14
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":14
  *         if initial_len > size:
  *             size = initial_len
  *         self.size = size             # <<<<<<<<<<<<<<
@@ -4760,7 +4759,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
  */
   __pyx_v_self->size = __pyx_v_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":15
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":15
  *             size = initial_len
  *         self.size = size
  *         self.increment = increment             # <<<<<<<<<<<<<<
@@ -4769,7 +4768,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
  */
   __pyx_v_self->increment = __pyx_v_increment;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":16
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":16
  *         self.size = size
  *         self.increment = increment
  *         self.len = initial_len             # <<<<<<<<<<<<<<
@@ -4778,7 +4777,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
  */
   __pyx_v_self->len = __pyx_v_initial_len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":17
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":17
  *         self.increment = increment
  *         self.len = initial_len
  *         self.arr = <int*> malloc(size*sizeof(int))             # <<<<<<<<<<<<<<
@@ -4787,7 +4786,7 @@ static int __pyx_pf_3_sa_7IntList___cinit__(struct __pyx_obj_3_sa_IntList *__pyx
  */
   __pyx_v_self->arr = ((int *)malloc((__pyx_v_size * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":18
  *         self.len = initial_len
  *         self.arr = <int*> malloc(size*sizeof(int))
  *         memset(self.arr, 0, initial_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -4812,7 +4811,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_3__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":20
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":20
  *         memset(self.arr, 0, initial_len*sizeof(int))
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -4835,7 +4834,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":22
  *     def __str__(self):
  *         cdef unsigned i
  *         ret = "IntList["             # <<<<<<<<<<<<<<
@@ -4845,7 +4844,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_3));
   __pyx_v_ret = ((PyObject *)__pyx_kp_s_3);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":23
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":23
  *         cdef unsigned i
  *         ret = "IntList["
  *         for idx in range(self.size):             # <<<<<<<<<<<<<<
@@ -4856,7 +4855,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_idx = __pyx_t_2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":24
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":24
  *         ret = "IntList["
  *         for idx in range(self.size):
  *             if idx>0:             # <<<<<<<<<<<<<<
@@ -4866,7 +4865,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
     __pyx_t_3 = (__pyx_v_idx > 0);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":25
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":25
  *         for idx in range(self.size):
  *             if idx>0:
  *                 ret += ","             # <<<<<<<<<<<<<<
@@ -4882,7 +4881,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":26
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":26
  *             if idx>0:
  *                 ret += ","
  *             ret += str(self.arr[idx])             # <<<<<<<<<<<<<<
@@ -4907,7 +4906,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
     __pyx_t_5 = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":27
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":27
  *                 ret += ","
  *             ret += str(self.arr[idx])
  *         ret += "]"             # <<<<<<<<<<<<<<
@@ -4920,7 +4919,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   __pyx_v_ret = __pyx_t_5;
   __pyx_t_5 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":28
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":28
  *             ret += str(self.arr[idx])
  *         ret += "]"
  *         ret += "len="             # <<<<<<<<<<<<<<
@@ -4933,7 +4932,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   __pyx_v_ret = __pyx_t_5;
   __pyx_t_5 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":29
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":29
  *         ret += "]"
  *         ret += "len="
  *         ret += str(self.len)             # <<<<<<<<<<<<<<
@@ -4957,7 +4956,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_2__str__(struct __pyx_obj_3_sa_IntList *
   __pyx_v_ret = __pyx_t_4;
   __pyx_t_4 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":30
  *         ret += "len="
  *         ret += str(self.len)
  *         return ret             # <<<<<<<<<<<<<<
@@ -4994,7 +4993,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_5index(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":32
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":32
  *         return ret
  * 
  *     def index(self, val):             # <<<<<<<<<<<<<<
@@ -5016,7 +5015,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_4index(struct __pyx_obj_3_sa_IntList *__
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("index", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":34
  *     def index(self, val):
  *         cdef unsigned i
  *         for i in range(self.len):             # <<<<<<<<<<<<<<
@@ -5027,7 +5026,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_4index(struct __pyx_obj_3_sa_IntList *__
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":35
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":35
  *         cdef unsigned i
  *         for i in range(self.len):
  *             if self.arr[i] == val:             # <<<<<<<<<<<<<<
@@ -5036,13 +5035,14 @@ static PyObject *__pyx_pf_3_sa_7IntList_4index(struct __pyx_obj_3_sa_IntList *__
  */
     __pyx_t_3 = PyInt_FromLong((__pyx_v_self->arr[__pyx_v_i])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
-    __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_val, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_val, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_4);
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":36
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":36
  *         for i in range(self.len):
  *             if self.arr[i] == val:
  *                 return i             # <<<<<<<<<<<<<<
@@ -5060,7 +5060,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_4index(struct __pyx_obj_3_sa_IntList *__
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":37
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":37
  *             if self.arr[i] == val:
  *                 return i
  *         return IndexError             # <<<<<<<<<<<<<<
@@ -5090,11 +5090,11 @@ static PyObject *__pyx_pw_3_sa_7IntList_7partition(PyObject *__pyx_v_self, PyObj
 static PyObject *__pyx_pw_3_sa_7IntList_7partition(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_start = 0;
   PyObject *__pyx_v_end = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("partition (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
     PyObject* values[2] = {0,0};
     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -5108,10 +5108,12 @@ static PyObject *__pyx_pw_3_sa_7IntList_7partition(PyObject *__pyx_v_self, PyObj
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("partition", 1, 2, 2, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
@@ -5141,7 +5143,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_7partition(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":39
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":39
  *         return IndexError
  * 
  *     def partition(self,start,end):             # <<<<<<<<<<<<<<
@@ -5167,7 +5169,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("partition", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":40
  * 
  *     def partition(self,start,end):
  *         pivot = self.arr[end]             # <<<<<<<<<<<<<<
@@ -5180,7 +5182,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
   __pyx_v_pivot = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":41
  *     def partition(self,start,end):
  *         pivot = self.arr[end]
  *         bottom = start-1             # <<<<<<<<<<<<<<
@@ -5192,7 +5194,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
   __pyx_v_bottom = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":42
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":42
  *         pivot = self.arr[end]
  *         bottom = start-1
  *         top = end             # <<<<<<<<<<<<<<
@@ -5202,7 +5204,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
   __Pyx_INCREF(__pyx_v_end);
   __pyx_v_top = __pyx_v_end;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":43
  *         bottom = start-1
  *         top = end
  *         done = 0             # <<<<<<<<<<<<<<
@@ -5211,7 +5213,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
  */
   __pyx_v_done = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":44
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":44
  *         top = end
  *         done = 0
  *         while not done:             # <<<<<<<<<<<<<<
@@ -5222,7 +5224,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
     __pyx_t_3 = (!__pyx_v_done);
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":45
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":45
  *         done = 0
  *         while not done:
  *             while not done:             # <<<<<<<<<<<<<<
@@ -5233,7 +5235,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
       __pyx_t_3 = (!__pyx_v_done);
       if (!__pyx_t_3) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":46
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":46
  *         while not done:
  *             while not done:
  *                 bottom += 1             # <<<<<<<<<<<<<<
@@ -5246,19 +5248,20 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
       __pyx_v_bottom = __pyx_t_2;
       __pyx_t_2 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":47
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":47
  *             while not done:
  *                 bottom += 1
  *                 if bottom == top:             # <<<<<<<<<<<<<<
  *                     done = 1
  *                     break
  */
-      __pyx_t_2 = PyObject_RichCompare(__pyx_v_bottom, __pyx_v_top, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_RichCompare(__pyx_v_bottom, __pyx_v_top, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_2);
       __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":48
+        /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":48
  *                 bottom += 1
  *                 if bottom == top:
  *                     done = 1             # <<<<<<<<<<<<<<
@@ -5267,7 +5270,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
  */
         __pyx_v_done = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":49
+        /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":49
  *                 if bottom == top:
  *                     done = 1
  *                     break             # <<<<<<<<<<<<<<
@@ -5279,7 +5282,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_6partition(struct __pyx_obj_3_sa_IntList
       }
       __pyx_L7:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":50
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":50
  *                     done = 1
  *                     break
  *                 if self.arr[bottom] > pivot:             # <<<<<<<<<<<<<<
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+      __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_v_pivot, Py_GT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":51
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":52
+        /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":52
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":53
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":53
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-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":54
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-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":55
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":56
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":57
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-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":58
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":59
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-        /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":60
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":61
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":62
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":64
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":65
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":66
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":67
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":68
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":70
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":72
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":73
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":75
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":79
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":83
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-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":84
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":86
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":88
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  *     def __getitem__(self, index):
  *         cdef int i, j, k
  *         if isinstance(index, int):             # <<<<<<<<<<<<<<
@@ -5969,7 +5977,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":89
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":89
  *         cdef int i, j, k
  *         if isinstance(index, int):
  *             j = index             # <<<<<<<<<<<<<<
@@ -5979,7 +5987,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_v_index); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_j = __pyx_t_3;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":90
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":90
  *         if isinstance(index, int):
  *             j = index
  *             if j < 0:             # <<<<<<<<<<<<<<
@@ -5989,7 +5997,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __pyx_t_2 = (__pyx_v_j < 0);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":91
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":91
  *             j = index
  *             if j < 0:
  *                 j = self.len + j             # <<<<<<<<<<<<<<
@@ -6001,7 +6009,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":92
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":92
  *             if j < 0:
  *                 j = self.len + j
  *             if j<0 or j>=self.len:             # <<<<<<<<<<<<<<
@@ -6017,7 +6025,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":93
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":93
  *                 j = self.len + j
  *             if j<0 or j>=self.len:
  *                 raise IndexError("Requested index %d of %d-length IntList" % (index, self.len))             # <<<<<<<<<<<<<<
@@ -6052,7 +6060,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":94
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":94
  *             if j<0 or j>=self.len:
  *                 raise IndexError("Requested index %d of %d-length IntList" % (index, self.len))
  *             return self.arr[j]             # <<<<<<<<<<<<<<
@@ -6068,7 +6076,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":95
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":95
  *                 raise IndexError("Requested index %d of %d-length IntList" % (index, self.len))
  *             return self.arr[j]
  *         elif isinstance(index, slice):             # <<<<<<<<<<<<<<
@@ -6081,7 +6089,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   if (__pyx_t_5) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":96
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":96
  *             return self.arr[j]
  *         elif isinstance(index, slice):
  *             i = index.start             # <<<<<<<<<<<<<<
@@ -6094,7 +6102,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
     __pyx_v_i = __pyx_t_3;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":97
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":97
  *         elif isinstance(index, slice):
  *             i = index.start
  *             j = index.stop             # <<<<<<<<<<<<<<
@@ -6107,7 +6115,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
     __pyx_v_j = __pyx_t_3;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":98
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":98
  *             i = index.start
  *             j = index.stop
  *             if i < 0:             # <<<<<<<<<<<<<<
@@ -6117,7 +6125,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __pyx_t_5 = (__pyx_v_i < 0);
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":99
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":99
  *             j = index.stop
  *             if i < 0:
  *                 i = self.len + i             # <<<<<<<<<<<<<<
@@ -6129,7 +6137,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     __pyx_L6:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":100
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":100
  *             if i < 0:
  *                 i = self.len + i
  *             if j < 0:             # <<<<<<<<<<<<<<
@@ -6139,7 +6147,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __pyx_t_5 = (__pyx_v_j < 0);
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":101
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":101
  *                 i = self.len + i
  *             if j < 0:
  *                 j = self.len + j             # <<<<<<<<<<<<<<
@@ -6151,7 +6159,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     __pyx_L7:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":102
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":102
  *             if j < 0:
  *                 j = self.len + j
  *             if i < 0 or i >= self.len or j < 0 or j > self.len:             # <<<<<<<<<<<<<<
@@ -6179,7 +6187,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":103
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":103
  *                 j = self.len + j
  *             if i < 0 or i >= self.len or j < 0 or j > self.len:
  *                 raise IndexError("Requested index %d:%d of %d-length IntList" % (index.start, index.stop, self.len))             # <<<<<<<<<<<<<<
@@ -6221,7 +6229,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     }
     __pyx_L8:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":104
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":104
  *             if i < 0 or i >= self.len or j < 0 or j > self.len:
  *                 raise IndexError("Requested index %d:%d of %d-length IntList" % (index.start, index.stop, self.len))
  *             result = ()             # <<<<<<<<<<<<<<
@@ -6231,7 +6239,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __Pyx_INCREF(((PyObject *)__pyx_empty_tuple));
     __pyx_v_result = __pyx_empty_tuple;
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":105
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":105
  *                 raise IndexError("Requested index %d:%d of %d-length IntList" % (index.start, index.stop, self.len))
  *             result = ()
  *             for k from i <= k < j:             # <<<<<<<<<<<<<<
@@ -6241,7 +6249,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
     __pyx_t_3 = __pyx_v_j;
     for (__pyx_v_k = __pyx_v_i; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":106
+      /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":106
  *             result = ()
  *             for k from i <= k < j:
  *                 result = result + (self.arr[k],)             # <<<<<<<<<<<<<<
@@ -6263,7 +6271,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
       __pyx_t_9 = 0;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":107
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":107
  *             for k from i <= k < j:
  *                 result = result + (self.arr[k],)
  *             return result             # <<<<<<<<<<<<<<
@@ -6278,7 +6286,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":109
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":109
  *             return result
  *         else:
  *             raise TypeError("Illegal key type %s for IntList" % type(index))             # <<<<<<<<<<<<<<
@@ -6317,7 +6325,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntL
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":111
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":111
  *             raise TypeError("Illegal key type %s for IntList" % type(index))
  * 
  *     cdef void set(self, int i, int val):             # <<<<<<<<<<<<<<
@@ -6339,7 +6347,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("set", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":112
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":112
  * 
  *     cdef void set(self, int i, int val):
  *         j = i             # <<<<<<<<<<<<<<
@@ -6348,7 +6356,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
  */
   __pyx_v_j = __pyx_v_i;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":113
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":113
  *     cdef void set(self, int i, int val):
  *         j = i
  *         if i<0:             # <<<<<<<<<<<<<<
@@ -6358,7 +6366,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
   __pyx_t_1 = (__pyx_v_i < 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":114
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":114
  *         j = i
  *         if i<0:
  *             j = self.len + i             # <<<<<<<<<<<<<<
@@ -6370,7 +6378,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":115
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":115
  *         if i<0:
  *             j = self.len + i
  *         if j<0 or j>=self.len:             # <<<<<<<<<<<<<<
@@ -6386,7 +6394,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":116
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":116
  *             j = self.len + i
  *         if j<0 or j>=self.len:
  *             raise IndexError("Requested index %d of %d-length IntList" % (i, self.len))             # <<<<<<<<<<<<<<
@@ -6423,7 +6431,7 @@ static void __pyx_f_3_sa_7IntList_set(struct __pyx_obj_3_sa_IntList *__pyx_v_sel
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":117
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":117
  *         if j<0 or j>=self.len:
  *             raise IndexError("Requested index %d of %d-length IntList" % (i, self.len))
  *         self.arr[j] = val             # <<<<<<<<<<<<<<
@@ -6453,7 +6461,7 @@ static int __pyx_pw_3_sa_7IntList_22__setitem__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":119
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":119
  *         self.arr[j] = val
  * 
  *     def __setitem__(self, i, val):             # <<<<<<<<<<<<<<
@@ -6471,7 +6479,7 @@ static int __pyx_pf_3_sa_7IntList_21__setitem__(struct __pyx_obj_3_sa_IntList *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__setitem__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":120
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":120
  * 
  *     def __setitem__(self, i, val):
  *         self.set(i, val)             # <<<<<<<<<<<<<<
@@ -6503,7 +6511,7 @@ static Py_ssize_t __pyx_pw_3_sa_7IntList_24__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":122
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":122
  *         self.set(i, val)
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -6516,7 +6524,7 @@ static Py_ssize_t __pyx_pf_3_sa_7IntList_23__len__(struct __pyx_obj_3_sa_IntList
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":123
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":123
  * 
  *     def __len__(self):
  *         return self.len             # <<<<<<<<<<<<<<
@@ -6543,7 +6551,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_26get_size(PyObject *__pyx_v_self, CYTHO
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":125
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":125
  *         return self.len
  * 
  *     def get_size(self):             # <<<<<<<<<<<<<<
@@ -6560,7 +6568,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_25get_size(struct __pyx_obj_3_sa_IntList
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("get_size", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":126
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":126
  * 
  *     def get_size(self):
  *         return self.size             # <<<<<<<<<<<<<<
@@ -6607,7 +6615,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_28append(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":128
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":128
  *         return self.size
  * 
  *     def append(self, int val):             # <<<<<<<<<<<<<<
@@ -6620,7 +6628,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_27append(struct __pyx_obj_3_sa_IntList *
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("append", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":129
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":129
  * 
  *     def append(self, int val):
  *         self._append(val)             # <<<<<<<<<<<<<<
@@ -6635,7 +6643,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_27append(struct __pyx_obj_3_sa_IntList *
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":131
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":131
  *         self._append(val)
  * 
  *     cdef void _append(self, int val):             # <<<<<<<<<<<<<<
@@ -6648,7 +6656,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("_append", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":132
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":132
  * 
  *     cdef void _append(self, int val):
  *         if self.len == self.size:             # <<<<<<<<<<<<<<
@@ -6658,7 +6666,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
   __pyx_t_1 = (__pyx_v_self->len == __pyx_v_self->size);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":133
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":133
  *     cdef void _append(self, int val):
  *         if self.len == self.size:
  *             self.size = self.size + self.increment             # <<<<<<<<<<<<<<
@@ -6667,7 +6675,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
  */
     __pyx_v_self->size = (__pyx_v_self->size + __pyx_v_self->increment);
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":134
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":134
  *         if self.len == self.size:
  *             self.size = self.size + self.increment
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))             # <<<<<<<<<<<<<<
@@ -6679,7 +6687,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":135
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":135
  *             self.size = self.size + self.increment
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         self.arr[self.len] = val             # <<<<<<<<<<<<<<
@@ -6688,7 +6696,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
  */
   (__pyx_v_self->arr[__pyx_v_self->len]) = __pyx_v_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":136
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":136
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         self.arr[self.len] = val
  *         self.len = self.len + 1             # <<<<<<<<<<<<<<
@@ -6711,7 +6719,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_30extend(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":138
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":138
  *         self.len = self.len + 1
  * 
  *     def extend(self, other):             # <<<<<<<<<<<<<<
@@ -6728,7 +6736,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_29extend(struct __pyx_obj_3_sa_IntList *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("extend", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":139
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":139
  * 
  *     def extend(self, other):
  *         self._extend(other)             # <<<<<<<<<<<<<<
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":141
+/* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":141
  *         self._extend(other)
  * 
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":142
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  * 
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":144
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":145
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  * 
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   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":146
+    /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":146
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     __pyx_v_self->size = (__pyx_v_self->len + __pyx_v_other_len);
 
-    /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":147
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":148
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":148
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":149
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":149
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":152
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   free(__pyx_v_self->arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":153
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":153
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":154
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":155
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":158
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   fwrite((&__pyx_v_self->len), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":159
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":159
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":164
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":165
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":167
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":168
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":169
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":169
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   fread((&__pyx_v_self->len), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":170
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":170
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":171
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":171
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":172
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-/* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":174
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":176
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":177
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":177
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-  /* "/home/m/workspace/cdec/python/src/sa/int_list.pxi":178
+  /* "/home/paulb/workspace/cdec/python/src/sa/int_list.pxi":178
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":13
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-  /* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":14
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-/* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":16
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-  /* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":17
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":22
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-  /* "/home/m/workspace/cdec/python/src/sa/str_map.pxi":23
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   int __pyx_v_use_sent_id;
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":17
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":18
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  *     def __cinit__(self, from_binary=None, from_text=None, side=None, bint use_sent_id=False):
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@@ -7371,7 +7383,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_v_self->word2id = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":19
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":19
  *     def __cinit__(self, from_binary=None, from_text=None, side=None, bint use_sent_id=False):
  *         self.word2id = {"END_OF_FILE":0, "END_OF_LINE":1}
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]             # <<<<<<<<<<<<<<
@@ -7392,7 +7404,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_v_self->id2word = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":20
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":20
  *         self.word2id = {"END_OF_FILE":0, "END_OF_LINE":1}
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
  *         self.data = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -7407,7 +7419,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_v_self->data = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":21
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":21
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -7422,7 +7434,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_v_self->sent_id = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":22
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -7437,7 +7449,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_v_self->sent_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":23
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":23
  *         self.sent_id = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)
  *         self.use_sent_id = use_sent_id             # <<<<<<<<<<<<<<
@@ -7446,7 +7458,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
  */
   __pyx_v_self->use_sent_id = __pyx_v_use_sent_id;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":24
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":24
  *         self.sent_index = IntList(1000,1000)
  *         self.use_sent_id = use_sent_id
  *         if from_binary:             # <<<<<<<<<<<<<<
@@ -7456,7 +7468,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":25
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":25
  *         self.use_sent_id = use_sent_id
  *         if from_binary:
  *             self.read_binary(from_binary)             # <<<<<<<<<<<<<<
@@ -7478,7 +7490,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":26
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":26
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_text:             # <<<<<<<<<<<<<<
@@ -7488,7 +7500,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_text); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":27
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":27
  *             self.read_binary(from_binary)
  *         elif from_text:
  *             if side:             # <<<<<<<<<<<<<<
@@ -7498,7 +7510,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
     __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_side); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":28
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":28
  *         elif from_text:
  *             if side:
  *                 self.read_bitext(from_text, (0 if side == 'source' else 1))             # <<<<<<<<<<<<<<
@@ -7507,9 +7519,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
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       __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__read_bitext); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_4);
-      __pyx_t_3 = PyObject_RichCompare(__pyx_v_side, ((PyObject *)__pyx_n_s__source), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+      __pyx_t_2 = __Pyx_PyString_Equals(__pyx_v_side, ((PyObject *)__pyx_n_s__source), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       if (__pyx_t_2) {
         __pyx_t_5 = 0;
       } else {
@@ -7534,7 +7544,7 @@ static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *_
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":30
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":30
  *                 self.read_bitext(from_text, (0 if side == 'source' else 1))
  *             else:
  *                 self.read_text(from_text)             # <<<<<<<<<<<<<<
@@ -7583,7 +7593,7 @@ static Py_ssize_t __pyx_pw_3_sa_9DataArray_3__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":32
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":32
  *                 self.read_text(from_text)
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -7601,7 +7611,7 @@ static Py_ssize_t __pyx_pf_3_sa_9DataArray_2__len__(struct __pyx_obj_3_sa_DataAr
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   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":33
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":33
  * 
  *     def __len__(self):
  *         return len(self.data)             # <<<<<<<<<<<<<<
@@ -7637,7 +7647,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_5get_sentence_id(PyObject *__pyx_v_sel
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":35
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":35
  *         return len(self.data)
  * 
  *     def get_sentence_id(self, i):             # <<<<<<<<<<<<<<
@@ -7655,7 +7665,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_4get_sentence_id(struct __pyx_obj_3_sa
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   __Pyx_RefNannySetupContext("get_sentence_id", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":36
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":36
  * 
  *     def get_sentence_id(self, i):
  *         return self.sent_id.arr[i]             # <<<<<<<<<<<<<<
@@ -7693,7 +7703,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_7get_sentence(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":38
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":38
  *         return self.sent_id.arr[i]
  * 
  *     def get_sentence(self, i):             # <<<<<<<<<<<<<<
@@ -7718,7 +7728,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
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   __Pyx_INCREF(__pyx_v_i);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":40
  *     def get_sentence(self, i):
  *         cdef int j, start, stop
  *         sent = []             # <<<<<<<<<<<<<<
@@ -7730,7 +7740,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
   __pyx_v_sent = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":41
  *         cdef int j, start, stop
  *         sent = []
  *         start = self.sent_index.arr[i]             # <<<<<<<<<<<<<<
@@ -7740,7 +7750,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
   __pyx_t_2 = __Pyx_PyIndex_AsSsize_t(__pyx_v_i); if (unlikely((__pyx_t_2 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_start = (__pyx_v_self->sent_index->arr[__pyx_t_2]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":42
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":42
  *         sent = []
  *         start = self.sent_index.arr[i]
  *         stop = self.sent_index.arr[i+1]             # <<<<<<<<<<<<<<
@@ -7753,7 +7763,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_v_stop = (__pyx_v_self->sent_index->arr[__pyx_t_2]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":43
  *         start = self.sent_index.arr[i]
  *         stop = self.sent_index.arr[i+1]
  *         for i from start <= i < stop:             # <<<<<<<<<<<<<<
@@ -7768,7 +7778,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
     __pyx_v_i = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":44
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":44
  *         stop = self.sent_index.arr[i+1]
  *         for i from start <= i < stop:
  *             sent.append(self.id2word[self.data.arr[i]])             # <<<<<<<<<<<<<<
@@ -7783,7 +7793,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
     __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_i); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":43
  *         start = self.sent_index.arr[i]
  *         stop = self.sent_index.arr[i+1]
  *         for i from start <= i < stop:             # <<<<<<<<<<<<<<
@@ -7796,7 +7806,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_Da
   __pyx_v_i = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":45
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":45
  *         for i from start <= i < stop:
  *             sent.append(self.id2word[self.data.arr[i]])
  *         return sent             # <<<<<<<<<<<<<<
@@ -7833,7 +7843,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_9get_id(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":47
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":47
  *         return sent
  * 
  *     def get_id(self, word):             # <<<<<<<<<<<<<<
@@ -7853,18 +7863,18 @@ static PyObject *__pyx_pf_3_sa_9DataArray_8get_id(struct __pyx_obj_3_sa_DataArra
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   __Pyx_RefNannySetupContext("get_id", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":48
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":48
  * 
  *     def get_id(self, word):
  *         if not word in self.word2id:             # <<<<<<<<<<<<<<
  *             self.word2id[word] = len(self.id2word)
  *             self.id2word.append(word)
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-  __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_word, __pyx_v_self->word2id, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->word2id, __pyx_v_word))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_t_2 = (!__pyx_t_1);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":49
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":49
  *     def get_id(self, word):
  *         if not word in self.word2id:
  *             self.word2id[word] = len(self.id2word)             # <<<<<<<<<<<<<<
@@ -7880,7 +7890,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_8get_id(struct __pyx_obj_3_sa_DataArra
     if (PyObject_SetItem(__pyx_v_self->word2id, __pyx_v_word, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":50
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":50
  *         if not word in self.word2id:
  *             self.word2id[word] = len(self.id2word)
  *             self.id2word.append(word)             # <<<<<<<<<<<<<<
@@ -7894,7 +7904,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_8get_id(struct __pyx_obj_3_sa_DataArra
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":51
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":51
  *             self.word2id[word] = len(self.id2word)
  *             self.id2word.append(word)
  *         return self.word2id[word]             # <<<<<<<<<<<<<<
@@ -7931,7 +7941,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_11__getitem__(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":53
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":53
  *         return self.word2id[word]
  * 
  *     def __getitem__(self, loc):             # <<<<<<<<<<<<<<
@@ -7949,7 +7959,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_10__getitem__(struct __pyx_obj_3_sa_Da
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   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":54
  * 
  *     def __getitem__(self, loc):
  *         return self.id2word[self.data.arr[loc]]             # <<<<<<<<<<<<<<
@@ -7987,7 +7997,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_13get_sentence_bounds(PyObject *__pyx_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":56
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":56
  *         return self.id2word[self.data.arr[loc]]
  * 
  *     def get_sentence_bounds(self, loc):             # <<<<<<<<<<<<<<
@@ -8008,7 +8018,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_12get_sentence_bounds(struct __pyx_obj
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   __Pyx_RefNannySetupContext("get_sentence_bounds", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":57
  * 
  *     def get_sentence_bounds(self, loc):
  *         cdef int sid = self.sent_id.arr[loc]             # <<<<<<<<<<<<<<
@@ -8018,7 +8028,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_12get_sentence_bounds(struct __pyx_obj
   __pyx_t_1 = __Pyx_PyIndex_AsSsize_t(__pyx_v_loc); if (unlikely((__pyx_t_1 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_sid = (__pyx_v_self->sent_id->arr[__pyx_t_1]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":58
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":58
  *     def get_sentence_bounds(self, loc):
  *         cdef int sid = self.sent_id.arr[loc]
  *         return (self.sent_index.arr[sid], self.sent_index.arr[sid+1])             # <<<<<<<<<<<<<<
@@ -8077,7 +8087,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_15write_text(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":60
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":60
  *         return (self.sent_index.arr[sid], self.sent_index.arr[sid+1])
  * 
  *     def write_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -8109,7 +8119,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_14write_text(struct __pyx_obj_3_sa_Dat
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("write_text", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":61
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":61
  * 
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       if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_6)) {
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-        #if CYTHON_COMPILING_IN_CPYTHON
-        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_5); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        #else
-        __pyx_t_5 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        #endif
+        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_5); __pyx_t_7++;
       } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_6)) {
         if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
-        #if CYTHON_COMPILING_IN_CPYTHON
-        __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_5); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        #else
-        __pyx_t_5 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        #endif
+        __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_5); __pyx_t_7++;
       } else {
         __pyx_t_5 = __pyx_t_8(__pyx_t_6);
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@@ -9186,7 +9167,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
       __pyx_v_word = __pyx_t_5;
       __pyx_t_5 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":82
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":82
  *             self.sent_index.append(word_count)
  *             for word in line.split():
  *                 self.data.append(self.get_id(word))             # <<<<<<<<<<<<<<
@@ -9209,7 +9190,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
       __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
       __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":83
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":83
  *             for word in line.split():
  *                 self.data.append(self.get_id(word))
  *                 if self.use_sent_id:             # <<<<<<<<<<<<<<
@@ -9218,7 +9199,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
  */
       if (__pyx_v_self->use_sent_id) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":84
+        /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":84
  *                 self.data.append(self.get_id(word))
  *                 if self.use_sent_id:
  *                     self.sent_id.append(line_num)             # <<<<<<<<<<<<<<
@@ -9232,7 +9213,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
       }
       __pyx_L7:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":85
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":85
  *                 if self.use_sent_id:
  *                     self.sent_id.append(line_num)
  *                 word_count = word_count + 1             # <<<<<<<<<<<<<<
@@ -9243,7 +9224,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
     }
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":86
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":86
  *                     self.sent_id.append(line_num)
  *                 word_count = word_count + 1
  *             self.data.append(1)             # <<<<<<<<<<<<<<
@@ -9254,7 +9235,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":87
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":87
  *                 word_count = word_count + 1
  *             self.data.append(1)
  *             if self.use_sent_id:             # <<<<<<<<<<<<<<
@@ -9263,7 +9244,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
  */
     if (__pyx_v_self->use_sent_id) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":88
+      /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":88
  *             self.data.append(1)
  *             if self.use_sent_id:
  *                 self.sent_id.append(line_num)             # <<<<<<<<<<<<<<
@@ -9277,7 +9258,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
     }
     __pyx_L8:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":89
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":89
  *             if self.use_sent_id:
  *                 self.sent_id.append(line_num)
  *             word_count = word_count + 1             # <<<<<<<<<<<<<<
@@ -9289,7 +9270,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":90
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":90
  *                 self.sent_id.append(line_num)
  *             word_count = word_count + 1
  *         self.data.append(0)             # <<<<<<<<<<<<<<
@@ -9300,7 +9281,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_20read_text_data(struct __pyx_obj_3_sa
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":91
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":91
  *             word_count = word_count + 1
  *         self.data.append(0)
  *         self.sent_index.append(word_count)             # <<<<<<<<<<<<<<
@@ -9355,7 +9336,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_23read_binary(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":94
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":94
  * 
  * 
  *     def read_binary(self, char* filename):             # <<<<<<<<<<<<<<
@@ -9369,7 +9350,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_22read_binary(struct __pyx_obj_3_sa_Da
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("read_binary", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":96
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":96
  *     def read_binary(self, char* filename):
  *         cdef FILE* f
  *         f = fopen(filename, "r")             # <<<<<<<<<<<<<<
@@ -9378,7 +9359,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_22read_binary(struct __pyx_obj_3_sa_Da
  */
   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":97
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":97
  *         cdef FILE* f
  *         f = fopen(filename, "r")
  *         self.read_handle(f)             # <<<<<<<<<<<<<<
@@ -9387,7 +9368,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_22read_binary(struct __pyx_obj_3_sa_Da
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   ((struct __pyx_vtabstruct_3_sa_DataArray *)__pyx_v_self->__pyx_vtab)->read_handle(__pyx_v_self, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":98
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":98
  *         f = fopen(filename, "r")
  *         self.read_handle(f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -9402,7 +9383,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_22read_binary(struct __pyx_obj_3_sa_Da
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":100
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":100
  *         fclose(f)
  * 
  *     cdef void read_handle(self, FILE* f):             # <<<<<<<<<<<<<<
@@ -9427,7 +9408,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
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   __Pyx_RefNannySetupContext("read_handle", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":105
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":105
  *         cdef char* word
  * 
  *         self.data.read_handle(f)             # <<<<<<<<<<<<<<
@@ -9436,7 +9417,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->data->__pyx_vtab)->read_handle(__pyx_v_self->data, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":106
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":106
  * 
  *         self.data.read_handle(f)
  *         self.sent_index.read_handle(f)             # <<<<<<<<<<<<<<
@@ -9445,7 +9426,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_index->__pyx_vtab)->read_handle(__pyx_v_self->sent_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":107
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":107
  *         self.data.read_handle(f)
  *         self.sent_index.read_handle(f)
  *         self.sent_id.read_handle(f)             # <<<<<<<<<<<<<<
@@ -9454,7 +9435,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_id->__pyx_vtab)->read_handle(__pyx_v_self->sent_id, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":108
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":108
  *         self.sent_index.read_handle(f)
  *         self.sent_id.read_handle(f)
  *         fread(&(num_words), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -9463,7 +9444,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
   fread((&__pyx_v_num_words), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":109
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":109
  *         self.sent_id.read_handle(f)
  *         fread(&(num_words), sizeof(int), 1, f)
  *         for i in range(num_words):             # <<<<<<<<<<<<<<
@@ -9474,7 +9455,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
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     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":110
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":110
  *         fread(&(num_words), sizeof(int), 1, f)
  *         for i in range(num_words):
  *             fread(&(word_len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -9483,7 +9464,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
     fread((&__pyx_v_word_len), (sizeof(int)), 1, __pyx_v_f);
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":111
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":111
  *         for i in range(num_words):
  *             fread(&(word_len), sizeof(int), 1, f)
  *             word = <char*> malloc (word_len * sizeof(char))             # <<<<<<<<<<<<<<
@@ -9492,7 +9473,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
     __pyx_v_word = ((char *)malloc((__pyx_v_word_len * (sizeof(char)))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":112
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":112
  *             fread(&(word_len), sizeof(int), 1, f)
  *             word = <char*> malloc (word_len * sizeof(char))
  *             fread(word, sizeof(char), word_len, f)             # <<<<<<<<<<<<<<
@@ -9501,7 +9482,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
  */
     fread(__pyx_v_word, (sizeof(char)), __pyx_v_word_len, __pyx_v_f);
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":113
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":113
  *             word = <char*> malloc (word_len * sizeof(char))
  *             fread(word, sizeof(char), word_len, f)
  *             self.word2id[word] = len(self.id2word)             # <<<<<<<<<<<<<<
@@ -9520,7 +9501,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
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     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":114
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":114
  *             fread(word, sizeof(char), word_len, f)
  *             self.word2id[word] = len(self.id2word)
  *             self.id2word.append(word)             # <<<<<<<<<<<<<<
@@ -9534,7 +9515,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
     __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
     __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":115
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":115
  *             self.word2id[word] = len(self.id2word)
  *             self.id2word.append(word)
  *             free(word)             # <<<<<<<<<<<<<<
@@ -9544,7 +9525,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
     free(__pyx_v_word);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":116
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":116
  *             self.id2word.append(word)
  *             free(word)
  *         if len(self.sent_id) == 0:             # <<<<<<<<<<<<<<
@@ -9558,7 +9539,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
   __pyx_t_6 = (__pyx_t_4 == 0);
   if (__pyx_t_6) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":117
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":117
  *             free(word)
  *         if len(self.sent_id) == 0:
  *             self.use_sent_id = False             # <<<<<<<<<<<<<<
@@ -9570,7 +9551,7 @@ static void __pyx_f_3_sa_9DataArray_read_handle(struct __pyx_obj_3_sa_DataArray
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":119
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":119
  *             self.use_sent_id = False
  *         else:
  *             self.use_sent_id = True             # <<<<<<<<<<<<<<
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   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":121
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":121
  *             self.use_sent_id = True
  * 
  *     cdef void write_handle(self, FILE* f):             # <<<<<<<<<<<<<<
@@ -9614,7 +9595,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
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   __Pyx_RefNannySetupContext("write_handle", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":125
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":125
  *         cdef int num_words
  * 
  *         self.data.write_handle(f)             # <<<<<<<<<<<<<<
@@ -9623,7 +9604,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->data->__pyx_vtab)->write_handle(__pyx_v_self->data, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":126
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":126
  * 
  *         self.data.write_handle(f)
  *         self.sent_index.write_handle(f)             # <<<<<<<<<<<<<<
@@ -9632,7 +9613,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_index->__pyx_vtab)->write_handle(__pyx_v_self->sent_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":127
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":127
  *         self.data.write_handle(f)
  *         self.sent_index.write_handle(f)
  *         self.sent_id.write_handle(f)             # <<<<<<<<<<<<<<
@@ -9641,7 +9622,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_id->__pyx_vtab)->write_handle(__pyx_v_self->sent_id, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":128
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":128
  *         self.sent_index.write_handle(f)
  *         self.sent_id.write_handle(f)
  *         num_words = len(self.id2word) - 2             # <<<<<<<<<<<<<<
@@ -9654,7 +9635,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_v_num_words = (__pyx_t_2 - 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":129
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":129
  *         self.sent_id.write_handle(f)
  *         num_words = len(self.id2word) - 2
  *         fwrite(&(num_words), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -9663,7 +9644,7 @@ static void __pyx_f_3_sa_9DataArray_write_handle(struct __pyx_obj_3_sa_DataArray
  */
   fwrite((&__pyx_v_num_words), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":130
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":130
  *         num_words = len(self.id2word) - 2
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":131
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":132
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":133
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 }
 
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":137
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":138
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":139
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":139
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":142
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":143
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":144
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":145
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":145
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":146
+    /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":146
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":147
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":147
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":148
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":148
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":149
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":150
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":150
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":151
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":151
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@@ -10149,7 +10090,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_26write_enhanced_handle(struct __pyx_o
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-    /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":152
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-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":153
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":155
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":155
  *         f.write("\n")
  * 
  *     def write_enhanced(self, char* filename):             # <<<<<<<<<<<<<<
@@ -10264,7 +10205,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_28write_enhanced(struct __pyx_obj_3_sa
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   __Pyx_RefNannySetupContext("write_enhanced", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":156
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":156
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -10303,7 +10244,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_28write_enhanced(struct __pyx_obj_3_sa
           __pyx_v_f = __pyx_t_4;
           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":157
+          /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":157
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:
  *             self.write_enhanced_handle(self, f)             # <<<<<<<<<<<<<<
@@ -10333,7 +10274,7 @@ static PyObject *__pyx_pf_3_sa_9DataArray_28write_enhanced(struct __pyx_obj_3_sa
         __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":156
+        /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":156
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -10439,7 +10380,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_7word2id_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":10
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":10
  * 
  * cdef class DataArray:
  *     cdef public word2id             # <<<<<<<<<<<<<<
@@ -10526,7 +10467,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_7id2word_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":11
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":11
  * cdef class DataArray:
  *     cdef public word2id
  *     cdef public id2word             # <<<<<<<<<<<<<<
@@ -10613,7 +10554,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_4data_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":12
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":12
  *     cdef public word2id
  *     cdef public id2word
  *     cdef public IntList data             # <<<<<<<<<<<<<<
@@ -10709,7 +10650,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_7sent_id_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":13
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":13
  *     cdef public id2word
  *     cdef public IntList data
  *     cdef public IntList sent_id             # <<<<<<<<<<<<<<
@@ -10805,7 +10746,7 @@ static PyObject *__pyx_pw_3_sa_9DataArray_10sent_index_1__get__(PyObject *__pyx_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":14
+/* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":14
  *     cdef public IntList data
  *     cdef public IntList sent_id
  *     cdef public IntList sent_index             # <<<<<<<<<<<<<<
@@ -10890,7 +10831,7 @@ static int __pyx_pf_3_sa_9DataArray_10sent_index_4__del__(struct __pyx_obj_3_sa_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":12
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":12
  *     cdef IntList sent_index
  * 
  *     cdef int link(self, int i, int j):             # <<<<<<<<<<<<<<
@@ -10903,7 +10844,7 @@ static int __pyx_f_3_sa_9Alignment_link(CYTHON_UNUSED struct __pyx_obj_3_sa_Alig
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   __Pyx_RefNannySetupContext("link", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":14
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":14
  *     cdef int link(self, int i, int j):
  *         """Integerizes an alignment link pair"""
  *         return i*65536 + j             # <<<<<<<<<<<<<<
@@ -10931,7 +10872,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_1unlink(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":16
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":16
  *         return i*65536 + j
  * 
  *     def unlink(self, link):             # <<<<<<<<<<<<<<
@@ -10950,7 +10891,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_unlink(CYTHON_UNUSED struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("unlink", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":18
  *     def unlink(self, link):
  *         """De-integerizes an alignment link pair"""
  *         return (link/65536, link%65536)             # <<<<<<<<<<<<<<
@@ -10988,7 +10929,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_unlink(CYTHON_UNUSED struct __pyx_obj_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":20
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":20
  *         return (link/65536, link%65536)
  * 
  *     cdef _unlink(self, int link, int* f, int* e):             # <<<<<<<<<<<<<<
@@ -11001,7 +10942,7 @@ static PyObject *__pyx_f_3_sa_9Alignment__unlink(CYTHON_UNUSED struct __pyx_obj_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("_unlink", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":21
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":21
  * 
  *     cdef _unlink(self, int link, int* f, int* e):
  *         f[0] = link/65536             # <<<<<<<<<<<<<<
@@ -11010,7 +10951,7 @@ static PyObject *__pyx_f_3_sa_9Alignment__unlink(CYTHON_UNUSED struct __pyx_obj_
  */
   (__pyx_v_f[0]) = __Pyx_div_long(__pyx_v_link, 65536);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":22
  *     cdef _unlink(self, int link, int* f, int* e):
  *         f[0] = link/65536
  *         e[0] = link%65536             # <<<<<<<<<<<<<<
@@ -11046,7 +10987,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_3get_sent_links(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":24
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":24
  *         e[0] = link%65536
  * 
  *     def get_sent_links(self, int sent_id):             # <<<<<<<<<<<<<<
@@ -11066,7 +11007,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("get_sent_links", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":28
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":28
  *         cdef int* arr
  *         cdef int arr_len
  *         sent_links = IntList()             # <<<<<<<<<<<<<<
@@ -11078,7 +11019,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
   __pyx_v_sent_links = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":29
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":29
  *         cdef int arr_len
  *         sent_links = IntList()
  *         arr = self._get_sent_links(sent_id, &arr_len)             # <<<<<<<<<<<<<<
@@ -11087,7 +11028,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
  */
   __pyx_v_arr = ((struct __pyx_vtabstruct_3_sa_Alignment *)__pyx_v_self->__pyx_vtab)->_get_sent_links(__pyx_v_self, __pyx_v_sent_id, (&__pyx_v_arr_len));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":30
  *         sent_links = IntList()
  *         arr = self._get_sent_links(sent_id, &arr_len)
  *         sent_links._extend_arr(arr, arr_len*2)             # <<<<<<<<<<<<<<
@@ -11096,7 +11037,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_sent_links->__pyx_vtab)->_extend_arr(__pyx_v_sent_links, __pyx_v_arr, (__pyx_v_arr_len * 2));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":31
  *         arr = self._get_sent_links(sent_id, &arr_len)
  *         sent_links._extend_arr(arr, arr_len*2)
  *         free(arr)             # <<<<<<<<<<<<<<
@@ -11105,7 +11046,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
  */
   free(__pyx_v_arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":32
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":32
  *         sent_links._extend_arr(arr, arr_len*2)
  *         free(arr)
  *         return sent_links             # <<<<<<<<<<<<<<
@@ -11130,7 +11071,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":34
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":34
  *         return sent_links
  * 
  *     cdef int* _get_sent_links(self, int sent_id, int* num_links):             # <<<<<<<<<<<<<<
@@ -11152,7 +11093,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
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   __Pyx_RefNannySetupContext("_get_sent_links", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":37
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":37
  *         cdef int* sent_links
  *         cdef int i, start, end
  *         start = self.sent_index.arr[sent_id]             # <<<<<<<<<<<<<<
@@ -11161,7 +11102,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
  */
   __pyx_v_start = (__pyx_v_self->sent_index->arr[__pyx_v_sent_id]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":38
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":38
  *         cdef int i, start, end
  *         start = self.sent_index.arr[sent_id]
  *         end = self.sent_index.arr[sent_id+1]             # <<<<<<<<<<<<<<
@@ -11170,7 +11111,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
  */
   __pyx_v_end = (__pyx_v_self->sent_index->arr[(__pyx_v_sent_id + 1)]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":39
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":39
  *         start = self.sent_index.arr[sent_id]
  *         end = self.sent_index.arr[sent_id+1]
  *         num_links[0] = end - start             # <<<<<<<<<<<<<<
@@ -11179,7 +11120,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
  */
   (__pyx_v_num_links[0]) = (__pyx_v_end - __pyx_v_start);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":40
  *         end = self.sent_index.arr[sent_id+1]
  *         num_links[0] = end - start
  *         sent_links = <int*> malloc(2*num_links[0]*sizeof(int))             # <<<<<<<<<<<<<<
@@ -11188,7 +11129,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
  */
   __pyx_v_sent_links = ((int *)malloc(((2 * (__pyx_v_num_links[0])) * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":41
  *         num_links[0] = end - start
  *         sent_links = <int*> malloc(2*num_links[0]*sizeof(int))
  *         for i from 0 <= i < num_links[0]:             # <<<<<<<<<<<<<<
@@ -11198,7 +11139,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
   __pyx_t_1 = (__pyx_v_num_links[0]);
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":42
+    /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":42
  *         sent_links = <int*> malloc(2*num_links[0]*sizeof(int))
  *         for i from 0 <= i < num_links[0]:
  *             self._unlink(self.links.arr[start + i], sent_links + (2*i), sent_links + (2*i) + 1)             # <<<<<<<<<<<<<<
@@ -11210,7 +11151,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":43
  *         for i from 0 <= i < num_links[0]:
  *             self._unlink(self.links.arr[start + i], sent_links + (2*i), sent_links + (2*i) + 1)
  *         return sent_links             # <<<<<<<<<<<<<<
@@ -11236,14 +11177,14 @@ static int __pyx_pw_3_sa_9Alignment_5__cinit__(PyObject *__pyx_v_self, PyObject
 static int __pyx_pw_3_sa_9Alignment_5__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_from_binary = 0;
   PyObject *__pyx_v_from_text = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_binary,&__pyx_n_s__from_text,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
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-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_binary,&__pyx_n_s__from_text,0};
     PyObject* values[2] = {0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":45
+    /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":45
  *         return sent_links
  * 
  *     def __cinit__(self, from_binary=None, from_text=None):             # <<<<<<<<<<<<<<
@@ -11313,7 +11254,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":46
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":46
  * 
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -11328,7 +11269,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_v_self->links = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":47
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":47
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -11343,7 +11284,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_v_self->sent_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":48
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":48
  *         self.links = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)
  *         if from_binary:             # <<<<<<<<<<<<<<
@@ -11353,7 +11294,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":49
+    /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":49
  *         self.sent_index = IntList(1000,1000)
  *         if from_binary:
  *             self.read_binary(from_binary)             # <<<<<<<<<<<<<<
@@ -11375,7 +11316,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":50
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":50
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_text:             # <<<<<<<<<<<<<<
@@ -11385,7 +11326,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_text); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":51
+    /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":51
  *             self.read_binary(from_binary)
  *         elif from_text:
  *             self.read_text(from_text)             # <<<<<<<<<<<<<<
@@ -11442,7 +11383,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_7read_text(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":53
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":53
  *             self.read_text(from_text)
  * 
  *     def read_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -11484,7 +11425,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("read_text", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":54
  * 
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -11524,7 +11465,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
           __pyx_v_f = __pyx_t_1;
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":55
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":55
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:
  *             for line in f:             # <<<<<<<<<<<<<<
@@ -11542,18 +11483,10 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
           for (;;) {
             if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_1)) {
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #endif
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
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-              #endif
+              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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             __pyx_v_line = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":56
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":56
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@@ -11587,7 +11520,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
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             __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":57
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":57
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  *                 self.sent_index.append(len(self.links))
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             __pyx_v_pairs = __pyx_t_2;
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-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":58
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":58
  *                 self.sent_index.append(len(self.links))
  *                 pairs = line.split()
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-                #else
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-                #endif
+                __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
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-                #if CYTHON_COMPILING_IN_CPYTHON
-                __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-                #else
-                __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-                #endif
+                __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
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@@ -11648,7 +11573,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
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-              /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":59
+              /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":59
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-                  {__pyx_filename = __pyx_f[4]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-                #if CYTHON_COMPILING_IN_CPYTHON
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+                    else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                    {__pyx_filename = __pyx_f[4]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                  }
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-                #endif
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-              {
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-                __pyx_t_15 = NULL;
-                if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+                if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+                if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
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               __pyx_t_13 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":60
+              /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":60
  *                 for pair in pairs:
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":61
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":61
  *                     (i, j) = map(int, pair.split('-'))
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  *             self.sent_index.append(len(self.links))             # <<<<<<<<<<<<<<
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         __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":54
+        /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":54
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":63
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":63
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":65
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":65
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":66
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":66
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  *         self.links.read_handle(f)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":67
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":67
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   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_index->__pyx_vtab)->read_handle(__pyx_v_self->sent_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":68
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":68
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  *         self.sent_index.read_handle(f)
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":70
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":70
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":71
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":72
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":72
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":73
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":73
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-              #endif
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-              #endif
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-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":74
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":74
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+              __pyx_t_10 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_GE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":75
+              /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":75
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-              /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":76
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             }
 
-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":77
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":77
  *                     f.write("\n")
  *                     sent_num = sent_num + 1
  *                 f.write("%d-%d " % self.unlink(link))             # <<<<<<<<<<<<<<
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           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":78
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":78
  *                     sent_num = sent_num + 1
  *                 f.write("%d-%d " % self.unlink(link))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -12225,7 +12136,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_10write_text(struct __pyx_obj_3_sa_Ali
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         __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":71
+        /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":71
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  *     def write_text(self, char* filename):
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@@ -12347,7 +12258,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_13write_binary(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":80
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":80
  *             f.write("\n")
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":82
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":82
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":83
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":83
  *         cdef FILE* f
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  *         self.links.write_handle(f)             # <<<<<<<<<<<<<<
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   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->links->__pyx_vtab)->write_handle(__pyx_v_self->links, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":84
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":84
  *         f = fopen(filename, "w")
  *         self.links.write_handle(f)
  *         self.sent_index.write_handle(f)             # <<<<<<<<<<<<<<
@@ -12388,7 +12299,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_12write_binary(struct __pyx_obj_3_sa_A
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":85
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":85
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  *         self.sent_index.write_handle(f)
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":87
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":87
  *         fclose(f)
  * 
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":88
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":88
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  *     def write_enhanced(self, char* filename):
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@@ -12497,7 +12408,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_14write_enhanced(struct __pyx_obj_3_sa
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":89
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":89
  *     def write_enhanced(self, char* filename):
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           __pyx_v_sent_num = 1;
 
-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":90
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":90
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@@ -12524,18 +12435,10 @@ static PyObject *__pyx_pf_3_sa_9Alignment_14write_enhanced(struct __pyx_obj_3_sa
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-              #endif
+              __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++;
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-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":91
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":91
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":92
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":92
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":93
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":93
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-              #endif
+              __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_4); __pyx_t_8++;
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@@ -12634,7 +12529,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_14write_enhanced(struct __pyx_obj_3_sa
             __pyx_v_i = __pyx_t_4;
             __pyx_t_4 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":94
+            /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":94
  *             f.write("\n")
  *             for i in self.sent_index:
  *                 f.write("%d " % i)             # <<<<<<<<<<<<<<
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-          /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":95
+          /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":95
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-        /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":88
+        /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":88
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@@ -12792,7 +12687,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_17alignment(PyObject *__pyx_v_self, Py
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":97
+/* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":97
  *             f.write("\n")
  * 
  *     def alignment(self, i):             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":100
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":100
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":101
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":101
  *         cdef int j, start, end
  *         result = []
  *         start = self.sent_index.arr[i]             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":102
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":102
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":103
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":103
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  *         for j from start <= j < end:             # <<<<<<<<<<<<<<
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-    /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":104
+    /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":104
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-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":105
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-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":15
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":17
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":18
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":19
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":19
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":20
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":20
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  *     n.bigger = NULL
  *     n.key = key             # <<<<<<<<<<<<<<
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   __pyx_v_n->key = __pyx_v_key;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":21
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":21
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  *     n.key = key
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   __pyx_v_n->val = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":22
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":25
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":26
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  * cdef del_node(_node* n):
  *     if n.smaller != NULL:             # <<<<<<<<<<<<<<
@@ -13014,7 +12909,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   __pyx_t_1 = (__pyx_v_n->smaller != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":27
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":27
  * cdef del_node(_node* n):
  *     if n.smaller != NULL:
  *         del_node(n.smaller)             # <<<<<<<<<<<<<<
@@ -13028,7 +12923,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":28
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":28
  *     if n.smaller != NULL:
  *         del_node(n.smaller)
  *     if n.bigger != NULL:             # <<<<<<<<<<<<<<
@@ -13038,7 +12933,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   __pyx_t_1 = (__pyx_v_n->bigger != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":29
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":29
  *         del_node(n.smaller)
  *     if n.bigger != NULL:
  *         del_node(n.bigger)             # <<<<<<<<<<<<<<
@@ -13052,7 +12947,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":30
  *     if n.bigger != NULL:
  *         del_node(n.bigger)
  *     free(n)             # <<<<<<<<<<<<<<
@@ -13073,7 +12968,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":32
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":32
  *     free(n)
  * 
  * cdef int* get_val(_node* n, int key):             # <<<<<<<<<<<<<<
@@ -13087,7 +12982,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("get_val", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":33
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":33
  * 
  * cdef int* get_val(_node* n, int key):
  *     if key == n.key:             # <<<<<<<<<<<<<<
@@ -13097,7 +12992,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   __pyx_t_1 = (__pyx_v_key == __pyx_v_n->key);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":34
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":34
  * cdef int* get_val(_node* n, int key):
  *     if key == n.key:
  *         return &n.val             # <<<<<<<<<<<<<<
@@ -13109,7 +13004,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":35
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":35
  *     if key == n.key:
  *         return &n.val
  *     elif key < n.key:             # <<<<<<<<<<<<<<
@@ -13119,7 +13014,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   __pyx_t_1 = (__pyx_v_key < __pyx_v_n->key);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":36
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":36
  *         return &n.val
  *     elif key < n.key:
  *         if n.smaller == NULL:             # <<<<<<<<<<<<<<
@@ -13129,7 +13024,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     __pyx_t_1 = (__pyx_v_n->smaller == NULL);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":37
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":37
  *     elif key < n.key:
  *         if n.smaller == NULL:
  *             n.smaller = new_node(key)             # <<<<<<<<<<<<<<
@@ -13138,7 +13033,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
  */
       __pyx_v_n->smaller = __pyx_f_3_sa_new_node(__pyx_v_key);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":38
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":38
  *         if n.smaller == NULL:
  *             n.smaller = new_node(key)
  *             return &(n.smaller.val)             # <<<<<<<<<<<<<<
@@ -13151,7 +13046,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":39
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":39
  *             n.smaller = new_node(key)
  *             return &(n.smaller.val)
  *         return get_val(n.smaller, key)             # <<<<<<<<<<<<<<
@@ -13164,7 +13059,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":41
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":41
  *         return get_val(n.smaller, key)
  *     else:
  *         if n.bigger == NULL:             # <<<<<<<<<<<<<<
@@ -13174,7 +13069,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     __pyx_t_1 = (__pyx_v_n->bigger == NULL);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":42
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":42
  *     else:
  *         if n.bigger == NULL:
  *             n.bigger = new_node(key)             # <<<<<<<<<<<<<<
@@ -13183,7 +13078,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
  */
       __pyx_v_n->bigger = __pyx_f_3_sa_new_node(__pyx_v_key);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":43
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":43
  *         if n.bigger == NULL:
  *             n.bigger = new_node(key)
  *             return &(n.bigger.val)             # <<<<<<<<<<<<<<
@@ -13196,7 +13091,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":44
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":44
  *             n.bigger = new_node(key)
  *             return &(n.bigger.val)
  *         return get_val(n.bigger, key)             # <<<<<<<<<<<<<<
@@ -13223,14 +13118,14 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
   PyObject *__pyx_v_earray = 0;
   PyObject *__pyx_v_fsarray = 0;
   PyObject *__pyx_v_alignment = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_text,&__pyx_n_s__from_data,&__pyx_n_s__from_binary,&__pyx_n_s__earray,&__pyx_n_s__fsarray,&__pyx_n_s__alignment,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_text,&__pyx_n_s__from_data,&__pyx_n_s__from_binary,&__pyx_n_s__earray,&__pyx_n_s__fsarray,&__pyx_n_s__alignment,0};
     PyObject* values[6] = {0,0,0,0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":54
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":54
  *     cdef id2eword, id2fword, eword2id, fword2id
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,             # <<<<<<<<<<<<<<
@@ -13241,7 +13136,7 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
     values[1] = __pyx_k_41;
     values[2] = ((PyObject *)Py_None);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":55
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":55
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,
  *             earray=None, fsarray=None, alignment=None):             # <<<<<<<<<<<<<<
@@ -13332,7 +13227,7 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":54
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":54
  *     cdef id2eword, id2fword, eword2id, fword2id
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,             # <<<<<<<<<<<<<<
@@ -13353,7 +13248,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":56
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":56
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,
  *             earray=None, fsarray=None, alignment=None):
  *         self.id2eword = []             # <<<<<<<<<<<<<<
@@ -13368,7 +13263,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->id2eword = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":57
  *             earray=None, fsarray=None, alignment=None):
  *         self.id2eword = []
  *         self.id2fword = []             # <<<<<<<<<<<<<<
@@ -13383,7 +13278,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->id2fword = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":58
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":58
  *         self.id2eword = []
  *         self.id2fword = []
  *         self.eword2id = {}             # <<<<<<<<<<<<<<
@@ -13398,7 +13293,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->eword2id = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":59
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":59
  *         self.id2fword = []
  *         self.eword2id = {}
  *         self.fword2id = {}             # <<<<<<<<<<<<<<
@@ -13413,7 +13308,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->fword2id = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":60
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":60
  *         self.eword2id = {}
  *         self.fword2id = {}
  *         self.e_index = IntList()             # <<<<<<<<<<<<<<
@@ -13428,7 +13323,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->e_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":61
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":61
  *         self.fword2id = {}
  *         self.e_index = IntList()
  *         self.f_index = IntList()             # <<<<<<<<<<<<<<
@@ -13443,7 +13338,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->f_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":62
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":62
  *         self.e_index = IntList()
  *         self.f_index = IntList()
  *         self.col1 = FloatList()             # <<<<<<<<<<<<<<
@@ -13458,7 +13353,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->col1 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":63
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":63
  *         self.f_index = IntList()
  *         self.col1 = FloatList()
  *         self.col2 = FloatList()             # <<<<<<<<<<<<<<
@@ -13473,7 +13368,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->col2 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":64
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":64
  *         self.col1 = FloatList()
  *         self.col2 = FloatList()
  *         if from_binary:             # <<<<<<<<<<<<<<
@@ -13483,7 +13378,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":65
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":65
  *         self.col2 = FloatList()
  *         if from_binary:
  *             self.read_binary(from_binary)             # <<<<<<<<<<<<<<
@@ -13505,7 +13400,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":66
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":66
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_data:             # <<<<<<<<<<<<<<
@@ -13515,7 +13410,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_data); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":67
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":67
  *             self.read_binary(from_binary)
  *         elif from_data:
  *             self.compute_from_data(fsarray, earray, alignment)             # <<<<<<<<<<<<<<
@@ -13541,7 +13436,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":69
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":69
  *             self.compute_from_data(fsarray, earray, alignment)
  *         else:
  *             self.read_text(from_text)             # <<<<<<<<<<<<<<
@@ -13577,7 +13472,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":72
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":72
  * 
  * 
  *     cdef compute_from_data(self, SuffixArray fsa, DataArray eda, Alignment aa):             # <<<<<<<<<<<<<<
@@ -13631,7 +13526,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("compute_from_data", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":79
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":79
  *         cdef int null_word
  * 
  *         null_word = 0             # <<<<<<<<<<<<<<
@@ -13640,7 +13535,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_null_word = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":80
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":80
  * 
  *         null_word = 0
  *         for word in fsa.darray.id2word: # I miss list comprehensions             # <<<<<<<<<<<<<<
@@ -13658,18 +13553,10 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else {
       __pyx_t_4 = __pyx_t_3(__pyx_t_1);
       if (unlikely(!__pyx_t_4)) {
@@ -13685,7 +13572,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_v_word = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":81
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":81
  *         null_word = 0
  *         for word in fsa.darray.id2word: # I miss list comprehensions
  *             self.id2fword.append(word)             # <<<<<<<<<<<<<<
@@ -13698,7 +13585,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":82
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":82
  *         for word in fsa.darray.id2word: # I miss list comprehensions
  *             self.id2fword.append(word)
  *         self.id2fword[null_word] = "NULL"             # <<<<<<<<<<<<<<
@@ -13707,7 +13594,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   if (__Pyx_SetItemInt(__pyx_v_self->id2fword, __pyx_v_null_word, ((PyObject *)__pyx_n_s__NULL), sizeof(int), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":83
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":83
  *             self.id2fword.append(word)
  *         self.id2fword[null_word] = "NULL"
  *         for id, word in enumerate(self.id2fword):             # <<<<<<<<<<<<<<
@@ -13727,18 +13614,10 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_4)) {
       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_4)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_4)) {
       if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
     } else {
       __pyx_t_5 = __pyx_t_3(__pyx_t_4);
       if (unlikely(!__pyx_t_5)) {
@@ -13762,7 +13641,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_1 = __pyx_t_5;
     __pyx_t_5 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":84
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":84
  *         self.id2fword[null_word] = "NULL"
  *         for id, word in enumerate(self.id2fword):
  *             self.fword2id[word] = id             # <<<<<<<<<<<<<<
@@ -13774,7 +13653,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":86
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":86
  *             self.fword2id[word] = id
  * 
  *         for word in eda.id2word:             # <<<<<<<<<<<<<<
@@ -13792,18 +13671,10 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else {
       __pyx_t_4 = __pyx_t_3(__pyx_t_1);
       if (unlikely(!__pyx_t_4)) {
@@ -13819,7 +13690,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_v_word = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":87
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":87
  * 
  *         for word in eda.id2word:
  *             self.id2eword.append(word)             # <<<<<<<<<<<<<<
@@ -13832,7 +13703,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":88
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":88
  *         for word in eda.id2word:
  *             self.id2eword.append(word)
  *         self.id2eword[null_word] = "NULL"             # <<<<<<<<<<<<<<
@@ -13841,7 +13712,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   if (__Pyx_SetItemInt(__pyx_v_self->id2eword, __pyx_v_null_word, ((PyObject *)__pyx_n_s__NULL), sizeof(int), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":89
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":89
  *             self.id2eword.append(word)
  *         self.id2eword[null_word] = "NULL"
  *         for id, word in enumerate(self.id2eword):             # <<<<<<<<<<<<<<
@@ -13861,18 +13732,10 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_4)) {
       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_4)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_4)) {
       if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
     } else {
       __pyx_t_5 = __pyx_t_3(__pyx_t_4);
       if (unlikely(!__pyx_t_5)) {
@@ -13896,7 +13759,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_1 = __pyx_t_5;
     __pyx_t_5 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":90
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":90
  *         self.id2eword[null_word] = "NULL"
  *         for id, word in enumerate(self.id2eword):
  *             self.eword2id[word] = id             # <<<<<<<<<<<<<<
@@ -13908,7 +13771,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":92
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":92
  *             self.eword2id[word] = id
  * 
  *         num_pairs = 0             # <<<<<<<<<<<<<<
@@ -13917,7 +13780,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_num_pairs = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":94
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":94
  *         num_pairs = 0
  * 
  *         V_E = len(eda.id2word)             # <<<<<<<<<<<<<<
@@ -13930,7 +13793,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_v_V_E = __pyx_t_2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":95
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":95
  * 
  *         V_E = len(eda.id2word)
  *         V_F = len(fsa.darray.id2word)             # <<<<<<<<<<<<<<
@@ -13943,7 +13806,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_v_V_F = __pyx_t_2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":96
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":96
  *         V_E = len(eda.id2word)
  *         V_F = len(fsa.darray.id2word)
  *         fmargin = <int*> malloc(V_F*sizeof(int))             # <<<<<<<<<<<<<<
@@ -13952,7 +13815,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_fmargin = ((int *)malloc((__pyx_v_V_F * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":97
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":97
  *         V_F = len(fsa.darray.id2word)
  *         fmargin = <int*> malloc(V_F*sizeof(int))
  *         emargin = <int*> malloc(V_E*sizeof(int))             # <<<<<<<<<<<<<<
@@ -13961,7 +13824,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_emargin = ((int *)malloc((__pyx_v_V_E * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":98
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":98
  *         fmargin = <int*> malloc(V_F*sizeof(int))
  *         emargin = <int*> malloc(V_E*sizeof(int))
  *         memset(fmargin, 0, V_F*sizeof(int))             # <<<<<<<<<<<<<<
@@ -13970,7 +13833,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   memset(__pyx_v_fmargin, 0, (__pyx_v_V_F * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":99
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":99
  *         emargin = <int*> malloc(V_E*sizeof(int))
  *         memset(fmargin, 0, V_F*sizeof(int))
  *         memset(emargin, 0, V_E*sizeof(int))             # <<<<<<<<<<<<<<
@@ -13979,7 +13842,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   memset(__pyx_v_emargin, 0, (__pyx_v_V_E * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":101
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":101
  *         memset(emargin, 0, V_E*sizeof(int))
  * 
  *         dict = <_node**> malloc(V_F*sizeof(_node*))             # <<<<<<<<<<<<<<
@@ -13988,7 +13851,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_dict = ((struct __pyx_t_3_sa__node **)malloc((__pyx_v_V_F * (sizeof(struct __pyx_t_3_sa__node *)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":102
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":102
  * 
  *         dict = <_node**> malloc(V_F*sizeof(_node*))
  *         memset(dict, 0, V_F*sizeof(_node*))             # <<<<<<<<<<<<<<
@@ -13997,7 +13860,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   memset(__pyx_v_dict, 0, (__pyx_v_V_F * (sizeof(struct __pyx_t_3_sa__node *))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":104
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":104
  *         memset(dict, 0, V_F*sizeof(_node*))
  * 
  *         num_sents = len(fsa.darray.sent_index)             # <<<<<<<<<<<<<<
@@ -14013,7 +13876,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_num_sents = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":105
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":105
  * 
  *         num_sents = len(fsa.darray.sent_index)
  *         for sent_id from 0 <= sent_id < num_sents-1:             # <<<<<<<<<<<<<<
@@ -14026,7 +13889,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   for (__pyx_v_sent_id = 0; __pyx_v_sent_id < __pyx_t_6; __pyx_v_sent_id++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":107
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":107
  *         for sent_id from 0 <= sent_id < num_sents-1:
  * 
  *             fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]             # <<<<<<<<<<<<<<
@@ -14035,7 +13898,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_fsent = (__pyx_v_fsa->darray->data->arr + (__pyx_v_fsa->darray->sent_index->arr[__pyx_v_sent_id]));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":108
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":108
  * 
  *             fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1             # <<<<<<<<<<<<<<
@@ -14044,7 +13907,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_I = (((__pyx_v_fsa->darray->sent_index->arr[(__pyx_v_sent_id + 1)]) - (__pyx_v_fsa->darray->sent_index->arr[__pyx_v_sent_id])) - 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":109
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":109
  *             fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1
  *             faligned = <int*> malloc(I*sizeof(int))             # <<<<<<<<<<<<<<
@@ -14053,7 +13916,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_faligned = ((int *)malloc((__pyx_v_I * (sizeof(int)))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":110
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":110
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1
  *             faligned = <int*> malloc(I*sizeof(int))
  *             memset(faligned, 0, I*sizeof(int))             # <<<<<<<<<<<<<<
@@ -14062,7 +13925,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     memset(__pyx_v_faligned, 0, (__pyx_v_I * (sizeof(int))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":112
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":112
  *             memset(faligned, 0, I*sizeof(int))
  * 
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]             # <<<<<<<<<<<<<<
@@ -14071,7 +13934,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_esent = (__pyx_v_eda->data->arr + (__pyx_v_eda->sent_index->arr[__pyx_v_sent_id]));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":113
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":113
  * 
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1             # <<<<<<<<<<<<<<
@@ -14080,7 +13943,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_J = (((__pyx_v_eda->sent_index->arr[(__pyx_v_sent_id + 1)]) - (__pyx_v_eda->sent_index->arr[__pyx_v_sent_id])) - 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":114
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":114
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1
  *             ealigned = <int*> malloc(J*sizeof(int))             # <<<<<<<<<<<<<<
@@ -14089,7 +13952,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_ealigned = ((int *)malloc((__pyx_v_J * (sizeof(int)))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":115
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":115
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1
  *             ealigned = <int*> malloc(J*sizeof(int))
  *             memset(ealigned, 0, J*sizeof(int))             # <<<<<<<<<<<<<<
@@ -14098,7 +13961,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     memset(__pyx_v_ealigned, 0, (__pyx_v_J * (sizeof(int))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":117
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":117
  *             memset(ealigned, 0, J*sizeof(int))
  * 
  *             links = aa._get_sent_links(sent_id, &num_links)             # <<<<<<<<<<<<<<
@@ -14107,7 +13970,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_links = ((struct __pyx_vtabstruct_3_sa_Alignment *)__pyx_v_aa->__pyx_vtab)->_get_sent_links(__pyx_v_aa, __pyx_v_sent_id, (&__pyx_v_num_links));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":119
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":119
  *             links = aa._get_sent_links(sent_id, &num_links)
  * 
  *             for l from 0 <= l < num_links:             # <<<<<<<<<<<<<<
@@ -14117,7 +13980,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_num_links;
     for (__pyx_v_l = 0; __pyx_v_l < __pyx_t_7; __pyx_v_l++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":120
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":120
  * 
  *             for l from 0 <= l < num_links:
  *                 i = links[l*2]             # <<<<<<<<<<<<<<
@@ -14126,7 +13989,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_i = (__pyx_v_links[(__pyx_v_l * 2)]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":121
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":121
  *             for l from 0 <= l < num_links:
  *                 i = links[l*2]
  *                 j = links[l*2+1]             # <<<<<<<<<<<<<<
@@ -14135,7 +13998,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_j = (__pyx_v_links[((__pyx_v_l * 2) + 1)]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":122
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":122
  *                 i = links[l*2]
  *                 j = links[l*2+1]
  *                 if i >= I or j >= J:             # <<<<<<<<<<<<<<
@@ -14151,7 +14014,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       if (__pyx_t_10) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":123
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":123
  *                 j = links[l*2+1]
  *                 if i >= I or j >= J:
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))             # <<<<<<<<<<<<<<
@@ -14203,7 +14066,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       __pyx_L15:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":124
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":124
  *                 if i >= I or j >= J:
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))
  *                 f_i = fsent[i]             # <<<<<<<<<<<<<<
@@ -14212,7 +14075,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_f_i = (__pyx_v_fsent[__pyx_v_i]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":125
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":125
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))
  *                 f_i = fsent[i]
  *                 e_j = esent[j]             # <<<<<<<<<<<<<<
@@ -14221,7 +14084,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_e_j = (__pyx_v_esent[__pyx_v_j]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":126
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":126
  *                 f_i = fsent[i]
  *                 e_j = esent[j]
  *                 fmargin[f_i] = fmargin[f_i]+1             # <<<<<<<<<<<<<<
@@ -14230,7 +14093,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_fmargin[__pyx_v_f_i]) = ((__pyx_v_fmargin[__pyx_v_f_i]) + 1);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":127
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":127
  *                 e_j = esent[j]
  *                 fmargin[f_i] = fmargin[f_i]+1
  *                 emargin[e_j] = emargin[e_j]+1             # <<<<<<<<<<<<<<
@@ -14239,7 +14102,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_emargin[__pyx_v_e_j]) = ((__pyx_v_emargin[__pyx_v_e_j]) + 1);
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":128
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":128
  *                 fmargin[f_i] = fmargin[f_i]+1
  *                 emargin[e_j] = emargin[e_j]+1
  *                 if dict[f_i] == NULL:             # <<<<<<<<<<<<<<
@@ -14249,7 +14112,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_dict[__pyx_v_f_i]) == NULL);
       if (__pyx_t_10) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":129
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":129
  *                 emargin[e_j] = emargin[e_j]+1
  *                 if dict[f_i] == NULL:
  *                     dict[f_i] = new_node(e_j)             # <<<<<<<<<<<<<<
@@ -14258,7 +14121,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_dict[__pyx_v_f_i]) = __pyx_f_3_sa_new_node(__pyx_v_e_j);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":130
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":130
  *                 if dict[f_i] == NULL:
  *                     dict[f_i] = new_node(e_j)
  *                     dict[f_i].val = 1             # <<<<<<<<<<<<<<
@@ -14267,7 +14130,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_dict[__pyx_v_f_i])->val = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":131
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":131
  *                     dict[f_i] = new_node(e_j)
  *                     dict[f_i].val = 1
  *                     num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14279,7 +14142,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":133
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":133
  *                     num_pairs = num_pairs + 1
  *                 else:
  *                     count = get_val(dict[f_i], e_j)             # <<<<<<<<<<<<<<
@@ -14288,7 +14151,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_f_i]), __pyx_v_e_j);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":134
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":134
  *                 else:
  *                     count = get_val(dict[f_i], e_j)
  *                     if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -14298,7 +14161,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_count[0]) == 0);
         if (__pyx_t_10) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":135
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":135
  *                     count = get_val(dict[f_i], e_j)
  *                     if count[0] == 0:
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14310,7 +14173,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         __pyx_L17:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":136
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":136
  *                     if count[0] == 0:
  *                         num_pairs = num_pairs + 1
  *                     count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -14321,7 +14184,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       __pyx_L16:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":138
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":138
  *                     count[0] = count[0] + 1
  *                 # add count
  *                 faligned[i] = 1             # <<<<<<<<<<<<<<
@@ -14330,7 +14193,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_faligned[__pyx_v_i]) = 1;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":139
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":139
  *                 # add count
  *                 faligned[i] = 1
  *                 ealigned[j] = 1             # <<<<<<<<<<<<<<
@@ -14340,7 +14203,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       (__pyx_v_ealigned[__pyx_v_j]) = 1;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":140
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":140
  *                 faligned[i] = 1
  *                 ealigned[j] = 1
  *             for i from 0 <= i < I:             # <<<<<<<<<<<<<<
@@ -14350,7 +14213,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_I;
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":141
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":141
  *                 ealigned[j] = 1
  *             for i from 0 <= i < I:
  *                 if faligned[i] == 0:             # <<<<<<<<<<<<<<
@@ -14360,7 +14223,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_faligned[__pyx_v_i]) == 0);
       if (__pyx_t_10) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":142
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":142
  *             for i from 0 <= i < I:
  *                 if faligned[i] == 0:
  *                     f_i = fsent[i]             # <<<<<<<<<<<<<<
@@ -14369,7 +14232,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_f_i = (__pyx_v_fsent[__pyx_v_i]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":143
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":143
  *                 if faligned[i] == 0:
  *                     f_i = fsent[i]
  *                     fmargin[f_i] = fmargin[f_i] + 1             # <<<<<<<<<<<<<<
@@ -14378,7 +14241,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_fmargin[__pyx_v_f_i]) = ((__pyx_v_fmargin[__pyx_v_f_i]) + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":144
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":144
  *                     f_i = fsent[i]
  *                     fmargin[f_i] = fmargin[f_i] + 1
  *                     emargin[null_word] = emargin[null_word] + 1             # <<<<<<<<<<<<<<
@@ -14387,7 +14250,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_emargin[__pyx_v_null_word]) = ((__pyx_v_emargin[__pyx_v_null_word]) + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":145
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":145
  *                     fmargin[f_i] = fmargin[f_i] + 1
  *                     emargin[null_word] = emargin[null_word] + 1
  *                     if dict[f_i] == NULL:             # <<<<<<<<<<<<<<
@@ -14397,7 +14260,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_dict[__pyx_v_f_i]) == NULL);
         if (__pyx_t_10) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":146
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":146
  *                     emargin[null_word] = emargin[null_word] + 1
  *                     if dict[f_i] == NULL:
  *                         dict[f_i] = new_node(null_word)             # <<<<<<<<<<<<<<
@@ -14406,7 +14269,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_f_i]) = __pyx_f_3_sa_new_node(__pyx_v_null_word);
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":147
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":147
  *                     if dict[f_i] == NULL:
  *                         dict[f_i] = new_node(null_word)
  *                         dict[f_i].val = 1             # <<<<<<<<<<<<<<
@@ -14415,7 +14278,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_f_i])->val = 1;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":148
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":148
  *                         dict[f_i] = new_node(null_word)
  *                         dict[f_i].val = 1
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14427,7 +14290,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":150
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":150
  *                         num_pairs = num_pairs + 1
  *                     else:
  *                         count = get_val(dict[f_i], null_word)             # <<<<<<<<<<<<<<
@@ -14436,7 +14299,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_f_i]), __pyx_v_null_word);
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":151
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":151
  *                     else:
  *                         count = get_val(dict[f_i], null_word)
  *                         if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -14446,7 +14309,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           __pyx_t_10 = ((__pyx_v_count[0]) == 0);
           if (__pyx_t_10) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":152
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":152
  *                         count = get_val(dict[f_i], null_word)
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14458,7 +14321,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           }
           __pyx_L22:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":153
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":153
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -14473,7 +14336,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_L20:;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":154
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":154
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1
  *             for j from 0 <= j < J:             # <<<<<<<<<<<<<<
@@ -14483,7 +14346,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_J;
     for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_7; __pyx_v_j++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":155
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":155
  *                         count[0] = count[0] + 1
  *             for j from 0 <= j < J:
  *                 if ealigned[j] == 0:             # <<<<<<<<<<<<<<
@@ -14493,7 +14356,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_ealigned[__pyx_v_j]) == 0);
       if (__pyx_t_10) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":156
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":156
  *             for j from 0 <= j < J:
  *                 if ealigned[j] == 0:
  *                     e_j = esent[j]             # <<<<<<<<<<<<<<
@@ -14502,7 +14365,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_e_j = (__pyx_v_esent[__pyx_v_j]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":157
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":157
  *                 if ealigned[j] == 0:
  *                     e_j = esent[j]
  *                     fmargin[null_word] = fmargin[null_word] + 1             # <<<<<<<<<<<<<<
@@ -14511,7 +14374,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_fmargin[__pyx_v_null_word]) = ((__pyx_v_fmargin[__pyx_v_null_word]) + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":158
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":158
  *                     e_j = esent[j]
  *                     fmargin[null_word] = fmargin[null_word] + 1
  *                     emargin[e_j] = emargin[e_j] + 1             # <<<<<<<<<<<<<<
@@ -14520,7 +14383,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_emargin[__pyx_v_e_j]) = ((__pyx_v_emargin[__pyx_v_e_j]) + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":159
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":159
  *                     fmargin[null_word] = fmargin[null_word] + 1
  *                     emargin[e_j] = emargin[e_j] + 1
  *                     if dict[null_word] == NULL:             # <<<<<<<<<<<<<<
@@ -14530,7 +14393,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_dict[__pyx_v_null_word]) == NULL);
         if (__pyx_t_10) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":160
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":160
  *                     emargin[e_j] = emargin[e_j] + 1
  *                     if dict[null_word] == NULL:
  *                         dict[null_word] = new_node(e_j)             # <<<<<<<<<<<<<<
@@ -14539,7 +14402,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_null_word]) = __pyx_f_3_sa_new_node(__pyx_v_e_j);
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":161
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":161
  *                     if dict[null_word] == NULL:
  *                         dict[null_word] = new_node(e_j)
  *                         dict[null_word].val = 1             # <<<<<<<<<<<<<<
@@ -14548,7 +14411,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_null_word])->val = 1;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":162
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":162
  *                         dict[null_word] = new_node(e_j)
  *                         dict[null_word].val = 1
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14560,7 +14423,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":164
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":164
  *                         num_pairs = num_pairs + 1
  *                     else:
  *                         count = get_val(dict[null_word], e_j)             # <<<<<<<<<<<<<<
@@ -14569,7 +14432,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_null_word]), __pyx_v_e_j);
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":165
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":165
  *                     else:
  *                         count = get_val(dict[null_word], e_j)
  *                         if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -14579,7 +14442,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           __pyx_t_10 = ((__pyx_v_count[0]) == 0);
           if (__pyx_t_10) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":166
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":166
  *                         count = get_val(dict[null_word], e_j)
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -14591,7 +14454,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           }
           __pyx_L27:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":167
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":167
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -14606,7 +14469,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_L25:;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":168
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":168
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1
  *             free(links)             # <<<<<<<<<<<<<<
@@ -14615,7 +14478,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     free(__pyx_v_links);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":169
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":169
  *                         count[0] = count[0] + 1
  *             free(links)
  *             free(faligned)             # <<<<<<<<<<<<<<
@@ -14624,7 +14487,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     free(__pyx_v_faligned);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":170
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":170
  *             free(links)
  *             free(faligned)
  *             free(ealigned)             # <<<<<<<<<<<<<<
@@ -14634,7 +14497,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     free(__pyx_v_ealigned);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":171
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":171
  *             free(faligned)
  *             free(ealigned)
  *         self.f_index = IntList(initial_len=V_F)             # <<<<<<<<<<<<<<
@@ -14656,7 +14519,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->f_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_13);
   __pyx_t_13 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":172
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":172
  *             free(ealigned)
  *         self.f_index = IntList(initial_len=V_F)
  *         self.e_index = IntList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
@@ -14678,7 +14541,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->e_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_12);
   __pyx_t_12 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":173
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":173
  *         self.f_index = IntList(initial_len=V_F)
  *         self.e_index = IntList(initial_len=num_pairs)
  *         self.col1 = FloatList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
@@ -14700,7 +14563,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->col1 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_13);
   __pyx_t_13 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":174
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":174
  *         self.e_index = IntList(initial_len=num_pairs)
  *         self.col1 = FloatList(initial_len=num_pairs)
  *         self.col2 = FloatList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
@@ -14722,7 +14585,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->col2 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_12);
   __pyx_t_12 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":176
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":176
  *         self.col2 = FloatList(initial_len=num_pairs)
  * 
  *         num_pairs = 0             # <<<<<<<<<<<<<<
@@ -14731,7 +14594,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_num_pairs = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":177
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":177
  * 
  *         num_pairs = 0
  *         for i from 0 <= i < V_F:             # <<<<<<<<<<<<<<
@@ -14741,7 +14604,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_t_6 = __pyx_v_V_F;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_6; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":179
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":179
  *         for i from 0 <= i < V_F:
  *             #self.f_index[i] = num_pairs
  *             self.f_index.set(i, num_pairs)             # <<<<<<<<<<<<<<
@@ -14750,7 +14613,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->f_index->__pyx_vtab)->set(__pyx_v_self->f_index, __pyx_v_i, __pyx_v_num_pairs);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":180
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":180
  *             #self.f_index[i] = num_pairs
  *             self.f_index.set(i, num_pairs)
  *             if dict[i] != NULL:             # <<<<<<<<<<<<<<
@@ -14760,7 +14623,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_10 = ((__pyx_v_dict[__pyx_v_i]) != NULL);
     if (__pyx_t_10) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":181
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":181
  *             self.f_index.set(i, num_pairs)
  *             if dict[i] != NULL:
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)             # <<<<<<<<<<<<<<
@@ -14771,7 +14634,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __Pyx_GOTREF(__pyx_t_12);
       __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":182
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":182
  *             if dict[i] != NULL:
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)
  *                 del_node(dict[i])             # <<<<<<<<<<<<<<
@@ -14786,7 +14649,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_L30:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":183
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":183
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)
  *                 del_node(dict[i])
  *         free(fmargin)             # <<<<<<<<<<<<<<
@@ -14795,7 +14658,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_fmargin);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":184
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":184
  *                 del_node(dict[i])
  *         free(fmargin)
  *         free(emargin)             # <<<<<<<<<<<<<<
@@ -14804,7 +14667,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_emargin);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":185
  *         free(fmargin)
  *         free(emargin)
  *         free(dict)             # <<<<<<<<<<<<<<
@@ -14813,7 +14676,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_dict);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":186
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":186
  *         free(emargin)
  *         free(dict)
  *         return             # <<<<<<<<<<<<<<
@@ -14844,7 +14707,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":189
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":189
  * 
  * 
  *     cdef _add_node(self, _node* n, int* num_pairs, float fmargin, int* emargin):             # <<<<<<<<<<<<<<
@@ -14863,7 +14726,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("_add_node", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":191
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":191
  *     cdef _add_node(self, _node* n, int* num_pairs, float fmargin, int* emargin):
  *         cdef int loc
  *         if n.smaller != NULL:             # <<<<<<<<<<<<<<
@@ -14873,7 +14736,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   __pyx_t_1 = (__pyx_v_n->smaller != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":192
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":192
  *         cdef int loc
  *         if n.smaller != NULL:
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)             # <<<<<<<<<<<<<<
@@ -14887,7 +14750,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":193
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":193
  *         if n.smaller != NULL:
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)
  *         loc = num_pairs[0]             # <<<<<<<<<<<<<<
@@ -14896,7 +14759,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   __pyx_v_loc = (__pyx_v_num_pairs[0]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":194
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":194
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)
  *         loc = num_pairs[0]
  *         self.e_index.set(loc, n.key)             # <<<<<<<<<<<<<<
@@ -14905,7 +14768,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->e_index->__pyx_vtab)->set(__pyx_v_self->e_index, __pyx_v_loc, __pyx_v_n->key);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":195
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":195
  *         loc = num_pairs[0]
  *         self.e_index.set(loc, n.key)
  *         self.col1.set(loc, float(n.val)/fmargin)             # <<<<<<<<<<<<<<
@@ -14918,7 +14781,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   }
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col1->__pyx_vtab)->set(__pyx_v_self->col1, __pyx_v_loc, (((double)__pyx_v_n->val) / __pyx_v_fmargin));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":196
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":196
  *         self.e_index.set(loc, n.key)
  *         self.col1.set(loc, float(n.val)/fmargin)
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))             # <<<<<<<<<<<<<<
@@ -14931,7 +14794,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   }
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col2->__pyx_vtab)->set(__pyx_v_self->col2, __pyx_v_loc, (((double)__pyx_v_n->val) / ((double)(__pyx_v_emargin[__pyx_v_n->key]))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":197
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":197
  *         self.col1.set(loc, float(n.val)/fmargin)
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))
  *         num_pairs[0] = loc + 1             # <<<<<<<<<<<<<<
@@ -14940,7 +14803,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   (__pyx_v_num_pairs[0]) = (__pyx_v_loc + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":198
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":198
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))
  *         num_pairs[0] = loc + 1
  *         if n.bigger != NULL:             # <<<<<<<<<<<<<<
@@ -14950,7 +14813,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   __pyx_t_1 = (__pyx_v_n->bigger != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":199
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":199
  *         num_pairs[0] = loc + 1
  *         if n.bigger != NULL:
  *             self._add_node(n.bigger, num_pairs, fmargin, emargin)             # <<<<<<<<<<<<<<
@@ -14997,7 +14860,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_3write_binary(PyObject *__pyx_v_self, PyOb
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":202
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":202
  * 
  * 
  *     def write_binary(self, char* filename):             # <<<<<<<<<<<<<<
@@ -15016,7 +14879,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("write_binary", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":204
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":204
  *     def write_binary(self, char* filename):
  *         cdef FILE* f
  *         f = fopen(filename, "w")             # <<<<<<<<<<<<<<
@@ -15025,7 +14888,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__w);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":205
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":205
  *         cdef FILE* f
  *         f = fopen(filename, "w")
  *         self.f_index.write_handle(f)             # <<<<<<<<<<<<<<
@@ -15034,7 +14897,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->f_index->__pyx_vtab)->write_handle(__pyx_v_self->f_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":206
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":206
  *         f = fopen(filename, "w")
  *         self.f_index.write_handle(f)
  *         self.e_index.write_handle(f)             # <<<<<<<<<<<<<<
@@ -15043,7 +14906,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->e_index->__pyx_vtab)->write_handle(__pyx_v_self->e_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":207
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":207
  *         self.f_index.write_handle(f)
  *         self.e_index.write_handle(f)
  *         self.col1.write_handle(f)             # <<<<<<<<<<<<<<
@@ -15052,7 +14915,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col1->__pyx_vtab)->write_handle(__pyx_v_self->col1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":208
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":208
  *         self.e_index.write_handle(f)
  *         self.col1.write_handle(f)
  *         self.col2.write_handle(f)             # <<<<<<<<<<<<<<
@@ -15061,7 +14924,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col2->__pyx_vtab)->write_handle(__pyx_v_self->col2, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":209
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":209
  *         self.col1.write_handle(f)
  *         self.col2.write_handle(f)
  *         self.write_wordlist(self.id2fword, f)             # <<<<<<<<<<<<<<
@@ -15075,7 +14938,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":210
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":210
  *         self.col2.write_handle(f)
  *         self.write_wordlist(self.id2fword, f)
  *         self.write_wordlist(self.id2eword, f)             # <<<<<<<<<<<<<<
@@ -15089,7 +14952,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":211
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":211
  *         self.write_wordlist(self.id2fword, f)
  *         self.write_wordlist(self.id2eword, f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -15111,7 +14974,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":214
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":214
  * 
  * 
  *     cdef write_wordlist(self, wordlist, FILE* f):             # <<<<<<<<<<<<<<
@@ -15136,7 +14999,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("write_wordlist", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":218
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":218
  *         cdef int num_words
  * 
  *         num_words = len(wordlist)             # <<<<<<<<<<<<<<
@@ -15146,7 +15009,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
   __pyx_t_1 = PyObject_Length(__pyx_v_wordlist); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_num_words = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":219
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":219
  * 
  *         num_words = len(wordlist)
  *         fwrite(&(num_words), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -15155,7 +15018,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
  */
   fwrite((&__pyx_v_num_words), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":220
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":220
  *         num_words = len(wordlist)
  *         fwrite(&(num_words), sizeof(int), 1, f)
  *         for word in wordlist:             # <<<<<<<<<<<<<<
@@ -15173,18 +15036,10 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_2)) {
       if (__pyx_t_1 >= PyList_GET_SIZE(__pyx_t_2)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_2)) {
       if (__pyx_t_1 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++;
     } else {
       __pyx_t_4 = __pyx_t_3(__pyx_t_2);
       if (unlikely(!__pyx_t_4)) {
@@ -15200,7 +15055,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
     __pyx_v_word = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":221
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":221
  *         fwrite(&(num_words), sizeof(int), 1, f)
  *         for word in wordlist:
  *             word_len = len(word) + 1             # <<<<<<<<<<<<<<
@@ -15210,7 +15065,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
     __pyx_t_5 = PyObject_Length(__pyx_v_word); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_word_len = (__pyx_t_5 + 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":222
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":222
  *         for word in wordlist:
  *             word_len = len(word) + 1
  *             fwrite(&(word_len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -15219,7 +15074,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
  */
     fwrite((&__pyx_v_word_len), (sizeof(int)), 1, __pyx_v_f);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":223
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":223
  *             word_len = len(word) + 1
  *             fwrite(&(word_len), sizeof(int), 1, f)
  *             fwrite(<char *>word, sizeof(char), word_len, f)             # <<<<<<<<<<<<<<
@@ -15245,7 +15100,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":226
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":226
  * 
  * 
  *     cdef read_wordlist(self, word2id, id2word, FILE* f):             # <<<<<<<<<<<<<<
@@ -15269,7 +15124,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("read_wordlist", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":231
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":231
  *         cdef char* word
  * 
  *         fread(&(num_words), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -15278,7 +15133,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
  */
   fread((&__pyx_v_num_words), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":232
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":232
  * 
  *         fread(&(num_words), sizeof(int), 1, f)
  *         for i from 0 <= i < num_words:             # <<<<<<<<<<<<<<
@@ -15288,7 +15143,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
   __pyx_t_1 = __pyx_v_num_words;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":233
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":233
  *         fread(&(num_words), sizeof(int), 1, f)
  *         for i from 0 <= i < num_words:
  *             fread(&(word_len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -15297,7 +15152,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
  */
     fread((&__pyx_v_word_len), (sizeof(int)), 1, __pyx_v_f);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":234
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":234
  *         for i from 0 <= i < num_words:
  *             fread(&(word_len), sizeof(int), 1, f)
  *             word = <char*> malloc (word_len * sizeof(char))             # <<<<<<<<<<<<<<
@@ -15306,7 +15161,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
  */
     __pyx_v_word = ((char *)malloc((__pyx_v_word_len * (sizeof(char)))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":235
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":235
  *             fread(&(word_len), sizeof(int), 1, f)
  *             word = <char*> malloc (word_len * sizeof(char))
  *             fread(word, sizeof(char), word_len, f)             # <<<<<<<<<<<<<<
@@ -15315,7 +15170,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
  */
     fread(__pyx_v_word, (sizeof(char)), __pyx_v_word_len, __pyx_v_f);
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":236
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":236
  *             word = <char*> malloc (word_len * sizeof(char))
  *             fread(word, sizeof(char), word_len, f)
  *             word2id[word] = len(id2word)             # <<<<<<<<<<<<<<
@@ -15331,7 +15186,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
     __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":237
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":237
  *             fread(word, sizeof(char), word_len, f)
  *             word2id[word] = len(id2word)
  *             id2word.append(word)             # <<<<<<<<<<<<<<
@@ -15345,7 +15200,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_read_wordlist(CYTHON_UNUSED struct __pyx_ob
     __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":238
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":238
  *             word2id[word] = len(id2word)
  *             id2word.append(word)
  *             free(word)             # <<<<<<<<<<<<<<
@@ -15389,7 +15244,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_5read_binary(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":240
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":240
  *             free(word)
  * 
  *     def read_binary(self, char* filename):             # <<<<<<<<<<<<<<
@@ -15409,7 +15264,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("read_binary", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":242
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":242
  *     def read_binary(self, char* filename):
  *         cdef FILE* f
  *         f = fopen(filename, "r")             # <<<<<<<<<<<<<<
@@ -15418,7 +15273,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
  */
   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":243
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":243
  *         cdef FILE* f
  *         f = fopen(filename, "r")
  *         self.f_index.read_handle(f)             # <<<<<<<<<<<<<<
@@ -15427,7 +15282,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->f_index->__pyx_vtab)->read_handle(__pyx_v_self->f_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":244
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":244
  *         f = fopen(filename, "r")
  *         self.f_index.read_handle(f)
  *         self.e_index.read_handle(f)             # <<<<<<<<<<<<<<
@@ -15436,7 +15291,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->e_index->__pyx_vtab)->read_handle(__pyx_v_self->e_index, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":245
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":245
  *         self.f_index.read_handle(f)
  *         self.e_index.read_handle(f)
  *         self.col1.read_handle(f)             # <<<<<<<<<<<<<<
@@ -15445,7 +15300,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
  */
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col1->__pyx_vtab)->read_handle(__pyx_v_self->col1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":246
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":246
  *         self.e_index.read_handle(f)
  *         self.col1.read_handle(f)
  *         self.col2.read_handle(f)             # <<<<<<<<<<<<<<
@@ -15454,7 +15309,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
  */
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col2->__pyx_vtab)->read_handle(__pyx_v_self->col2, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":247
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":247
  *         self.col1.read_handle(f)
  *         self.col2.read_handle(f)
  *         self.read_wordlist(self.fword2id, self.id2fword, f)             # <<<<<<<<<<<<<<
@@ -15471,7 +15326,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":248
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":248
  *         self.col2.read_handle(f)
  *         self.read_wordlist(self.fword2id, self.id2fword, f)
  *         self.read_wordlist(self.eword2id, self.id2eword, f)             # <<<<<<<<<<<<<<
@@ -15488,7 +15343,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_4read_binary(struct __pyx_obj_3_sa_BiLex *
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":249
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":249
  *         self.read_wordlist(self.fword2id, self.id2fword, f)
  *         self.read_wordlist(self.eword2id, self.id2eword, f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -15522,7 +15377,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_7get_e_id(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":252
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":252
  * 
  * 
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   __Pyx_RefNannySetupContext("get_e_id", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":253
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":253
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+  __pyx_t_1 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_self->eword2id, __pyx_v_eword))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":254
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":254
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@@ -15568,7 +15423,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_6get_e_id(struct __pyx_obj_3_sa_BiLex *__p
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     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":255
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":255
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@@ -15579,7 +15434,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_6get_e_id(struct __pyx_obj_3_sa_BiLex *__p
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     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":256
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":256
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":257
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":257
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":260
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":260
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  * 
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":261
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":261
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+  __pyx_t_1 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_self->fword2id, __pyx_v_fword))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":262
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":262
  *     def get_f_id(self, fword):
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  *             f_id = len(self.id2fword)             # <<<<<<<<<<<<<<
@@ -15675,7 +15530,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_8get_f_id(struct __pyx_obj_3_sa_BiLex *__p
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     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":263
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":263
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@@ -15686,7 +15541,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_8get_f_id(struct __pyx_obj_3_sa_BiLex *__p
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     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":264
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":264
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@@ -15698,7 +15553,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_8get_f_id(struct __pyx_obj_3_sa_BiLex *__p
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":265
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":265
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@@ -15746,7 +15601,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_11read_text(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":268
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":268
  * 
  * 
  *     def read_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -15801,7 +15656,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
   int __pyx_clineno = 0;
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":272
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":272
  *         cdef IntList fcount
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@@ -15813,7 +15668,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":273
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":273
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  *         fcount = IntList()
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -15853,7 +15708,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
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           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":275
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":275
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
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-              #endif
+              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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               __pyx_t_2 = __pyx_t_9(__pyx_t_1);
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@@ -15898,7 +15745,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_line = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":276
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":276
  *             # first loop merely establishes size of array objects
  *             for line in f:
  *                 (fword, eword, score1, score2) = line.split()             # <<<<<<<<<<<<<<
@@ -15912,23 +15759,22 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #endif
-              if (unlikely(size != 4)) {
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-                else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              }
-              #if CYTHON_COMPILING_IN_CPYTHON
               if (likely(PyTuple_CheckExact(sequence))) {
+                if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+                  if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+                  else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0); 
                 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1); 
                 __pyx_t_11 = PyTuple_GET_ITEM(sequence, 2); 
                 __pyx_t_12 = PyTuple_GET_ITEM(sequence, 3); 
               } else {
+                if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+                  if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+                  else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_2 = PyList_GET_ITEM(sequence, 0); 
                 __pyx_t_10 = PyList_GET_ITEM(sequence, 1); 
                 __pyx_t_11 = PyList_GET_ITEM(sequence, 2); 
@@ -15938,36 +15784,28 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
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-              for (i=0; i < 4; i++) {
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-                *(temps[i]) = item;
-              }
-              #endif
               __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-            } else
-            {
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               Py_ssize_t index = -1;
-              PyObject** temps[4] = {&__pyx_t_2,&__pyx_t_10,&__pyx_t_11,&__pyx_t_12};
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-              for (index=0; index < 4; index++) {
-                PyObject* item = __pyx_t_14(__pyx_t_13); if (unlikely(!item)) goto __pyx_L18_unpacking_failed;
-                __Pyx_GOTREF(item);
-                *(temps[index]) = item;
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+              index = 0; __pyx_t_2 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_2)) goto __pyx_L18_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_2);
+              index = 1; __pyx_t_10 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_10)) goto __pyx_L18_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_10);
+              index = 2; __pyx_t_11 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_11)) goto __pyx_L18_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_11);
+              index = 3; __pyx_t_12 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_12)) goto __pyx_L18_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_12);
               if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_13), 4) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              __pyx_t_14 = NULL;
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               __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
-              __pyx_t_14 = NULL;
-              if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+              if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+              if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
               {__pyx_filename = __pyx_f[5]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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             __pyx_v_score2 = __pyx_t_12;
             __pyx_t_12 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":277
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":277
  *             for line in f:
  *                 (fword, eword, score1, score2) = line.split()
  *                 f_id = self.get_f_id(fword)             # <<<<<<<<<<<<<<
@@ -16006,7 +15844,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
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             __pyx_t_11 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":278
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":278
  *                 (fword, eword, score1, score2) = line.split()
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             __pyx_t_3 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":279
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":279
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  *                 e_id = self.get_e_id(eword)
  *                 while f_id >= len(fcount):             # <<<<<<<<<<<<<<
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-              __pyx_t_12 = PyObject_RichCompare(__pyx_v_f_id, __pyx_t_3, Py_GE); __Pyx_XGOTREF(__pyx_t_12); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+              __pyx_t_12 = PyObject_RichCompare(__pyx_v_f_id, __pyx_t_3, Py_GE); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+              __Pyx_GOTREF(__pyx_t_12);
               __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
               __pyx_t_16 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely(__pyx_t_16 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":280
+              /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":280
  *                 e_id = self.get_e_id(eword)
  *                 while f_id >= len(fcount):
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@@ -16057,7 +15896,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
               __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
             }
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":281
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":281
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           }
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":284
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":284
  * 
  *             # Allocate space for dictionary in arrays
  *             N = 0             # <<<<<<<<<<<<<<
@@ -16080,7 +15919,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __Pyx_INCREF(__pyx_int_0);
           __pyx_v_N = __pyx_int_0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":285
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":285
  *             # Allocate space for dictionary in arrays
  *             N = 0
  *             n_f = len(fcount)             # <<<<<<<<<<<<<<
@@ -16093,7 +15932,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_n_f = __pyx_t_1;
           __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":286
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":286
  *             N = 0
  *             n_f = len(fcount)
  *             self.f_index = IntList(initial_len=n_f+1)             # <<<<<<<<<<<<<<
@@ -16115,7 +15954,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_self->f_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_12);
           __pyx_t_12 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":287
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":287
  *             n_f = len(fcount)
  *             self.f_index = IntList(initial_len=n_f+1)
  *             for i from 0 <= i < n_f:             # <<<<<<<<<<<<<<
@@ -16130,7 +15969,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_i = __pyx_t_12;
             __pyx_t_12 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":288
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":288
  *             self.f_index = IntList(initial_len=n_f+1)
  *             for i from 0 <= i < n_f:
  *                 self.f_index.arr[i] = N             # <<<<<<<<<<<<<<
@@ -16141,7 +15980,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_t_8 = __Pyx_PyIndex_AsSsize_t(__pyx_v_i); if (unlikely((__pyx_t_8 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
             (__pyx_v_self->f_index->arr[__pyx_t_8]) = __pyx_t_20;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":289
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":289
  *             for i from 0 <= i < n_f:
  *                 self.f_index.arr[i] = N
  *                 N = N + fcount.arr[i]             # <<<<<<<<<<<<<<
@@ -16158,7 +15997,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_N = __pyx_t_1;
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":290
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":290
  *                 self.f_index.arr[i] = N
  *                 N = N + fcount.arr[i]
  *                 fcount.arr[i] = 0             # <<<<<<<<<<<<<<
@@ -16170,7 +16009,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_t_19 = __Pyx_PyInt_AsLong(__pyx_v_i); if (unlikely((__pyx_t_19 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
           }
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":287
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":287
  *             n_f = len(fcount)
  *             self.f_index = IntList(initial_len=n_f+1)
  *             for i from 0 <= i < n_f:             # <<<<<<<<<<<<<<
@@ -16183,7 +16022,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_i = __pyx_t_1;
           __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":291
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":291
  *                 N = N + fcount.arr[i]
  *                 fcount.arr[i] = 0
  *             self.f_index.arr[n_f] = N             # <<<<<<<<<<<<<<
@@ -16194,7 +16033,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_t_8 = __Pyx_PyIndex_AsSsize_t(__pyx_v_n_f); if (unlikely((__pyx_t_8 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
           (__pyx_v_self->f_index->arr[__pyx_t_8]) = __pyx_t_20;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":292
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":292
  *                 fcount.arr[i] = 0
  *             self.f_index.arr[n_f] = N
  *             self.e_index = IntList(initial_len=N)             # <<<<<<<<<<<<<<
@@ -16213,7 +16052,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_self->e_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_12);
           __pyx_t_12 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":293
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":293
  *             self.f_index.arr[n_f] = N
  *             self.e_index = IntList(initial_len=N)
  *             self.col1 = FloatList(initial_len=N)             # <<<<<<<<<<<<<<
@@ -16232,7 +16071,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_self->col1 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_1);
           __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":294
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":294
  *             self.e_index = IntList(initial_len=N)
  *             self.col1 = FloatList(initial_len=N)
  *             self.col2 = FloatList(initial_len=N)             # <<<<<<<<<<<<<<
@@ -16251,7 +16090,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __pyx_v_self->col2 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_12);
           __pyx_t_12 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":297
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":297
  * 
  *             # Re-read file, placing words into buckets
  *             f.seek(0)             # <<<<<<<<<<<<<<
@@ -16265,7 +16104,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":298
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":298
  *             # Re-read file, placing words into buckets
  *             f.seek(0)
  *             for line in f:             # <<<<<<<<<<<<<<
@@ -16283,18 +16122,10 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
           for (;;) {
             if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_1)) {
               if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_12 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_12); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_12 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_12 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_12); __pyx_t_8++;
             } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_1)) {
               if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_12); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_12 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_12); __pyx_t_8++;
             } else {
               __pyx_t_12 = __pyx_t_9(__pyx_t_1);
               if (unlikely(!__pyx_t_12)) {
@@ -16310,7 +16141,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_line = __pyx_t_12;
             __pyx_t_12 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":299
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":299
  *             f.seek(0)
  *             for line in f:
  *                 (fword, eword, score1, score2) = line.split()             # <<<<<<<<<<<<<<
@@ -16324,23 +16155,22 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
             if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
               PyObject* sequence = __pyx_t_3;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              Py_ssize_t size = Py_SIZE(sequence);
-              #else
-              Py_ssize_t size = PySequence_Size(sequence);
-              #endif
-              if (unlikely(size != 4)) {
-                if (size > 4) __Pyx_RaiseTooManyValuesError(4);
-                else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              }
-              #if CYTHON_COMPILING_IN_CPYTHON
               if (likely(PyTuple_CheckExact(sequence))) {
+                if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+                  if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+                  else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_12 = PyTuple_GET_ITEM(sequence, 0); 
                 __pyx_t_11 = PyTuple_GET_ITEM(sequence, 1); 
                 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 2); 
                 __pyx_t_2 = PyTuple_GET_ITEM(sequence, 3); 
               } else {
+                if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+                  if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+                  else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_12 = PyList_GET_ITEM(sequence, 0); 
                 __pyx_t_11 = PyList_GET_ITEM(sequence, 1); 
                 __pyx_t_10 = PyList_GET_ITEM(sequence, 2); 
@@ -16350,36 +16180,28 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
               __Pyx_INCREF(__pyx_t_11);
               __Pyx_INCREF(__pyx_t_10);
               __Pyx_INCREF(__pyx_t_2);
-              #else
-              Py_ssize_t i;
-              PyObject** temps[4] = {&__pyx_t_12,&__pyx_t_11,&__pyx_t_10,&__pyx_t_2};
-              for (i=0; i < 4; i++) {
-                PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-                *(temps[i]) = item;
-              }
-              #endif
               __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-            } else
-            {
+            } else {
               Py_ssize_t index = -1;
-              PyObject** temps[4] = {&__pyx_t_12,&__pyx_t_11,&__pyx_t_10,&__pyx_t_2};
               __pyx_t_13 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               __Pyx_GOTREF(__pyx_t_13);
               __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
               __pyx_t_14 = Py_TYPE(__pyx_t_13)->tp_iternext;
-              for (index=0; index < 4; index++) {
-                PyObject* item = __pyx_t_14(__pyx_t_13); if (unlikely(!item)) goto __pyx_L26_unpacking_failed;
-                __Pyx_GOTREF(item);
-                *(temps[index]) = item;
-              }
+              index = 0; __pyx_t_12 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_12)) goto __pyx_L26_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_12);
+              index = 1; __pyx_t_11 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_11)) goto __pyx_L26_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_11);
+              index = 2; __pyx_t_10 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_10)) goto __pyx_L26_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_10);
+              index = 3; __pyx_t_2 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_2)) goto __pyx_L26_unpacking_failed;
+              __Pyx_GOTREF(__pyx_t_2);
               if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_13), 4) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              __pyx_t_14 = NULL;
               __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
               goto __pyx_L27_unpacking_done;
               __pyx_L26_unpacking_failed:;
               __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
-              __pyx_t_14 = NULL;
-              if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+              if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+              if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
               {__pyx_filename = __pyx_f[5]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               __pyx_L27_unpacking_done:;
             }
@@ -16396,7 +16218,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_score2 = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":300
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":300
  *             for line in f:
  *                 (fword, eword, score1, score2) = line.split()
  *                 f_id = self.get_f_id(fword)             # <<<<<<<<<<<<<<
@@ -16418,7 +16240,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_f_id = __pyx_t_10;
             __pyx_t_10 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":301
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":301
  *                 (fword, eword, score1, score2) = line.split()
  *                 f_id = self.get_f_id(fword)
  *                 e_id = self.get_e_id(eword)             # <<<<<<<<<<<<<<
@@ -16440,7 +16262,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_e_id = __pyx_t_3;
             __pyx_t_3 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":302
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":302
  *                 f_id = self.get_f_id(fword)
  *                 e_id = self.get_e_id(eword)
  *                 index = self.f_index.arr[f_id] + fcount.arr[f_id]             # <<<<<<<<<<<<<<
@@ -16455,7 +16277,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_v_index = __pyx_t_3;
             __pyx_t_3 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":303
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":303
  *                 e_id = self.get_e_id(eword)
  *                 index = self.f_index.arr[f_id] + fcount.arr[f_id]
  *                 fcount.arr[f_id] = fcount.arr[f_id] + 1             # <<<<<<<<<<<<<<
@@ -16466,7 +16288,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_t_15 = __Pyx_PyIndex_AsSsize_t(__pyx_v_f_id); if (unlikely((__pyx_t_15 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
             (__pyx_v_fcount->arr[__pyx_t_15]) = ((__pyx_v_fcount->arr[__pyx_t_17]) + 1);
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":304
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":304
  *                 index = self.f_index.arr[f_id] + fcount.arr[f_id]
  *                 fcount.arr[f_id] = fcount.arr[f_id] + 1
  *                 self.e_index.arr[index] = int(e_id)             # <<<<<<<<<<<<<<
@@ -16486,7 +16308,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             __pyx_t_17 = __Pyx_PyIndex_AsSsize_t(__pyx_v_index); if (unlikely((__pyx_t_17 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
             (__pyx_v_self->e_index->arr[__pyx_t_17]) = __pyx_t_20;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":305
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":305
  *                 fcount.arr[f_id] = fcount.arr[f_id] + 1
  *                 self.e_index.arr[index] = int(e_id)
  *                 self.col1[index] = float(score1)             # <<<<<<<<<<<<<<
@@ -16499,7 +16321,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
             if (PyObject_SetItem(((PyObject *)__pyx_v_self->col1), __pyx_v_index, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
             __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":306
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":306
  *                 self.e_index.arr[index] = int(e_id)
  *                 self.col1[index] = float(score1)
  *                 self.col2[index] = float(score2)             # <<<<<<<<<<<<<<
@@ -16527,7 +16349,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
         __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
         __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":273
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":273
  * 
  *         fcount = IntList()
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -16607,7 +16429,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
     __pyx_L31:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":309
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":309
  * 
  *         # Sort buckets by eword
  *         for b from 0 <= b < n_f:             # <<<<<<<<<<<<<<
@@ -16623,7 +16445,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
     __pyx_v_b = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":310
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":310
  *         # Sort buckets by eword
  *         for b from 0 <= b < n_f:
  *             i = self.f_index.arr[b]             # <<<<<<<<<<<<<<
@@ -16637,7 +16459,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
     __pyx_v_i = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":311
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":311
  *         for b from 0 <= b < n_f:
  *             i = self.f_index.arr[b]
  *             j = self.f_index.arr[b+1]             # <<<<<<<<<<<<<<
@@ -16654,7 +16476,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
     __pyx_v_j = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":312
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":312
  *             i = self.f_index.arr[b]
  *             j = self.f_index.arr[b+1]
  *             self.qsort(i,j, "")             # <<<<<<<<<<<<<<
@@ -16672,7 +16494,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
     __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_b); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":309
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":309
  * 
  *         # Sort buckets by eword
  *         for b from 0 <= b < n_f:             # <<<<<<<<<<<<<<
@@ -16718,7 +16540,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_10read_text(struct __pyx_obj_3_sa_BiLex *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":315
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":315
  * 
  * 
  *     cdef swap(self, int i, int j):             # <<<<<<<<<<<<<<
@@ -16734,7 +16556,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("swap", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":319
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":319
  *         cdef float ftmp
  * 
  *         if i == j:             # <<<<<<<<<<<<<<
@@ -16744,7 +16566,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_t_1 = (__pyx_v_i == __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":320
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":320
  * 
  *         if i == j:
  *             return             # <<<<<<<<<<<<<<
@@ -16758,7 +16580,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":322
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":322
  *             return
  * 
  *         itmp = self.e_index.arr[i]             # <<<<<<<<<<<<<<
@@ -16767,7 +16589,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_itmp = (__pyx_v_self->e_index->arr[__pyx_v_i]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":323
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":323
  * 
  *         itmp = self.e_index.arr[i]
  *         self.e_index.arr[i] = self.e_index.arr[j]             # <<<<<<<<<<<<<<
@@ -16776,7 +16598,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->e_index->arr[__pyx_v_i]) = (__pyx_v_self->e_index->arr[__pyx_v_j]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":324
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":324
  *         itmp = self.e_index.arr[i]
  *         self.e_index.arr[i] = self.e_index.arr[j]
  *         self.e_index.arr[j] = itmp             # <<<<<<<<<<<<<<
@@ -16785,7 +16607,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->e_index->arr[__pyx_v_j]) = __pyx_v_itmp;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":326
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":326
  *         self.e_index.arr[j] = itmp
  * 
  *         ftmp = self.col1.arr[i]             # <<<<<<<<<<<<<<
@@ -16794,7 +16616,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_ftmp = (__pyx_v_self->col1->arr[__pyx_v_i]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":327
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":327
  * 
  *         ftmp = self.col1.arr[i]
  *         self.col1.arr[i] = self.col1.arr[j]             # <<<<<<<<<<<<<<
@@ -16803,7 +16625,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col1->arr[__pyx_v_i]) = (__pyx_v_self->col1->arr[__pyx_v_j]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":328
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":328
  *         ftmp = self.col1.arr[i]
  *         self.col1.arr[i] = self.col1.arr[j]
  *         self.col1.arr[j] = ftmp             # <<<<<<<<<<<<<<
@@ -16812,7 +16634,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col1->arr[__pyx_v_j]) = __pyx_v_ftmp;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":330
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":330
  *         self.col1.arr[j] = ftmp
  * 
  *         ftmp = self.col2.arr[i]             # <<<<<<<<<<<<<<
@@ -16821,7 +16643,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_ftmp = (__pyx_v_self->col2->arr[__pyx_v_i]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":331
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":331
  * 
  *         ftmp = self.col2.arr[i]
  *         self.col2.arr[i] = self.col2.arr[j]             # <<<<<<<<<<<<<<
@@ -16830,7 +16652,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col2->arr[__pyx_v_i]) = (__pyx_v_self->col2->arr[__pyx_v_j]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":332
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":332
  *         ftmp = self.col2.arr[i]
  *         self.col2.arr[i] = self.col2.arr[j]
  *         self.col2.arr[j] = ftmp             # <<<<<<<<<<<<<<
@@ -16846,7 +16668,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":335
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":335
  * 
  * 
  *     cdef qsort(self, int i, int j, pad):             # <<<<<<<<<<<<<<
@@ -16869,7 +16691,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("qsort", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":338
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":338
  *         cdef int pval, p
  * 
  *         if i > j:             # <<<<<<<<<<<<<<
@@ -16879,7 +16701,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i > __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":339
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":339
  * 
  *         if i > j:
  *             raise Exception("Sort error in CLex")             # <<<<<<<<<<<<<<
@@ -16895,7 +16717,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":340
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":340
  *         if i > j:
  *             raise Exception("Sort error in CLex")
  *         if i == j: #empty interval             # <<<<<<<<<<<<<<
@@ -16905,7 +16727,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i == __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":341
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":341
  *             raise Exception("Sort error in CLex")
  *         if i == j: #empty interval
  *             return             # <<<<<<<<<<<<<<
@@ -16919,7 +16741,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":342
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":342
  *         if i == j: #empty interval
  *             return
  *         if i == j-1: # singleton interval             # <<<<<<<<<<<<<<
@@ -16929,7 +16751,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i == (__pyx_v_j - 1));
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":343
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":343
  *             return
  *         if i == j-1: # singleton interval
  *             return             # <<<<<<<<<<<<<<
@@ -16943,7 +16765,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":345
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":345
  *             return
  * 
  *         p = (i+j)/2             # <<<<<<<<<<<<<<
@@ -16952,7 +16774,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_p = __Pyx_div_long((__pyx_v_i + __pyx_v_j), 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":346
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":346
  * 
  *         p = (i+j)/2
  *         pval = self.e_index.arr[p]             # <<<<<<<<<<<<<<
@@ -16961,7 +16783,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_pval = (__pyx_v_self->e_index->arr[__pyx_v_p]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":347
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":347
  *         p = (i+j)/2
  *         pval = self.e_index.arr[p]
  *         self.swap(i, p)             # <<<<<<<<<<<<<<
@@ -16972,7 +16794,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":348
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":348
  *         pval = self.e_index.arr[p]
  *         self.swap(i, p)
  *         p = i             # <<<<<<<<<<<<<<
@@ -16981,7 +16803,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_p = __pyx_v_i;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":349
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":349
  *         self.swap(i, p)
  *         p = i
  *         for k from i+1 <= k < j:             # <<<<<<<<<<<<<<
@@ -16991,7 +16813,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_3 = __pyx_v_j;
   for (__pyx_v_k = (__pyx_v_i + 1); __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":350
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":350
  *         p = i
  *         for k from i+1 <= k < j:
  *             if pval >= self.e_index.arr[k]:             # <<<<<<<<<<<<<<
@@ -17001,7 +16823,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
     __pyx_t_1 = (__pyx_v_pval >= (__pyx_v_self->e_index->arr[__pyx_v_k]));
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":351
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":351
  *         for k from i+1 <= k < j:
  *             if pval >= self.e_index.arr[k]:
  *                 self.swap(p+1, k)             # <<<<<<<<<<<<<<
@@ -17012,7 +16834,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":352
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":352
  *             if pval >= self.e_index.arr[k]:
  *                 self.swap(p+1, k)
  *                 self.swap(p, p+1)             # <<<<<<<<<<<<<<
@@ -17023,7 +16845,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":353
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":353
  *                 self.swap(p+1, k)
  *                 self.swap(p, p+1)
  *                 p = p + 1             # <<<<<<<<<<<<<<
@@ -17036,7 +16858,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
     __pyx_L8:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":354
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":354
  *                 self.swap(p, p+1)
  *                 p = p + 1
  *         self.qsort(i,p, pad+"    ")             # <<<<<<<<<<<<<<
@@ -17050,7 +16872,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":355
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":355
  *                 p = p + 1
  *         self.qsort(i,p, pad+"    ")
  *         self.qsort(p+1,j, pad+"    ")             # <<<<<<<<<<<<<<
@@ -17098,7 +16920,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_13write_enhanced(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":358
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":358
  * 
  * 
  *     def write_enhanced(self, char* filename):             # <<<<<<<<<<<<<<
@@ -17135,7 +16957,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("write_enhanced", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":359
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":359
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -17175,7 +16997,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
           __pyx_v_f = __pyx_t_4;
           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":360
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":360
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:
  *             for i in self.f_index:             # <<<<<<<<<<<<<<
@@ -17193,18 +17015,10 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
           for (;;) {
             if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_4)) {
               if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_4)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++;
             } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_4)) {
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++;
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               __pyx_t_1 = __pyx_t_9(__pyx_t_4);
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@@ -17220,7 +17034,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
             __pyx_v_i = __pyx_t_1;
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":361
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":361
  *         with open(filename, "w") as f:
  *             for i in self.f_index:
  *                 f.write("%d " % i)             # <<<<<<<<<<<<<<
@@ -17244,7 +17058,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":362
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":362
  *             for i in self.f_index:
  *                 f.write("%d " % i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -17258,7 +17072,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":363
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":363
  *                 f.write("%d " % i)
  *             f.write("\n")
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):             # <<<<<<<<<<<<<<
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
-              __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_4); __pyx_t_8++;
             } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_2)) {
               if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_4); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_4); __pyx_t_8++;
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               __pyx_t_4 = __pyx_t_9(__pyx_t_2);
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@@ -17316,22 +17122,21 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              Py_ssize_t size = Py_SIZE(sequence);
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-              Py_ssize_t size = PySequence_Size(sequence);
-              #endif
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-                if (size > 3) __Pyx_RaiseTooManyValuesError(3);
-                else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              }
-              #if CYTHON_COMPILING_IN_CPYTHON
               if (likely(PyTuple_CheckExact(sequence))) {
+                if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
+                  if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+                  else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 0); 
                 __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1); 
                 __pyx_t_11 = PyTuple_GET_ITEM(sequence, 2); 
               } else {
+                if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
+                  if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+                  else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                }
                 __pyx_t_10 = PyList_GET_ITEM(sequence, 0); 
                 __pyx_t_1 = PyList_GET_ITEM(sequence, 1); 
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@@ -17339,14 +17144,8 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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-              #else
-              __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              __pyx_t_11 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
               __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-            } else
-            {
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@@ -17359,13 +17158,12 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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-              __pyx_t_13 = NULL;
               __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
               goto __pyx_L21_unpacking_done;
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               __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
-              __pyx_t_13 = NULL;
-              if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+              if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+              if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
               {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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@@ -17379,7 +17177,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
             __pyx_v_s2 = __pyx_t_11;
             __pyx_t_11 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":364
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":364
  *             f.write("\n")
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
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@@ -17415,7 +17213,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":365
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":365
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
  *                 f.write("%d %f %f " % (i, s1, s2))
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@@ -17429,7 +17227,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":366
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":366
  *                 f.write("%d %f %f " % (i, s1, s2))
  *             f.write("\n")
  *             for i, w in enumerate(self.id2fword):             # <<<<<<<<<<<<<<
@@ -17449,18 +17247,10 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
-              __pyx_t_11 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_11 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_11); __pyx_t_8++;
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_11); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
-              __pyx_t_11 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_11); __pyx_t_8++;
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@@ -17484,7 +17274,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
             __pyx_t_1 = __pyx_t_11;
             __pyx_t_11 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":367
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":367
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-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":368
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":368
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":369
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":369
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  *             for i, w in enumerate(self.id2eword):             # <<<<<<<<<<<<<<
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
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-              #endif
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
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-              #endif
+              __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_10); __pyx_t_8++;
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@@ -17587,7 +17369,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
             __pyx_t_2 = __pyx_t_10;
             __pyx_t_10 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":370
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":370
  *             f.write("\n")
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":371
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":371
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-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":359
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":359
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   PyObject *__pyx_v_eword = 0;
   PyObject *__pyx_v_col = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fword,&__pyx_n_s__eword,&__pyx_n_s__col,0};
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       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fword)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fword);
+        if (likely(values[0])) kw_args--;
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+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__eword);
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-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__col)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__col);
+        if (likely(values[2])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("get_score", 1, 3, 3, 2); {__pyx_filename = __pyx_f[5]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -17814,7 +17599,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_15get_score(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":374
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":374
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  * 
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@@ -17840,17 +17625,17 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("get_score", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":377
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":377
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-  __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_eword, __pyx_v_self->eword2id, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_self->eword2id, __pyx_v_eword))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":378
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":378
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  *         if eword not in self.eword2id:
  *             return None             # <<<<<<<<<<<<<<
@@ -17865,17 +17650,17 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":379
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":379
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  *         if fword not in self.fword2id:             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_fword, __pyx_v_self->fword2id, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_self->fword2id, __pyx_v_fword))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":380
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":380
  *             return None
  *         if fword not in self.fword2id:
  *             return None             # <<<<<<<<<<<<<<
@@ -17890,7 +17675,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   }
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":381
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":381
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  *             return None
  *         f_id = self.fword2id[fword]             # <<<<<<<<<<<<<<
@@ -17902,7 +17687,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   __pyx_v_f_id = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":382
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":382
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  *         e_id = self.eword2id[eword]             # <<<<<<<<<<<<<<
@@ -17914,7 +17699,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
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   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":383
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":383
  *         f_id = self.fword2id[fword]
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  *         low = self.f_index.arr[f_id]             # <<<<<<<<<<<<<<
@@ -17927,7 +17712,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   __pyx_v_low = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":384
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":384
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  *         high = self.f_index.arr[f_id+1]             # <<<<<<<<<<<<<<
@@ -17943,7 +17728,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
   __pyx_v_high = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":385
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":385
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  *         high = self.f_index.arr[f_id+1]
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@@ -17953,13 +17738,14 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
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+    __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_4);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     if (!__pyx_t_1) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":386
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":386
  *         high = self.f_index.arr[f_id+1]
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@@ -17975,7 +17761,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
     __pyx_v_midpoint = __pyx_t_2;
     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":387
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":387
  *         while high - low > 0:
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  *             val = self.e_index.arr[midpoint]             # <<<<<<<<<<<<<<
@@ -17989,31 +17775,33 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
     __pyx_v_val = __pyx_t_2;
     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":388
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":388
  *             midpoint = (low+high)/2
  *             val = self.e_index.arr[midpoint]
  *             if val == e_id:             # <<<<<<<<<<<<<<
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-    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_2);
     __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":389
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":389
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-      __pyx_t_2 = PyObject_RichCompare(__pyx_v_col, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_RichCompare(__pyx_v_col, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_2);
       __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":390
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":390
  *             if val == e_id:
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@@ -18031,19 +17819,20 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
       }
       __pyx_L8:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":391
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":391
  *                 if col == 0:
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  *                 if col == 1:             # <<<<<<<<<<<<<<
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-      __pyx_t_2 = PyObject_RichCompare(__pyx_v_col, __pyx_int_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_RichCompare(__pyx_v_col, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_2);
       __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":392
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":392
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  *                 if col == 1:
  *                     return self.col2.arr[midpoint]             # <<<<<<<<<<<<<<
@@ -18064,19 +17853,20 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
     }
     __pyx_L7:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":393
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":393
  *                 if col == 1:
  *                     return self.col2.arr[midpoint]
  *             if val > e_id:             # <<<<<<<<<<<<<<
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-    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_2);
     __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":394
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":394
  *                     return self.col2.arr[midpoint]
  *             if val > e_id:
  *                 high = midpoint             # <<<<<<<<<<<<<<
@@ -18090,19 +17880,20 @@ static PyObject *__pyx_pf_3_sa_5BiLex_14get_score(struct __pyx_obj_3_sa_BiLex *_
     }
     __pyx_L10:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":395
+    /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":395
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  *             if val < e_id:             # <<<<<<<<<<<<<<
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-    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_RichCompare(__pyx_v_val, __pyx_v_e_id, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_2);
     __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":396
+      /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":396
  *                 high = midpoint
  *             if val < e_id:
  *                 low = midpoint + 1             # <<<<<<<<<<<<<<
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     __pyx_L11:;
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":397
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":397
  *             if val < e_id:
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  *         return None             # <<<<<<<<<<<<<<
@@ -18172,7 +17963,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_17write_text(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":400
+/* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":400
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  *     def write_text(self, char* filename):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("write_text", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":404
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":404
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  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
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-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":405
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":405
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  *         with open(filename, "w") as f:
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@@ -18265,7 +18056,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
           __pyx_v_N = __pyx_t_4;
           __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":406
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":406
  *         with open(filename, "w") as f:
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  *             f_id = 0             # <<<<<<<<<<<<<<
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           __pyx_v_f_id = __pyx_int_0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":407
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":407
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  *             for i from 0 <= i < N:             # <<<<<<<<<<<<<<
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             __pyx_v_i = __pyx_t_4;
             __pyx_t_4 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":408
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":408
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-              __pyx_t_1 = PyObject_RichCompare(__pyx_t_4, __pyx_v_i, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+              __pyx_t_1 = PyObject_RichCompare(__pyx_t_4, __pyx_v_i, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+              __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
               __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               if (!__pyx_t_11) break;
 
-              /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":409
+              /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":409
  *             for i from 0 <= i < N:
  *                 while self.f_index.arr[f_id+1] == i:
  *                     f_id = f_id + 1             # <<<<<<<<<<<<<<
@@ -18324,7 +18116,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
               __pyx_t_1 = 0;
             }
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":410
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":410
  *                 while self.f_index.arr[f_id+1] == i:
  *                     f_id = f_id + 1
  *                 e_id = self.e_index.arr[i]             # <<<<<<<<<<<<<<
@@ -18338,7 +18130,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
             __pyx_v_e_id = __pyx_t_1;
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":411
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":411
  *                     f_id = f_id + 1
  *                 e_id = self.e_index.arr[i]
  *                 score1 = self.col1.arr[i]             # <<<<<<<<<<<<<<
@@ -18352,7 +18144,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
             __pyx_v_score1 = __pyx_t_1;
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":412
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":412
  *                 e_id = self.e_index.arr[i]
  *                 score1 = self.col1.arr[i]
  *                 score2 = self.col2.arr[i]             # <<<<<<<<<<<<<<
@@ -18365,7 +18157,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
             __pyx_v_score2 = __pyx_t_1;
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":413
+            /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":413
  *                 score1 = self.col1.arr[i]
  *                 score2 = self.col2.arr[i]
  *                 f.write("%s %s %.6f %.6f\n" % (self.id2fword[f_id], self.id2eword[e_id], score1, score2))             # <<<<<<<<<<<<<<
@@ -18406,7 +18198,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
             __pyx_t_10 = __Pyx_PyInt_AsLong(__pyx_v_i); if (unlikely((__pyx_t_10 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
           }
 
-          /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":407
+          /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":407
  *             N = len(self.e_index)
  *             f_id = 0
  *             for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -18429,7 +18221,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
         __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
         __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":404
+        /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":404
  *         cdef i, N, e_id, f_id
  * 
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -18531,7 +18323,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_16write_text(struct __pyx_obj_3_sa_BiLex *
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":21
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":21
  * cdef int LOWER_MASK[32]
  * 
  * cdef void _init_lower_mask():             # <<<<<<<<<<<<<<
@@ -18547,7 +18339,7 @@ static void __pyx_f_3_sa__init_lower_mask(void) {
   unsigned int __pyx_t_2;
   __Pyx_RefNannySetupContext("_init_lower_mask", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":23
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":23
  * cdef void _init_lower_mask():
  *     cdef unsigned i
  *     cdef int mask = 0             # <<<<<<<<<<<<<<
@@ -18556,7 +18348,7 @@ static void __pyx_f_3_sa__init_lower_mask(void) {
  */
   __pyx_v_mask = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":24
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":24
  *     cdef unsigned i
  *     cdef int mask = 0
  *     for i in range(MIN_BOTTOM_SIZE):             # <<<<<<<<<<<<<<
@@ -18567,7 +18359,7 @@ static void __pyx_f_3_sa__init_lower_mask(void) {
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_i = __pyx_t_2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":25
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":25
  *     cdef int mask = 0
  *     for i in range(MIN_BOTTOM_SIZE):
  *         mask = (mask << 1) + 1             # <<<<<<<<<<<<<<
@@ -18576,7 +18368,7 @@ static void __pyx_f_3_sa__init_lower_mask(void) {
  */
     __pyx_v_mask = ((__pyx_v_mask << 1) + 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":26
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":26
  *     for i in range(MIN_BOTTOM_SIZE):
  *         mask = (mask << 1) + 1
  *         LOWER_MASK[i] = mask             # <<<<<<<<<<<<<<
@@ -18589,7 +18381,7 @@ static void __pyx_f_3_sa__init_lower_mask(void) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":37
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":37
  * 
  * 
  * cdef _BitSet* new_BitSet():             # <<<<<<<<<<<<<<
@@ -18603,7 +18395,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("new_BitSet", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":40
  *     cdef _BitSet* b
  * 
  *     b = <_BitSet*> malloc(sizeof(_BitSet))             # <<<<<<<<<<<<<<
@@ -18612,7 +18404,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b = ((struct __pyx_t_3_sa__BitSet *)malloc((sizeof(struct __pyx_t_3_sa__BitSet))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":41
  * 
  *     b = <_BitSet*> malloc(sizeof(_BitSet))
  *     b.bitset = 0             # <<<<<<<<<<<<<<
@@ -18621,7 +18413,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->bitset = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":42
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":42
  *     b = <_BitSet*> malloc(sizeof(_BitSet))
  *     b.bitset = 0
  *     b.min_val = -1             # <<<<<<<<<<<<<<
@@ -18630,7 +18422,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->min_val = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":43
  *     b.bitset = 0
  *     b.min_val = -1
  *     b.max_val = -1             # <<<<<<<<<<<<<<
@@ -18639,7 +18431,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->max_val = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":44
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":44
  *     b.min_val = -1
  *     b.max_val = -1
  *     b.size = 0             # <<<<<<<<<<<<<<
@@ -18648,7 +18440,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->size = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":45
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":45
  *     b.max_val = -1
  *     b.size = 0
  *     return b             # <<<<<<<<<<<<<<
@@ -18664,7 +18456,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":48
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":48
  * 
  * 
  * cdef int bitset_findsucc(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -18685,7 +18477,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("bitset_findsucc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":52
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":52
  *     cdef int low, high, mid
  * 
  *     if b.max_val == -1 or i >= b.max_val:             # <<<<<<<<<<<<<<
@@ -18701,7 +18493,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":53
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":53
  * 
  *     if b.max_val == -1 or i >= b.max_val:
  *         return -1             # <<<<<<<<<<<<<<
@@ -18714,7 +18506,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":54
  *     if b.max_val == -1 or i >= b.max_val:
  *         return -1
  *     if i < b.min_val:             # <<<<<<<<<<<<<<
@@ -18724,7 +18516,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   __pyx_t_3 = (__pyx_v_i < __pyx_v_b->min_val);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":55
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":55
  *         return -1
  *     if i < b.min_val:
  *         return b.min_val             # <<<<<<<<<<<<<<
@@ -18737,7 +18529,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":57
  *         return b.min_val
  * 
  *     bitset = b.bitset & ~LOWER_MASK[i]             # <<<<<<<<<<<<<<
@@ -18746,7 +18538,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_bitset = (__pyx_v_b->bitset & (~(__pyx_v_3_sa_LOWER_MASK[__pyx_v_i])));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":58
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":58
  * 
  *     bitset = b.bitset & ~LOWER_MASK[i]
  *     low = i+1             # <<<<<<<<<<<<<<
@@ -18755,7 +18547,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_low = (__pyx_v_i + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":59
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":59
  *     bitset = b.bitset & ~LOWER_MASK[i]
  *     low = i+1
  *     high = b.max_val+1             # <<<<<<<<<<<<<<
@@ -18764,7 +18556,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_high = (__pyx_v_b->max_val + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":60
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":60
  *     low = i+1
  *     high = b.max_val+1
  *     while low < high-1:             # <<<<<<<<<<<<<<
@@ -18775,7 +18567,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_t_3 = (__pyx_v_low < (__pyx_v_high - 1));
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":61
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":61
  *     high = b.max_val+1
  *     while low < high-1:
  *         mid = (high + low)/2             # <<<<<<<<<<<<<<
@@ -18784,7 +18576,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
     __pyx_v_mid = __Pyx_div_long((__pyx_v_high + __pyx_v_low), 2);
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":62
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":62
  *     while low < high-1:
  *         mid = (high + low)/2
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])             # <<<<<<<<<<<<<<
@@ -18793,7 +18585,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
     __pyx_v_mask = (~((__pyx_v_3_sa_LOWER_MASK[(__pyx_v_high - 1)]) ^ (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_mid - 1)])));
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":63
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":63
  *         mid = (high + low)/2
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])
  *         if bitset & mask == 0:             # <<<<<<<<<<<<<<
@@ -18803,7 +18595,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_t_3 = ((__pyx_v_bitset & __pyx_v_mask) == 0);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":64
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":64
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])
  *         if bitset & mask == 0:
  *             low = mid             # <<<<<<<<<<<<<<
@@ -18815,7 +18607,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":66
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":66
  *             low = mid
  *         else:
  *             bitset = bitset & mask             # <<<<<<<<<<<<<<
@@ -18824,7 +18616,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
       __pyx_v_bitset = (__pyx_v_bitset & __pyx_v_mask);
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":67
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":67
  *         else:
  *             bitset = bitset & mask
  *             high = mid             # <<<<<<<<<<<<<<
@@ -18836,7 +18628,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_L7:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":68
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":68
  *             bitset = bitset & mask
  *             high = mid
  *     return low             # <<<<<<<<<<<<<<
@@ -18852,7 +18644,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":71
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":71
  * 
  * 
  * cdef int bitset_insert(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -18867,7 +18659,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("bitset_insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":74
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":74
  *     cdef int val
  * 
  *     val = 1 << i             # <<<<<<<<<<<<<<
@@ -18876,7 +18668,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
   __pyx_v_val = (1 << __pyx_v_i);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":75
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":75
  * 
  *     val = 1 << i
  *     if b.bitset & val == 0:             # <<<<<<<<<<<<<<
@@ -18886,7 +18678,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   __pyx_t_1 = ((__pyx_v_b->bitset & __pyx_v_val) == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":76
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":76
  *     val = 1 << i
  *     if b.bitset & val == 0:
  *         b.bitset = b.bitset | val             # <<<<<<<<<<<<<<
@@ -18895,7 +18687,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
     __pyx_v_b->bitset = (__pyx_v_b->bitset | __pyx_v_val);
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":77
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":77
  *     if b.bitset & val == 0:
  *         b.bitset = b.bitset | val
  *         if b.size == 0:             # <<<<<<<<<<<<<<
@@ -18905,7 +18697,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     __pyx_t_1 = (__pyx_v_b->size == 0);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":78
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":78
  *         b.bitset = b.bitset | val
  *         if b.size == 0:
  *             b.min_val = i             # <<<<<<<<<<<<<<
@@ -18914,7 +18706,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
       __pyx_v_b->min_val = __pyx_v_i;
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":79
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":79
  *         if b.size == 0:
  *             b.min_val = i
  *             b.max_val = i             # <<<<<<<<<<<<<<
@@ -18926,7 +18718,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":81
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":81
  *             b.max_val = i
  *         else:
  *             if i < b.min_val:             # <<<<<<<<<<<<<<
@@ -18936,7 +18728,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       __pyx_t_1 = (__pyx_v_i < __pyx_v_b->min_val);
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":82
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":82
  *         else:
  *             if i < b.min_val:
  *                 b.min_val = i             # <<<<<<<<<<<<<<
@@ -18948,7 +18740,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       }
       __pyx_L5:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":83
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":83
  *             if i < b.min_val:
  *                 b.min_val = i
  *             if i > b.max_val:             # <<<<<<<<<<<<<<
@@ -18958,7 +18750,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       __pyx_t_1 = (__pyx_v_i > __pyx_v_b->max_val);
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":84
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":84
  *                 b.min_val = i
  *             if i > b.max_val:
  *                 b.max_val = i             # <<<<<<<<<<<<<<
@@ -18972,7 +18764,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":85
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":85
  *             if i > b.max_val:
  *                 b.max_val = i
  *         b.size = b.size + 1             # <<<<<<<<<<<<<<
@@ -18981,7 +18773,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
     __pyx_v_b->size = (__pyx_v_b->size + 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":86
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":86
  *                 b.max_val = i
  *         b.size = b.size + 1
  *         return 1             # <<<<<<<<<<<<<<
@@ -18994,7 +18786,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":87
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":87
  *         b.size = b.size + 1
  *         return 1
  *     return 0             # <<<<<<<<<<<<<<
@@ -19010,7 +18802,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":90
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":90
  * 
  * 
  * cdef int bitset_contains(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -19025,7 +18817,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("bitset_contains", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":93
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":93
  *     cdef int val
  * 
  *     val = 1 << i             # <<<<<<<<<<<<<<
@@ -19034,7 +18826,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_val = (1 << __pyx_v_i);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":94
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":94
  * 
  *     val = 1 << i
  *     if b.bitset & val == 0:             # <<<<<<<<<<<<<<
@@ -19044,7 +18836,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   __pyx_t_1 = ((__pyx_v_b->bitset & __pyx_v_val) == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":95
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":95
  *     val = 1 << i
  *     if b.bitset & val == 0:
  *         return 0             # <<<<<<<<<<<<<<
@@ -19057,7 +18849,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":97
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":97
  *         return 0
  *     else:
  *         return 1             # <<<<<<<<<<<<<<
@@ -19086,7 +18878,7 @@ static PyObject *__pyx_pw_3_sa_14BitSetIterator_1__next__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":104
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":104
  *     cdef int next_val
  * 
  *     def __next__(self):             # <<<<<<<<<<<<<<
@@ -19105,7 +18897,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__next__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":107
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":107
  *         cdef int ret_val
  * 
  *         if self.next_val == -1:             # <<<<<<<<<<<<<<
@@ -19115,7 +18907,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   __pyx_t_1 = (__pyx_v_self->next_val == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":108
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":108
  * 
  *         if self.next_val == -1:
  *             raise StopIteration()             # <<<<<<<<<<<<<<
@@ -19131,7 +18923,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":109
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":109
  *         if self.next_val == -1:
  *             raise StopIteration()
  *         ret_val = self.next_val             # <<<<<<<<<<<<<<
@@ -19140,7 +18932,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
  */
   __pyx_v_ret_val = __pyx_v_self->next_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":110
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":110
  *             raise StopIteration()
  *         ret_val = self.next_val
  *         self.next_val = bitset_findsucc(self.b, ret_val)             # <<<<<<<<<<<<<<
@@ -19149,7 +18941,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
  */
   __pyx_v_self->next_val = __pyx_f_3_sa_bitset_findsucc(__pyx_v_self->b, __pyx_v_ret_val);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":111
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":111
  *         ret_val = self.next_val
  *         self.next_val = bitset_findsucc(self.b, ret_val)
  *         return ret_val             # <<<<<<<<<<<<<<
@@ -19189,7 +18981,7 @@ static int __pyx_pw_3_sa_6BitSet_1__cinit__(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":122
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":122
  *     cdef _BitSet* b
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -19202,7 +18994,7 @@ static int __pyx_pf_3_sa_6BitSet___cinit__(struct __pyx_obj_3_sa_BitSet *__pyx_v
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":123
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":123
  * 
  *     def __cinit__(self):
  *         self.b = new_BitSet()             # <<<<<<<<<<<<<<
@@ -19225,7 +19017,7 @@ static void __pyx_pw_3_sa_6BitSet_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":125
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":125
  *         self.b = new_BitSet()
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -19237,7 +19029,7 @@ static void __pyx_pf_3_sa_6BitSet_2__dealloc__(struct __pyx_obj_3_sa_BitSet *__p
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":126
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":126
  * 
  *     def __dealloc__(self):
  *         free(self.b)             # <<<<<<<<<<<<<<
@@ -19260,7 +19052,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_5__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":128
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":128
  *         free(self.b)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -19278,7 +19070,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__iter__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":130
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":130
  *     def __iter__(self):
  *         cdef BitSetIterator it
  *         it = BitSetIterator()             # <<<<<<<<<<<<<<
@@ -19290,7 +19082,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
   __pyx_v_it = ((struct __pyx_obj_3_sa_BitSetIterator *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":131
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":131
  *         cdef BitSetIterator it
  *         it = BitSetIterator()
  *         it.b = self.b             # <<<<<<<<<<<<<<
@@ -19299,7 +19091,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
  */
   __pyx_v_it->b = __pyx_v_self->b;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":132
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":132
  *         it = BitSetIterator()
  *         it.b = self.b
  *         it.next_val = self.b.min_val             # <<<<<<<<<<<<<<
@@ -19308,7 +19100,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
  */
   __pyx_v_it->next_val = __pyx_v_self->b->min_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":133
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":133
  *         it.b = self.b
  *         it.next_val = self.b.min_val
  *         return it             # <<<<<<<<<<<<<<
@@ -19344,7 +19136,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_7insert(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":135
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":135
  *         return it
  * 
  *     def insert(self, i):             # <<<<<<<<<<<<<<
@@ -19362,7 +19154,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_6insert(struct __pyx_obj_3_sa_BitSet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":136
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":136
  * 
  *     def insert(self, i):
  *         return bitset_insert(self.b, i)             # <<<<<<<<<<<<<<
@@ -19400,7 +19192,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_9findsucc(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":138
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":138
  *         return bitset_insert(self.b, i)
  * 
  *     def findsucc(self, i):             # <<<<<<<<<<<<<<
@@ -19418,7 +19210,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_8findsucc(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("findsucc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":139
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":139
  * 
  *     def findsucc(self, i):
  *         return bitset_findsucc(self.b, i)             # <<<<<<<<<<<<<<
@@ -19456,7 +19248,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_11__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":141
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":141
  *         return bitset_findsucc(self.b, i)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -19475,7 +19267,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_10__str__(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":142
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":142
  * 
  *     def __str__(self):
  *         return dec2bin(self.b.bitset)+"  ("+str(self.b.size)+","+str(self.b.min_val)+","+str(self.b.max_val)+")"             # <<<<<<<<<<<<<<
@@ -19568,7 +19360,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_13min(PyObject *__pyx_v_self, CYTHON_UNUS
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":144
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":144
  *         return dec2bin(self.b.bitset)+"  ("+str(self.b.size)+","+str(self.b.min_val)+","+str(self.b.max_val)+")"
  * 
  *     def min(self):             # <<<<<<<<<<<<<<
@@ -19585,7 +19377,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_12min(struct __pyx_obj_3_sa_BitSet *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("min", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":145
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":145
  * 
  *     def min(self):
  *         return self.b.min_val             # <<<<<<<<<<<<<<
@@ -19622,7 +19414,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_15max(PyObject *__pyx_v_self, CYTHON_UNUS
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":147
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":147
  *         return self.b.min_val
  * 
  *     def max(self):             # <<<<<<<<<<<<<<
@@ -19639,7 +19431,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_14max(struct __pyx_obj_3_sa_BitSet *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("max", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":148
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":148
  * 
  *     def max(self):
  *         return self.b.max_val             # <<<<<<<<<<<<<<
@@ -19676,7 +19468,7 @@ static Py_ssize_t __pyx_pw_3_sa_6BitSet_17__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":150
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":150
  *         return self.b.max_val
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -19689,7 +19481,7 @@ static Py_ssize_t __pyx_pf_3_sa_6BitSet_16__len__(struct __pyx_obj_3_sa_BitSet *
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":151
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":151
  * 
  *     def __len__(self):
  *         return self.b.size             # <<<<<<<<<<<<<<
@@ -19716,7 +19508,7 @@ static int __pyx_pw_3_sa_6BitSet_19__contains__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":153
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":153
  *         return self.b.size
  * 
  *     def __contains__(self, i):             # <<<<<<<<<<<<<<
@@ -19735,7 +19527,7 @@ static int __pyx_pf_3_sa_6BitSet_18__contains__(struct __pyx_obj_3_sa_BitSet *__
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__contains__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":154
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":154
  * 
  *     def __contains__(self, i):
  *         return bool(bitset_contains(self.b, i))             # <<<<<<<<<<<<<<
@@ -19761,7 +19553,7 @@ static int __pyx_pf_3_sa_6BitSet_18__contains__(struct __pyx_obj_3_sa_BitSet *__
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":157
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":157
  * 
  * 
  * cdef str dec2bin(long i):             # <<<<<<<<<<<<<<
@@ -19783,7 +19575,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("dec2bin", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":158
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":158
  * 
  * cdef str dec2bin(long i):
  *     cdef str result = ""             # <<<<<<<<<<<<<<
@@ -19793,7 +19585,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
   __pyx_v_result = __pyx_kp_s_45;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":160
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":160
  *     cdef str result = ""
  *     cdef unsigned d
  *     for d in range(MIN_BOTTOM_SIZE):             # <<<<<<<<<<<<<<
@@ -19804,7 +19596,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_d = __pyx_t_2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":161
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":161
  *     cdef unsigned d
  *     for d in range(MIN_BOTTOM_SIZE):
  *         if i & LOWER_MASK[0] == 0:             # <<<<<<<<<<<<<<
@@ -19814,7 +19606,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     __pyx_t_3 = ((__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[0])) == 0);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":162
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":162
  *     for d in range(MIN_BOTTOM_SIZE):
  *         if i & LOWER_MASK[0] == 0:
  *             result = "0"+result             # <<<<<<<<<<<<<<
@@ -19830,7 +19622,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":164
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":164
  *             result = "0"+result
  *         else:
  *             result = "1"+result             # <<<<<<<<<<<<<<
@@ -19845,7 +19637,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":165
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":165
  *         else:
  *             result = "1"+result
  *         i = i >> 1             # <<<<<<<<<<<<<<
@@ -19855,7 +19647,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     __pyx_v_i = (__pyx_v_i >> 1);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":166
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":166
  *             result = "1"+result
  *         i = i >> 1
  *     return result             # <<<<<<<<<<<<<<
@@ -19880,7 +19672,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":177
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":177
  *     void** bottom
  * 
  * cdef _VEB* new_VEB(int n):             # <<<<<<<<<<<<<<
@@ -19901,7 +19693,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("new_VEB", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":181
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":181
  *     cdef int num_bits, num_top_bits, i
  * 
  *     veb = <_VEB*> malloc(sizeof(_VEB))             # <<<<<<<<<<<<<<
@@ -19910,7 +19702,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb = ((struct __pyx_t_3_sa__VEB *)malloc((sizeof(struct __pyx_t_3_sa__VEB))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":183
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":183
  *     veb = <_VEB*> malloc(sizeof(_VEB))
  * 
  *     num_bits = int(ceil(log(n) / log(2)))             # <<<<<<<<<<<<<<
@@ -19925,7 +19717,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_v_num_bits = ((int)ceil((__pyx_t_1 / __pyx_t_2)));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":184
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":184
  * 
  *     num_bits = int(ceil(log(n) / log(2)))
  *     veb.num_bottom_bits = num_bits/2             # <<<<<<<<<<<<<<
@@ -19934,7 +19726,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->num_bottom_bits = __Pyx_div_long(__pyx_v_num_bits, 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":185
  *     num_bits = int(ceil(log(n) / log(2)))
  *     veb.num_bottom_bits = num_bits/2
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -19944,7 +19736,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   __pyx_t_3 = (__pyx_v_veb->num_bottom_bits < __pyx_v_3_sa_MIN_BOTTOM_BITS);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":186
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":186
  *     veb.num_bottom_bits = num_bits/2
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:
  *         veb.num_bottom_bits = MIN_BOTTOM_BITS             # <<<<<<<<<<<<<<
@@ -19956,7 +19748,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":187
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":187
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:
  *         veb.num_bottom_bits = MIN_BOTTOM_BITS
  *     veb.top_universe_size = (n >> veb.num_bottom_bits) + 1             # <<<<<<<<<<<<<<
@@ -19965,7 +19757,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->top_universe_size = ((__pyx_v_n >> __pyx_v_veb->num_bottom_bits) + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":189
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":189
  *     veb.top_universe_size = (n >> veb.num_bottom_bits) + 1
  * 
  *     veb.bottom = <void**> malloc(veb.top_universe_size * sizeof(void*))             # <<<<<<<<<<<<<<
@@ -19974,7 +19766,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->bottom = ((void **)malloc((__pyx_v_veb->top_universe_size * (sizeof(void *)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":190
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":190
  * 
  *     veb.bottom = <void**> malloc(veb.top_universe_size * sizeof(void*))
  *     memset(veb.bottom, 0, veb.top_universe_size * sizeof(void*))             # <<<<<<<<<<<<<<
@@ -19983,7 +19775,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   memset(__pyx_v_veb->bottom, 0, (__pyx_v_veb->top_universe_size * (sizeof(void *))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":192
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":192
  *     memset(veb.bottom, 0, veb.top_universe_size * sizeof(void*))
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -19993,7 +19785,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":193
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":193
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         veb.top = new_VEB(veb.top_universe_size)             # <<<<<<<<<<<<<<
@@ -20005,7 +19797,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":195
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":195
  *         veb.top = new_VEB(veb.top_universe_size)
  *     else:
  *         veb.top = new_BitSet()             # <<<<<<<<<<<<<<
@@ -20016,7 +19808,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":197
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":197
  *         veb.top = new_BitSet()
  * 
  *     veb.max_val = -1             # <<<<<<<<<<<<<<
@@ -20025,7 +19817,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->max_val = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":198
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":198
  * 
  *     veb.max_val = -1
  *     veb.min_val = -1             # <<<<<<<<<<<<<<
@@ -20034,7 +19826,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->min_val = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":199
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":199
  *     veb.max_val = -1
  *     veb.min_val = -1
  *     veb.size = 0             # <<<<<<<<<<<<<<
@@ -20043,7 +19835,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->size = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":200
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":200
  *     veb.min_val = -1
  *     veb.size = 0
  *     return veb             # <<<<<<<<<<<<<<
@@ -20063,7 +19855,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":203
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":203
  * 
  * 
  * cdef int VEB_insert(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -20084,7 +19876,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("VEB_insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":208
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":208
  *     cdef int a, b, tmp
  * 
  *     if veb.size == 0:             # <<<<<<<<<<<<<<
@@ -20094,7 +19886,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   __pyx_t_1 = (__pyx_v_veb->size == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":209
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":209
  * 
  *     if veb.size == 0:
  *         veb.min_val = i             # <<<<<<<<<<<<<<
@@ -20103,7 +19895,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_veb->min_val = __pyx_v_i;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":210
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":210
  *     if veb.size == 0:
  *         veb.min_val = i
  *         veb.max_val = i             # <<<<<<<<<<<<<<
@@ -20114,7 +19906,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":211
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":211
  *         veb.min_val = i
  *         veb.max_val = i
  *     elif i == veb.min_val or i == veb.max_val:             # <<<<<<<<<<<<<<
@@ -20130,7 +19922,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":212
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":212
  *         veb.max_val = i
  *     elif i == veb.min_val or i == veb.max_val:
  *         return 0             # <<<<<<<<<<<<<<
@@ -20143,7 +19935,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":214
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":214
  *         return 0
  *     else:
  *         if i < veb.min_val:             # <<<<<<<<<<<<<<
@@ -20153,7 +19945,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_i < __pyx_v_veb->min_val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":215
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":215
  *     else:
  *         if i < veb.min_val:
  *             tmp = i             # <<<<<<<<<<<<<<
@@ -20162,7 +19954,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_tmp = __pyx_v_i;
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":216
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":216
  *         if i < veb.min_val:
  *             tmp = i
  *             i = veb.min_val             # <<<<<<<<<<<<<<
@@ -20171,7 +19963,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_i = __pyx_v_veb->min_val;
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":217
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":217
  *             tmp = i
  *             i = veb.min_val
  *             veb.min_val = tmp             # <<<<<<<<<<<<<<
@@ -20183,7 +19975,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":218
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":218
  *             i = veb.min_val
  *             veb.min_val = tmp
  *         a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -20192,7 +19984,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":219
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":219
  *             veb.min_val = tmp
  *         a = i >> veb.num_bottom_bits
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -20201,7 +19993,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":220
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":220
  *         a = i >> veb.num_bottom_bits
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *         if veb.bottom[a] == NULL:             # <<<<<<<<<<<<<<
@@ -20211,7 +20003,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = ((__pyx_v_veb->bottom[__pyx_v_a]) == NULL);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":221
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":221
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *         if veb.bottom[a] == NULL:
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -20221,7 +20013,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":222
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":222
  *         if veb.bottom[a] == NULL:
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *                 subv = <_VEB*> veb.top             # <<<<<<<<<<<<<<
@@ -20230,7 +20022,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
         __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)__pyx_v_veb->top);
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":223
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":223
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *                 subv = <_VEB*> veb.top
  *                 VEB_insert(subv, a)             # <<<<<<<<<<<<<<
@@ -20242,7 +20034,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":225
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":225
  *                 VEB_insert(subv, a)
  *             else:
  *                 subb = <_BitSet*> veb.top             # <<<<<<<<<<<<<<
@@ -20251,7 +20043,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
         __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)__pyx_v_veb->top);
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":226
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":226
  *             else:
  *                 subb = <_BitSet*> veb.top
  *                 bitset_insert(subb, a)             # <<<<<<<<<<<<<<
@@ -20262,7 +20054,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       __pyx_L6:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":227
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":227
  *                 subb = <_BitSet*> veb.top
  *                 bitset_insert(subb, a)
  *             if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -20272,7 +20064,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":228
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":228
  *                 bitset_insert(subb, a)
  *             if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *                 veb.bottom[a] = new_VEB(1 << veb.num_bottom_bits)             # <<<<<<<<<<<<<<
@@ -20284,7 +20076,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":230
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":230
  *                 veb.bottom[a] = new_VEB(1 << veb.num_bottom_bits)
  *             else:
  *                 veb.bottom[a] = new_BitSet()             # <<<<<<<<<<<<<<
@@ -20298,7 +20090,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":231
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":231
  *             else:
  *                 veb.bottom[a] = new_BitSet()
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -20308,7 +20100,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":232
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":232
  *                 veb.bottom[a] = new_BitSet()
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -20317,7 +20109,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":233
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":233
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             if VEB_insert(subv, b) == 0:             # <<<<<<<<<<<<<<
@@ -20327,7 +20119,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_f_3_sa_VEB_insert(__pyx_v_subv, __pyx_v_b) == 0);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":234
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":234
  *             subv = <_VEB*> veb.bottom[a]
  *             if VEB_insert(subv, b) == 0:
  *                 return 0             # <<<<<<<<<<<<<<
@@ -20343,7 +20135,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":236
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":236
  *                 return 0
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -20352,7 +20144,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":237
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":237
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             if bitset_insert(subb, b) == 0:             # <<<<<<<<<<<<<<
@@ -20362,7 +20154,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_f_3_sa_bitset_insert(__pyx_v_subb, __pyx_v_b) == 0);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":238
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":238
  *             subb = <_BitSet*> veb.bottom[a]
  *             if bitset_insert(subb, b) == 0:
  *                 return 0             # <<<<<<<<<<<<<<
@@ -20377,7 +20169,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L8:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":240
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":240
  *                 return 0
  * 
  *         if i > veb.max_val:             # <<<<<<<<<<<<<<
@@ -20387,7 +20179,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_i > __pyx_v_veb->max_val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":241
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":241
  * 
  *         if i > veb.max_val:
  *             veb.max_val = i             # <<<<<<<<<<<<<<
@@ -20401,7 +20193,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":242
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":242
  *         if i > veb.max_val:
  *             veb.max_val = i
  *     veb.size = veb.size + 1             # <<<<<<<<<<<<<<
@@ -20410,7 +20202,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
   __pyx_v_veb->size = (__pyx_v_veb->size + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":243
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":243
  *             veb.max_val = i
  *     veb.size = veb.size + 1
  *     return 1             # <<<<<<<<<<<<<<
@@ -20426,7 +20218,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":246
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":246
  * 
  * 
  * cdef del_VEB(_VEB* veb):             # <<<<<<<<<<<<<<
@@ -20445,7 +20237,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("del_VEB", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":249
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":249
  *     cdef int i
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -20455,7 +20247,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":250
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":250
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         i = (<_VEB*> veb.top).min_val             # <<<<<<<<<<<<<<
@@ -20467,7 +20259,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":252
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":252
  *         i = (<_VEB*> veb.top).min_val
  *     else:
  *         i = (<_BitSet*> veb.top).min_val             # <<<<<<<<<<<<<<
@@ -20478,7 +20270,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":254
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":254
  *         i = (<_BitSet*> veb.top).min_val
  * 
  *     while i != -1:             # <<<<<<<<<<<<<<
@@ -20489,7 +20281,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_i != -1);
     if (!__pyx_t_1) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":255
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":255
  * 
  *     while i != -1:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -20499,7 +20291,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":256
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":256
  *     while i != -1:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             del_VEB(<_VEB*> veb.bottom[i])             # <<<<<<<<<<<<<<
@@ -20513,7 +20305,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":258
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":258
  *             del_VEB(<_VEB*> veb.bottom[i])
  *         else:
  *             free(<_BitSet*> veb.bottom[i])             # <<<<<<<<<<<<<<
@@ -20524,7 +20316,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     __pyx_L6:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":260
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":260
  *             free(<_BitSet*> veb.bottom[i])
  * 
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -20534,7 +20326,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":261
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":261
  * 
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             i = VEB_findsucc(<_VEB*> veb.top, i)             # <<<<<<<<<<<<<<
@@ -20546,7 +20338,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":263
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":263
  *             i = VEB_findsucc(<_VEB*> veb.top, i)
  *         else:
  *             i = bitset_findsucc(<_BitSet*> veb.top, i)             # <<<<<<<<<<<<<<
@@ -20558,7 +20350,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_L7:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":265
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":265
  *             i = bitset_findsucc(<_BitSet*> veb.top, i)
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -20568,7 +20360,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":266
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":266
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         del_VEB(<_VEB*> veb.top)             # <<<<<<<<<<<<<<
@@ -20582,7 +20374,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":268
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":268
  *         del_VEB(<_VEB*> veb.top)
  *     else:
  *         free(<_BitSet*> veb.top)             # <<<<<<<<<<<<<<
@@ -20593,7 +20385,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   __pyx_L8:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":269
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":269
  *     else:
  *         free(<_BitSet*> veb.top)
  *     free(veb.bottom)             # <<<<<<<<<<<<<<
@@ -20602,7 +20394,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
  */
   free(__pyx_v_veb->bottom);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":270
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":270
  *         free(<_BitSet*> veb.top)
  *     free(veb.bottom)
  *     free(veb)             # <<<<<<<<<<<<<<
@@ -20623,7 +20415,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":273
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":273
  * 
  * 
  * cdef int VEB_findsucc(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -20646,7 +20438,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("VEB_findsucc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":278
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":278
  *     cdef int a, b, j, c, found
  * 
  *     if veb.max_val == -1 or i>=veb.max_val:             # <<<<<<<<<<<<<<
@@ -20662,7 +20454,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":279
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":279
  * 
  *     if veb.max_val == -1 or i>=veb.max_val:
  *         return -1             # <<<<<<<<<<<<<<
@@ -20675,7 +20467,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":280
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":280
  *     if veb.max_val == -1 or i>=veb.max_val:
  *         return -1
  *     if i < veb.min_val:             # <<<<<<<<<<<<<<
@@ -20685,7 +20477,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = (__pyx_v_i < __pyx_v_veb->min_val);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":281
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":281
  *         return -1
  *     if i < veb.min_val:
  *         return veb.min_val             # <<<<<<<<<<<<<<
@@ -20698,7 +20490,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":283
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":283
  *         return veb.min_val
  * 
  *     a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -20707,7 +20499,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":284
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":284
  * 
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -20716,7 +20508,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":285
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":285
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     found = 0             # <<<<<<<<<<<<<<
@@ -20725,7 +20517,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_found = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":286
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":286
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     found = 0
  *     if veb.bottom[a] != NULL:             # <<<<<<<<<<<<<<
@@ -20735,7 +20527,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = ((__pyx_v_veb->bottom[__pyx_v_a]) != NULL);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":287
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":287
  *     found = 0
  *     if veb.bottom[a] != NULL:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -20745,7 +20537,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":288
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":288
  *     if veb.bottom[a] != NULL:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -20754,7 +20546,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":289
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":289
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             if subv.max_val > b:             # <<<<<<<<<<<<<<
@@ -20764,7 +20556,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
       __pyx_t_3 = (__pyx_v_subv->max_val > __pyx_v_b);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":290
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":290
  *             subv = <_VEB*> veb.bottom[a]
  *             if subv.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + VEB_findsucc(subv, b)             # <<<<<<<<<<<<<<
@@ -20773,7 +20565,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
         __pyx_v_j = ((__pyx_v_a << __pyx_v_veb->num_bottom_bits) + __pyx_f_3_sa_VEB_findsucc(__pyx_v_subv, __pyx_v_b));
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":291
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":291
  *             if subv.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + VEB_findsucc(subv, b)
  *                 found = 1             # <<<<<<<<<<<<<<
@@ -20788,7 +20580,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":293
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":293
  *                 found = 1
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -20797,7 +20589,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":294
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":294
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             if subb.max_val > b:             # <<<<<<<<<<<<<<
@@ -20807,7 +20599,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
       __pyx_t_3 = (__pyx_v_subb->max_val > __pyx_v_b);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":295
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":295
  *             subb = <_BitSet*> veb.bottom[a]
  *             if subb.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)             # <<<<<<<<<<<<<<
@@ -20816,7 +20608,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
         __pyx_v_j = ((__pyx_v_a << __pyx_v_veb->num_bottom_bits) + __pyx_f_3_sa_bitset_findsucc(__pyx_v_subb, __pyx_v_b));
 
-        /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":296
+        /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":296
  *             if subb.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)
  *                 found = 1             # <<<<<<<<<<<<<<
@@ -20833,7 +20625,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":297
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":297
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)
  *                 found = 1
  *     if found==0:             # <<<<<<<<<<<<<<
@@ -20843,7 +20635,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = (__pyx_v_found == 0);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":298
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":298
  *                 found = 1
  *     if found==0:
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -20853,7 +20645,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":299
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":299
  *     if found==0:
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             subv = <_VEB*> veb.top             # <<<<<<<<<<<<<<
@@ -20862,7 +20654,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)__pyx_v_veb->top);
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":300
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":300
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             subv = <_VEB*> veb.top
  *             c = VEB_findsucc(subv, a)             # <<<<<<<<<<<<<<
@@ -20874,7 +20666,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":302
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":302
  *             c = VEB_findsucc(subv, a)
  *         else:
  *             subb = <_BitSet*> veb.top             # <<<<<<<<<<<<<<
@@ -20883,7 +20675,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)__pyx_v_veb->top);
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":303
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":303
  *         else:
  *             subb = <_BitSet*> veb.top
  *             c = bitset_findsucc(subb, a)             # <<<<<<<<<<<<<<
@@ -20894,7 +20686,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     __pyx_L10:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":304
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":304
  *             subb = <_BitSet*> veb.top
  *             c = bitset_findsucc(subb, a)
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -20904,7 +20696,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":305
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":305
  *             c = bitset_findsucc(subb, a)
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[c]             # <<<<<<<<<<<<<<
@@ -20913,7 +20705,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_c]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":306
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":306
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subv.min_val             # <<<<<<<<<<<<<<
@@ -20925,7 +20717,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":308
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":308
  *             j = (c << veb.num_bottom_bits) + subv.min_val
  *         else:
  *             subb = <_BitSet*> veb.bottom[c]             # <<<<<<<<<<<<<<
@@ -20934,7 +20726,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_c]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":309
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":309
  *         else:
  *             subb = <_BitSet*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subb.min_val             # <<<<<<<<<<<<<<
@@ -20948,7 +20740,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L9:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":310
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":310
  *             subb = <_BitSet*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subb.min_val
  *     return j             # <<<<<<<<<<<<<<
@@ -20964,7 +20756,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":313
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":313
  * 
  * 
  * cdef int VEB_contains(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -20985,7 +20777,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("VEB_contains", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":318
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":318
  *     cdef int a, b
  * 
  *     if veb.size == 0 or i < veb.min_val or i > veb.max_val:             # <<<<<<<<<<<<<<
@@ -21007,7 +20799,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":319
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":319
  * 
  *     if veb.size == 0 or i < veb.min_val or i > veb.max_val:
  *         return 0             # <<<<<<<<<<<<<<
@@ -21020,7 +20812,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":321
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":321
  *         return 0
  * 
  *     if veb.min_val == i:             # <<<<<<<<<<<<<<
@@ -21030,7 +20822,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_2 = (__pyx_v_veb->min_val == __pyx_v_i);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":322
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":322
  * 
  *     if veb.min_val == i:
  *         return 1             # <<<<<<<<<<<<<<
@@ -21043,7 +20835,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":324
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":324
  *         return 1
  *     else:
  *         if veb.size == 1:             # <<<<<<<<<<<<<<
@@ -21053,7 +20845,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_2 = (__pyx_v_veb->size == 1);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":325
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":325
  *     else:
  *         if veb.size == 1:
  *             return 0             # <<<<<<<<<<<<<<
@@ -21068,7 +20860,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":327
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":327
  *             return 0
  * 
  *     a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -21077,7 +20869,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":328
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":328
  * 
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -21086,7 +20878,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":329
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":329
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     if veb.bottom[a] == NULL:             # <<<<<<<<<<<<<<
@@ -21096,7 +20888,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_2 = ((__pyx_v_veb->bottom[__pyx_v_a]) == NULL);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":330
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":330
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     if veb.bottom[a] == NULL:
  *         return 0             # <<<<<<<<<<<<<<
@@ -21109,7 +20901,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":332
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":332
  *         return 0
  *     else:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -21119,7 +20911,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_2 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":333
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":333
  *     else:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -21128,7 +20920,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":334
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":334
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             return VEB_contains(subv, b)             # <<<<<<<<<<<<<<
@@ -21141,7 +20933,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":336
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":336
  *             return VEB_contains(subv, b)
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -21150,7 +20942,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":337
+      /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":337
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             return bitset_contains(subb, b)             # <<<<<<<<<<<<<<
@@ -21181,7 +20973,7 @@ static PyObject *__pyx_pw_3_sa_11VEBIterator_1__next__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":344
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":344
  *     cdef int next_val
  * 
  *     def __next__(self):             # <<<<<<<<<<<<<<
@@ -21200,7 +20992,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__next__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":347
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":347
  *         cdef int ret_val
  * 
  *         if self.next_val == -1:             # <<<<<<<<<<<<<<
@@ -21210,7 +21002,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   __pyx_t_1 = (__pyx_v_self->next_val == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":348
+    /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":348
  * 
  *         if self.next_val == -1:
  *             raise StopIteration()             # <<<<<<<<<<<<<<
@@ -21226,7 +21018,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":349
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":349
  *         if self.next_val == -1:
  *             raise StopIteration()
  *         ret_val = self.next_val             # <<<<<<<<<<<<<<
@@ -21235,7 +21027,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
  */
   __pyx_v_ret_val = __pyx_v_self->next_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":350
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":350
  *             raise StopIteration()
  *         ret_val = self.next_val
  *         self.next_val = VEB_findsucc(self.v, ret_val)             # <<<<<<<<<<<<<<
@@ -21244,7 +21036,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
  */
   __pyx_v_self->next_val = __pyx_f_3_sa_VEB_findsucc(__pyx_v_self->v, __pyx_v_ret_val);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":351
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":351
  *         ret_val = self.next_val
  *         self.next_val = VEB_findsucc(self.v, ret_val)
  *         return ret_val             # <<<<<<<<<<<<<<
@@ -21274,11 +21066,11 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
 static int __pyx_pw_3_sa_3VEB_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_3_sa_3VEB_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   int __pyx_v_size;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size,0};
     PyObject* values[1] = {0};
     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -21291,7 +21083,8 @@ static int __pyx_pw_3_sa_3VEB_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
       }
       if (unlikely(kw_args > 0)) {
@@ -21317,7 +21110,7 @@ static int __pyx_pw_3_sa_3VEB_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":360
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":360
  *     cdef int _first(self)
  * 
  *     def __cinit__(self, int size):             # <<<<<<<<<<<<<<
@@ -21330,7 +21123,7 @@ static int __pyx_pf_3_sa_3VEB___cinit__(struct __pyx_obj_3_sa_VEB *__pyx_v_self,
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":361
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":361
  * 
  *     def __cinit__(self, int size):
  *         self.veb = new_VEB(size)             # <<<<<<<<<<<<<<
@@ -21353,7 +21146,7 @@ static void __pyx_pw_3_sa_3VEB_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":363
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":363
  *         self.veb = new_VEB(size)
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -21369,7 +21162,7 @@ static void __pyx_pf_3_sa_3VEB_2__dealloc__(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":364
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":364
  * 
  *     def __dealloc__(self):
  *         del_VEB(self.veb)             # <<<<<<<<<<<<<<
@@ -21399,7 +21192,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_5__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":366
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":366
  *         del_VEB(self.veb)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -21417,7 +21210,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__iter__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":368
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":368
  *     def __iter__(self):
  *         cdef VEBIterator it
  *         it = VEBIterator()             # <<<<<<<<<<<<<<
@@ -21429,7 +21222,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
   __pyx_v_it = ((struct __pyx_obj_3_sa_VEBIterator *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":369
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":369
  *         cdef VEBIterator it
  *         it = VEBIterator()
  *         it.v = self.veb             # <<<<<<<<<<<<<<
@@ -21438,7 +21231,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
  */
   __pyx_v_it->v = __pyx_v_self->veb;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":370
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":370
  *         it = VEBIterator()
  *         it.v = self.veb
  *         it.next_val = self.veb.min_val             # <<<<<<<<<<<<<<
@@ -21447,7 +21240,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
  */
   __pyx_v_it->next_val = __pyx_v_self->veb->min_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":371
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":371
  *         it.v = self.veb
  *         it.next_val = self.veb.min_val
  *         return it             # <<<<<<<<<<<<<<
@@ -21483,7 +21276,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_7insert(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":373
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":373
  *         return it
  * 
  *     def insert(self, i):             # <<<<<<<<<<<<<<
@@ -21501,7 +21294,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_6insert(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":374
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":374
  * 
  *     def insert(self, i):
  *         return VEB_insert(self.veb, i)             # <<<<<<<<<<<<<<
@@ -21528,7 +21321,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_6insert(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":376
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":376
  *         return VEB_insert(self.veb, i)
  * 
  *     cdef int _insert(self, int i):             # <<<<<<<<<<<<<<
@@ -21541,7 +21334,7 @@ static int __pyx_f_3_sa_3VEB__insert(struct __pyx_obj_3_sa_VEB *__pyx_v_self, in
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("_insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":377
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":377
  * 
  *     cdef int _insert(self, int i):
  *         return VEB_insert(self.veb, i)             # <<<<<<<<<<<<<<
@@ -21568,7 +21361,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_9findsucc(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":379
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":379
  *         return VEB_insert(self.veb, i)
  * 
  *     def findsucc(self, i):             # <<<<<<<<<<<<<<
@@ -21586,7 +21379,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_8findsucc(struct __pyx_obj_3_sa_VEB *__pyx_v
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   __Pyx_RefNannySetupContext("findsucc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":380
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":380
  * 
  *     def findsucc(self, i):
  *         return VEB_findsucc(self.veb, i)             # <<<<<<<<<<<<<<
@@ -21613,7 +21406,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_8findsucc(struct __pyx_obj_3_sa_VEB *__pyx_v
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":382
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":382
  *         return VEB_findsucc(self.veb, i)
  * 
  *     cdef int _first(self):             # <<<<<<<<<<<<<<
@@ -21626,7 +21419,7 @@ static int __pyx_f_3_sa_3VEB__first(struct __pyx_obj_3_sa_VEB *__pyx_v_self) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("_first", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":383
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":383
  * 
  *     cdef int _first(self):
  *         return self.veb.min_val             # <<<<<<<<<<<<<<
@@ -21642,7 +21435,7 @@ static int __pyx_f_3_sa_3VEB__first(struct __pyx_obj_3_sa_VEB *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":385
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":385
  *         return self.veb.min_val
  * 
  *     cdef int _findsucc(self, int i):             # <<<<<<<<<<<<<<
@@ -21655,7 +21448,7 @@ static int __pyx_f_3_sa_3VEB__findsucc(struct __pyx_obj_3_sa_VEB *__pyx_v_self,
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   __Pyx_RefNannySetupContext("_findsucc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":386
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":386
  * 
  *     cdef int _findsucc(self, int i):
  *         return VEB_findsucc(self.veb, i)             # <<<<<<<<<<<<<<
@@ -21682,7 +21475,7 @@ static Py_ssize_t __pyx_pw_3_sa_3VEB_11__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":388
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":388
  *         return VEB_findsucc(self.veb, i)
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -21695,7 +21488,7 @@ static Py_ssize_t __pyx_pf_3_sa_3VEB_10__len__(struct __pyx_obj_3_sa_VEB *__pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":389
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":389
  * 
  *     def __len__(self):
  *         return self.veb.size             # <<<<<<<<<<<<<<
@@ -21722,7 +21515,7 @@ static int __pyx_pw_3_sa_3VEB_13__contains__(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/veb.pxi":391
+/* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":391
  *         return self.veb.size
  * 
  *     def __contains__(self, i):             # <<<<<<<<<<<<<<
@@ -21738,7 +21531,7 @@ static int __pyx_pf_3_sa_3VEB_12__contains__(struct __pyx_obj_3_sa_VEB *__pyx_v_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__contains__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":392
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":392
  * 
  *     def __contains__(self, i):
  *         return VEB_contains(self.veb, i)             # <<<<<<<<<<<<<<
@@ -21761,11 +21554,11 @@ static int __pyx_pf_3_sa_3VEB_12__contains__(struct __pyx_obj_3_sa_VEB *__pyx_v_
 static int __pyx_pw_3_sa_3LCP_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_3_sa_3LCP_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   struct __pyx_obj_3_sa_SuffixArray *__pyx_v_sa = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__sa,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__sa,0};
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     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -21778,7 +21571,8 @@ static int __pyx_pw_3_sa_3LCP_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__sa)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__sa);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
       }
       if (unlikely(kw_args > 0)) {
@@ -21809,7 +21603,7 @@ static int __pyx_pw_3_sa_3LCP_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":9
+/* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":9
  *     cdef IntList lcp
  * 
  *     def __cinit__(self, SuffixArray sa):             # <<<<<<<<<<<<<<
@@ -21838,7 +21632,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":13
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":13
  *         cdef IntList rank
  * 
  *         logger.info("Constructing LCP array")             # <<<<<<<<<<<<<<
@@ -21855,7 +21649,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":14
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":14
  * 
  *         logger.info("Constructing LCP array")
  *         self.sa = sa             # <<<<<<<<<<<<<<
@@ -21868,7 +21662,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __Pyx_DECREF(((PyObject *)__pyx_v_self->sa));
   __pyx_v_self->sa = __pyx_v_sa;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":15
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":15
  *         logger.info("Constructing LCP array")
  *         self.sa = sa
  *         n = self.sa.sa.len             # <<<<<<<<<<<<<<
@@ -21877,7 +21671,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
   __pyx_v_n = __pyx_v_self->sa->sa->len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":16
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":16
  *         self.sa = sa
  *         n = self.sa.sa.len
  *         self.lcp = IntList(initial_len=n)             # <<<<<<<<<<<<<<
@@ -21899,7 +21693,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_v_self->lcp = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":18
  *         self.lcp = IntList(initial_len=n)
  * 
  *         rank = IntList(initial_len=n)             # <<<<<<<<<<<<<<
@@ -21918,7 +21712,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_v_rank = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":19
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":19
  * 
  *         rank = IntList(initial_len=n)
  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
@@ -21928,7 +21722,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_t_3 = __pyx_v_n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":20
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":20
  *         rank = IntList(initial_len=n)
  *         for i from 0 <= i < n:
  *             rank.arr[sa.sa.arr[i]] = i             # <<<<<<<<<<<<<<
@@ -21938,7 +21732,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     (__pyx_v_rank->arr[(__pyx_v_sa->sa->arr[__pyx_v_i])]) = __pyx_v_i;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":22
  *             rank.arr[sa.sa.arr[i]] = i
  * 
  *         h = 0             # <<<<<<<<<<<<<<
@@ -21947,7 +21741,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
   __pyx_v_h = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":23
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":23
  * 
  *         h = 0
  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
@@ -21957,7 +21751,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_t_3 = __pyx_v_n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":24
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":24
  *         h = 0
  *         for i from 0 <= i < n:
  *             k = rank.arr[i]             # <<<<<<<<<<<<<<
@@ -21966,7 +21760,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
     __pyx_v_k = (__pyx_v_rank->arr[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":25
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":25
  *         for i from 0 <= i < n:
  *             k = rank.arr[i]
  *             if k == 0:             # <<<<<<<<<<<<<<
@@ -21976,7 +21770,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     __pyx_t_4 = (__pyx_v_k == 0);
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":26
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":26
  *             k = rank.arr[i]
  *             if k == 0:
  *                 self.lcp.arr[k] = -1             # <<<<<<<<<<<<<<
@@ -21988,7 +21782,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":28
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":28
  *                 self.lcp.arr[k] = -1
  *             else:
  *                 j = sa.sa.arr[k-1]             # <<<<<<<<<<<<<<
@@ -21997,7 +21791,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
       __pyx_v_j = (__pyx_v_sa->sa->arr[(__pyx_v_k - 1)]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":29
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":29
  *             else:
  *                 j = sa.sa.arr[k-1]
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:             # <<<<<<<<<<<<<<
@@ -22020,7 +21814,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
         }
         if (!__pyx_t_5) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":30
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":30
  *                 j = sa.sa.arr[k-1]
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:
  *                     h = h+1             # <<<<<<<<<<<<<<
@@ -22030,7 +21824,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
         __pyx_v_h = (__pyx_v_h + 1);
       }
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":31
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":31
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:
  *                     h = h+1
  *                 self.lcp.arr[k] = h             # <<<<<<<<<<<<<<
@@ -22041,7 +21835,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     }
     __pyx_L7:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":32
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":32
  *                     h = h+1
  *                 self.lcp.arr[k] = h
  *             if h > 0:             # <<<<<<<<<<<<<<
@@ -22051,7 +21845,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     __pyx_t_5 = (__pyx_v_h > 0);
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":33
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":33
  *                 self.lcp.arr[k] = h
  *             if h > 0:
  *                 h = h-1             # <<<<<<<<<<<<<<
@@ -22064,7 +21858,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     __pyx_L10:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":34
  *             if h > 0:
  *                 h = h-1
  *         logger.info("LCP array completed")             # <<<<<<<<<<<<<<
@@ -22117,7 +21911,7 @@ static PyObject *__pyx_pw_3_sa_3LCP_3compute_stats(PyObject *__pyx_v_self, PyObj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":36
+/* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":36
  *         logger.info("LCP array completed")
  * 
  *     def compute_stats(self, int max_n):             # <<<<<<<<<<<<<<
@@ -22188,7 +21982,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_L3_first_run:;
   if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":48
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":48
  *         cdef VEB veb
  * 
  *         N = self.sa.sa.len             # <<<<<<<<<<<<<<
@@ -22197,7 +21991,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
   __pyx_cur_scope->__pyx_v_N = __pyx_cur_scope->__pyx_v_self->sa->sa->len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":50
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":50
  *         N = self.sa.sa.len
  * 
  *         ngram_starts = []             # <<<<<<<<<<<<<<
@@ -22210,7 +22004,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_cur_scope->__pyx_v_ngram_starts = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":51
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":51
  * 
  *         ngram_starts = []
  *         for n from 0 <= n < max_n:             # <<<<<<<<<<<<<<
@@ -22220,7 +22014,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_t_2 = __pyx_cur_scope->__pyx_v_max_n;
   for (__pyx_cur_scope->__pyx_v_n = 0; __pyx_cur_scope->__pyx_v_n < __pyx_t_2; __pyx_cur_scope->__pyx_v_n++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":52
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":52
  *         ngram_starts = []
  *         for n from 0 <= n < max_n:
  *             ngram_starts.append(IntList(initial_len=N))             # <<<<<<<<<<<<<<
@@ -22240,7 +22034,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":54
  *             ngram_starts.append(IntList(initial_len=N))
  * 
  *         run_start = IntList(initial_len=max_n)             # <<<<<<<<<<<<<<
@@ -22260,7 +22054,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_cur_scope->__pyx_v_run_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":55
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":55
  * 
  *         run_start = IntList(initial_len=max_n)
  *         veb = VEB(N)             # <<<<<<<<<<<<<<
@@ -22281,7 +22075,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_cur_scope->__pyx_v_veb = ((struct __pyx_obj_3_sa_VEB *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":57
  *         veb = VEB(N)
  * 
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -22291,7 +22085,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_t_2 = __pyx_cur_scope->__pyx_v_N;
   for (__pyx_cur_scope->__pyx_v_i = 0; __pyx_cur_scope->__pyx_v_i < __pyx_t_2; __pyx_cur_scope->__pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":58
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":58
  * 
  *         for i from 0 <= i < N:
  *             h = self.lcp.arr[i]             # <<<<<<<<<<<<<<
@@ -22300,7 +22094,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
     __pyx_cur_scope->__pyx_v_h = (__pyx_cur_scope->__pyx_v_self->lcp->arr[__pyx_cur_scope->__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":59
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":59
  *         for i from 0 <= i < N:
  *             h = self.lcp.arr[i]
  *             if h < 0:             # <<<<<<<<<<<<<<
@@ -22310,7 +22104,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     __pyx_t_5 = (__pyx_cur_scope->__pyx_v_h < 0);
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":60
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":60
  *             h = self.lcp.arr[i]
  *             if h < 0:
  *                 h = 0             # <<<<<<<<<<<<<<
@@ -22322,7 +22116,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     }
     __pyx_L8:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":61
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":61
  *             if h < 0:
  *                 h = 0
  *             for n from h <= n < max_n:             # <<<<<<<<<<<<<<
@@ -22332,7 +22126,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     __pyx_t_6 = __pyx_cur_scope->__pyx_v_max_n;
     for (__pyx_cur_scope->__pyx_v_n = __pyx_cur_scope->__pyx_v_h; __pyx_cur_scope->__pyx_v_n < __pyx_t_6; __pyx_cur_scope->__pyx_v_n++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":62
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":62
  *                 h = 0
  *             for n from h <= n < max_n:
  *                 rs = run_start.arr[n]             # <<<<<<<<<<<<<<
@@ -22341,7 +22135,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
       __pyx_cur_scope->__pyx_v_rs = (__pyx_cur_scope->__pyx_v_run_start->arr[__pyx_cur_scope->__pyx_v_n]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":63
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":63
  *             for n from h <= n < max_n:
  *                 rs = run_start.arr[n]
  *                 run_start.arr[n] = i             # <<<<<<<<<<<<<<
@@ -22350,7 +22144,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
       (__pyx_cur_scope->__pyx_v_run_start->arr[__pyx_cur_scope->__pyx_v_n]) = __pyx_cur_scope->__pyx_v_i;
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":64
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":64
  *                 rs = run_start.arr[n]
  *                 run_start.arr[n] = i
  *                 freq = i - rs             # <<<<<<<<<<<<<<
@@ -22359,7 +22153,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
       __pyx_cur_scope->__pyx_v_freq = (__pyx_cur_scope->__pyx_v_i - __pyx_cur_scope->__pyx_v_rs);
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":65
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":65
  *                 run_start.arr[n] = i
  *                 freq = i - rs
  *                 if freq > 1000: # arbitrary, but see note below             # <<<<<<<<<<<<<<
@@ -22369,7 +22163,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
       __pyx_t_5 = (__pyx_cur_scope->__pyx_v_freq > 1000);
       if (__pyx_t_5) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":66
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":66
  *                 freq = i - rs
  *                 if freq > 1000: # arbitrary, but see note below
  *                     veb._insert(freq)             # <<<<<<<<<<<<<<
@@ -22378,7 +22172,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
         ((struct __pyx_vtabstruct_3_sa_VEB *)__pyx_cur_scope->__pyx_v_veb->__pyx_vtab)->_insert(__pyx_cur_scope->__pyx_v_veb, __pyx_cur_scope->__pyx_v_freq);
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":67
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":67
  *                 if freq > 1000: # arbitrary, but see note below
  *                     veb._insert(freq)
  *                     ngram_start = ngram_starts[n]             # <<<<<<<<<<<<<<
@@ -22394,7 +22188,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
         __pyx_cur_scope->__pyx_v_ngram_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
         __pyx_t_1 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":68
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":68
  *                     veb._insert(freq)
  *                     ngram_start = ngram_starts[n]
  *                     while ngram_start.arr[freq] > 0:             # <<<<<<<<<<<<<<
@@ -22405,7 +22199,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
           __pyx_t_5 = ((__pyx_cur_scope->__pyx_v_ngram_start->arr[__pyx_cur_scope->__pyx_v_freq]) > 0);
           if (!__pyx_t_5) break;
 
-          /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":69
+          /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":69
  *                     ngram_start = ngram_starts[n]
  *                     while ngram_start.arr[freq] > 0:
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram             # <<<<<<<<<<<<<<
@@ -22415,7 +22209,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
           __pyx_cur_scope->__pyx_v_freq = (__pyx_cur_scope->__pyx_v_freq + 1);
         }
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":70
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":70
  *                     while ngram_start.arr[freq] > 0:
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram
  *                     ngram_start.arr[freq] = rs             # <<<<<<<<<<<<<<
@@ -22429,7 +22223,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     }
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":71
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram
  *                     ngram_start.arr[freq] = rs
  *         i = veb.veb.min_val             # <<<<<<<<<<<<<<
@@ -22438,7 +22232,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
   __pyx_cur_scope->__pyx_v_i = __pyx_cur_scope->__pyx_v_veb->veb->min_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":72
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":72
  *                     ngram_start.arr[freq] = rs
  *         i = veb.veb.min_val
  *         while i != -1:             # <<<<<<<<<<<<<<
@@ -22449,7 +22243,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     __pyx_t_5 = (__pyx_cur_scope->__pyx_v_i != -1);
     if (!__pyx_t_5) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":73
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":73
  *         i = veb.veb.min_val
  *         while i != -1:
  *             ii = veb._findsucc(i)             # <<<<<<<<<<<<<<
@@ -22458,7 +22252,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
     __pyx_cur_scope->__pyx_v_ii = ((struct __pyx_vtabstruct_3_sa_VEB *)__pyx_cur_scope->__pyx_v_veb->__pyx_vtab)->_findsucc(__pyx_cur_scope->__pyx_v_veb, __pyx_cur_scope->__pyx_v_i);
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":74
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":74
  *         while i != -1:
  *             ii = veb._findsucc(i)
  *             for n from 0 <= n < max_n:             # <<<<<<<<<<<<<<
@@ -22468,7 +22262,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
     __pyx_t_2 = __pyx_cur_scope->__pyx_v_max_n;
     for (__pyx_cur_scope->__pyx_v_n = 0; __pyx_cur_scope->__pyx_v_n < __pyx_t_2; __pyx_cur_scope->__pyx_v_n++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":75
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":75
  *             ii = veb._findsucc(i)
  *             for n from 0 <= n < max_n:
  *                 ngram_start = ngram_starts[n]             # <<<<<<<<<<<<<<
@@ -22484,7 +22278,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
       __pyx_cur_scope->__pyx_v_ngram_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
       __pyx_t_1 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":76
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":76
  *             for n from 0 <= n < max_n:
  *                 ngram_start = ngram_starts[n]
  *                 iii = i             # <<<<<<<<<<<<<<
@@ -22493,7 +22287,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
       __pyx_cur_scope->__pyx_v_iii = __pyx_cur_scope->__pyx_v_i;
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":77
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":77
  *                 ngram_start = ngram_starts[n]
  *                 iii = i
  *                 rs = ngram_start.arr[iii]             # <<<<<<<<<<<<<<
@@ -22502,7 +22296,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
       __pyx_cur_scope->__pyx_v_rs = (__pyx_cur_scope->__pyx_v_ngram_start->arr[__pyx_cur_scope->__pyx_v_iii]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":78
+      /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":78
  *                 iii = i
  *                 rs = ngram_start.arr[iii]
  *                 while (ii==-1 or iii < ii) and rs != 0:             # <<<<<<<<<<<<<<
@@ -22525,7 +22319,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
         }
         if (!__pyx_t_7) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":79
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":79
  *                 rs = ngram_start.arr[iii]
  *                 while (ii==-1 or iii < ii) and rs != 0:
  *                     j = self.sa.sa.arr[rs]             # <<<<<<<<<<<<<<
@@ -22534,7 +22328,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
         __pyx_cur_scope->__pyx_v_j = (__pyx_cur_scope->__pyx_v_self->sa->sa->arr[__pyx_cur_scope->__pyx_v_rs]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":80
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":80
  *                 while (ii==-1 or iii < ii) and rs != 0:
  *                     j = self.sa.sa.arr[rs]
  *                     valid = 1             # <<<<<<<<<<<<<<
@@ -22543,7 +22337,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
         __pyx_cur_scope->__pyx_v_valid = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":81
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":81
  *                     j = self.sa.sa.arr[rs]
  *                     valid = 1
  *                     for k from 0 <= k < n+1:             # <<<<<<<<<<<<<<
@@ -22553,7 +22347,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
         __pyx_t_9 = (__pyx_cur_scope->__pyx_v_n + 1);
         for (__pyx_cur_scope->__pyx_v_k = 0; __pyx_cur_scope->__pyx_v_k < __pyx_t_9; __pyx_cur_scope->__pyx_v_k++) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":82
+          /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":82
  *                     valid = 1
  *                     for k from 0 <= k < n+1:
  *                         if self.sa.darray.data.arr[j+k] < 2:             # <<<<<<<<<<<<<<
@@ -22563,7 +22357,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
           __pyx_t_7 = ((__pyx_cur_scope->__pyx_v_self->sa->darray->data->arr[(__pyx_cur_scope->__pyx_v_j + __pyx_cur_scope->__pyx_v_k)]) < 2);
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":83
+            /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":83
  *                     for k from 0 <= k < n+1:
  *                         if self.sa.darray.data.arr[j+k] < 2:
  *                             valid = 0             # <<<<<<<<<<<<<<
@@ -22576,7 +22370,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
           __pyx_L22:;
         }
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":84
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":84
  *                         if self.sa.darray.data.arr[j+k] < 2:
  *                             valid = 0
  *                     if valid:             # <<<<<<<<<<<<<<
@@ -22585,7 +22379,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
         if (__pyx_cur_scope->__pyx_v_valid) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":85
+          /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":85
  *                             valid = 0
  *                     if valid:
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])             # <<<<<<<<<<<<<<
@@ -22599,7 +22393,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
             __pyx_cur_scope->__pyx_v_k = __pyx_t_6;
             __pyx_t_3 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_self->sa->darray->data->arr[(__pyx_cur_scope->__pyx_v_j + __pyx_cur_scope->__pyx_v_k)])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_3);
-            if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
           }
           __pyx_t_3 = ((PyObject *)PyList_AsTuple(__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -22611,7 +22405,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
           __pyx_cur_scope->__pyx_v_ngram = __pyx_t_3;
           __pyx_t_3 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":86
+          /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":86
  *                     if valid:
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])
  *                         yield i, n+1, ngram             # <<<<<<<<<<<<<<
@@ -22648,7 +22442,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
         }
         __pyx_L23:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":87
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":87
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])
  *                         yield i, n+1, ngram
  *                     iii = iii + 1             # <<<<<<<<<<<<<<
@@ -22657,7 +22451,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
  */
         __pyx_cur_scope->__pyx_v_iii = (__pyx_cur_scope->__pyx_v_iii + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":88
+        /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":88
  *                         yield i, n+1, ngram
  *                     iii = iii + 1
  *                     rs = ngram_start.arr[iii]             # <<<<<<<<<<<<<<
@@ -22667,7 +22461,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
       }
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":89
+    /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":89
  *                     iii = iii + 1
  *                     rs = ngram_start.arr[iii]
  *             i = ii             # <<<<<<<<<<<<<<
@@ -22684,7 +22478,6 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_gen
   __pyx_L0:;
   __Pyx_XDECREF(__pyx_r);
   __pyx_generator->resume_label = -1;
-  __Pyx_Generator_clear((PyObject*)__pyx_generator);
   __Pyx_RefNannyFinishContext();
   return NULL;
 }
@@ -22703,7 +22496,7 @@ static int __pyx_pw_3_sa_8Alphabet_1__cinit__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":12
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":12
  *     cdef dict id2sym
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -22720,7 +22513,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":13
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":13
  * 
  *     def __cinit__(self):
  *         self.terminals = StringMap()             # <<<<<<<<<<<<<<
@@ -22735,7 +22528,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->terminals = ((struct __pyx_obj_3_sa_StringMap *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":14
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":14
  *     def __cinit__(self):
  *         self.terminals = StringMap()
  *         self.nonterminals = StringMap()             # <<<<<<<<<<<<<<
@@ -22750,7 +22543,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->nonterminals = ((struct __pyx_obj_3_sa_StringMap *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":15
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":15
  *         self.terminals = StringMap()
  *         self.nonterminals = StringMap()
  *         self.id2sym = {}             # <<<<<<<<<<<<<<
@@ -22765,7 +22558,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->id2sym = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":16
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":16
  *         self.nonterminals = StringMap()
  *         self.id2sym = {}
  *         self.first_nonterminal = -1             # <<<<<<<<<<<<<<
@@ -22794,7 +22587,7 @@ static void __pyx_pw_3_sa_8Alphabet_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":18
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":18
  *         self.first_nonterminal = -1
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -22809,7 +22602,7 @@ static void __pyx_pf_3_sa_8Alphabet_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":21
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":21
  *         pass
  * 
  *     cdef int isvar(self, int sym):             # <<<<<<<<<<<<<<
@@ -22822,7 +22615,7 @@ static int __pyx_f_3_sa_8Alphabet_isvar(CYTHON_UNUSED struct __pyx_obj_3_sa_Alph
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("isvar", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":22
  * 
  *     cdef int isvar(self, int sym):
  *         return sym < 0             # <<<<<<<<<<<<<<
@@ -22838,7 +22631,7 @@ static int __pyx_f_3_sa_8Alphabet_isvar(CYTHON_UNUSED struct __pyx_obj_3_sa_Alph
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":24
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":24
  *         return sym < 0
  * 
  *     cdef int isword(self, int sym):             # <<<<<<<<<<<<<<
@@ -22851,7 +22644,7 @@ static int __pyx_f_3_sa_8Alphabet_isword(CYTHON_UNUSED struct __pyx_obj_3_sa_Alp
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("isword", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":25
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":25
  * 
  *     cdef int isword(self, int sym):
  *         return sym >= 0             # <<<<<<<<<<<<<<
@@ -22867,7 +22660,7 @@ static int __pyx_f_3_sa_8Alphabet_isword(CYTHON_UNUSED struct __pyx_obj_3_sa_Alp
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":27
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":27
  *         return sym >= 0
  * 
  *     cdef int getindex(self, int sym):             # <<<<<<<<<<<<<<
@@ -22880,7 +22673,7 @@ static int __pyx_f_3_sa_8Alphabet_getindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("getindex", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":28
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":28
  * 
  *     cdef int getindex(self, int sym):
  *         return -sym & INDEX_MASK             # <<<<<<<<<<<<<<
@@ -22896,7 +22689,7 @@ static int __pyx_f_3_sa_8Alphabet_getindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":30
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":30
  *         return -sym & INDEX_MASK
  * 
  *     cdef int setindex(self, int sym, int ind):             # <<<<<<<<<<<<<<
@@ -22909,7 +22702,7 @@ static int __pyx_f_3_sa_8Alphabet_setindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("setindex", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":31
  * 
  *     cdef int setindex(self, int sym, int ind):
  *         return -(-sym & ~INDEX_MASK | ind)             # <<<<<<<<<<<<<<
@@ -22925,7 +22718,7 @@ static int __pyx_f_3_sa_8Alphabet_setindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":33
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":33
  *         return -(-sym & ~INDEX_MASK | ind)
  * 
  *     cdef int clearindex(self, int sym):             # <<<<<<<<<<<<<<
@@ -22938,7 +22731,7 @@ static int __pyx_f_3_sa_8Alphabet_clearindex(CYTHON_UNUSED struct __pyx_obj_3_sa
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("clearindex", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":34
  * 
  *     cdef int clearindex(self, int sym):
  *         return -(-sym& ~INDEX_MASK)             # <<<<<<<<<<<<<<
@@ -22954,7 +22747,7 @@ static int __pyx_f_3_sa_8Alphabet_clearindex(CYTHON_UNUSED struct __pyx_obj_3_sa
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":36
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":36
  *         return -(-sym& ~INDEX_MASK)
  * 
  *     cdef int match(self, int sym1, int sym2):             # <<<<<<<<<<<<<<
@@ -22967,7 +22760,7 @@ static int __pyx_f_3_sa_8Alphabet_match(struct __pyx_obj_3_sa_Alphabet *__pyx_v_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("match", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":37
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":37
  * 
  *     cdef int match(self, int sym1, int sym2):
  *         return self.clearindex(sym1) == self.clearindex(sym2);             # <<<<<<<<<<<<<<
@@ -22983,7 +22776,7 @@ static int __pyx_f_3_sa_8Alphabet_match(struct __pyx_obj_3_sa_Alphabet *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":39
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":39
  *         return self.clearindex(sym1) == self.clearindex(sym2);
  * 
  *     cdef char* tocat(self, int sym):             # <<<<<<<<<<<<<<
@@ -22996,7 +22789,7 @@ static char *__pyx_f_3_sa_8Alphabet_tocat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("tocat", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":40
  * 
  *     cdef char* tocat(self, int sym):
  *         return self.nonterminals.word((-sym >> INDEX_SHIFT)-1)             # <<<<<<<<<<<<<<
@@ -23012,7 +22805,7 @@ static char *__pyx_f_3_sa_8Alphabet_tocat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":42
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":42
  *         return self.nonterminals.word((-sym >> INDEX_SHIFT)-1)
  * 
  *     cdef int fromcat(self, char *s):             # <<<<<<<<<<<<<<
@@ -23027,7 +22820,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("fromcat", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":44
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":44
  *     cdef int fromcat(self, char *s):
  *         cdef int i
  *         i = self.nonterminals.index(s)             # <<<<<<<<<<<<<<
@@ -23036,7 +22829,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
  */
   __pyx_v_i = ((struct __pyx_vtabstruct_3_sa_StringMap *)__pyx_v_self->nonterminals->__pyx_vtab)->index(__pyx_v_self->nonterminals, __pyx_v_s);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":45
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":45
  *         cdef int i
  *         i = self.nonterminals.index(s)
  *         if self.first_nonterminal == -1:             # <<<<<<<<<<<<<<
@@ -23046,7 +22839,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __pyx_t_1 = (__pyx_v_self->first_nonterminal == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":46
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":46
  *         i = self.nonterminals.index(s)
  *         if self.first_nonterminal == -1:
  *             self.first_nonterminal = i             # <<<<<<<<<<<<<<
@@ -23058,7 +22851,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":47
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":47
  *         if self.first_nonterminal == -1:
  *             self.first_nonterminal = i
  *         if i > self.last_nonterminal:             # <<<<<<<<<<<<<<
@@ -23068,7 +22861,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __pyx_t_1 = (__pyx_v_i > __pyx_v_self->last_nonterminal);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":48
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":48
  *             self.first_nonterminal = i
  *         if i > self.last_nonterminal:
  *             self.last_nonterminal = i             # <<<<<<<<<<<<<<
@@ -23080,7 +22873,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":49
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":49
  *         if i > self.last_nonterminal:
  *             self.last_nonterminal = i
  *         return -(i+1 << INDEX_SHIFT)             # <<<<<<<<<<<<<<
@@ -23096,7 +22889,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":51
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":51
  *         return -(i+1 << INDEX_SHIFT)
  * 
  *     cdef char* tostring(self, int sym):             # <<<<<<<<<<<<<<
@@ -23119,7 +22912,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("tostring", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":53
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":53
  *     cdef char* tostring(self, int sym):
  *         cdef int ind
  *         if self.isvar(sym):             # <<<<<<<<<<<<<<
@@ -23129,7 +22922,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Alphabet *)__pyx_v_self->__pyx_vtab)->isvar(__pyx_v_self, __pyx_v_sym);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":54
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":54
  *         cdef int ind
  *         if self.isvar(sym):
  *             if sym in self.id2sym:             # <<<<<<<<<<<<<<
@@ -23139,24 +22932,19 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     __pyx_t_2 = PyInt_FromLong(__pyx_v_sym); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     if (unlikely(((PyObject *)__pyx_v_self->id2sym) == Py_None)) {
-      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 
     }
-    __pyx_t_3 = (__Pyx_PyDict_Contains(__pyx_t_2, ((PyObject *)__pyx_v_self->id2sym), Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = ((PyDict_Contains(((PyObject *)__pyx_v_self->id2sym), __pyx_t_2))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":55
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":55
  *         if self.isvar(sym):
  *             if sym in self.id2sym:
  *                 return self.id2sym[sym]             # <<<<<<<<<<<<<<
  *             ind = self.getindex(sym)
  *             if ind > 0:
  */
-      if (unlikely(((PyObject *)__pyx_v_self->id2sym) == Py_None)) {
-        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
-        {__pyx_filename = __pyx_f[10]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      }
       __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->id2sym), __pyx_v_sym, sizeof(int), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __pyx_t_4 = PyBytes_AsString(__pyx_t_2); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -23167,7 +22955,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":56
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":56
  *             if sym in self.id2sym:
  *                 return self.id2sym[sym]
  *             ind = self.getindex(sym)             # <<<<<<<<<<<<<<
@@ -23176,7 +22964,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     __pyx_v_ind = ((struct __pyx_vtabstruct_3_sa_Alphabet *)__pyx_v_self->__pyx_vtab)->getindex(__pyx_v_self, __pyx_v_sym);
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":57
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":57
  *                 return self.id2sym[sym]
  *             ind = self.getindex(sym)
  *             if ind > 0:             # <<<<<<<<<<<<<<
@@ -23186,7 +22974,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     __pyx_t_3 = (__pyx_v_ind > 0);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":58
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":58
  *             ind = self.getindex(sym)
  *             if ind > 0:
  *                 self.id2sym[sym] = "[%s,%d]" % (self.tocat(sym), ind)             # <<<<<<<<<<<<<<
@@ -23208,17 +22996,13 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
       __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_64), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_5));
       __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
-      if (unlikely(((PyObject *)__pyx_v_self->id2sym) == Py_None)) {
-        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
-        {__pyx_filename = __pyx_f[10]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      }
       if (__Pyx_SetItemInt(((PyObject *)__pyx_v_self->id2sym), __pyx_v_sym, ((PyObject *)__pyx_t_5), sizeof(int), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
       goto __pyx_L5;
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":60
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":60
  *                 self.id2sym[sym] = "[%s,%d]" % (self.tocat(sym), ind)
  *             else:
  *                 self.id2sym[sym] = "[%s]" % self.tocat(sym)             # <<<<<<<<<<<<<<
@@ -23230,26 +23014,18 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
       __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_65), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_6));
       __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
-      if (unlikely(((PyObject *)__pyx_v_self->id2sym) == Py_None)) {
-        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
-        {__pyx_filename = __pyx_f[10]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      }
       if (__Pyx_SetItemInt(((PyObject *)__pyx_v_self->id2sym), __pyx_v_sym, ((PyObject *)__pyx_t_6), sizeof(int), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":61
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":61
  *             else:
  *                 self.id2sym[sym] = "[%s]" % self.tocat(sym)
  *             return self.id2sym[sym]             # <<<<<<<<<<<<<<
  *         else:
  *             return self.terminals.word(sym)
  */
-    if (unlikely(((PyObject *)__pyx_v_self->id2sym) == Py_None)) {
-      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
-      {__pyx_filename = __pyx_f[10]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    }
     __pyx_t_6 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->id2sym), __pyx_v_sym, sizeof(int), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __pyx_t_4 = PyBytes_AsString(__pyx_t_6); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -23260,7 +23036,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":63
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":63
  *             return self.id2sym[sym]
  *         else:
  *             return self.terminals.word(sym)             # <<<<<<<<<<<<<<
@@ -23285,7 +23061,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":65
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":65
  *             return self.terminals.word(sym)
  * 
  *     cdef int fromstring(self, char *s, bint terminal):             # <<<<<<<<<<<<<<
@@ -23313,7 +23089,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("fromstring", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":69
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":69
  *         cdef char *comma
  *         cdef int n
  *         n = strlen(s)             # <<<<<<<<<<<<<<
@@ -23322,7 +23098,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
   __pyx_v_n = strlen(__pyx_v_s);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":71
  *         n = strlen(s)
  *         cdef char *sep
  *         sep = strstr(s,"_SEP_")             # <<<<<<<<<<<<<<
@@ -23331,7 +23107,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
   __pyx_v_sep = strstr(__pyx_v_s, __pyx_k___SEP_);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":72
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":72
  *         cdef char *sep
  *         sep = strstr(s,"_SEP_")
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:             # <<<<<<<<<<<<<<
@@ -23359,7 +23135,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
   }
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":73
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":73
  *         sep = strstr(s,"_SEP_")
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:
  *             if terminal:             # <<<<<<<<<<<<<<
@@ -23368,7 +23144,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     if (__pyx_v_terminal) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":74
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":74
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:
  *             if terminal:
  *                 s1 = "\\"+s             # <<<<<<<<<<<<<<
@@ -23383,7 +23159,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
       __pyx_v_s1 = __pyx_t_7;
       __pyx_t_7 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":75
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":75
  *             if terminal:
  *                 s1 = "\\"+s
  *                 return self.terminals.index(s1)             # <<<<<<<<<<<<<<
@@ -23397,7 +23173,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     __pyx_L4:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":76
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":76
  *                 s1 = "\\"+s
  *                 return self.terminals.index(s1)
  *             s[n-1] = c'\0'             # <<<<<<<<<<<<<<
@@ -23406,7 +23182,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     (__pyx_v_s[(__pyx_v_n - 1)]) = '\x00';
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":77
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":77
  *                 return self.terminals.index(s1)
  *             s[n-1] = c'\0'
  *             s = s + 1             # <<<<<<<<<<<<<<
@@ -23415,7 +23191,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     __pyx_v_s = (__pyx_v_s + 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":78
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":78
  *             s[n-1] = c'\0'
  *             s = s + 1
  *             comma = strrchr(s, c',')             # <<<<<<<<<<<<<<
@@ -23424,7 +23200,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     __pyx_v_comma = strrchr(__pyx_v_s, ',');
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":79
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":79
  *             s = s + 1
  *             comma = strrchr(s, c',')
  *             if comma != NULL:             # <<<<<<<<<<<<<<
@@ -23434,7 +23210,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
     __pyx_t_2 = (__pyx_v_comma != NULL);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":80
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":80
  *             comma = strrchr(s, c',')
  *             if comma != NULL:
  *                 comma[0] = c'\0'             # <<<<<<<<<<<<<<
@@ -23443,7 +23219,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
       (__pyx_v_comma[0]) = '\x00';
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":81
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":81
  *             if comma != NULL:
  *                 comma[0] = c'\0'
  *                 return self.setindex(self.fromcat(s), strtol(comma+1, NULL, 10))             # <<<<<<<<<<<<<<
@@ -23456,7 +23232,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":83
+      /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":83
  *                 return self.setindex(self.fromcat(s), strtol(comma+1, NULL, 10))
  *             else:
  *                 return self.fromcat(s)             # <<<<<<<<<<<<<<
@@ -23471,7 +23247,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":85
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":85
  *                 return self.fromcat(s)
  *         else:
  *             return self.terminals.index(s)             # <<<<<<<<<<<<<<
@@ -23507,7 +23283,7 @@ static PyObject *__pyx_pw_3_sa_8Alphabet_9terminals_1__get__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":8
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":8
  * 
  * cdef class Alphabet:
  *     cdef readonly StringMap terminals, nonterminals             # <<<<<<<<<<<<<<
@@ -23558,7 +23334,7 @@ static PyObject *__pyx_pf_3_sa_8Alphabet_12nonterminals___get__(struct __pyx_obj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":89
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":89
  * cdef Alphabet ALPHABET = Alphabet()
  * 
  * cdef char* sym_tostring(int sym):             # <<<<<<<<<<<<<<
@@ -23571,7 +23347,7 @@ static char *__pyx_f_3_sa_sym_tostring(int __pyx_v_sym) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_tostring", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":90
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":90
  * 
  * cdef char* sym_tostring(int sym):
  *     return ALPHABET.tostring(sym)             # <<<<<<<<<<<<<<
@@ -23587,7 +23363,7 @@ static char *__pyx_f_3_sa_sym_tostring(int __pyx_v_sym) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":92
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":92
  *     return ALPHABET.tostring(sym)
  * 
  * cdef char* sym_tocat(int sym):             # <<<<<<<<<<<<<<
@@ -23600,7 +23376,7 @@ static char *__pyx_f_3_sa_sym_tocat(int __pyx_v_sym) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_tocat", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":93
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":93
  * 
  * cdef char* sym_tocat(int sym):
  *     return ALPHABET.tocat(sym)             # <<<<<<<<<<<<<<
@@ -23616,7 +23392,7 @@ static char *__pyx_f_3_sa_sym_tocat(int __pyx_v_sym) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":95
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":95
  *     return ALPHABET.tocat(sym)
  * 
  * cdef int sym_isvar(int sym):             # <<<<<<<<<<<<<<
@@ -23629,7 +23405,7 @@ static int __pyx_f_3_sa_sym_isvar(int __pyx_v_sym) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_isvar", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":96
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":96
  * 
  * cdef int sym_isvar(int sym):
  *     return ALPHABET.isvar(sym)             # <<<<<<<<<<<<<<
@@ -23645,7 +23421,7 @@ static int __pyx_f_3_sa_sym_isvar(int __pyx_v_sym) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":98
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":98
  *     return ALPHABET.isvar(sym)
  * 
  * cdef int sym_getindex(int sym):             # <<<<<<<<<<<<<<
@@ -23658,7 +23434,7 @@ static int __pyx_f_3_sa_sym_getindex(int __pyx_v_sym) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_getindex", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":99
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":99
  * 
  * cdef int sym_getindex(int sym):
  *     return ALPHABET.getindex(sym)             # <<<<<<<<<<<<<<
@@ -23674,7 +23450,7 @@ static int __pyx_f_3_sa_sym_getindex(int __pyx_v_sym) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":101
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":101
  *     return ALPHABET.getindex(sym)
  * 
  * cdef int sym_setindex(int sym, int id):             # <<<<<<<<<<<<<<
@@ -23687,7 +23463,7 @@ static int __pyx_f_3_sa_sym_setindex(int __pyx_v_sym, int __pyx_v_id) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_setindex", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":102
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":102
  * 
  * cdef int sym_setindex(int sym, int id):
  *     return ALPHABET.setindex(sym, id)             # <<<<<<<<<<<<<<
@@ -23703,7 +23479,7 @@ static int __pyx_f_3_sa_sym_setindex(int __pyx_v_sym, int __pyx_v_id) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":104
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":104
  *     return ALPHABET.setindex(sym, id)
  * 
  * cdef int sym_fromstring(char* string, bint terminal):             # <<<<<<<<<<<<<<
@@ -23716,7 +23492,7 @@ static int __pyx_f_3_sa_sym_fromstring(char *__pyx_v_string, int __pyx_v_termina
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sym_fromstring", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":105
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":105
  * 
  * cdef int sym_fromstring(char* string, bint terminal):
  *     return ALPHABET.fromstring(string, terminal)             # <<<<<<<<<<<<<<
@@ -23733,18 +23509,19 @@ static int __pyx_f_3_sa_sym_fromstring(char *__pyx_v_string, int __pyx_v_termina
 }
 
 /* Python wrapper */
-static PyObject *__pyx_pw_3_sa_3isvar(PyObject *__pyx_self, PyObject *__pyx_v_sym); /*proto*/
-static PyMethodDef __pyx_mdef_3_sa_3isvar = {__Pyx_NAMESTR("isvar"), (PyCFunction)__pyx_pw_3_sa_3isvar, METH_O, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pw_3_sa_3isvar(PyObject *__pyx_self, PyObject *__pyx_v_sym) {
+static PyObject *__pyx_pw_3_sa_5isvar(PyObject *__pyx_self, PyObject *__pyx_v_sym); /*proto*/
+static PyMethodDef __pyx_mdef_3_sa_5isvar = {__Pyx_NAMESTR("isvar"), (PyCFunction)__pyx_pw_3_sa_5isvar, METH_O, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pw_3_sa_5isvar(PyObject *__pyx_self, PyObject *__pyx_v_sym) {
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("isvar (wrapper)", 0);
-  __pyx_r = __pyx_pf_3_sa_2isvar(__pyx_self, ((PyObject *)__pyx_v_sym));
+  __pyx_self = __pyx_self;
+  __pyx_r = __pyx_pf_3_sa_4isvar(__pyx_self, ((PyObject *)__pyx_v_sym));
   __Pyx_RefNannyFinishContext();
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":107
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  */
 
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+static PyObject *__pyx_pf_3_sa_4isvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_sym) {
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+static PyObject *__pyx_pw_3_sa_7make_lattice(PyObject *__pyx_self, PyObject *__pyx_v_words) {
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+  __pyx_self = __pyx_self;
+  __pyx_r = __pyx_pf_3_sa_6make_lattice(__pyx_self, ((PyObject *)__pyx_v_words));
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":111
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":111
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-      #endif
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":112
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-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
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-      #endif
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-static PyObject *__pyx_pf_3_sa_4make_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words) {
+static PyObject *__pyx_pf_3_sa_6make_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words) {
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":111
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":111
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":112
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":112
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+static PyObject *__pyx_pw_3_sa_9decode_lattice(PyObject *__pyx_self, PyObject *__pyx_v_lattice) {
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":115
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":115
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":116
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":116
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-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":115
+    /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":115
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-      #endif
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-    /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":116
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":115
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":119
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 static PyObject *__pyx_gb_3_sa_12encode_words_2generator11(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":122
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":122
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-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
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-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":121
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":121
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@@ -25116,7 +24814,7 @@ static PyObject *__pyx_gb_3_sa_12encode_words_2generator11(__pyx_GeneratorObject
  * 
  */
 
-static PyObject *__pyx_pf_3_sa_10encode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words) {
+static PyObject *__pyx_pf_3_sa_12encode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words) {
   struct __pyx_obj_3_sa___pyx_scope_struct_11_encode_words *__pyx_cur_scope;
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   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_words);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":122
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":122
  * 
  * def encode_words(words):
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@@ -25173,19 +24871,20 @@ static PyObject *__pyx_pf_3_sa_10encode_words(CYTHON_UNUSED PyObject *__pyx_self
 }
 
 /* Python wrapper */
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-static PyObject *__pyx_pw_3_sa_13decode_words(PyObject *__pyx_self, PyObject *__pyx_v_syms) {
+static PyObject *__pyx_pw_3_sa_15decode_words(PyObject *__pyx_self, PyObject *__pyx_v_syms); /*proto*/
+static PyMethodDef __pyx_mdef_3_sa_15decode_words = {__Pyx_NAMESTR("decode_words"), (PyCFunction)__pyx_pw_3_sa_15decode_words, METH_O, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pw_3_sa_15decode_words(PyObject *__pyx_self, PyObject *__pyx_v_syms) {
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-  __pyx_r = __pyx_pf_3_sa_12decode_words(__pyx_self, ((PyObject *)__pyx_v_syms));
+  __pyx_self = __pyx_self;
+  __pyx_r = __pyx_pf_3_sa_14decode_words(__pyx_self, ((PyObject *)__pyx_v_syms));
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 static PyObject *__pyx_gb_3_sa_12decode_words_2generator12(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":125
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":125
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  * def decode_words(syms):
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-      #else
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-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
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-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
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-/* "/home/m/workspace/cdec/python/src/sa/sym.pxi":124
+/* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":124
  *     return tuple(sym_fromstring(word, True) for word in words)
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  * def decode_words(syms):             # <<<<<<<<<<<<<<
  *     return tuple(sym_tostring(sym) for sym in syms)
  */
 
-static PyObject *__pyx_pf_3_sa_12decode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_syms) {
+static PyObject *__pyx_pf_3_sa_14decode_words(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_syms) {
   struct __pyx_obj_3_sa___pyx_scope_struct_13_decode_words *__pyx_cur_scope;
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   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_syms);
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":125
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":125
  * 
  * def decode_words(syms):
  *     return tuple(sym_tostring(sym) for sym in syms)             # <<<<<<<<<<<<<<
@@ -25389,11 +25079,11 @@ static PyObject *__pyx_pf_3_sa_12decode_words(CYTHON_UNUSED PyObject *__pyx_self
 static int __pyx_pw_3_sa_6Phrase_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_3_sa_6Phrase_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_words = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__words,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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@@ -25406,7 +25096,8 @@ static int __pyx_pw_3_sa_6Phrase_1__cinit__(PyObject *__pyx_v_self, PyObject *__
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       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__words)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__words);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
       }
       if (unlikely(kw_args > 0)) {
@@ -25432,7 +25123,7 @@ static int __pyx_pw_3_sa_6Phrase_1__cinit__(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":6
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":6
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":8
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":8
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  */
   __pyx_v_n_vars = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":9
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":9
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  *         n = len(words)             # <<<<<<<<<<<<<<
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   __pyx_v_n = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":10
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":10
  *         n_vars = 0
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   __pyx_v_self->syms = ((int *)malloc((__pyx_v_n * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":11
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":11
  *         n = len(words)
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  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":12
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":12
  *         self.syms = <int *>malloc(n*sizeof(int))
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     (__pyx_v_self->syms[__pyx_v_i]) = __pyx_t_4;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":13
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":13
  *         for i from 0 <= i < n:
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     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":14
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":14
  *             self.syms[i] = words[i]
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     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":15
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":15
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  *         self.n = n             # <<<<<<<<<<<<<<
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   __pyx_v_self->n = __pyx_v_n;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":16
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":16
  *                 n_vars += 1
  *         self.n = n
  *         self.n_vars = n_vars             # <<<<<<<<<<<<<<
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   __pyx_v_self->n_vars = __pyx_v_n_vars;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":17
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":17
  *         self.n = n
  *         self.n_vars = n_vars
  *         self.varpos = <int *>malloc(n_vars*sizeof(int))             # <<<<<<<<<<<<<<
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   __pyx_v_self->varpos = ((int *)malloc((__pyx_v_n_vars * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":18
  *         self.n_vars = n_vars
  *         self.varpos = <int *>malloc(n_vars*sizeof(int))
  *         j = 0             # <<<<<<<<<<<<<<
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  */
   __pyx_v_j = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":19
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":19
  *         self.varpos = <int *>malloc(n_vars*sizeof(int))
  *         j = 0
  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
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   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_2; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":20
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":20
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     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":21
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":21
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  *                 self.varpos[j] = i             # <<<<<<<<<<<<<<
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  */
       (__pyx_v_self->varpos[__pyx_v_j]) = __pyx_v_i;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":22
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":22
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  *                 self.varpos[j] = i
  *                 j = j + 1             # <<<<<<<<<<<<<<
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":24
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  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":25
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   free(__pyx_v_self->syms);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":26
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":26
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":28
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":28
  *         free(self.varpos)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":29
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":29
  * 
  *     def __str__(self):
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@@ -25708,7 +25399,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__
   __pyx_v_strs = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":31
  *         strs = []
  *         cdef int i, s
  *         for i from 0 <= i < self.n:             # <<<<<<<<<<<<<<
@@ -25718,7 +25409,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__
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   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_2; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":32
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":32
  *         cdef int i, s
  *         for i from 0 <= i < self.n:
  *             s = self.syms[i]             # <<<<<<<<<<<<<<
@@ -25727,7 +25418,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__
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     __pyx_v_s = (__pyx_v_self->syms[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":33
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":33
  *         for i from 0 <= i < self.n:
  *             s = self.syms[i]
  *             strs.append(sym_tostring(s))             # <<<<<<<<<<<<<<
@@ -25740,7 +25431,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__
     __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":34
  *             s = self.syms[i]
  *             strs.append(sym_tostring(s))
  *         return ' '.join(strs)             # <<<<<<<<<<<<<<
@@ -25790,7 +25481,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_7handle(PyObject *__pyx_v_self, CYTHON_UN
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":36
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":36
  *         return ' '.join(strs)
  * 
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@@ -25814,7 +25505,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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   __Pyx_RefNannySetupContext("handle", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":39
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":39
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  *         norm = []             # <<<<<<<<<<<<<<
@@ -25826,7 +25517,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
   __pyx_v_norm = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":41
  *         norm = []
  *         cdef int i, j, s
  *         i = 1             # <<<<<<<<<<<<<<
@@ -25835,7 +25526,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
  */
   __pyx_v_i = 1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":42
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":42
  *         cdef int i, j, s
  *         i = 1
  *         j = 0             # <<<<<<<<<<<<<<
@@ -25844,7 +25535,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":43
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":43
  *         i = 1
  *         j = 0
  *         for j from 0 <= j < self.n:             # <<<<<<<<<<<<<<
@@ -25854,7 +25545,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":44
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":44
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  *             s = self.syms[j]             # <<<<<<<<<<<<<<
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":45
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":45
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-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":46
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":46
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-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":47
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":47
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@@ -25894,7 +25585,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":48
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":48
  *                 s = sym_setindex(s,i)
  *                 i = i + 1
  *             norm.append(s)             # <<<<<<<<<<<<<<
@@ -25907,7 +25598,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":49
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":49
  *                 i = i + 1
  *             norm.append(s)
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@@ -25945,7 +25636,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_9strhandle(PyObject *__pyx_v_self, CYTHON
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":51
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":51
  *         return tuple(norm)
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  *     def strhandle(self):             # <<<<<<<<<<<<<<
@@ -25972,7 +25663,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":52
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":52
  * 
  *     def strhandle(self):
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":53
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":53
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":55
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":55
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":56
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":56
  *         cdef int i, j, s
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":57
  *         i = 1
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  *         for j from 0 <= j < self.n:             # <<<<<<<<<<<<<<
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":58
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":58
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":59
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":59
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-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":60
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":60
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-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":61
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":61
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":62
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":62
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":63
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":63
  *                 i = i + 1
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":65
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":65
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":66
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":66
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  *     def arity(self):
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":68
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":68
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":69
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":69
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+  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_1);
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":70
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":70
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":72
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":74
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":75
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":75
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-  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_1);
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":76
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":76
  *     def getvar(self, i):
  *         if 0 <= i < self.n_vars:
  *             return self.syms[self.varpos[i]]             # <<<<<<<<<<<<<<
@@ -26331,7 +26026,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_14getvar(struct __pyx_obj_3_sa_Phrase *__
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":78
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":78
  *             return self.syms[self.varpos[i]]
  *         else:
  *             raise IndexError             # <<<<<<<<<<<<<<
@@ -26356,7 +26051,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_14getvar(struct __pyx_obj_3_sa_Phrase *__
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":80
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":80
  *             raise IndexError
  * 
  *     cdef int chunkpos(self, int k):             # <<<<<<<<<<<<<<
@@ -26370,7 +26065,7 @@ int __pyx_f_3_sa_6Phrase_chunkpos(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("chunkpos", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":81
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":81
  * 
  *     cdef int chunkpos(self, int k):
  *         if k == 0:             # <<<<<<<<<<<<<<
@@ -26380,7 +26075,7 @@ int __pyx_f_3_sa_6Phrase_chunkpos(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_k == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":82
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":82
  *     cdef int chunkpos(self, int k):
  *         if k == 0:
  *             return 0             # <<<<<<<<<<<<<<
@@ -26393,7 +26088,7 @@ int __pyx_f_3_sa_6Phrase_chunkpos(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":84
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":84
  *             return 0
  *         else:
  *             return self.varpos[k-1]+1             # <<<<<<<<<<<<<<
@@ -26411,7 +26106,7 @@ int __pyx_f_3_sa_6Phrase_chunkpos(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":86
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":86
  *             return self.varpos[k-1]+1
  * 
  *     cdef int chunklen(self, int k):             # <<<<<<<<<<<<<<
@@ -26425,7 +26120,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("chunklen", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":87
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":87
  * 
  *     cdef int chunklen(self, int k):
  *         if self.n_vars == 0:             # <<<<<<<<<<<<<<
@@ -26435,7 +26130,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_self->n_vars == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":88
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":88
  *     cdef int chunklen(self, int k):
  *         if self.n_vars == 0:
  *             return self.n             # <<<<<<<<<<<<<<
@@ -26447,7 +26142,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":89
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":89
  *         if self.n_vars == 0:
  *             return self.n
  *         elif k == 0:             # <<<<<<<<<<<<<<
@@ -26457,7 +26152,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_k == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":90
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":90
  *             return self.n
  *         elif k == 0:
  *             return self.varpos[0]             # <<<<<<<<<<<<<<
@@ -26469,7 +26164,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":91
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":91
  *         elif k == 0:
  *             return self.varpos[0]
  *         elif k == self.n_vars:             # <<<<<<<<<<<<<<
@@ -26479,7 +26174,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_k == __pyx_v_self->n_vars);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":92
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":92
  *             return self.varpos[0]
  *         elif k == self.n_vars:
  *             return self.n-self.varpos[k-1]-1             # <<<<<<<<<<<<<<
@@ -26492,7 +26187,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":94
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":94
  *             return self.n-self.varpos[k-1]-1
  *         else:
  *             return self.varpos[k]-self.varpos[k-1]-1             # <<<<<<<<<<<<<<
@@ -26521,7 +26216,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_17clen(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":96
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":96
  *             return self.varpos[k]-self.varpos[k-1]-1
  * 
  *     def clen(self, k):             # <<<<<<<<<<<<<<
@@ -26539,7 +26234,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_16clen(struct __pyx_obj_3_sa_Phrase *__py
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("clen", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":97
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":97
  * 
  *     def clen(self, k):
  *          return self.chunklen(k)             # <<<<<<<<<<<<<<
@@ -26577,7 +26272,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_19getchunk(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":99
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":99
  *          return self.chunklen(k)
  * 
  *     def getchunk(self, ci):             # <<<<<<<<<<<<<<
@@ -26600,7 +26295,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("getchunk", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":101
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":101
  *     def getchunk(self, ci):
  *         cdef int start, stop
  *         start = self.chunkpos(ci)             # <<<<<<<<<<<<<<
@@ -26610,7 +26305,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_ci); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_start = ((struct __pyx_vtabstruct_3_sa_Phrase *)__pyx_v_self->__pyx_vtab)->chunkpos(__pyx_v_self, __pyx_t_1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":102
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":102
  *         cdef int start, stop
  *         start = self.chunkpos(ci)
  *         stop = start+self.chunklen(ci)             # <<<<<<<<<<<<<<
@@ -26620,7 +26315,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_ci); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_stop = (__pyx_v_start + ((struct __pyx_vtabstruct_3_sa_Phrase *)__pyx_v_self->__pyx_vtab)->chunklen(__pyx_v_self, __pyx_t_1));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":103
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":103
  *         start = self.chunkpos(ci)
  *         stop = start+self.chunklen(ci)
  *         chunk = []             # <<<<<<<<<<<<<<
@@ -26632,7 +26327,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_v_chunk = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":104
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":104
  *         stop = start+self.chunklen(ci)
  *         chunk = []
  *         for i from start <= i < stop:             # <<<<<<<<<<<<<<
@@ -26642,7 +26337,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __pyx_v_stop;
   for (__pyx_v_i = __pyx_v_start; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":105
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":105
  *         chunk = []
  *         for i from start <= i < stop:
  *             chunk.append(self.syms[i])             # <<<<<<<<<<<<<<
@@ -26655,7 +26350,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":106
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":106
  *         for i from start <= i < stop:
  *             chunk.append(self.syms[i])
  *         return chunk             # <<<<<<<<<<<<<<
@@ -26693,7 +26388,7 @@ static int __pyx_pw_3_sa_6Phrase_21__cmp__(PyObject *__pyx_v_self, PyObject *__p
 }
 #endif /*!(#if PY_MAJOR_VERSION < 3)*/
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":108
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":108
  *         return chunk
  * 
  *     def __cmp__(self, other):             # <<<<<<<<<<<<<<
@@ -26716,7 +26411,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cmp__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":111
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":111
  *         cdef Phrase otherp
  *         cdef int i
  *         otherp = other             # <<<<<<<<<<<<<<
@@ -26727,7 +26422,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __Pyx_INCREF(__pyx_v_other);
   __pyx_v_otherp = ((struct __pyx_obj_3_sa_Phrase *)__pyx_v_other);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":112
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":112
  *         cdef int i
  *         otherp = other
  *         for i from 0 <= i < min(self.n, otherp.n):             # <<<<<<<<<<<<<<
@@ -26744,7 +26439,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_1 = __pyx_t_3;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":113
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":113
  *         otherp = other
  *         for i from 0 <= i < min(self.n, otherp.n):
  *             if self.syms[i] < otherp.syms[i]:             # <<<<<<<<<<<<<<
@@ -26754,7 +26449,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_t_4 = ((__pyx_v_self->syms[__pyx_v_i]) < (__pyx_v_otherp->syms[__pyx_v_i]));
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":114
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":114
  *         for i from 0 <= i < min(self.n, otherp.n):
  *             if self.syms[i] < otherp.syms[i]:
  *                 return -1             # <<<<<<<<<<<<<<
@@ -26766,7 +26461,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
       goto __pyx_L5;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":115
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":115
  *             if self.syms[i] < otherp.syms[i]:
  *                 return -1
  *             elif self.syms[i] > otherp.syms[i]:             # <<<<<<<<<<<<<<
@@ -26776,7 +26471,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_t_4 = ((__pyx_v_self->syms[__pyx_v_i]) > (__pyx_v_otherp->syms[__pyx_v_i]));
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":116
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":116
  *                 return -1
  *             elif self.syms[i] > otherp.syms[i]:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -26790,7 +26485,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":117
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":117
  *             elif self.syms[i] > otherp.syms[i]:
  *                 return 1
  *         if self.n < otherp.n:             # <<<<<<<<<<<<<<
@@ -26800,7 +26495,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_4 = (__pyx_v_self->n < __pyx_v_otherp->n);
   if (__pyx_t_4) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":118
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":118
  *                 return 1
  *         if self.n < otherp.n:
  *             return -1             # <<<<<<<<<<<<<<
@@ -26812,7 +26507,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     goto __pyx_L6;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":119
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":119
  *         if self.n < otherp.n:
  *             return -1
  *         elif self.n > otherp.n:             # <<<<<<<<<<<<<<
@@ -26822,7 +26517,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_4 = (__pyx_v_self->n > __pyx_v_otherp->n);
   if (__pyx_t_4) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":120
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":120
  *             return -1
  *         elif self.n > otherp.n:
  *             return 1             # <<<<<<<<<<<<<<
@@ -26835,7 +26530,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":122
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":122
  *             return 1
  *         else:
  *             return 0             # <<<<<<<<<<<<<<
@@ -26870,7 +26565,7 @@ static Py_hash_t __pyx_pw_3_sa_6Phrase_23__hash__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":124
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":124
  *             return 0
  * 
  *     def __hash__(self):             # <<<<<<<<<<<<<<
@@ -26887,7 +26582,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
   int __pyx_t_2;
   __Pyx_RefNannySetupContext("__hash__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":127
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":127
  *         cdef int i
  *         cdef unsigned h
  *         h = 0             # <<<<<<<<<<<<<<
@@ -26896,7 +26591,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
  */
   __pyx_v_h = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":128
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":128
  *         cdef unsigned h
  *         h = 0
  *         for i from 0 <= i < self.n:             # <<<<<<<<<<<<<<
@@ -26906,7 +26601,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __pyx_v_self->n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":129
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":129
  *         h = 0
  *         for i from 0 <= i < self.n:
  *             if self.syms[i] > 0:             # <<<<<<<<<<<<<<
@@ -26916,7 +26611,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     __pyx_t_2 = ((__pyx_v_self->syms[__pyx_v_i]) > 0);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":130
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":130
  *         for i from 0 <= i < self.n:
  *             if self.syms[i] > 0:
  *                 h = (h << 1) + self.syms[i]             # <<<<<<<<<<<<<<
@@ -26928,7 +26623,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":132
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":132
  *                 h = (h << 1) + self.syms[i]
  *             else:
  *                 h = (h << 1) + -self.syms[i]             # <<<<<<<<<<<<<<
@@ -26940,7 +26635,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":133
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":133
  *             else:
  *                 h = (h << 1) + -self.syms[i]
  *         return h             # <<<<<<<<<<<<<<
@@ -26968,7 +26663,7 @@ static Py_ssize_t __pyx_pw_3_sa_6Phrase_25__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":135
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":135
  *         return h
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -26981,7 +26676,7 @@ static Py_ssize_t __pyx_pf_3_sa_6Phrase_24__len__(struct __pyx_obj_3_sa_Phrase *
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":136
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":136
  * 
  *     def __len__(self):
  *         return self.n             # <<<<<<<<<<<<<<
@@ -27008,7 +26703,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_27__getitem__(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":138
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":138
  *         return self.n
  * 
  *     def __getitem__(self, i):             # <<<<<<<<<<<<<<
@@ -27026,7 +26721,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_26__getitem__(struct __pyx_obj_3_sa_Phras
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":139
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":139
  * 
  *     def __getitem__(self, i):
  *         return self.syms[i]             # <<<<<<<<<<<<<<
@@ -27065,7 +26760,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_29__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":141
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":141
  *         return self.syms[i]
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -27127,7 +26822,7 @@ static PyObject *__pyx_gb_3_sa_6Phrase_30generator2(__pyx_GeneratorObject *__pyx
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":143
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":143
  *     def __iter__(self):
  *         cdef int i
  *         for i from 0 <= i < self.n:             # <<<<<<<<<<<<<<
@@ -27137,7 +26832,7 @@ static PyObject *__pyx_gb_3_sa_6Phrase_30generator2(__pyx_GeneratorObject *__pyx
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":144
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":144
  *         cdef int i
  *         for i from 0 <= i < self.n:
  *             yield self.syms[i]             # <<<<<<<<<<<<<<
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-  __Pyx_Generator_clear((PyObject*)__pyx_generator);
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 static PyObject *__pyx_pw_3_sa_6Phrase_32subst(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_start = 0;
   PyObject *__pyx_v_children = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__children,0};
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@@ -27194,10 +26888,12 @@ static PyObject *__pyx_pw_3_sa_6Phrase_32subst(PyObject *__pyx_v_self, PyObject
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__children)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__children);
+        if (likely(values[1])) kw_args--;
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@@ -27227,7 +26923,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_32subst(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":146
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":146
  *             yield self.syms[i]
  * 
  *     def subst(self, start, children):             # <<<<<<<<<<<<<<
@@ -27250,7 +26946,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":148
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":148
  *     def subst(self, start, children):
  *         cdef int i
  *         for i from 0 <= i < self.n:             # <<<<<<<<<<<<<<
@@ -27260,7 +26956,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":149
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":149
  *         cdef int i
  *         for i from 0 <= i < self.n:
  *             if sym_isvar(self.syms[i]):             # <<<<<<<<<<<<<<
@@ -27270,7 +26966,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
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     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":150
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":150
  *         for i from 0 <= i < self.n:
  *             if sym_isvar(self.syms[i]):
  *                 start = start + children[sym_getindex(self.syms[i])-1]             # <<<<<<<<<<<<<<
@@ -27290,7 +26986,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":152
+      /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":152
  *                 start = start + children[sym_getindex(self.syms[i])-1]
  *             else:
  *                 start = start + (self.syms[i],)             # <<<<<<<<<<<<<<
@@ -27314,7 +27010,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":153
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":153
  *             else:
  *                 start = start + (self.syms[i],)
  *         return start             # <<<<<<<<<<<<<<
@@ -27351,7 +27047,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_5words_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":156
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":156
  * 
  *     property words:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -27375,7 +27071,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_5words___get__(struct __pyx_obj_3_sa_Phra
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":157
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":157
  *     property words:
  *         def __get__(self):
  *             return [sym_tostring(w) for w in self if not sym_isvar(w)]             # <<<<<<<<<<<<<<
@@ -27396,18 +27092,10 @@ static PyObject *__pyx_pf_3_sa_6Phrase_5words___get__(struct __pyx_obj_3_sa_Phra
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-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++;
     } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
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-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++;
     } else {
       __pyx_t_5 = __pyx_t_4(__pyx_t_2);
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@@ -27428,7 +27116,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_5words___get__(struct __pyx_obj_3_sa_Phra
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       __Pyx_GOTREF(((PyObject *)__pyx_t_5));
-      if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       goto __pyx_L5;
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@@ -27463,14 +27151,14 @@ static int __pyx_pw_3_sa_4Rule_1__cinit__(PyObject *__pyx_v_self, PyObject *__py
   struct __pyx_obj_3_sa_Phrase *__pyx_v_e = 0;
   PyObject *__pyx_v_scores = 0;
   PyObject *__pyx_v_word_alignments = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__lhs,&__pyx_n_s__f,&__pyx_n_s__e,&__pyx_n_s__scores,&__pyx_n_s__word_alignments,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__lhs,&__pyx_n_s__f,&__pyx_n_s__e,&__pyx_n_s__scores,&__pyx_n_s__word_alignments,0};
     PyObject* values[5] = {0,0,0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":161
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":161
  * cdef class Rule:
  * 
  *     def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):             # <<<<<<<<<<<<<<
@@ -27494,15 +27182,18 @@ static int __pyx_pw_3_sa_4Rule_1__cinit__(PyObject *__pyx_v_self, PyObject *__py
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__lhs)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__lhs);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 1); {__pyx_filename = __pyx_f[7]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e);
+        if (likely(values[2])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 2); {__pyx_filename = __pyx_f[7]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
@@ -27567,7 +27258,7 @@ static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_sel
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":162
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":162
  * 
  *     def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):
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@@ -27596,7 +27287,7 @@ static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_sel
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":163
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":163
  *     def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):
  *         if not sym_isvar(lhs): raise Exception('Invalid LHS symbol: %d' % lhs)
  *         self.lhs = lhs             # <<<<<<<<<<<<<<
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  */
   __pyx_v_self->lhs = __pyx_v_lhs;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":164
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":164
  *         if not sym_isvar(lhs): raise Exception('Invalid LHS symbol: %d' % lhs)
  *         self.lhs = lhs
  *         self.f = f             # <<<<<<<<<<<<<<
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   __pyx_v_self->f = __pyx_v_f;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":165
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":165
  *         self.lhs = lhs
  *         self.f = f
  *         self.e = e             # <<<<<<<<<<<<<<
@@ -27631,7 +27322,7 @@ static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_sel
   __Pyx_DECREF(((PyObject *)__pyx_v_self->e));
   __pyx_v_self->e = __pyx_v_e;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":166
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":166
  *         self.f = f
  *         self.e = e
  *         self.word_alignments = word_alignments             # <<<<<<<<<<<<<<
@@ -27644,7 +27335,7 @@ static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_sel
   __Pyx_DECREF(__pyx_v_self->word_alignments);
   __pyx_v_self->word_alignments = __pyx_v_word_alignments;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":167
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":167
  *         self.e = e
  *         self.word_alignments = word_alignments
  *         self.scores = scores             # <<<<<<<<<<<<<<
@@ -27681,7 +27372,7 @@ static Py_hash_t __pyx_pw_3_sa_4Rule_3__hash__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":169
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":169
  *         self.scores = scores
  * 
  *     def __hash__(self):             # <<<<<<<<<<<<<<
@@ -27700,7 +27391,7 @@ static Py_hash_t __pyx_pf_3_sa_4Rule_2__hash__(struct __pyx_obj_3_sa_Rule *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__hash__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":170
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":170
  * 
  *     def __hash__(self):
  *         return hash((self.lhs, self.f, self.e))             # <<<<<<<<<<<<<<
@@ -27756,7 +27447,7 @@ static int __pyx_pw_3_sa_4Rule_5__cmp__(PyObject *__pyx_v_self, PyObject *__pyx_
 }
 #endif /*!(#if PY_MAJOR_VERSION < 3)*/
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":172
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":172
  *         return hash((self.lhs, self.f, self.e))
  * 
  *     def __cmp__(self, Rule other):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("__cmp__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":173
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":173
  * 
  *     def __cmp__(self, Rule other):
  *         return cmp((self.lhs, self.f, self.e, self.word_alignments),             # <<<<<<<<<<<<<<
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":174
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":174
  *     def __cmp__(self, Rule other):
  *         return cmp((self.lhs, self.f, self.e, self.word_alignments),
  *                 (other.lhs, other.f, other.e, self.word_alignments))             # <<<<<<<<<<<<<<
@@ -27870,7 +27561,7 @@ static PyObject *__pyx_pw_3_sa_4Rule_7fmerge(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":176
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":176
  *                 (other.lhs, other.f, other.e, self.word_alignments))
  * 
  *     def fmerge(self, Phrase f):             # <<<<<<<<<<<<<<
@@ -27888,19 +27579,20 @@ static PyObject *__pyx_pf_3_sa_4Rule_6fmerge(struct __pyx_obj_3_sa_Rule *__pyx_v
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":177
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+  __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_v_self->f), ((PyObject *)__pyx_v_f), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":178
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":178
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":180
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":180
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":181
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":181
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":187
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":187
  *         fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
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-      #endif
+      __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":183
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   __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":185
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   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":186
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":186
  *         cdef unsigned i
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":187
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":187
  *         fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":188
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":188
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   return __pyx_r;
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-/* "/home/m/workspace/cdec/python/src/sa/rule.pxi":190
+/* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":190
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-  /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":191
+  /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":191
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  *     def alignments(self):
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-      #endif
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-      #endif
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-    /* "/home/m/workspace/cdec/python/src/sa/rule.pxi":192
+    /* "/home/paulb/workspace/cdec/python/src/sa/rule.pxi":192
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":21
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":24
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":24
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":25
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":25
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":26
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":26
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":27
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":27
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":29
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":31
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":32
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":32
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":33
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":33
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":34
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":35
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":35
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":36
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":38
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":39
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":40
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":40
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":41
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":43
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  * cdef free_trie_edge(_Trie_Edge* edge):             # <<<<<<<<<<<<<<
@@ -28766,7 +28440,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("free_trie_edge", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":44
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":44
  * 
  * cdef free_trie_edge(_Trie_Edge* edge):
  *     if edge != NULL:             # <<<<<<<<<<<<<<
@@ -28776,7 +28450,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   __pyx_t_1 = (__pyx_v_edge != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":45
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":45
  * cdef free_trie_edge(_Trie_Edge* edge):
  *     if edge != NULL:
  *         free_trie_node(edge.node)             # <<<<<<<<<<<<<<
@@ -28787,7 +28461,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":46
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":46
  *     if edge != NULL:
  *         free_trie_node(edge.node)
  *         free_trie_edge(edge.bigger)             # <<<<<<<<<<<<<<
@@ -28798,7 +28472,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":47
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":47
  *         free_trie_node(edge.node)
  *         free_trie_edge(edge.bigger)
  *         free_trie_edge(edge.smaller)             # <<<<<<<<<<<<<<
@@ -28824,7 +28498,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":49
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":49
  *         free_trie_edge(edge.smaller)
  * 
  * cdef _Trie_Node* trie_find(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -28841,7 +28515,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("trie_find", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":51
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":51
  * cdef _Trie_Node* trie_find(_Trie_Node* node, int val):
  *     cdef _Trie_Edge* cur
  *     cur = node.root             # <<<<<<<<<<<<<<
@@ -28850,7 +28524,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
  */
   __pyx_v_cur = __pyx_v_node->root;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":52
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":52
  *     cdef _Trie_Edge* cur
  *     cur = node.root
  *     while cur != NULL and cur.val != val:             # <<<<<<<<<<<<<<
@@ -28867,7 +28541,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     }
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":53
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":53
  *     cur = node.root
  *     while cur != NULL and cur.val != val:
  *         if val > cur.val:             # <<<<<<<<<<<<<<
@@ -28877,7 +28551,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_t_3 = (__pyx_v_val > __pyx_v_cur->val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":54
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":54
  *     while cur != NULL and cur.val != val:
  *         if val > cur.val:
  *             cur = cur.bigger             # <<<<<<<<<<<<<<
@@ -28888,7 +28562,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
       goto __pyx_L5;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":55
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":55
  *         if val > cur.val:
  *             cur = cur.bigger
  *         elif val < cur.val:             # <<<<<<<<<<<<<<
@@ -28898,7 +28572,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_t_3 = (__pyx_v_val < __pyx_v_cur->val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":56
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":56
  *             cur = cur.bigger
  *         elif val < cur.val:
  *             cur = cur.smaller             # <<<<<<<<<<<<<<
@@ -28911,7 +28585,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":57
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":57
  *         elif val < cur.val:
  *             cur = cur.smaller
  *     if cur == NULL:             # <<<<<<<<<<<<<<
@@ -28921,7 +28595,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   __pyx_t_3 = (__pyx_v_cur == NULL);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":58
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":58
  *             cur = cur.smaller
  *     if cur == NULL:
  *         return NULL             # <<<<<<<<<<<<<<
@@ -28934,7 +28608,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":60
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":60
  *         return NULL
  *     else:
  *         return cur.node             # <<<<<<<<<<<<<<
@@ -28952,7 +28626,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":62
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":62
  *         return cur.node
  * 
  * cdef trie_node_data_append(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -28966,7 +28640,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("trie_node_data_append", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":64
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":64
  * cdef trie_node_data_append(_Trie_Node* node, int val):
  *     cdef int new_len
  *     new_len = node.arr_len + 1             # <<<<<<<<<<<<<<
@@ -28975,7 +28649,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_new_len = (__pyx_v_node->arr_len + 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":65
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":65
  *     cdef int new_len
  *     new_len = node.arr_len + 1
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -28984,7 +28658,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_node->arr = ((int *)realloc(__pyx_v_node->arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":66
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":66
  *     new_len = node.arr_len + 1
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     node.arr[node.arr_len] = val             # <<<<<<<<<<<<<<
@@ -28993,7 +28667,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   (__pyx_v_node->arr[__pyx_v_node->arr_len]) = __pyx_v_val;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":67
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":67
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     node.arr[node.arr_len] = val
  *     node.arr_len = new_len             # <<<<<<<<<<<<<<
@@ -29008,7 +28682,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":69
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":69
  *     node.arr_len = new_len
  * 
  * cdef trie_node_data_extend(_Trie_Node* node, int* vals, int num_vals):             # <<<<<<<<<<<<<<
@@ -29022,7 +28696,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("trie_node_data_extend", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":71
  * cdef trie_node_data_extend(_Trie_Node* node, int* vals, int num_vals):
  *     cdef int new_len
  *     new_len = node.arr_len + num_vals             # <<<<<<<<<<<<<<
@@ -29031,7 +28705,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_new_len = (__pyx_v_node->arr_len + __pyx_v_num_vals);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":72
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":72
  *     cdef int new_len
  *     new_len = node.arr_len + num_vals
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -29040,7 +28714,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_node->arr = ((int *)realloc(__pyx_v_node->arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":73
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":73
  *     new_len = node.arr_len + num_vals
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     memcpy(node.arr + node.arr_len, vals, num_vals*sizeof(int))             # <<<<<<<<<<<<<<
@@ -29049,7 +28723,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   memcpy((__pyx_v_node->arr + __pyx_v_node->arr_len), __pyx_v_vals, (__pyx_v_num_vals * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":74
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":74
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     memcpy(node.arr + node.arr_len, vals, num_vals*sizeof(int))
  *     node.arr_len = new_len             # <<<<<<<<<<<<<<
@@ -29064,7 +28738,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":77
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":77
  * 
  * 
  * cdef _Trie_Node* trie_insert(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -29081,7 +28755,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("trie_insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":79
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":79
  * cdef _Trie_Node* trie_insert(_Trie_Node* node, int val):
  *     cdef _Trie_Edge** cur
  *     cur = &node.root             # <<<<<<<<<<<<<<
@@ -29090,7 +28764,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
  */
   __pyx_v_cur = (&__pyx_v_node->root);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":80
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":80
  *     cdef _Trie_Edge** cur
  *     cur = &node.root
  *     while cur[0] != NULL and cur[0].val != val:             # <<<<<<<<<<<<<<
@@ -29107,7 +28781,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     }
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":81
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":81
  *     cur = &node.root
  *     while cur[0] != NULL and cur[0].val != val:
  *         if val > cur[0].val:             # <<<<<<<<<<<<<<
@@ -29117,7 +28791,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_t_3 = (__pyx_v_val > (__pyx_v_cur[0])->val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":82
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":82
  *     while cur[0] != NULL and cur[0].val != val:
  *         if val > cur[0].val:
  *             cur = &cur[0].bigger             # <<<<<<<<<<<<<<
@@ -29128,7 +28802,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
       goto __pyx_L5;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":83
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":83
  *         if val > cur[0].val:
  *             cur = &cur[0].bigger
  *         elif val < cur[0].val:             # <<<<<<<<<<<<<<
@@ -29138,7 +28812,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_t_3 = (__pyx_v_val < (__pyx_v_cur[0])->val);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":84
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":84
  *             cur = &cur[0].bigger
  *         elif val < cur[0].val:
  *             cur = &cur[0].smaller             # <<<<<<<<<<<<<<
@@ -29151,7 +28825,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":85
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":85
  *         elif val < cur[0].val:
  *             cur = &cur[0].smaller
  *     if cur[0] == NULL:             # <<<<<<<<<<<<<<
@@ -29161,7 +28835,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
   __pyx_t_3 = ((__pyx_v_cur[0]) == NULL);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":86
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":86
  *             cur = &cur[0].smaller
  *     if cur[0] == NULL:
  *         cur[0] = new_trie_edge(val)             # <<<<<<<<<<<<<<
@@ -29173,7 +28847,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
   }
   __pyx_L6:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":87
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":87
  *     if cur[0] == NULL:
  *         cur[0] = new_trie_edge(val)
  *     return cur[0].node             # <<<<<<<<<<<<<<
@@ -29189,7 +28863,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":89
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":89
  *     return cur[0].node
  * 
  * cdef trie_node_to_map(_Trie_Node* node, result, prefix, int include_zeros):             # <<<<<<<<<<<<<<
@@ -29209,7 +28883,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("trie_node_to_map", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":92
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":92
  *     cdef IntList arr
  * 
  *     if include_zeros or node.arr_len > 0:             # <<<<<<<<<<<<<<
@@ -29224,7 +28898,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
   }
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":93
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":93
  * 
  *     if include_zeros or node.arr_len > 0:
  *         arr = IntList()             # <<<<<<<<<<<<<<
@@ -29236,7 +28910,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
     __pyx_v_arr = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_3);
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":94
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":94
  *     if include_zeros or node.arr_len > 0:
  *         arr = IntList()
  *         free(arr.arr)             # <<<<<<<<<<<<<<
@@ -29245,7 +28919,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
  */
     free(__pyx_v_arr->arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":95
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":95
  *         arr = IntList()
  *         free(arr.arr)
  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))             # <<<<<<<<<<<<<<
@@ -29254,7 +28928,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
  */
     __pyx_v_arr->arr = ((int *)malloc((__pyx_v_node->arr_len * (sizeof(int)))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":96
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":96
  *         free(arr.arr)
  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))             # <<<<<<<<<<<<<<
@@ -29263,7 +28937,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
  */
     memcpy(__pyx_v_arr->arr, __pyx_v_node->arr, (__pyx_v_node->arr_len * (sizeof(int))));
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":97
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":97
  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))
  *         arr.len = node.arr_len             # <<<<<<<<<<<<<<
@@ -29272,7 +28946,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
  */
     __pyx_v_arr->len = __pyx_v_node->arr_len;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":98
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":98
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))
  *         arr.len = node.arr_len
  *         arr.size = node.arr_len             # <<<<<<<<<<<<<<
@@ -29281,7 +28955,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
  */
     __pyx_v_arr->size = __pyx_v_node->arr_len;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":99
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":99
  *         arr.len = node.arr_len
  *         arr.size = node.arr_len
  *         result[prefix] = arr             # <<<<<<<<<<<<<<
@@ -29293,7 +28967,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":100
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":100
  *         arr.size = node.arr_len
  *         result[prefix] = arr
  *     trie_edge_to_map(node.root, result, prefix, include_zeros)             # <<<<<<<<<<<<<<
@@ -29317,7 +28991,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":102
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":102
  *     trie_edge_to_map(node.root, result, prefix, include_zeros)
  * 
  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):             # <<<<<<<<<<<<<<
@@ -29337,7 +29011,7 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
   __Pyx_RefNannySetupContext("trie_edge_to_map", 0);
   __Pyx_INCREF(__pyx_v_prefix);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":103
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":103
  * 
  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):
  *     if edge != NULL:             # <<<<<<<<<<<<<<
@@ -29347,7 +29021,7 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
   __pyx_t_1 = (__pyx_v_edge != NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":104
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":104
  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):
  *     if edge != NULL:
  *         trie_edge_to_map(edge.smaller, result, prefix, include_zeros)             # <<<<<<<<<<<<<<
@@ -29358,7 +29032,7 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":105
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":105
  *     if edge != NULL:
  *         trie_edge_to_map(edge.smaller, result, prefix, include_zeros)
  *         trie_edge_to_map(edge.bigger, result, prefix, include_zeros)             # <<<<<<<<<<<<<<
@@ -29369,7 +29043,7 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":106
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":106
  *         trie_edge_to_map(edge.smaller, result, prefix, include_zeros)
  *         trie_edge_to_map(edge.bigger, result, prefix, include_zeros)
  *         prefix = prefix + (edge.val,)             # <<<<<<<<<<<<<<
@@ -29390,7 +29064,7 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
     __pyx_v_prefix = __pyx_t_2;
     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":107
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":107
  *         trie_edge_to_map(edge.bigger, result, prefix, include_zeros)
  *         prefix = prefix + (edge.val,)
  *         trie_node_to_map(edge.node, result, prefix, include_zeros)             # <<<<<<<<<<<<<<
@@ -29422,11 +29096,11 @@ static PyObject *__pyx_f_3_sa_trie_edge_to_map(struct __pyx_t_3_sa__Trie_Edge *_
 static int __pyx_pw_3_sa_7TrieMap_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_3_sa_7TrieMap_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   int __pyx_v_alphabet_size;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__alphabet_size,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__alphabet_size,0};
     PyObject* values[1] = {0};
     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -29439,7 +29113,8 @@ static int __pyx_pw_3_sa_7TrieMap_1__cinit__(PyObject *__pyx_v_self, PyObject *_
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alphabet_size)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alphabet_size);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
       }
       if (unlikely(kw_args > 0)) {
@@ -29465,7 +29140,7 @@ static int __pyx_pw_3_sa_7TrieMap_1__cinit__(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":114
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":114
  *     cdef int V
  * 
  *     def __cinit__(self, int alphabet_size):             # <<<<<<<<<<<<<<
@@ -29478,7 +29153,7 @@ static int __pyx_pf_3_sa_7TrieMap___cinit__(struct __pyx_obj_3_sa_TrieMap *__pyx
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":115
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":115
  * 
  *     def __cinit__(self, int alphabet_size):
  *         self.V = alphabet_size             # <<<<<<<<<<<<<<
@@ -29487,7 +29162,7 @@ static int __pyx_pf_3_sa_7TrieMap___cinit__(struct __pyx_obj_3_sa_TrieMap *__pyx
  */
   __pyx_v_self->V = __pyx_v_alphabet_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":116
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":116
  *     def __cinit__(self, int alphabet_size):
  *         self.V = alphabet_size
  *         self.root = <_Trie_Node**> malloc(self.V * sizeof(_Trie_Node*))             # <<<<<<<<<<<<<<
@@ -29496,7 +29171,7 @@ static int __pyx_pf_3_sa_7TrieMap___cinit__(struct __pyx_obj_3_sa_TrieMap *__pyx
  */
   __pyx_v_self->root = ((struct __pyx_t_3_sa__Trie_Node **)malloc((__pyx_v_self->V * (sizeof(struct __pyx_t_3_sa__Trie_Node *)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":117
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":117
  *         self.V = alphabet_size
  *         self.root = <_Trie_Node**> malloc(self.V * sizeof(_Trie_Node*))
  *         memset(self.root, 0, self.V * sizeof(_Trie_Node*))             # <<<<<<<<<<<<<<
@@ -29519,7 +29194,7 @@ static void __pyx_pw_3_sa_7TrieMap_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":120
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":120
  * 
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -29538,7 +29213,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":122
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":122
  *     def __dealloc__(self):
  *         cdef int i
  *         for i from 0 <= i < self.V:             # <<<<<<<<<<<<<<
@@ -29548,7 +29223,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
   __pyx_t_1 = __pyx_v_self->V;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":123
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":123
  *         cdef int i
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:             # <<<<<<<<<<<<<<
@@ -29558,7 +29233,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
     __pyx_t_2 = ((__pyx_v_self->root[__pyx_v_i]) != NULL);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":124
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":124
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:
  *                 free_trie_node(self.root[i])             # <<<<<<<<<<<<<<
@@ -29573,7 +29248,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
     __pyx_L5:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":125
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":125
  *             if self.root[i] != NULL:
  *                 free_trie_node(self.root[i])
  *         free(self.root)             # <<<<<<<<<<<<<<
@@ -29601,7 +29276,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_5insert(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":128
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":128
  * 
  * 
  *     def insert(self, pattern):             # <<<<<<<<<<<<<<
@@ -29624,7 +29299,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":131
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":131
  *         cdef int* p
  *         cdef int i, l
  *         l = len(pattern)             # <<<<<<<<<<<<<<
@@ -29634,7 +29309,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
   __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_l = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":132
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":132
  *         cdef int i, l
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))             # <<<<<<<<<<<<<<
@@ -29643,7 +29318,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
  */
   __pyx_v_p = ((int *)malloc((__pyx_v_l * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":133
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":133
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:             # <<<<<<<<<<<<<<
@@ -29653,7 +29328,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
   __pyx_t_2 = __pyx_v_l;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_2; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":134
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":134
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:
  *             p[i] = pattern[i]             # <<<<<<<<<<<<<<
@@ -29667,7 +29342,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
     (__pyx_v_p[__pyx_v_i]) = __pyx_t_4;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":135
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":135
  *         for i from 0 <= i < l:
  *             p[i] = pattern[i]
  *         self._insert(p,l)             # <<<<<<<<<<<<<<
@@ -29676,7 +29351,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
  */
   ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_self->__pyx_vtab)->_insert(__pyx_v_self, __pyx_v_p, __pyx_v_l);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":136
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":136
  *             p[i] = pattern[i]
  *         self._insert(p,l)
  *         free(p)             # <<<<<<<<<<<<<<
@@ -29697,7 +29372,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":139
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":139
  * 
  * 
  *     cdef _Trie_Node* _insert(self, int* pattern, int pattern_len):             # <<<<<<<<<<<<<<
@@ -29714,7 +29389,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
   int __pyx_t_2;
   __Pyx_RefNannySetupContext("_insert", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":142
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":142
  *         cdef int i
  *         cdef _Trie_Node* node
  *         if self.root[pattern[0]] == NULL:             # <<<<<<<<<<<<<<
@@ -29724,7 +29399,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
   __pyx_t_1 = ((__pyx_v_self->root[(__pyx_v_pattern[0])]) == NULL);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":143
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":143
  *         cdef _Trie_Node* node
  *         if self.root[pattern[0]] == NULL:
  *             self.root[pattern[0]] = new_trie_node()             # <<<<<<<<<<<<<<
@@ -29736,7 +29411,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":144
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":144
  *         if self.root[pattern[0]] == NULL:
  *             self.root[pattern[0]] = new_trie_node()
  *         node = self.root[pattern[0]]             # <<<<<<<<<<<<<<
@@ -29745,7 +29420,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
  */
   __pyx_v_node = (__pyx_v_self->root[(__pyx_v_pattern[0])]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":145
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":145
  *             self.root[pattern[0]] = new_trie_node()
  *         node = self.root[pattern[0]]
  *         for i from 1 <= i < pattern_len:             # <<<<<<<<<<<<<<
@@ -29755,7 +29430,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
   __pyx_t_2 = __pyx_v_pattern_len;
   for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_2; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":146
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":146
  *         node = self.root[pattern[0]]
  *         for i from 1 <= i < pattern_len:
  *             node = trie_insert(node, pattern[i])             # <<<<<<<<<<<<<<
@@ -29765,7 +29440,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
     __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_pattern[__pyx_v_i]));
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":147
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":147
  *         for i from 1 <= i < pattern_len:
  *             node = trie_insert(node, pattern[i])
  *         return node             # <<<<<<<<<<<<<<
@@ -29792,7 +29467,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_7contains(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":149
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":149
  *         return node
  * 
  *     def contains(self, pattern):             # <<<<<<<<<<<<<<
@@ -29817,7 +29492,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("contains", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":153
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":153
  *         cdef int i, l
  *         cdef _Trie_Node* node
  *         l = len(pattern)             # <<<<<<<<<<<<<<
@@ -29827,7 +29502,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_l = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":154
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":154
  *         cdef _Trie_Node* node
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))             # <<<<<<<<<<<<<<
@@ -29836,7 +29511,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
  */
   __pyx_v_p = ((int *)malloc((__pyx_v_l * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":155
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":155
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:             # <<<<<<<<<<<<<<
@@ -29846,7 +29521,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   __pyx_t_2 = __pyx_v_l;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_2; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":156
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":156
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:
  *             p[i] = pattern[i]             # <<<<<<<<<<<<<<
@@ -29860,7 +29535,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
     (__pyx_v_p[__pyx_v_i]) = __pyx_t_4;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":157
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":157
  *         for i from 0 <= i < l:
  *             p[i] = pattern[i]
  *         node = self._contains(p,l)             # <<<<<<<<<<<<<<
@@ -29869,7 +29544,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
  */
   __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_self->__pyx_vtab)->_contains(__pyx_v_self, __pyx_v_p, __pyx_v_l);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":158
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":158
  *             p[i] = pattern[i]
  *         node = self._contains(p,l)
  *         free(p)             # <<<<<<<<<<<<<<
@@ -29878,7 +29553,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
  */
   free(__pyx_v_p);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":159
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":159
  *         node = self._contains(p,l)
  *         free(p)
  *         if node == NULL:             # <<<<<<<<<<<<<<
@@ -29888,7 +29563,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   __pyx_t_5 = (__pyx_v_node == NULL);
   if (__pyx_t_5) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":160
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":160
  *         free(p)
  *         if node == NULL:
  *             return False             # <<<<<<<<<<<<<<
@@ -29905,7 +29580,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":162
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":162
  *             return False
  *         else:
  *             return True             # <<<<<<<<<<<<<<
@@ -29933,7 +29608,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":164
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":164
  *             return True
  * 
  *     cdef _Trie_Node* _contains(self, int* pattern, int pattern_len):             # <<<<<<<<<<<<<<
@@ -29951,7 +29626,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("_contains", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":167
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":167
  *         cdef int i
  *         cdef _Trie_Node* node
  *         node = self.root[pattern[0]]             # <<<<<<<<<<<<<<
@@ -29960,7 +29635,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
  */
   __pyx_v_node = (__pyx_v_self->root[(__pyx_v_pattern[0])]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":168
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":168
  *         cdef _Trie_Node* node
  *         node = self.root[pattern[0]]
  *         i = 1             # <<<<<<<<<<<<<<
@@ -29969,7 +29644,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
  */
   __pyx_v_i = 1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":169
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":169
  *         node = self.root[pattern[0]]
  *         i = 1
  *         while node != NULL and i < pattern_len:             # <<<<<<<<<<<<<<
@@ -29986,7 +29661,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
     }
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":170
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":170
  *         i = 1
  *         while node != NULL and i < pattern_len:
  *             node = trie_find(node, pattern[i])             # <<<<<<<<<<<<<<
@@ -29995,7 +29670,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
  */
     __pyx_v_node = __pyx_f_3_sa_trie_find(__pyx_v_node, (__pyx_v_pattern[__pyx_v_i]));
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":171
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":171
  *         while node != NULL and i < pattern_len:
  *             node = trie_find(node, pattern[i])
  *             i = i+1             # <<<<<<<<<<<<<<
@@ -30005,7 +29680,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
     __pyx_v_i = (__pyx_v_i + 1);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":172
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":172
  *             node = trie_find(node, pattern[i])
  *             i = i+1
  *         return node             # <<<<<<<<<<<<<<
@@ -30032,7 +29707,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_9toMap(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":174
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":174
  *         return node
  * 
  *     def toMap(self, flag):             # <<<<<<<<<<<<<<
@@ -30055,7 +29730,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("toMap", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":177
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":177
  *         cdef int i, include_zeros
  * 
  *         if flag:             # <<<<<<<<<<<<<<
@@ -30065,7 +29740,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_flag); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":178
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":178
  * 
  *         if flag:
  *             include_zeros=1             # <<<<<<<<<<<<<<
@@ -30077,7 +29752,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":180
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":180
  *             include_zeros=1
  *         else:
  *             include_zeros=0             # <<<<<<<<<<<<<<
@@ -30088,7 +29763,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":181
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":181
  *         else:
  *             include_zeros=0
  *         result = {}             # <<<<<<<<<<<<<<
@@ -30100,7 +29775,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   __pyx_v_result = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":182
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":182
  *             include_zeros=0
  *         result = {}
  *         for i from 0 <= i < self.V:             # <<<<<<<<<<<<<<
@@ -30110,7 +29785,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   __pyx_t_3 = __pyx_v_self->V;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":183
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":183
  *         result = {}
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:             # <<<<<<<<<<<<<<
@@ -30120,7 +29795,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
     __pyx_t_1 = ((__pyx_v_self->root[__pyx_v_i]) != NULL);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":184
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":184
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:
  *                 trie_node_to_map(self.root[i], result, (i,), include_zeros)             # <<<<<<<<<<<<<<
@@ -30143,7 +29818,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
     __pyx_L6:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":185
  *             if self.root[i] != NULL:
  *                 trie_node_to_map(self.root[i], result, (i,), include_zeros)
  *         return result             # <<<<<<<<<<<<<<
@@ -30181,14 +29856,14 @@ static int __pyx_pw_3_sa_14Precomputation_1__cinit__(PyObject *__pyx_v_self, PyO
   PyObject *__pyx_v_max_nonterminals = 0;
   PyObject *__pyx_v_train_max_initial_size = 0;
   PyObject *__pyx_v_train_min_gap_size = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fsarray,&__pyx_n_s__from_stats,&__pyx_n_s__from_binary,&__pyx_n_s__precompute_rank,&__pyx_n_s_70,&__pyx_n_s__max_length,&__pyx_n_s__max_nonterminals,&__pyx_n_s_71,&__pyx_n_s__train_min_gap_size,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fsarray,&__pyx_n_s__from_stats,&__pyx_n_s__from_binary,&__pyx_n_s__precompute_rank,&__pyx_n_s_70,&__pyx_n_s__max_length,&__pyx_n_s__max_nonterminals,&__pyx_n_s_71,&__pyx_n_s__train_min_gap_size,0};
     PyObject* values[9] = {0,0,0,0,0,0,0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":200
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":200
  *     cdef write_map(self, m, FILE* f)
  * 
  *     def __cinit__(self, fsarray=None, from_stats=None, from_binary=None,             # <<<<<<<<<<<<<<
@@ -30322,7 +29997,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":204
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":204
  *             max_length=5, max_nonterminals=2,
  *             train_max_initial_size=10, train_min_gap_size=2):
  *         self.precompute_rank = precompute_rank             # <<<<<<<<<<<<<<
@@ -30332,7 +30007,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->precompute_rank = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":205
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":205
  *             train_max_initial_size=10, train_min_gap_size=2):
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank             # <<<<<<<<<<<<<<
@@ -30342,7 +30017,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_secondary_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->precompute_secondary_rank = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":206
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":206
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.max_length = max_length             # <<<<<<<<<<<<<<
@@ -30352,7 +30027,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_length); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->max_length = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":207
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":207
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.max_length = max_length
  *         self.max_nonterminals = max_nonterminals             # <<<<<<<<<<<<<<
@@ -30362,7 +30037,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_nonterminals); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->max_nonterminals = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":208
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":208
  *         self.max_length = max_length
  *         self.max_nonterminals = max_nonterminals
  *         self.train_max_initial_size = train_max_initial_size             # <<<<<<<<<<<<<<
@@ -30372,7 +30047,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_max_initial_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->train_max_initial_size = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":209
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":209
  *         self.max_nonterminals = max_nonterminals
  *         self.train_max_initial_size = train_max_initial_size
  *         self.train_min_gap_size = train_min_gap_size             # <<<<<<<<<<<<<<
@@ -30382,7 +30057,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_min_gap_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->train_min_gap_size = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":210
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":210
  *         self.train_max_initial_size = train_max_initial_size
  *         self.train_min_gap_size = train_min_gap_size
  *         if from_binary:             # <<<<<<<<<<<<<<
@@ -30392,7 +30067,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":211
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":211
  *         self.train_min_gap_size = train_min_gap_size
  *         if from_binary:
  *             self.read_binary(from_binary)             # <<<<<<<<<<<<<<
@@ -30414,7 +30089,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":212
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":212
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_stats:             # <<<<<<<<<<<<<<
@@ -30424,7 +30099,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_stats); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":213
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":213
  *             self.read_binary(from_binary)
  *         elif from_stats:
  *             self.precompute(from_stats, fsarray)             # <<<<<<<<<<<<<<
@@ -30484,7 +30159,7 @@ static PyObject *__pyx_pw_3_sa_14Precomputation_3read_binary(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":216
+/* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":216
  * 
  * 
  *     def read_binary(self, char* filename):             # <<<<<<<<<<<<<<
@@ -30502,7 +30177,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("read_binary", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":218
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":218
  *     def read_binary(self, char* filename):
  *         cdef FILE* f
  *         f = fopen(filename, "r")             # <<<<<<<<<<<<<<
@@ -30511,7 +30186,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
  */
   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":219
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":219
  *         cdef FILE* f
  *         f = fopen(filename, "r")
  *         fread(&(self.precompute_rank), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -30520,7 +30195,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
  */
   fread((&__pyx_v_self->precompute_rank), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":220
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":220
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":221
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":221
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  *         fread(&(self.precompute_secondary_rank), sizeof(int), 1, f)
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":222
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":222
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  *         fread(&(self.max_length), sizeof(int), 1, f)
  *         fread(&(self.max_nonterminals), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":223
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":223
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  *         fread(&(self.max_nonterminals), sizeof(int), 1, f)
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":224
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":224
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  *         fread(&(self.train_max_initial_size), sizeof(int), 1, f)
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":225
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":225
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  *         fread(&(self.train_min_gap_size), sizeof(int), 1, f)
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":226
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":226
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":227
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":227
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":230
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":232
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":232
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":233
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":233
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":234
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":234
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":235
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":235
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":236
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":236
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  *         fwrite(&(self.max_length), sizeof(int), 1, f)
  *         fwrite(&(self.max_nonterminals), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":237
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":237
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  *         fwrite(&(self.max_nonterminals), sizeof(int), 1, f)
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":238
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":239
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":239
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":240
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":240
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":241
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":241
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-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":244
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":249
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":250
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":251
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-    __pyx_v_N = __pyx_t_8;
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":252
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":253
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":254
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-      __pyx_v_i = __pyx_t_7;
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":255
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":256
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":257
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":257
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":264
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":265
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":266
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":267
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":268
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":269
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":270
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":271
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":272
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":273
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":273
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":274
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":275
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-/* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":278
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":285
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":287
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":289
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":289
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":291
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":293
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":294
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":301
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":303
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":304
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":305
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":306
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":307
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  *             I_set.add(phrase)
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":308
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":309
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-      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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+      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+      __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":310
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-  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":312
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":312
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  *         queue = IntList(increment=1000)             # <<<<<<<<<<<<<<
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-  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_3);
-  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-  __pyx_v_queue = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_3);
-  __pyx_t_3 = 0;
+  __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+  if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__increment), __pyx_int_1000) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":314
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":314
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  *         logger.info("    Computing inverted indexes...")             # <<<<<<<<<<<<<<
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+  __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+  __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_75), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":315
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":315
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  *         logger.info("    Computing inverted indexes...")
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@@ -31779,17 +31504,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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   __pyx_v_N = __pyx_t_2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":316
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":316
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-  __pyx_t_13 = __pyx_v_N;
-  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":317
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":317
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-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":318
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":318
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":319
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":319
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@@ -31820,17 +31545,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     }
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":321
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-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":322
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":322
  *             else:
  *                 for l from 1 <= l <= max_pattern_len:
  *                     node = frequent_patterns._contains(data.arr+i, l)             # <<<<<<<<<<<<<<
@@ -31839,17 +31564,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i), __pyx_v_l);
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":323
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":323
  *                 for l from 1 <= l <= max_pattern_len:
  *                     node = frequent_patterns._contains(data.arr+i, l)
  *                     if node == NULL:             # <<<<<<<<<<<<<<
  *                         break
  *                     queue._append(i)
  */
-        __pyx_t_11 = (__pyx_v_node == NULL);
-        if (__pyx_t_11) {
+        __pyx_t_12 = (__pyx_v_node == NULL);
+        if (__pyx_t_12) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":324
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":324
  *                     node = frequent_patterns._contains(data.arr+i, l)
  *                     if node == NULL:
  *                         break             # <<<<<<<<<<<<<<
@@ -31861,7 +31586,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         __pyx_L14:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":325
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":325
  *                     if node == NULL:
  *                         break
  *                     queue._append(i)             # <<<<<<<<<<<<<<
@@ -31870,7 +31595,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_queue->__pyx_vtab)->_append(__pyx_v_queue, __pyx_v_i);
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":326
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":326
  *                         break
  *                     queue._append(i)
  *                     queue._append(l)             # <<<<<<<<<<<<<<
@@ -31879,40 +31604,40 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_queue->__pyx_vtab)->_append(__pyx_v_queue, __pyx_v_l);
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":327
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":327
  *                     queue._append(i)
  *                     queue._append(l)
  *                     trie_node_data_append(node, i)             # <<<<<<<<<<<<<<
  * 
  *         logger.info("    Computing collocations...")
  */
-        __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        __Pyx_GOTREF(__pyx_t_3);
-        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+        __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(__pyx_t_1);
+        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
       }
       __pyx_L13_break:;
     }
     __pyx_L11:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":329
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":329
  *                     trie_node_data_append(node, i)
  * 
  *         logger.info("    Computing collocations...")             # <<<<<<<<<<<<<<
  *         N = len(queue)
  *         ptr1 = 0
  */
-  __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+  __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":330
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":330
  * 
  *         logger.info("    Computing collocations...")
  *         N = len(queue)             # <<<<<<<<<<<<<<
@@ -31922,7 +31647,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   __pyx_t_2 = PyObject_Length(((PyObject *)__pyx_v_queue)); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_N = __pyx_t_2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":331
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":331
  *         logger.info("    Computing collocations...")
  *         N = len(queue)
  *         ptr1 = 0             # <<<<<<<<<<<<<<
@@ -31931,7 +31656,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
   __pyx_v_ptr1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":332
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":332
  *         N = len(queue)
  *         ptr1 = 0
  *         sent_count = 0             # <<<<<<<<<<<<<<
@@ -31940,7 +31665,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
   __pyx_v_sent_count = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":333
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":333
  *         ptr1 = 0
  *         sent_count = 0
  *         while ptr1 < N:    # main loop             # <<<<<<<<<<<<<<
@@ -31948,10 +31673,10 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  *             if i1 > -1:
  */
   while (1) {
-    __pyx_t_11 = (__pyx_v_ptr1 < __pyx_v_N);
-    if (!__pyx_t_11) break;
+    __pyx_t_12 = (__pyx_v_ptr1 < __pyx_v_N);
+    if (!__pyx_t_12) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":334
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":334
  *         sent_count = 0
  *         while ptr1 < N:    # main loop
  *             i1 = queue.arr[ptr1]             # <<<<<<<<<<<<<<
@@ -31960,17 +31685,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
     __pyx_v_i1 = (__pyx_v_queue->arr[__pyx_v_ptr1]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":335
+    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":335
  *         while ptr1 < N:    # main loop
  *             i1 = queue.arr[ptr1]
  *             if i1 > -1:             # <<<<<<<<<<<<<<
  *                 l1 = queue.arr[ptr1+1]
  *                 ptr2 = ptr1 + 2
  */
-    __pyx_t_11 = (__pyx_v_i1 > -1);
-    if (__pyx_t_11) {
+    __pyx_t_12 = (__pyx_v_i1 > -1);
+    if (__pyx_t_12) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":336
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":336
  *             i1 = queue.arr[ptr1]
  *             if i1 > -1:
  *                 l1 = queue.arr[ptr1+1]             # <<<<<<<<<<<<<<
@@ -31979,7 +31704,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
       __pyx_v_l1 = (__pyx_v_queue->arr[(__pyx_v_ptr1 + 1)]);
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":337
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":337
  *             if i1 > -1:
  *                 l1 = queue.arr[ptr1+1]
  *                 ptr2 = ptr1 + 2             # <<<<<<<<<<<<<<
@@ -31988,7 +31713,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
       __pyx_v_ptr2 = (__pyx_v_ptr1 + 2);
 
-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":338
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":338
  *                 l1 = queue.arr[ptr1+1]
  *                 ptr2 = ptr1 + 2
  *                 while ptr2 < N:             # <<<<<<<<<<<<<<
@@ -31996,10 +31721,10 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:
  */
       while (1) {
-        __pyx_t_11 = (__pyx_v_ptr2 < __pyx_v_N);
-        if (!__pyx_t_11) break;
+        __pyx_t_12 = (__pyx_v_ptr2 < __pyx_v_N);
+        if (!__pyx_t_12) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":339
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":339
  *                 ptr2 = ptr1 + 2
  *                 while ptr2 < N:
  *                     i2 = queue.arr[ptr2]             # <<<<<<<<<<<<<<
@@ -32008,23 +31733,23 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         __pyx_v_i2 = (__pyx_v_queue->arr[__pyx_v_ptr2]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":340
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":340
  *                 while ptr2 < N:
  *                     i2 = queue.arr[ptr2]
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:             # <<<<<<<<<<<<<<
  *                         break
  *                     l2 = queue.arr[ptr2+1]
  */
-        __pyx_t_11 = (__pyx_v_i2 == -1);
-        if (!__pyx_t_11) {
-          __pyx_t_17 = ((__pyx_v_i2 - __pyx_v_i1) >= __pyx_v_self->train_max_initial_size);
-          __pyx_t_18 = __pyx_t_17;
+        __pyx_t_12 = (__pyx_v_i2 == -1);
+        if (!__pyx_t_12) {
+          __pyx_t_18 = ((__pyx_v_i2 - __pyx_v_i1) >= __pyx_v_self->train_max_initial_size);
+          __pyx_t_19 = __pyx_t_18;
         } else {
-          __pyx_t_18 = __pyx_t_11;
+          __pyx_t_19 = __pyx_t_12;
         }
-        if (__pyx_t_18) {
+        if (__pyx_t_19) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":341
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":341
  *                     i2 = queue.arr[ptr2]
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:
  *                         break             # <<<<<<<<<<<<<<
@@ -32036,7 +31761,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         __pyx_L20:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":342
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":342
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:
  *                         break
  *                     l2 = queue.arr[ptr2+1]             # <<<<<<<<<<<<<<
@@ -32045,45 +31770,45 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         __pyx_v_l2 = (__pyx_v_queue->arr[(__pyx_v_ptr2 + 1)]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":343
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":343
  *                         break
  *                     l2 = queue.arr[ptr2+1]
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
  *                             i2 + l2 - i1 <= self.train_max_initial_size and
  *                             l1+l2+1 <= self.max_length):
  */
-        __pyx_t_18 = (((__pyx_v_i2 - __pyx_v_i1) - __pyx_v_l1) >= __pyx_v_self->train_min_gap_size);
-        if (__pyx_t_18) {
+        __pyx_t_19 = (((__pyx_v_i2 - __pyx_v_i1) - __pyx_v_l1) >= __pyx_v_self->train_min_gap_size);
+        if (__pyx_t_19) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":344
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":344
  *                     l2 = queue.arr[ptr2+1]
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and
  *                             i2 + l2 - i1 <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
  *                             l1+l2+1 <= self.max_length):
  *                         node = collocations._insert(data.arr+i1, l1)
  */
-          __pyx_t_11 = (((__pyx_v_i2 + __pyx_v_l2) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
-          if (__pyx_t_11) {
+          __pyx_t_12 = (((__pyx_v_i2 + __pyx_v_l2) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
+          if (__pyx_t_12) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":345
+            /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":345
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and
  *                             i2 + l2 - i1 <= self.train_max_initial_size and
  *                             l1+l2+1 <= self.max_length):             # <<<<<<<<<<<<<<
  *                         node = collocations._insert(data.arr+i1, l1)
  *                         node = trie_insert(node, -1)
  */
-            __pyx_t_17 = (((__pyx_v_l1 + __pyx_v_l2) + 1) <= __pyx_v_self->max_length);
-            __pyx_t_19 = __pyx_t_17;
+            __pyx_t_18 = (((__pyx_v_l1 + __pyx_v_l2) + 1) <= __pyx_v_self->max_length);
+            __pyx_t_20 = __pyx_t_18;
           } else {
-            __pyx_t_19 = __pyx_t_11;
+            __pyx_t_20 = __pyx_t_12;
           }
-          __pyx_t_11 = __pyx_t_19;
+          __pyx_t_12 = __pyx_t_20;
         } else {
-          __pyx_t_11 = __pyx_t_18;
+          __pyx_t_12 = __pyx_t_19;
         }
-        if (__pyx_t_11) {
+        if (__pyx_t_12) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":346
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":346
  *                             i2 + l2 - i1 <= self.train_max_initial_size and
  *                             l1+l2+1 <= self.max_length):
  *                         node = collocations._insert(data.arr+i1, l1)             # <<<<<<<<<<<<<<
@@ -32092,7 +31817,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
           __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_collocations->__pyx_vtab)->_insert(__pyx_v_collocations, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":347
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":347
  *                             l1+l2+1 <= self.max_length):
  *                         node = collocations._insert(data.arr+i1, l1)
  *                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -32101,17 +31826,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
           __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":348
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":348
  *                         node = collocations._insert(data.arr+i1, l1)
  *                         node = trie_insert(node, -1)
  *                         for i from i2 <= i < i2+l2:             # <<<<<<<<<<<<<<
  *                             node = trie_insert(node, data.arr[i])
  *                         trie_node_data_append(node, i1)
  */
-          __pyx_t_13 = (__pyx_v_i2 + __pyx_v_l2);
-          for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
+          __pyx_t_14 = (__pyx_v_i2 + __pyx_v_l2);
+          for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_14; __pyx_v_i++) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":349
+            /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":349
  *                         node = trie_insert(node, -1)
  *                         for i from i2 <= i < i2+l2:
  *                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -32121,49 +31846,49 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
           }
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":350
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":350
  *                         for i from i2 <= i < i2+l2:
  *                             node = trie_insert(node, data.arr[i])
  *                         trie_node_data_append(node, i1)             # <<<<<<<<<<<<<<
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  */
-          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_3);
-          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+          __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_1);
+          __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":351
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":351
  *                             node = trie_insert(node, data.arr[i])
  *                         trie_node_data_append(node, i1)
  *                         trie_node_data_append(node, i2)             # <<<<<<<<<<<<<<
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:
  */
-          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_3);
-          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+          __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_1);
+          __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":352
+          /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":352
  *                         trie_node_data_append(node, i1)
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:             # <<<<<<<<<<<<<<
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:
  *                                 is_super = 1
  */
-          __pyx_t_11 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i2), __pyx_v_l2) != NULL);
-          if (__pyx_t_11) {
+          __pyx_t_12 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i2), __pyx_v_l2) != NULL);
+          if (__pyx_t_12) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":353
+            /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":353
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:             # <<<<<<<<<<<<<<
  *                                 is_super = 1
  *                             else:
  */
-            __pyx_t_11 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1) != NULL);
-            if (__pyx_t_11) {
+            __pyx_t_12 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1) != NULL);
+            if (__pyx_t_12) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":354
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":354
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:
  *                                 is_super = 1             # <<<<<<<<<<<<<<
@@ -32175,7 +31900,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             }
             /*else*/ {
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":356
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":356
  *                                 is_super = 1
  *                             else:
  *                                 is_super = 0             # <<<<<<<<<<<<<<
@@ -32186,7 +31911,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             }
             __pyx_L25:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":357
+            /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":357
  *                             else:
  *                                 is_super = 0
  *                             ptr3 = ptr2 + 2             # <<<<<<<<<<<<<<
@@ -32195,7 +31920,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
             __pyx_v_ptr3 = (__pyx_v_ptr2 + 2);
 
-            /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":358
+            /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":358
  *                                 is_super = 0
  *                             ptr3 = ptr2 + 2
  *                             while ptr3 < N:             # <<<<<<<<<<<<<<
@@ -32203,10 +31928,10 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:
  */
             while (1) {
-              __pyx_t_11 = (__pyx_v_ptr3 < __pyx_v_N);
-              if (!__pyx_t_11) break;
+              __pyx_t_12 = (__pyx_v_ptr3 < __pyx_v_N);
+              if (!__pyx_t_12) break;
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":359
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":359
  *                             ptr3 = ptr2 + 2
  *                             while ptr3 < N:
  *                                 i3 = queue.arr[ptr3]             # <<<<<<<<<<<<<<
@@ -32215,23 +31940,23 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
               __pyx_v_i3 = (__pyx_v_queue->arr[__pyx_v_ptr3]);
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":360
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":360
  *                             while ptr3 < N:
  *                                 i3 = queue.arr[ptr3]
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:             # <<<<<<<<<<<<<<
  *                                     break
  *                                 l3 = queue.arr[ptr3+1]
  */
-              __pyx_t_11 = (__pyx_v_i3 == -1);
-              if (!__pyx_t_11) {
-                __pyx_t_18 = ((__pyx_v_i3 - __pyx_v_i1) >= __pyx_v_self->train_max_initial_size);
-                __pyx_t_19 = __pyx_t_18;
+              __pyx_t_12 = (__pyx_v_i3 == -1);
+              if (!__pyx_t_12) {
+                __pyx_t_19 = ((__pyx_v_i3 - __pyx_v_i1) >= __pyx_v_self->train_max_initial_size);
+                __pyx_t_20 = __pyx_t_19;
               } else {
-                __pyx_t_19 = __pyx_t_11;
+                __pyx_t_20 = __pyx_t_12;
               }
-              if (__pyx_t_19) {
+              if (__pyx_t_20) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":361
+                /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":361
  *                                 i3 = queue.arr[ptr3]
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:
  *                                     break             # <<<<<<<<<<<<<<
@@ -32243,7 +31968,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               __pyx_L28:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":362
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":362
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:
  *                                     break
  *                                 l3 = queue.arr[ptr3+1]             # <<<<<<<<<<<<<<
@@ -32252,45 +31977,45 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
               __pyx_v_l3 = (__pyx_v_queue->arr[(__pyx_v_ptr3 + 1)]);
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":363
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":363
  *                                     break
  *                                 l3 = queue.arr[ptr3+1]
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and
  *                                         l1+l2+l3+2 <= self.max_length):
  */
-              __pyx_t_19 = (((__pyx_v_i3 - __pyx_v_i2) - __pyx_v_l2) >= __pyx_v_self->train_min_gap_size);
-              if (__pyx_t_19) {
+              __pyx_t_20 = (((__pyx_v_i3 - __pyx_v_i2) - __pyx_v_l2) >= __pyx_v_self->train_min_gap_size);
+              if (__pyx_t_20) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":364
+                /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":364
  *                                 l3 = queue.arr[ptr3+1]
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
  *                                         l1+l2+l3+2 <= self.max_length):
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  */
-                __pyx_t_11 = (((__pyx_v_i3 + __pyx_v_l3) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
-                if (__pyx_t_11) {
+                __pyx_t_12 = (((__pyx_v_i3 + __pyx_v_l3) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
+                if (__pyx_t_12) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":365
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":365
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and
  *                                         l1+l2+l3+2 <= self.max_length):             # <<<<<<<<<<<<<<
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  *                                         node = collocations._insert(data.arr+i1, l1)
  */
-                  __pyx_t_18 = ((((__pyx_v_l1 + __pyx_v_l2) + __pyx_v_l3) + 2) <= __pyx_v_self->max_length);
-                  __pyx_t_17 = __pyx_t_18;
+                  __pyx_t_19 = ((((__pyx_v_l1 + __pyx_v_l2) + __pyx_v_l3) + 2) <= __pyx_v_self->max_length);
+                  __pyx_t_18 = __pyx_t_19;
                 } else {
-                  __pyx_t_17 = __pyx_t_11;
+                  __pyx_t_18 = __pyx_t_12;
                 }
-                __pyx_t_11 = __pyx_t_17;
+                __pyx_t_12 = __pyx_t_18;
               } else {
-                __pyx_t_11 = __pyx_t_19;
+                __pyx_t_12 = __pyx_t_20;
               }
-              if (__pyx_t_11) {
+              if (__pyx_t_12) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":366
+                /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":366
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and
  *                                         l1+l2+l3+2 <= self.max_length):
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:             # <<<<<<<<<<<<<<
@@ -32298,14 +32023,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  *                                         node = trie_insert(node, -1)
  */
                 if (!__pyx_v_is_super) {
-                  __pyx_t_11 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i3), __pyx_v_l3) != NULL);
-                  __pyx_t_19 = __pyx_t_11;
+                  __pyx_t_12 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i3), __pyx_v_l3) != NULL);
+                  __pyx_t_20 = __pyx_t_12;
                 } else {
-                  __pyx_t_19 = __pyx_v_is_super;
+                  __pyx_t_20 = __pyx_v_is_super;
                 }
-                if (__pyx_t_19) {
+                if (__pyx_t_20) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":367
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":367
  *                                         l1+l2+l3+2 <= self.max_length):
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  *                                         node = collocations._insert(data.arr+i1, l1)             # <<<<<<<<<<<<<<
@@ -32314,7 +32039,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_collocations->__pyx_vtab)->_insert(__pyx_v_collocations, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":368
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":368
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  *                                         node = collocations._insert(data.arr+i1, l1)
  *                                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -32323,17 +32048,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":369
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":369
  *                                         node = collocations._insert(data.arr+i1, l1)
  *                                         node = trie_insert(node, -1)
  *                                         for i from i2 <= i < i2+l2:             # <<<<<<<<<<<<<<
  *                                             node = trie_insert(node, data.arr[i])
  *                                         node = trie_insert(node, -1)
  */
-                  __pyx_t_13 = (__pyx_v_i2 + __pyx_v_l2);
-                  for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
+                  __pyx_t_14 = (__pyx_v_i2 + __pyx_v_l2);
+                  for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_14; __pyx_v_i++) {
 
-                    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":370
+                    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":370
  *                                         node = trie_insert(node, -1)
  *                                         for i from i2 <= i < i2+l2:
  *                                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -32343,7 +32068,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                     __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
                   }
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":371
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":371
  *                                         for i from i2 <= i < i2+l2:
  *                                             node = trie_insert(node, data.arr[i])
  *                                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -32352,17 +32077,17 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":372
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":372
  *                                             node = trie_insert(node, data.arr[i])
  *                                         node = trie_insert(node, -1)
  *                                         for i from i3 <= i < i3+l3:             # <<<<<<<<<<<<<<
  *                                             node = trie_insert(node, data.arr[i])
  *                                         trie_node_data_append(node, i1)
  */
-                  __pyx_t_13 = (__pyx_v_i3 + __pyx_v_l3);
-                  for (__pyx_v_i = __pyx_v_i3; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
+                  __pyx_t_14 = (__pyx_v_i3 + __pyx_v_l3);
+                  for (__pyx_v_i = __pyx_v_i3; __pyx_v_i < __pyx_t_14; __pyx_v_i++) {
 
-                    /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":373
+                    /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":373
  *                                         node = trie_insert(node, -1)
  *                                         for i from i3 <= i < i3+l3:
  *                                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -32372,38 +32097,38 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                     __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
                   }
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":374
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":374
  *                                         for i from i3 <= i < i3+l3:
  *                                             node = trie_insert(node, data.arr[i])
  *                                         trie_node_data_append(node, i1)             # <<<<<<<<<<<<<<
  *                                         trie_node_data_append(node, i2)
  *                                         trie_node_data_append(node, i3)
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __Pyx_GOTREF(__pyx_t_3);
-                  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+                  __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __Pyx_GOTREF(__pyx_t_1);
+                  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":375
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":375
  *                                             node = trie_insert(node, data.arr[i])
  *                                         trie_node_data_append(node, i1)
  *                                         trie_node_data_append(node, i2)             # <<<<<<<<<<<<<<
  *                                         trie_node_data_append(node, i3)
  *                                 ptr3 = ptr3 + 2
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __Pyx_GOTREF(__pyx_t_3);
-                  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+                  __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __Pyx_GOTREF(__pyx_t_1);
+                  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-                  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":376
+                  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":376
  *                                         trie_node_data_append(node, i1)
  *                                         trie_node_data_append(node, i2)
  *                                         trie_node_data_append(node, i3)             # <<<<<<<<<<<<<<
  *                                 ptr3 = ptr3 + 2
  *                     ptr2 = ptr2 + 2
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __Pyx_GOTREF(__pyx_t_3);
-                  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+                  __pyx_t_1 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __Pyx_GOTREF(__pyx_t_1);
+                  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                   goto __pyx_L30;
                 }
                 __pyx_L30:;
@@ -32411,7 +32136,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               __pyx_L29:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":377
+              /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":377
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-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":378
+        /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":378
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":379
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":379
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":381
+      /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":381
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":382
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-        /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":383
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":384
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":386
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":387
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-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":389
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-      /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":392
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@@ -33872,7 +33650,7 @@ static int __pyx_pf_3_sa_11SuffixArray___cinit__(struct __pyx_obj_3_sa_SuffixArr
     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":17
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":17
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_text:             # <<<<<<<<<<<<<<
@@ -33882,7 +33660,7 @@ static int __pyx_pf_3_sa_11SuffixArray___cinit__(struct __pyx_obj_3_sa_SuffixArr
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_text); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":18
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":18
  *             self.read_binary(from_binary)
  *         elif from_text:
  *             self.read_text(from_text, side)             # <<<<<<<<<<<<<<
@@ -33932,7 +33710,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_3__getitem__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":20
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":20
  *             self.read_text(from_text, side)
  * 
  *     def __getitem__(self, i):             # <<<<<<<<<<<<<<
@@ -33950,7 +33728,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_2__getitem__(struct __pyx_obj_3_sa_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":21
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":21
  * 
  *     def __getitem__(self, i):
  *         return self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -33983,11 +33761,11 @@ static char __pyx_doc_3_sa_11SuffixArray_4read_text[] = "Constructs suffix array
 static PyObject *__pyx_pw_3_sa_11SuffixArray_5read_text(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_filename = 0;
   PyObject *__pyx_v_side = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__side,0};
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("read_text (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__side,0};
     PyObject* values[2] = {0,0};
     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -34001,10 +33779,12 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_5read_text(PyObject *__pyx_v_self,
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__side)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__side);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("read_text", 1, 2, 2, 1); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
@@ -34034,7 +33814,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_5read_text(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":23
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":23
  *         return self.sa.arr[i]
  * 
  *     def read_text(self, filename, side):             # <<<<<<<<<<<<<<
@@ -34061,20 +33841,21 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   PyObject *__pyx_t_1 = NULL;
   PyObject *__pyx_t_2 = NULL;
   Py_ssize_t __pyx_t_3;
-  int __pyx_t_4;
-  long __pyx_t_5;
-  int __pyx_t_6;
+  float __pyx_t_4;
+  int __pyx_t_5;
+  long __pyx_t_6;
   int __pyx_t_7;
   int __pyx_t_8;
-  PyObject *__pyx_t_9 = NULL;
+  int __pyx_t_9;
   PyObject *__pyx_t_10 = NULL;
   PyObject *__pyx_t_11 = NULL;
+  PyObject *__pyx_t_12 = NULL;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("read_text", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":29
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":29
  *         cdef IntList isa, word_count
  * 
  *         self.darray = DataArray(from_text=filename, side=side, use_sent_id=True)             # <<<<<<<<<<<<<<
@@ -34098,7 +33879,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __pyx_v_self->darray = ((struct __pyx_obj_3_sa_DataArray *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":30
  * 
  *         self.darray = DataArray(from_text=filename, side=side, use_sent_id=True)
  *         N = len(self.darray)             # <<<<<<<<<<<<<<
@@ -34111,7 +33892,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __pyx_v_N = __pyx_t_3;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":31
  *         self.darray = DataArray(from_text=filename, side=side, use_sent_id=True)
  *         N = len(self.darray)
  *         V = len(self.darray.id2word)             # <<<<<<<<<<<<<<
@@ -34124,7 +33905,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __pyx_v_V = __pyx_t_3;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":33
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":33
  *         V = len(self.darray.id2word)
  * 
  *         self.sa = IntList(initial_len=N)             # <<<<<<<<<<<<<<
@@ -34146,7 +33927,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __pyx_v_self->sa = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":34
  * 
  *         self.sa = IntList(initial_len=N)
  *         self.ha = IntList(initial_len=V+1)             # <<<<<<<<<<<<<<
@@ -34168,7 +33949,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __pyx_v_self->ha = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":36
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":36
  *         self.ha = IntList(initial_len=V+1)
  * 
  *         isa = IntList(initial_len=N)             # <<<<<<<<<<<<<<
@@ -34187,7 +33968,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __pyx_v_isa = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":37
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":37
  * 
  *         isa = IntList(initial_len=N)
  *         word_count = IntList(initial_len=V+1)             # <<<<<<<<<<<<<<
@@ -34206,16 +33987,23 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
   __pyx_v_word_count = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":40
  * 
  *         '''Step 1: bucket sort data'''
  *         cdef float sort_start_time = monitor_cpu()             # <<<<<<<<<<<<<<
  *         cdef float start_time = sort_start_time
  *         for i from 0 <= i < N:
  */
-  __pyx_v_sort_start_time = __pyx_f_3_sa_monitor_cpu();
+  __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__monitor_cpu); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_2);
+  __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+  __pyx_t_4 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_4 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+  __pyx_v_sort_start_time = __pyx_t_4;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":41
  *         '''Step 1: bucket sort data'''
  *         cdef float sort_start_time = monitor_cpu()
  *         cdef float start_time = sort_start_time             # <<<<<<<<<<<<<<
@@ -34224,17 +34012,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
   __pyx_v_start_time = __pyx_v_sort_start_time;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":42
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":42
  *         cdef float sort_start_time = monitor_cpu()
  *         cdef float start_time = sort_start_time
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
  *             a_i = self.darray.data.arr[i]
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1
  */
-  __pyx_t_4 = __pyx_v_N;
-  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
+  __pyx_t_5 = __pyx_v_N;
+  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":43
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":43
  *         cdef float start_time = sort_start_time
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]             # <<<<<<<<<<<<<<
@@ -34243,7 +34031,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     __pyx_v_a_i = (__pyx_v_self->darray->data->arr[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":44
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":44
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1             # <<<<<<<<<<<<<<
@@ -34253,7 +34041,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
     (__pyx_v_word_count->arr[__pyx_v_a_i]) = ((__pyx_v_word_count->arr[__pyx_v_a_i]) + 1);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":46
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":46
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1
  * 
  *         n = 0             # <<<<<<<<<<<<<<
@@ -34262,17 +34050,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
   __pyx_v_n = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":47
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":47
  * 
  *         n = 0
  *         for i from 0 <= i < V+1:             # <<<<<<<<<<<<<<
  *             self.ha.arr[i] = n
  *             n = n + word_count.arr[i]
  */
-  __pyx_t_5 = (__pyx_v_V + 1);
-  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+  __pyx_t_6 = (__pyx_v_V + 1);
+  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_6; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":48
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":48
  *         n = 0
  *         for i from 0 <= i < V+1:
  *             self.ha.arr[i] = n             # <<<<<<<<<<<<<<
@@ -34281,7 +34069,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     (__pyx_v_self->ha->arr[__pyx_v_i]) = __pyx_v_n;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":49
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":49
  *         for i from 0 <= i < V+1:
  *             self.ha.arr[i] = n
  *             n = n + word_count.arr[i]             # <<<<<<<<<<<<<<
@@ -34290,7 +34078,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     __pyx_v_n = (__pyx_v_n + (__pyx_v_word_count->arr[__pyx_v_i]));
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":50
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":50
  *             self.ha.arr[i] = n
  *             n = n + word_count.arr[i]
  *             word_count.arr[i] = 0             # <<<<<<<<<<<<<<
@@ -34300,17 +34088,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
     (__pyx_v_word_count->arr[__pyx_v_i]) = 0;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":52
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":52
  *             word_count.arr[i] = 0
  * 
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
  *             a_i = self.darray.data.arr[i]
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i
  */
-  __pyx_t_4 = __pyx_v_N;
-  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
+  __pyx_t_5 = __pyx_v_N;
+  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":53
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":53
  * 
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]             # <<<<<<<<<<<<<<
@@ -34319,7 +34107,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     __pyx_v_a_i = (__pyx_v_self->darray->data->arr[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":54
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":54
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i             # <<<<<<<<<<<<<<
@@ -34328,7 +34116,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     (__pyx_v_self->sa->arr[((__pyx_v_self->ha->arr[__pyx_v_a_i]) + (__pyx_v_word_count->arr[__pyx_v_a_i]))]) = __pyx_v_i;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":55
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":55
  *             a_i = self.darray.data.arr[i]
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i
  *             isa.arr[i] = self.ha.arr[a_i + 1] - 1 # bucket pointer is last index in bucket             # <<<<<<<<<<<<<<
@@ -34337,7 +34125,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
     (__pyx_v_isa->arr[__pyx_v_i]) = ((__pyx_v_self->ha->arr[(__pyx_v_a_i + 1)]) - 1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":56
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":56
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i
  *             isa.arr[i] = self.ha.arr[a_i + 1] - 1 # bucket pointer is last index in bucket
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1             # <<<<<<<<<<<<<<
@@ -34347,7 +34135,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
     (__pyx_v_word_count->arr[__pyx_v_a_i]) = ((__pyx_v_word_count->arr[__pyx_v_a_i]) + 1);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":59
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":59
  * 
  *         '''Determine size of initial runs'''
  *         current_run = 0             # <<<<<<<<<<<<<<
@@ -34356,33 +34144,33 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
   __pyx_v_current_run = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":60
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":60
  *         '''Determine size of initial runs'''
  *         current_run = 0
  *         for i from 0 <= i < V+1:             # <<<<<<<<<<<<<<
  *             if i < V and self.ha.arr[i+1] - self.ha.arr[i] == 1:
  *                 current_run = current_run + 1
  */
-  __pyx_t_5 = (__pyx_v_V + 1);
-  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+  __pyx_t_6 = (__pyx_v_V + 1);
+  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_6; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":61
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":61
  *         current_run = 0
  *         for i from 0 <= i < V+1:
  *             if i < V and self.ha.arr[i+1] - self.ha.arr[i] == 1:             # <<<<<<<<<<<<<<
  *                 current_run = current_run + 1
  *             else:
  */
-    __pyx_t_6 = (__pyx_v_i < __pyx_v_V);
-    if (__pyx_t_6) {
-      __pyx_t_7 = (((__pyx_v_self->ha->arr[(__pyx_v_i + 1)]) - (__pyx_v_self->ha->arr[__pyx_v_i])) == 1);
-      __pyx_t_8 = __pyx_t_7;
+    __pyx_t_7 = (__pyx_v_i < __pyx_v_V);
+    if (__pyx_t_7) {
+      __pyx_t_8 = (((__pyx_v_self->ha->arr[(__pyx_v_i + 1)]) - (__pyx_v_self->ha->arr[__pyx_v_i])) == 1);
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+      __pyx_t_9 = __pyx_t_7;
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-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":62
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":62
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@@ -34394,17 +34182,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":64
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":64
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  *                     current_run = 0
  */
-      __pyx_t_8 = (__pyx_v_current_run > 0);
-      if (__pyx_t_8) {
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-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":65
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":65
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  *                     self.sa.arr[self.ha.arr[i] - current_run] = -current_run             # <<<<<<<<<<<<<<
@@ -34413,7 +34201,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":66
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":66
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":68
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":68
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  *         logger.info("    Bucket sort took %f seconds", (monitor_cpu() - sort_start_time))             # <<<<<<<<<<<<<<
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+  __Pyx_GIVEREF(__pyx_t_11);
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+  __Pyx_GOTREF(__pyx_t_11);
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":71
  * 
  *         '''Step 2: prefix-doubling sort'''
  *         h = 1             # <<<<<<<<<<<<<<
@@ -34465,7 +34262,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
  */
   __pyx_v_h = 1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":72
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":72
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  *         while self.sa.arr[0] != -N:             # <<<<<<<<<<<<<<
@@ -34473,47 +34270,54 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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  */
   while (1) {
-    __pyx_t_8 = ((__pyx_v_self->sa->arr[0]) != (-__pyx_v_N));
-    if (!__pyx_t_8) break;
+    __pyx_t_9 = ((__pyx_v_self->sa->arr[0]) != (-__pyx_v_N));
+    if (!__pyx_t_9) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":73
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":73
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  *         while self.sa.arr[0] != -N:
  *             sort_start_time = monitor_cpu()             # <<<<<<<<<<<<<<
  *             logger.debug("    Refining, sort depth = %d", h)
  *             i = 0
  */
-    __pyx_v_sort_start_time = __pyx_f_3_sa_monitor_cpu();
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-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":74
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-    PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_90));
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+    __Pyx_GOTREF(__pyx_t_1);
+    __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
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-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":75
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":75
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  *             logger.debug("    Refining, sort depth = %d", h)
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  */
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-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":76
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":76
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  *             i = 0
  *             skip = 0             # <<<<<<<<<<<<<<
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  */
     __pyx_v_skip = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":77
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":77
  *             i = 0
  *             skip = 0
  *             while i < N:             # <<<<<<<<<<<<<<
@@ -34539,20 +34343,20 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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  */
     while (1) {
-      __pyx_t_8 = (__pyx_v_i < __pyx_v_N);
-      if (!__pyx_t_8) break;
+      __pyx_t_9 = (__pyx_v_i < __pyx_v_N);
+      if (!__pyx_t_9) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":78
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":78
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  *             while i < N:
  *                 if self.sa.arr[i] < 0:             # <<<<<<<<<<<<<<
  *                     skip = skip + self.sa.arr[i]
  *                     i = i - self.sa.arr[i]
  */
-      __pyx_t_8 = ((__pyx_v_self->sa->arr[__pyx_v_i]) < 0);
-      if (__pyx_t_8) {
+      __pyx_t_9 = ((__pyx_v_self->sa->arr[__pyx_v_i]) < 0);
+      if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":79
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":79
  *             while i < N:
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  *                     skip = skip + self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -34561,7 +34365,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":80
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":80
  *                 if self.sa.arr[i] < 0:
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  *                     i = i - self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -34573,17 +34377,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":82
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":82
  *                     i = i - self.sa.arr[i]
  *                 else:
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  *                         skip = 0
  */
-        __pyx_t_8 = (__pyx_v_skip < 0);
-        if (__pyx_t_8) {
+        __pyx_t_9 = (__pyx_v_skip < 0);
+        if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":83
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":83
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  *                         self.sa.arr[i+skip] = skip             # <<<<<<<<<<<<<<
@@ -34592,7 +34396,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
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-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":84
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":84
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@@ -34604,7 +34408,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_Su
         }
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-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":85
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":85
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  *                         skip = 0
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-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":86
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":86
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  *                     self.q3sort(i, j, h, isa)             # <<<<<<<<<<<<<<
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  *             if skip < 0:
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-  __Pyx_XDECREF(__pyx_t_9);
   __Pyx_XDECREF(__pyx_t_10);
   __Pyx_XDECREF(__pyx_t_11);
+  __Pyx_XDECREF(__pyx_t_12);
   __Pyx_AddTraceback("_sa.SuffixArray.read_text", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __pyx_r = NULL;
   __pyx_L0:;
@@ -34821,11 +34643,11 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_7q3sort(PyObject *__pyx_v_self, PyO
   int __pyx_v_h;
   struct __pyx_obj_3_sa_IntList *__pyx_v_isa = 0;
   PyObject *__pyx_v_pad = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__i,&__pyx_n_s__j,&__pyx_n_s__h,&__pyx_n_s__isa,&__pyx_n_s__pad,0};
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("q3sort (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__i,&__pyx_n_s__j,&__pyx_n_s__h,&__pyx_n_s__isa,&__pyx_n_s__pad,0};
     PyObject* values[5] = {0,0,0,0,0};
     values[4] = ((PyObject *)__pyx_kp_s_45);
     if (unlikely(__pyx_kwds)) {
@@ -34843,20 +34665,24 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_7q3sort(PyObject *__pyx_v_self, PyO
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__i)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__i);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__j)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__j);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("q3sort", 0, 4, 5, 1); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__h)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__h);
+        if (likely(values[2])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("q3sort", 0, 4, 5, 2); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  3:
-        if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__isa)) != 0)) kw_args--;
+        values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__isa);
+        if (likely(values[3])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("q3sort", 0, 4, 5, 3); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
@@ -34904,7 +34730,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_7q3sort(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":100
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":100
  *         logger.info("Suffix array construction took %f seconds", (monitor_cpu() - start_time))
  * 
  *     def q3sort(self, int i, int j, int h, IntList isa, pad=""):             # <<<<<<<<<<<<<<
@@ -34934,7 +34760,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("q3sort", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":107
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":107
  *         cdef int k, midpoint, pval, phead, ptail, tmp
  * 
  *         if j-i < -1:             # <<<<<<<<<<<<<<
@@ -34944,7 +34770,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   __pyx_t_1 = ((__pyx_v_j - __pyx_v_i) < -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":108
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":108
  * 
  *         if j-i < -1:
  *             raise Exception("Unexpected condition found in q3sort: sort from %d to %d" % (i,j))             # <<<<<<<<<<<<<<
@@ -34981,7 +34807,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":109
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":109
  *         if j-i < -1:
  *             raise Exception("Unexpected condition found in q3sort: sort from %d to %d" % (i,j))
  *         if j-i == -1:    # recursive base case -- empty interval             # <<<<<<<<<<<<<<
@@ -34991,7 +34817,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   __pyx_t_1 = ((__pyx_v_j - __pyx_v_i) == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":110
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":110
  *             raise Exception("Unexpected condition found in q3sort: sort from %d to %d" % (i,j))
  *         if j-i == -1:    # recursive base case -- empty interval
  *             return             # <<<<<<<<<<<<<<
@@ -35005,7 +34831,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":111
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":111
  *         if j-i == -1:    # recursive base case -- empty interval
  *             return
  *         if (j-i == 0):    # recursive base case -- singleton interval             # <<<<<<<<<<<<<<
@@ -35015,7 +34841,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   __pyx_t_1 = ((__pyx_v_j - __pyx_v_i) == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":112
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":112
  *             return
  *         if (j-i == 0):    # recursive base case -- singleton interval
  *             isa.arr[self.sa.arr[i]] = i             # <<<<<<<<<<<<<<
@@ -35024,7 +34850,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
     (__pyx_v_isa->arr[(__pyx_v_self->sa->arr[__pyx_v_i])]) = __pyx_v_i;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":113
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":113
  *         if (j-i == 0):    # recursive base case -- singleton interval
  *             isa.arr[self.sa.arr[i]] = i
  *             self.sa.arr[i] = -1             # <<<<<<<<<<<<<<
@@ -35033,7 +34859,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
     (__pyx_v_self->sa->arr[__pyx_v_i]) = -1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":114
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":114
  *             isa.arr[self.sa.arr[i]] = i
  *             self.sa.arr[i] = -1
  *             return             # <<<<<<<<<<<<<<
@@ -35047,7 +34873,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":123
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":123
  *         # If the method of assigning word_id's is changed, this method
  *         # may need to be reconsidered as well.
  *         midpoint = (i+j)/2             # <<<<<<<<<<<<<<
@@ -35056,7 +34882,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
   __pyx_v_midpoint = __Pyx_div_long((__pyx_v_i + __pyx_v_j), 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":124
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":124
  *         # may need to be reconsidered as well.
  *         midpoint = (i+j)/2
  *         pval = isa.arr[self.sa.arr[midpoint] + h]             # <<<<<<<<<<<<<<
@@ -35065,7 +34891,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
   __pyx_v_pval = (__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_h)]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":125
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":125
  *         midpoint = (i+j)/2
  *         pval = isa.arr[self.sa.arr[midpoint] + h]
  *         if i != midpoint:             # <<<<<<<<<<<<<<
@@ -35075,7 +34901,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   __pyx_t_1 = (__pyx_v_i != __pyx_v_midpoint);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":126
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":126
  *         pval = isa.arr[self.sa.arr[midpoint] + h]
  *         if i != midpoint:
  *             tmp = self.sa.arr[midpoint]             # <<<<<<<<<<<<<<
@@ -35084,7 +34910,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
     __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_midpoint]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":127
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":127
  *         if i != midpoint:
  *             tmp = self.sa.arr[midpoint]
  *             self.sa.arr[midpoint] = self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -35093,7 +34919,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
     (__pyx_v_self->sa->arr[__pyx_v_midpoint]) = (__pyx_v_self->sa->arr[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":128
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":128
  *             tmp = self.sa.arr[midpoint]
  *             self.sa.arr[midpoint] = self.sa.arr[i]
  *             self.sa.arr[i] = tmp             # <<<<<<<<<<<<<<
@@ -35105,7 +34931,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   }
   __pyx_L6:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":129
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":129
  *             self.sa.arr[midpoint] = self.sa.arr[i]
  *             self.sa.arr[i] = tmp
  *         phead = i             # <<<<<<<<<<<<<<
@@ -35114,7 +34940,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
   __pyx_v_phead = __pyx_v_i;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":130
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":130
  *             self.sa.arr[i] = tmp
  *         phead = i
  *         ptail = i             # <<<<<<<<<<<<<<
@@ -35123,7 +34949,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
   __pyx_v_ptail = __pyx_v_i;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":134
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":134
  *         # find the three partitions.    phead marks the first element
  *         # of the middle partition, and ptail marks the last element
  *         for k from i+1 <= k < j+1:             # <<<<<<<<<<<<<<
@@ -35133,7 +34959,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
   __pyx_t_5 = (__pyx_v_j + 1);
   for (__pyx_v_k = (__pyx_v_i + 1); __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":135
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":135
  *         # of the middle partition, and ptail marks the last element
  *         for k from i+1 <= k < j+1:
  *             if isa.arr[self.sa.arr[k] + h] < pval:             # <<<<<<<<<<<<<<
@@ -35143,7 +34969,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
     __pyx_t_1 = ((__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_k]) + __pyx_v_h)]) < __pyx_v_pval);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":136
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":136
  *         for k from i+1 <= k < j+1:
  *             if isa.arr[self.sa.arr[k] + h] < pval:
  *                 if k > ptail+1:             # <<<<<<<<<<<<<<
@@ -35153,7 +34979,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
       __pyx_t_1 = (__pyx_v_k > (__pyx_v_ptail + 1));
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":137
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":137
  *             if isa.arr[self.sa.arr[k] + h] < pval:
  *                 if k > ptail+1:
  *                     tmp = self.sa.arr[phead]             # <<<<<<<<<<<<<<
@@ -35162,7 +34988,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
         __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_phead]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":138
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":138
  *                 if k > ptail+1:
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]             # <<<<<<<<<<<<<<
@@ -35171,7 +34997,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
         (__pyx_v_self->sa->arr[__pyx_v_phead]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":139
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":139
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = self.sa.arr[ptail+1]             # <<<<<<<<<<<<<<
@@ -35180,7 +35006,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
         (__pyx_v_self->sa->arr[__pyx_v_k]) = (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":140
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":140
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = self.sa.arr[ptail+1]
  *                     self.sa.arr[ptail+1] = tmp             # <<<<<<<<<<<<<<
@@ -35192,7 +35018,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":142
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":142
  *                     self.sa.arr[ptail+1] = tmp
  *                 else: # k == ptail+1
  *                     tmp = self.sa.arr[phead]             # <<<<<<<<<<<<<<
@@ -35201,7 +35027,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
         __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_phead]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":143
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":143
  *                 else: # k == ptail+1
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]             # <<<<<<<<<<<<<<
@@ -35210,7 +35036,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
         (__pyx_v_self->sa->arr[__pyx_v_phead]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":144
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":144
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = tmp             # <<<<<<<<<<<<<<
@@ -35221,7 +35047,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
       }
       __pyx_L10:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":145
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":145
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = tmp
  *                 phead = phead + 1             # <<<<<<<<<<<<<<
@@ -35230,7 +35056,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
       __pyx_v_phead = (__pyx_v_phead + 1);
 
-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":146
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":146
  *                     self.sa.arr[k] = tmp
  *                 phead = phead + 1
  *                 ptail = ptail + 1             # <<<<<<<<<<<<<<
@@ -35242,7 +35068,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":148
+      /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":148
  *                 ptail = ptail + 1
  *             else:
  *                 if isa.arr[self.sa.arr[k] + h] == pval:             # <<<<<<<<<<<<<<
@@ -35252,7 +35078,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
       __pyx_t_1 = ((__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_k]) + __pyx_v_h)]) == __pyx_v_pval);
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":149
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":149
  *             else:
  *                 if isa.arr[self.sa.arr[k] + h] == pval:
  *                     if k > ptail+1:             # <<<<<<<<<<<<<<
@@ -35262,7 +35088,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
         __pyx_t_1 = (__pyx_v_k > (__pyx_v_ptail + 1));
         if (__pyx_t_1) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":150
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":150
  *                 if isa.arr[self.sa.arr[k] + h] == pval:
  *                     if k > ptail+1:
  *                         tmp = self.sa.arr[ptail+1]             # <<<<<<<<<<<<<<
@@ -35271,7 +35097,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
  */
           __pyx_v_tmp = (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]);
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":151
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":151
  *                     if k > ptail+1:
  *                         tmp = self.sa.arr[ptail+1]
  *                         self.sa.arr[ptail+1] = self.sa.arr[k]             # <<<<<<<<<<<<<<
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           (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":152
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":152
  *                         tmp = self.sa.arr[ptail+1]
  *                         self.sa.arr[ptail+1] = self.sa.arr[k]
  *                         self.sa.arr[k] = tmp             # <<<<<<<<<<<<<<
@@ -35292,7 +35118,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
         }
         __pyx_L12:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":153
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":153
  *                         self.sa.arr[ptail+1] = self.sa.arr[k]
  *                         self.sa.arr[k] = tmp
  *                     ptail = ptail + 1             # <<<<<<<<<<<<<<
@@ -35307,7 +35133,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
     __pyx_L9:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":156
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":156
  * 
  *         # recursively sort smaller suffixes
  *         self.q3sort(i, phead-1, h, isa, pad+"    ")             # <<<<<<<<<<<<<<
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   __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":160
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":160
  *         # update suffixes with pivot value
  *         # corresponds to update_group function in Larsson & Sadakane
  *         for k from phead <= k < ptail+1:             # <<<<<<<<<<<<<<
@@ -35357,7 +35183,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
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-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":161
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":161
  *         # corresponds to update_group function in Larsson & Sadakane
  *         for k from phead <= k < ptail+1:
  *             isa.arr[self.sa.arr[k]] = ptail             # <<<<<<<<<<<<<<
@@ -35367,7 +35193,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_Suffi
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   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":162
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":162
  *         for k from phead <= k < ptail+1:
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  *         if phead == ptail:             # <<<<<<<<<<<<<<
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   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":163
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":163
  *             isa.arr[self.sa.arr[k]] = ptail
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  *             self.sa.arr[phead] = -1             # <<<<<<<<<<<<<<
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   }
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":166
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":166
  * 
  *         # recursively sort larger suffixes
  *         self.q3sort(ptail+1, j, h, isa, pad+"    ")             # <<<<<<<<<<<<<<
@@ -35467,7 +35293,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_9write_text(PyObject *__pyx_v_self,
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":169
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":169
  * 
  * 
  *     def write_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -35486,7 +35312,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_8write_text(struct __pyx_obj_3_sa_S
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":170
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":170
  * 
  *     def write_text(self, char* filename):
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":172
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":172
  *         self.darray.write_text(filename)
  * 
  *     def read_binary(self, char* filename):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("read_binary", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":174
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":174
  *     def read_binary(self, char* filename):
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":175
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":175
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":176
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":176
  *         f = fopen(filename, "r")
  *         self.darray.read_handle(f)
  *         self.sa.read_handle(f)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":177
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":177
  *         self.darray.read_handle(f)
  *         self.sa.read_handle(f)
  *         self.ha.read_handle(f)             # <<<<<<<<<<<<<<
@@ -35593,7 +35419,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_binary(struct __pyx_obj_3_sa
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":178
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":178
  *         self.sa.read_handle(f)
  *         self.ha.read_handle(f)
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":180
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":180
  *         fclose(f)
  * 
  *     def write_binary(self, char* filename):             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":182
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":182
  *     def write_binary(self, char* filename):
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__w);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":183
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":183
  *         cdef FILE* f
  *         f = fopen(filename, "w")
  *         self.darray.write_handle(f)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":184
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":184
  *         f = fopen(filename, "w")
  *         self.darray.write_handle(f)
  *         self.sa.write_handle(f)             # <<<<<<<<<<<<<<
@@ -35670,7 +35496,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12write_binary(struct __pyx_obj_3_s
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":185
  *         self.darray.write_handle(f)
  *         self.sa.write_handle(f)
  *         self.ha.write_handle(f)             # <<<<<<<<<<<<<<
@@ -35679,7 +35505,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12write_binary(struct __pyx_obj_3_s
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":186
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":186
  *         self.sa.write_handle(f)
  *         self.ha.write_handle(f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -35715,7 +35541,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_15write_enhanced(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":188
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":188
  *         fclose(f)
  * 
  *     def write_enhanced(self, char* filename):             # <<<<<<<<<<<<<<
@@ -35747,7 +35573,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":189
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":189
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -35787,7 +35613,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":190
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":190
  *     def write_enhanced(self, char* filename):
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  *             self.darray.write_enhanced_handle(f)             # <<<<<<<<<<<<<<
@@ -35807,7 +35633,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":191
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":191
  *         with open(filename, "w") as f:
  *             self.darray.write_enhanced_handle(f)
  *             for a_i in self.sa:             # <<<<<<<<<<<<<<
@@ -35825,18 +35651,10 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
-              __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++;
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              #endif
+              __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++;
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@@ -35852,7 +35670,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":192
+            /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":192
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           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":193
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":193
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@@ -35890,7 +35708,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":194
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":194
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  *             for w_i in self.ha:             # <<<<<<<<<<<<<<
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-              #if CYTHON_COMPILING_IN_CPYTHON
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-              #else
-              __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #endif
+              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
-              #else
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-              #endif
+              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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@@ -35935,7 +35745,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":195
+            /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":195
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  *                 f.write("%d " % w_i)             # <<<<<<<<<<<<<<
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           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":196
+          /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":196
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  *                 f.write("%d " % w_i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -35983,7 +35793,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
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         __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":189
+        /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":189
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -36081,7 +35891,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":198
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":198
  *             f.write("\n")
  * 
  *     cdef int __search_high(self, int word_id, int offset, int low, int high):             # <<<<<<<<<<<<<<
@@ -36096,7 +35906,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("__search_high", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":201
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":201
  *         cdef int midpoint
  * 
  *         if low >= high:             # <<<<<<<<<<<<<<
@@ -36106,7 +35916,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   __pyx_t_1 = (__pyx_v_low >= __pyx_v_high);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":202
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":202
  * 
  *         if low >= high:
  *             return high             # <<<<<<<<<<<<<<
@@ -36119,7 +35929,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":203
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":203
  *         if low >= high:
  *             return high
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
@@ -36128,7 +35938,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
  */
   __pyx_v_midpoint = __Pyx_div_long((__pyx_v_high + __pyx_v_low), 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":204
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":204
  *             return high
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:             # <<<<<<<<<<<<<<
@@ -36138,7 +35948,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   __pyx_t_1 = ((__pyx_v_self->darray->data->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_offset)]) == __pyx_v_word_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":205
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":205
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:
  *             return self.__search_high(word_id, offset, midpoint+1, high)             # <<<<<<<<<<<<<<
@@ -36151,7 +35961,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":207
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":207
  *             return self.__search_high(word_id, offset, midpoint+1, high)
  *         else:
  *             return self.__search_high(word_id, offset, low, midpoint)             # <<<<<<<<<<<<<<
@@ -36169,7 +35979,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":209
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":209
  *             return self.__search_high(word_id, offset, low, midpoint)
  * 
  *     cdef int __search_low(self, int word_id, int offset, int low, int high):             # <<<<<<<<<<<<<<
@@ -36184,7 +35994,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("__search_low", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":212
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":212
  *         cdef int midpoint
  * 
  *         if low >= high:             # <<<<<<<<<<<<<<
@@ -36194,7 +36004,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   __pyx_t_1 = (__pyx_v_low >= __pyx_v_high);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":213
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":213
  * 
  *         if low >= high:
  *             return high             # <<<<<<<<<<<<<<
@@ -36207,7 +36017,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":214
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":214
  *         if low >= high:
  *             return high
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
@@ -36216,7 +36026,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
  */
   __pyx_v_midpoint = __Pyx_div_long((__pyx_v_high + __pyx_v_low), 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":215
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":215
  *             return high
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:             # <<<<<<<<<<<<<<
@@ -36226,7 +36036,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   __pyx_t_1 = ((__pyx_v_self->darray->data->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_offset)]) == __pyx_v_word_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":216
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":216
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:
  *             return self.__search_low(word_id, offset, low, midpoint)             # <<<<<<<<<<<<<<
@@ -36239,7 +36049,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":218
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":218
  *             return self.__search_low(word_id, offset, low, midpoint)
  *         else:
  *             return self.__search_low(word_id, offset, midpoint+1, high)             # <<<<<<<<<<<<<<
@@ -36257,7 +36067,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":220
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":220
  *             return self.__search_low(word_id, offset, midpoint+1, high)
  * 
  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):             # <<<<<<<<<<<<<<
@@ -36276,7 +36086,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___get_range(struct __pyx_obj_3_sa_Su
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get_range", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":221
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":221
  * 
  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):
  *         return (self.__search_low(word_id, offset, low, midpoint),             # <<<<<<<<<<<<<<
@@ -36287,7 +36097,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___get_range(struct __pyx_obj_3_sa_Su
   __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___search_low(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, __pyx_v_low, __pyx_v_midpoint)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":222
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":222
  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):
  *         return (self.__search_low(word_id, offset, low, midpoint),
  *                 self.__search_high(word_id, offset, midpoint, high))             # <<<<<<<<<<<<<<
@@ -36322,7 +36132,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___get_range(struct __pyx_obj_3_sa_Su
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":224
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":224
  *                 self.__search_high(word_id, offset, midpoint, high))
  * 
  *     cdef __lookup_helper(self, int word_id, int offset, int low, int high):             # <<<<<<<<<<<<<<
@@ -36343,7 +36153,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__lookup_helper", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":227
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":227
  *         cdef int midpoint
  * 
  *         if offset == 0:             # <<<<<<<<<<<<<<
@@ -36353,7 +36163,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   __pyx_t_1 = (__pyx_v_offset == 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":228
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":228
  * 
  *         if offset == 0:
  *             return (self.ha.arr[word_id], self.ha.arr[word_id+1])             # <<<<<<<<<<<<<<
@@ -36380,7 +36190,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":229
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":229
  *         if offset == 0:
  *             return (self.ha.arr[word_id], self.ha.arr[word_id+1])
  *         if low >= high:             # <<<<<<<<<<<<<<
@@ -36390,7 +36200,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   __pyx_t_1 = (__pyx_v_low >= __pyx_v_high);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":230
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":230
  *             return (self.ha.arr[word_id], self.ha.arr[word_id+1])
  *         if low >= high:
  *             return None             # <<<<<<<<<<<<<<
@@ -36405,7 +36215,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":232
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":232
  *             return None
  * 
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
@@ -36414,7 +36224,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
  */
   __pyx_v_midpoint = __Pyx_div_long((__pyx_v_high + __pyx_v_low), 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":233
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":233
  * 
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:             # <<<<<<<<<<<<<<
@@ -36424,7 +36234,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   __pyx_t_1 = ((__pyx_v_self->darray->data->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_offset)]) == __pyx_v_word_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":234
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":234
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:
  *             return self.__get_range(word_id, offset, low, high, midpoint)             # <<<<<<<<<<<<<<
@@ -36441,7 +36251,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":235
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":235
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:
  *             return self.__get_range(word_id, offset, low, high, midpoint)
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] > word_id:             # <<<<<<<<<<<<<<
@@ -36451,7 +36261,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   __pyx_t_1 = ((__pyx_v_self->darray->data->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_offset)]) > __pyx_v_word_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":236
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":236
  *             return self.__get_range(word_id, offset, low, high, midpoint)
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] > word_id:
  *             return self.__lookup_helper(word_id, offset, low, midpoint)             # <<<<<<<<<<<<<<
@@ -36468,7 +36278,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":238
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":238
  *             return self.__lookup_helper(word_id, offset, low, midpoint)
  *         else:
  *             return self.__lookup_helper(word_id, offset, midpoint+1, high)             # <<<<<<<<<<<<<<
@@ -36505,11 +36315,11 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_17lookup(PyObject *__pyx_v_self, Py
   int __pyx_v_offset;
   int __pyx_v_low;
   int __pyx_v_high;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__word,&__pyx_n_s__offset,&__pyx_n_s__low,&__pyx_n_s__high,0};
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("lookup (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__word,&__pyx_n_s__offset,&__pyx_n_s__low,&__pyx_n_s__high,0};
     PyObject* values[4] = {0,0,0,0};
     if (unlikely(__pyx_kwds)) {
       Py_ssize_t kw_args;
@@ -36525,20 +36335,24 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_17lookup(PyObject *__pyx_v_self, Py
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__word)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__word);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 1); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__low)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__low);
+        if (likely(values[2])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 2); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  3:
-        if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__high)) != 0)) kw_args--;
+        values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__high);
+        if (likely(values[3])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 3); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
@@ -36572,7 +36386,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_17lookup(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":240
+/* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":240
  *             return self.__lookup_helper(word_id, offset, midpoint+1, high)
  * 
  *     def lookup(self, word, int offset, int low, int high):             # <<<<<<<<<<<<<<
@@ -36593,7 +36407,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_Suff
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("lookup", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":242
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":242
  *     def lookup(self, word, int offset, int low, int high):
  *         cdef int wordid
  *         if low == -1:             # <<<<<<<<<<<<<<
@@ -36603,7 +36417,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_Suff
   __pyx_t_1 = (__pyx_v_low == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":243
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":243
  *         cdef int wordid
  *         if low == -1:
  *             low = 0             # <<<<<<<<<<<<<<
@@ -36615,7 +36429,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_Suff
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":244
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":244
  *         if low == -1:
  *             low = 0
  *         if high == -1:             # <<<<<<<<<<<<<<
@@ -36625,7 +36439,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_Suff
   __pyx_t_1 = (__pyx_v_high == -1);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":245
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":245
  *             low = 0
  *         if high == -1:
  *             high = len(self.sa)             # <<<<<<<<<<<<<<
@@ -36641,17 +36455,17 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_Suff
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":246
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":246
  *         if high == -1:
  *             high = len(self.sa)
  *         if word in self.darray.word2id:             # <<<<<<<<<<<<<<
  *             word_id = self.darray.word2id[word]
  *             return self.__lookup_helper(word_id, offset, low, high)
  */
-  __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_word, __pyx_v_self->darray->word2id, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->darray->word2id, __pyx_v_word))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":247
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":247
  *             high = len(self.sa)
  *         if word in self.darray.word2id:
  *             word_id = self.darray.word2id[word]             # <<<<<<<<<<<<<<
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     __pyx_t_2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":248
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":248
  *         if word in self.darray.word2id:
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  *             return self.__lookup_helper(word_id, offset, low, high)             # <<<<<<<<<<<<<<
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   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":250
+    /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":250
  *             return self.__lookup_helper(word_id, offset, low, high)
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":49
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":49
  *     cdef public children
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":50
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":50
  * 
  *     def __cinit__(self):
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":47
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":47
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  * cdef class TrieNode:
  *     cdef public children             # <<<<<<<<<<<<<<
@@ -36856,14 +36670,14 @@ static int __pyx_pw_3_sa_16ExtendedTrieNode_1__cinit__(PyObject *__pyx_v_self, P
   PyObject *__pyx_v_phrase = 0;
   PyObject *__pyx_v_phrase_location = 0;
   PyObject *__pyx_v_suffix_link = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__phrase,&__pyx_n_s__phrase_location,&__pyx_n_s__suffix_link,0};
   int __pyx_r;
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     PyObject* values[3] = {0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":57
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":57
  *     cdef public suffix_link
  * 
  *     def __cinit__(self, phrase=None, phrase_location=None, suffix_link=None):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":58
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":58
  * 
  *     def __cinit__(self, phrase=None, phrase_location=None, suffix_link=None):
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   __pyx_v_self->phrase = __pyx_v_phrase;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":59
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":59
  *     def __cinit__(self, phrase=None, phrase_location=None, suffix_link=None):
  *         self.phrase = phrase
  *         self.phrase_location = phrase_location             # <<<<<<<<<<<<<<
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   __pyx_v_self->phrase_location = __pyx_v_phrase_location;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":60
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":60
  *         self.phrase = phrase
  *         self.phrase_location = phrase_location
  *         self.suffix_link = suffix_link             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":53
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":53
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  * cdef class ExtendedTrieNode(TrieNode):
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":54
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":54
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  *     cdef public phrase_location             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":55
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":55
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  *     cdef public phrase_location
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 static int __pyx_pw_3_sa_9TrieTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_3_sa_9TrieTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_extended = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__extended,0};
   int __pyx_r;
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@@ -37292,7 +37106,7 @@ static int __pyx_pw_3_sa_9TrieTable_1__cinit__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":67
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":67
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  *     cdef public root
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":68
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":68
  *     cdef public root
  *     def __cinit__(self, extended=False):
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   __pyx_v_self->count = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":69
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":69
  *     def __cinit__(self, extended=False):
  *         self.count = 0
  *         self.extended = extended             # <<<<<<<<<<<<<<
@@ -37330,7 +37144,7 @@ static int __pyx_pf_3_sa_9TrieTable___cinit__(struct __pyx_obj_3_sa_TrieTable *_
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   __pyx_v_self->extended = __pyx_t_1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":70
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":70
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  *         self.extended = extended
  *         if extended:             # <<<<<<<<<<<<<<
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":71
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":71
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  *         if extended:
  *             self.root = ExtendedTrieNode()             # <<<<<<<<<<<<<<
@@ -37358,7 +37172,7 @@ static int __pyx_pf_3_sa_9TrieTable___cinit__(struct __pyx_obj_3_sa_TrieTable *_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":73
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":73
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  *         else:
  *             self.root = TrieNode()             # <<<<<<<<<<<<<<
@@ -37397,7 +37211,7 @@ static PyObject *__pyx_pw_3_sa_9TrieTable_8extended_1__get__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":64
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":64
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  * cdef class TrieTable:
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@@ -37475,7 +37289,7 @@ static PyObject *__pyx_pw_3_sa_9TrieTable_5count_1__get__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":65
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":65
  * cdef class TrieTable:
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  *     cdef public int count             # <<<<<<<<<<<<<<
@@ -37553,7 +37367,7 @@ static PyObject *__pyx_pw_3_sa_9TrieTable_4root_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":66
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":66
  *     cdef public int extended
  *     cdef public int count
  *     cdef public root             # <<<<<<<<<<<<<<
@@ -37629,7 +37443,7 @@ static int __pyx_pf_3_sa_9TrieTable_4root_4__del__(struct __pyx_obj_3_sa_TrieTab
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":93
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":93
  * 
  *     # returns true if sent_id is contained
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":94
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":94
  *     # returns true if sent_id is contained
  *     cdef int contains(self, int sent_id):
  *         return 1             # <<<<<<<<<<<<<<
@@ -37667,14 +37481,14 @@ static int __pyx_pw_3_sa_14PhraseLocation_1__cinit__(PyObject *__pyx_v_self, PyO
   int __pyx_v_arr_high;
   PyObject *__pyx_v_arr = 0;
   int __pyx_v_num_subpatterns;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__sa_low,&__pyx_n_s__sa_high,&__pyx_n_s__arr_low,&__pyx_n_s__arr_high,&__pyx_n_s__arr,&__pyx_n_s__num_subpatterns,0};
   int __pyx_r;
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   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__sa_low,&__pyx_n_s__sa_high,&__pyx_n_s__arr_low,&__pyx_n_s__arr_high,&__pyx_n_s__arr,&__pyx_n_s__num_subpatterns,0};
     PyObject* values[6] = {0,0,0,0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":97
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":97
  * 
  *     def __cinit__(self, int sa_low=-1, int sa_high=-1, int arr_low=-1, int arr_high=-1,
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       }
+      if (values[0]) {
+      } else {
+        __pyx_v_sa_low = ((int)-1);
+      }
+      if (values[1]) {
+      } else {
+        __pyx_v_sa_high = ((int)-1);
+      }
+      if (values[2]) {
+      } else {
+        __pyx_v_arr_low = ((int)-1);
+      }
+      if (values[3]) {
+      } else {
+        __pyx_v_arr_high = ((int)-1);
+      }
+      if (values[5]) {
+      } else {
+        __pyx_v_num_subpatterns = ((int)1);
+      }
     } else {
       switch (PyTuple_GET_SIZE(__pyx_args)) {
         case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
@@ -37783,7 +37617,7 @@ static int __pyx_pw_3_sa_14PhraseLocation_1__cinit__(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":96
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":96
  *         return 1
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":98
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":98
  *     def __cinit__(self, int sa_low=-1, int sa_high=-1, int arr_low=-1, int arr_high=-1,
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  */
   __pyx_v_self->sa_low = __pyx_v_sa_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":99
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":99
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  *         self.sa_high = sa_high             # <<<<<<<<<<<<<<
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   __pyx_v_self->sa_high = __pyx_v_sa_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":100
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":100
  *         self.sa_low = sa_low
  *         self.sa_high = sa_high
  *         self.arr_low = arr_low             # <<<<<<<<<<<<<<
@@ -37826,7 +37660,7 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
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   __pyx_v_self->arr_low = __pyx_v_arr_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":101
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":101
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  *         self.arr_low = arr_low
  *         self.arr_high = arr_high             # <<<<<<<<<<<<<<
@@ -37835,7 +37669,7 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
  */
   __pyx_v_self->arr_high = __pyx_v_arr_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":102
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":102
  *         self.arr_low = arr_low
  *         self.arr_high = arr_high
  *         self.arr = arr             # <<<<<<<<<<<<<<
@@ -37849,7 +37683,7 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
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   __pyx_v_self->arr = ((struct __pyx_obj_3_sa_IntList *)__pyx_v_arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":103
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":103
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  *         self.arr = arr
  *         self.num_subpatterns = num_subpatterns             # <<<<<<<<<<<<<<
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 static int __pyx_pw_3_sa_7Sampler_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   int __pyx_v_sample_size;
   struct __pyx_obj_3_sa_SuffixArray *__pyx_v_fsarray = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__sample_size,&__pyx_n_s__fsarray,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
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       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__sample_size)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__sample_size);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fsarray)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fsarray);
+        if (likely(values[1])) kw_args--;
         else {
           __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":113
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":113
  *     cdef IntList sa
  * 
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):             # <<<<<<<<<<<<<<
@@ -37949,7 +37785,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":114
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":114
  * 
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):
  *         self.sample_size = sample_size             # <<<<<<<<<<<<<<
@@ -37958,7 +37794,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
  */
   __pyx_v_self->sample_size = __pyx_v_sample_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":115
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":115
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):
  *         self.sample_size = sample_size
  *         self.sa = fsarray.sa             # <<<<<<<<<<<<<<
@@ -37971,7 +37807,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   __Pyx_DECREF(((PyObject *)__pyx_v_self->sa));
   __pyx_v_self->sa = __pyx_v_fsarray->sa;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":116
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":116
  *         self.sample_size = sample_size
  *         self.sa = fsarray.sa
  *         if sample_size > 0:             # <<<<<<<<<<<<<<
@@ -37981,7 +37817,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   __pyx_t_1 = (__pyx_v_sample_size > 0);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":117
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":117
  *         self.sa = fsarray.sa
  *         if sample_size > 0:
  *             logger.info("Sampling strategy: uniform, max sample size = %d", sample_size)             # <<<<<<<<<<<<<<
@@ -38012,7 +37848,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":119
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":119
  *             logger.info("Sampling strategy: uniform, max sample size = %d", sample_size)
  *         else:
  *             logger.info("Sampling strategy: no sampling")             # <<<<<<<<<<<<<<
@@ -38061,7 +37897,7 @@ static PyObject *__pyx_pw_3_sa_7Sampler_3sample(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":121
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":121
  *             logger.info("Sampling strategy: no sampling")
  * 
  *     def sample(self, PhraseLocation phrase_location):             # <<<<<<<<<<<<<<
@@ -38088,7 +37924,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("sample", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":134
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":134
  *         cdef int num_locations, val, j
  * 
  *         sample = IntList()             # <<<<<<<<<<<<<<
@@ -38100,7 +37936,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   __pyx_v_sample = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":135
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":135
  * 
  *         sample = IntList()
  *         if phrase_location.arr is None:             # <<<<<<<<<<<<<<
@@ -38110,7 +37946,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   __pyx_t_2 = (((PyObject *)__pyx_v_phrase_location->arr) == Py_None);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":136
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":136
  *         sample = IntList()
  *         if phrase_location.arr is None:
  *             num_locations = phrase_location.sa_high - phrase_location.sa_low             # <<<<<<<<<<<<<<
@@ -38119,7 +37955,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
     __pyx_v_num_locations = (__pyx_v_phrase_location->sa_high - __pyx_v_phrase_location->sa_low);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":137
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":137
  *         if phrase_location.arr is None:
  *             num_locations = phrase_location.sa_high - phrase_location.sa_low
  *             if self.sample_size == -1 or num_locations <= self.sample_size:             # <<<<<<<<<<<<<<
@@ -38135,7 +37971,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":138
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":138
  *             num_locations = phrase_location.sa_high - phrase_location.sa_low
  *             if self.sample_size == -1 or num_locations <= self.sample_size:
  *                 sample._extend_arr(self.sa.arr + phrase_location.sa_low, num_locations)             # <<<<<<<<<<<<<<
@@ -38147,7 +37983,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":140
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":140
  *                 sample._extend_arr(self.sa.arr + phrase_location.sa_low, num_locations)
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)             # <<<<<<<<<<<<<<
@@ -38160,7 +37996,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
       }
       __pyx_v_stepsize = (((double)__pyx_v_num_locations) / ((double)__pyx_v_self->sample_size));
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":141
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":141
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.sa_low             # <<<<<<<<<<<<<<
@@ -38169,7 +38005,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
       __pyx_v_i = __pyx_v_phrase_location->sa_low;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":142
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":142
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.sa_low
  *                 while i < phrase_location.sa_high and sample.len < self.sample_size:             # <<<<<<<<<<<<<<
@@ -38186,7 +38022,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         if (!__pyx_t_3) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":145
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":145
  *                     '''Note: int(i) not guaranteed to have the desired
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:             # <<<<<<<<<<<<<<
@@ -38196,7 +38032,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         __pyx_t_3 = (fmod(__pyx_v_i, 1.0) > 0.5);
         if (__pyx_t_3) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":146
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":146
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:
  *                         val = int(ceil(i))             # <<<<<<<<<<<<<<
@@ -38208,7 +38044,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":148
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":148
  *                         val = int(ceil(i))
  *                     else:
  *                         val = int(floor(i))             # <<<<<<<<<<<<<<
@@ -38219,7 +38055,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         __pyx_L7:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":149
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":149
  *                     else:
  *                         val = int(floor(i))
  *                     sample._append(self.sa.arr[val])             # <<<<<<<<<<<<<<
@@ -38228,7 +38064,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_sample->__pyx_vtab)->_append(__pyx_v_sample, (__pyx_v_self->sa->arr[__pyx_v_val]));
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":150
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":150
  *                         val = int(floor(i))
  *                     sample._append(self.sa.arr[val])
  *                     i = i + stepsize             # <<<<<<<<<<<<<<
@@ -38243,7 +38079,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":152
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":152
  *                     i = i + stepsize
  *         else:
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns             # <<<<<<<<<<<<<<
@@ -38261,7 +38097,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     __pyx_v_num_locations = __Pyx_div_int(__pyx_t_5, __pyx_v_phrase_location->num_subpatterns);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":153
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":153
  *         else:
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns
  *             if self.sample_size == -1 or num_locations <= self.sample_size:             # <<<<<<<<<<<<<<
@@ -38277,7 +38113,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":154
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":154
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns
  *             if self.sample_size == -1 or num_locations <= self.sample_size:
  *                 sample = phrase_location.arr             # <<<<<<<<<<<<<<
@@ -38291,7 +38127,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":156
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":156
  *                 sample = phrase_location.arr
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)             # <<<<<<<<<<<<<<
@@ -38304,7 +38140,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
       }
       __pyx_v_stepsize = (((double)__pyx_v_num_locations) / ((double)__pyx_v_self->sample_size));
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":157
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":157
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.arr_low             # <<<<<<<<<<<<<<
@@ -38313,7 +38149,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
       __pyx_v_i = __pyx_v_phrase_location->arr_low;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":158
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":158
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.arr_low
  *                 while i < num_locations and sample.len < self.sample_size * phrase_location.num_subpatterns:             # <<<<<<<<<<<<<<
@@ -38330,7 +38166,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         if (!__pyx_t_4) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":161
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":161
  *                     '''Note: int(i) not guaranteed to have the desired
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:             # <<<<<<<<<<<<<<
@@ -38340,7 +38176,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         __pyx_t_4 = (fmod(__pyx_v_i, 1.0) > 0.5);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":162
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":162
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:
  *                         val = int(ceil(i))             # <<<<<<<<<<<<<<
@@ -38352,7 +38188,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":164
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":164
  *                         val = int(ceil(i))
  *                     else:
  *                         val = int(floor(i))             # <<<<<<<<<<<<<<
@@ -38363,7 +38199,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         __pyx_L11:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":165
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":165
  *                     else:
  *                         val = int(floor(i))
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)             # <<<<<<<<<<<<<<
@@ -38372,7 +38208,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         __pyx_v_j = (__pyx_v_phrase_location->arr_low + (__pyx_v_val * __pyx_v_phrase_location->num_subpatterns));
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":166
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":166
  *                         val = int(floor(i))
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)             # <<<<<<<<<<<<<<
@@ -38381,7 +38217,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_sample->__pyx_vtab)->_extend_arr(__pyx_v_sample, (__pyx_v_phrase_location->arr->arr + __pyx_v_j), __pyx_v_phrase_location->num_subpatterns);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":167
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":167
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)
  *                     i = i + stepsize             # <<<<<<<<<<<<<<
@@ -38395,7 +38231,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":168
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":168
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)
  *                     i = i + stepsize
  *         return sample             # <<<<<<<<<<<<<<
@@ -38420,7 +38256,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":180
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":180
  * 
  * 
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):             # <<<<<<<<<<<<<<
@@ -38432,7 +38268,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("assign_matching", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":181
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":181
  * 
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):
  *     m.arr = arr             # <<<<<<<<<<<<<<
@@ -38441,7 +38277,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->arr = __pyx_v_arr;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":182
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":182
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):
  *     m.arr = arr
  *     m.start = start             # <<<<<<<<<<<<<<
@@ -38450,7 +38286,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->start = __pyx_v_start;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":183
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":183
  *     m.arr = arr
  *     m.start = start
  *     m.end = start + step             # <<<<<<<<<<<<<<
@@ -38459,7 +38295,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->end = (__pyx_v_start + __pyx_v_step);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":184
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":184
  *     m.start = start
  *     m.end = start + step
  *     m.sent_id = sent_id_arr[arr[start]]             # <<<<<<<<<<<<<<
@@ -38468,7 +38304,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->sent_id = (__pyx_v_sent_id_arr[(__pyx_v_arr[__pyx_v_start])]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":185
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":185
  *     m.end = start + step
  *     m.sent_id = sent_id_arr[arr[start]]
  *     m.size = step             # <<<<<<<<<<<<<<
@@ -38480,7 +38316,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":188
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":188
  * 
  * 
  * cdef int* append_combined_matching(int* arr, Matching* loc1, Matching* loc2,             # <<<<<<<<<<<<<<
@@ -38497,7 +38333,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   int __pyx_t_2;
   __Pyx_RefNannySetupContext("append_combined_matching", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":192
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":192
  *     cdef int i, new_len
  * 
  *     new_len = result_len[0] + num_subpatterns             # <<<<<<<<<<<<<<
@@ -38506,7 +38342,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   __pyx_v_new_len = ((__pyx_v_result_len[0]) + __pyx_v_num_subpatterns);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":193
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":193
  * 
  *     new_len = result_len[0] + num_subpatterns
  *     arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -38515,7 +38351,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":195
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":195
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  * 
  *     for i from 0 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -38525,7 +38361,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   __pyx_t_1 = __pyx_v_loc1->size;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":196
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":196
  * 
  *     for i from 0 <= i < loc1.size:
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]             # <<<<<<<<<<<<<<
@@ -38535,7 +38371,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
     (__pyx_v_arr[((__pyx_v_result_len[0]) + __pyx_v_i)]) = (__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":197
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":197
  *     for i from 0 <= i < loc1.size:
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]
  *     if num_subpatterns > loc1.size:             # <<<<<<<<<<<<<<
@@ -38545,7 +38381,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   __pyx_t_2 = (__pyx_v_num_subpatterns > __pyx_v_loc1->size);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":198
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":198
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]
  *     if num_subpatterns > loc1.size:
  *         arr[new_len-1] = loc2.arr[loc2.end-1]             # <<<<<<<<<<<<<<
@@ -38557,7 +38393,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":199
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":199
  *     if num_subpatterns > loc1.size:
  *         arr[new_len-1] = loc2.arr[loc2.end-1]
  *     result_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -38566,7 +38402,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   (__pyx_v_result_len[0]) = __pyx_v_new_len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":200
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":200
  *         arr[new_len-1] = loc2.arr[loc2.end-1]
  *     result_len[0] = new_len
  *     return arr             # <<<<<<<<<<<<<<
@@ -38582,7 +38418,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":203
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":203
  * 
  * 
  * cdef int* extend_arr(int* arr, int* arr_len, int* appendix, int appendix_len):             # <<<<<<<<<<<<<<
@@ -38596,7 +38432,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("extend_arr", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":206
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":206
  *     cdef int new_len
  * 
  *     new_len = arr_len[0] + appendix_len             # <<<<<<<<<<<<<<
@@ -38605,7 +38441,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   __pyx_v_new_len = ((__pyx_v_arr_len[0]) + __pyx_v_appendix_len);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":207
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":207
  * 
  *     new_len = arr_len[0] + appendix_len
  *     arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -38614,7 +38450,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":208
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":208
  *     new_len = arr_len[0] + appendix_len
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -38623,7 +38459,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   memcpy((__pyx_v_arr + (__pyx_v_arr_len[0])), __pyx_v_appendix, (__pyx_v_appendix_len * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":209
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":209
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))
  *     arr_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -38632,7 +38468,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   (__pyx_v_arr_len[0]) = __pyx_v_new_len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":210
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":210
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))
  *     arr_len[0] = new_len
  *     return arr             # <<<<<<<<<<<<<<
@@ -38648,7 +38484,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":212
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":212
  *     return arr
  * 
  * cdef int median(int low, int high, int step):             # <<<<<<<<<<<<<<
@@ -38665,7 +38501,7 @@ static int __pyx_f_3_sa_median(int __pyx_v_low, int __pyx_v_high, int __pyx_v_st
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("median", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":213
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":213
  * 
  * cdef int median(int low, int high, int step):
  *     return low + (((high - low)/step)/2)*step             # <<<<<<<<<<<<<<
@@ -38694,7 +38530,7 @@ static int __pyx_f_3_sa_median(int __pyx_v_low, int __pyx_v_high, int __pyx_v_st
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":216
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":216
  * 
  * 
  * cdef void find_comparable_matchings(int low, int high, int* arr, int step, int loc, int* loc_minus, int* loc_plus):             # <<<<<<<<<<<<<<
@@ -38709,7 +38545,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("find_comparable_matchings", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":220
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":220
  *     # in which all matchings have the same first index as the one
  *     # starting at loc
  *     loc_plus[0] = loc + step             # <<<<<<<<<<<<<<
@@ -38718,7 +38554,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
  */
   (__pyx_v_loc_plus[0]) = (__pyx_v_loc + __pyx_v_step);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":221
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":221
  *     # starting at loc
  *     loc_plus[0] = loc + step
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:             # <<<<<<<<<<<<<<
@@ -38735,7 +38571,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
     }
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":222
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":222
  *     loc_plus[0] = loc + step
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:
  *         loc_plus[0] = loc_plus[0] + step             # <<<<<<<<<<<<<<
@@ -38745,7 +38581,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
     (__pyx_v_loc_plus[0]) = ((__pyx_v_loc_plus[0]) + __pyx_v_step);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":223
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":223
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:
  *         loc_plus[0] = loc_plus[0] + step
  *     loc_minus[0] = loc             # <<<<<<<<<<<<<<
@@ -38754,7 +38590,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
  */
   (__pyx_v_loc_minus[0]) = __pyx_v_loc;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":224
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":224
  *         loc_plus[0] = loc_plus[0] + step
  *     loc_minus[0] = loc
  *     while loc_minus[0]-step >= low and arr[loc_minus[0]-step] == arr[loc]:             # <<<<<<<<<<<<<<
@@ -38771,7 +38607,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
     }
     if (!__pyx_t_2) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":225
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":225
  *     loc_minus[0] = loc
  *     while loc_minus[0]-step >= low and arr[loc_minus[0]-step] == arr[loc]:
  *         loc_minus[0] = loc_minus[0] - step             # <<<<<<<<<<<<<<
@@ -38808,14 +38644,14 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
   int __pyx_v_use_baeza_yates;
   int __pyx_v_use_collocations;
   int __pyx_v_use_index;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__alignment,&__pyx_n_s__by_slack_factor,&__pyx_n_s__category,&__pyx_n_s__max_chunks,&__pyx_n_s__max_initial_size,&__pyx_n_s__max_length,&__pyx_n_s__max_nonterminals,&__pyx_n_s__max_target_chunks,&__pyx_n_s__max_target_length,&__pyx_n_s__min_gap_size,&__pyx_n_s__precompute_file,&__pyx_n_s_70,&__pyx_n_s__precompute_rank,&__pyx_n_s_103,&__pyx_n_s_104,&__pyx_n_s_71,&__pyx_n_s__train_min_gap_size,&__pyx_n_s__tight_phrases,&__pyx_n_s__use_baeza_yates,&__pyx_n_s__use_collocations,&__pyx_n_s__use_index,0};
   int __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__alignment,&__pyx_n_s__by_slack_factor,&__pyx_n_s__category,&__pyx_n_s__max_chunks,&__pyx_n_s__max_initial_size,&__pyx_n_s__max_length,&__pyx_n_s__max_nonterminals,&__pyx_n_s__max_target_chunks,&__pyx_n_s__max_target_length,&__pyx_n_s__min_gap_size,&__pyx_n_s__precompute_file,&__pyx_n_s_70,&__pyx_n_s__precompute_rank,&__pyx_n_s_103,&__pyx_n_s_104,&__pyx_n_s_71,&__pyx_n_s__train_min_gap_size,&__pyx_n_s__tight_phrases,&__pyx_n_s__use_baeza_yates,&__pyx_n_s__use_collocations,&__pyx_n_s__use_index,0};
     PyObject* values[21] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":295
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":296
  *             char* category="[X]",
  *             # maximum number of contiguous chunks of terminal symbols in RHS of a rule. If None, defaults to max_nonterminals+1
  *             max_chunks=None,             # <<<<<<<<<<<<<<
@@ -38824,7 +38660,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[3] = ((PyObject *)Py_None);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":303
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":304
  *             unsigned max_nonterminals=2,
  *             # maximum number of contiguous chunks of terminal symbols in target-side RHS of a rule. If None, defaults to max_nonterminals+1
  *             max_target_chunks=None,             # <<<<<<<<<<<<<<
@@ -38833,7 +38669,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[7] = ((PyObject *)Py_None);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":305
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":306
  *             max_target_chunks=None,
  *             # maximum number of target side symbols (both T and NT) allowed in a rule. If None, defaults to max_initial_size
  *             max_target_length=None,             # <<<<<<<<<<<<<<
@@ -38842,7 +38678,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[8] = ((PyObject *)Py_None);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":309
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":310
  *             unsigned min_gap_size=2,
  *             # filename of file containing precomputed collocations
  *             precompute_file=None,             # <<<<<<<<<<<<<<
@@ -38881,7 +38717,8 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alignment)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alignment);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
         if (kw_args > 0) {
@@ -38985,7 +38822,127 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
         }
       }
       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      }
+      if (values[1]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":292
+ *             Alignment alignment,
+ *             # parameter for double-binary search; doesn't seem to matter much
+ *             float by_slack_factor=1.0,             # <<<<<<<<<<<<<<
+ *             # name of generic nonterminal used by Hiero
+ *             char* category="[X]",
+ */
+        __pyx_v_by_slack_factor = ((float)1.0);
+      }
+      if (values[2]) {
+      } else {
+        __pyx_v_category = ((char *)__pyx_k_105);
+      }
+      if (values[4]) {
+      } else {
+        __pyx_v_max_initial_size = ((unsigned int)10);
+      }
+      if (values[5]) {
+      } else {
+        __pyx_v_max_length = ((unsigned int)5);
+      }
+      if (values[6]) {
+      } else {
+        __pyx_v_max_nonterminals = ((unsigned int)2);
+      }
+      if (values[9]) {
+      } else {
+        __pyx_v_min_gap_size = ((unsigned int)2);
+      }
+      if (values[11]) {
+      } else {
+        __pyx_v_precompute_secondary_rank = ((unsigned int)20);
+      }
+      if (values[12]) {
+      } else {
+        __pyx_v_precompute_rank = ((unsigned int)100);
+      }
+      if (values[13]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":316
+ *             unsigned precompute_rank=100,
+ *             # require extracted rules to have at least one aligned word
+ *             bint require_aligned_terminal=True,             # <<<<<<<<<<<<<<
+ *             # require each contiguous chunk of extracted rules to have at least one aligned word
+ *             bint require_aligned_chunks=False,
+ */
+        __pyx_v_require_aligned_terminal = ((int)1);
+      }
+      if (values[14]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":318
+ *             bint require_aligned_terminal=True,
+ *             # require each contiguous chunk of extracted rules to have at least one aligned word
+ *             bint require_aligned_chunks=False,             # <<<<<<<<<<<<<<
+ *             # maximum span of a grammar rule extracted from TRAINING DATA
+ *             unsigned train_max_initial_size=10,
+ */
+        __pyx_v_require_aligned_chunks = ((int)0);
+      }
+      if (values[15]) {
+      } else {
+        __pyx_v_train_max_initial_size = ((unsigned int)10);
+      }
+      if (values[16]) {
+      } else {
+        __pyx_v_train_min_gap_size = ((unsigned int)2);
+      }
+      if (values[17]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":324
+ *             unsigned train_min_gap_size=2,
+ *             # False if phrases should be loose (better but slower), True otherwise
+ *             bint tight_phrases=True,             # <<<<<<<<<<<<<<
+ *             # True to require use of double-binary alg, false otherwise
+ *             bint use_baeza_yates=True,
+ */
+        __pyx_v_tight_phrases = ((int)1);
+      }
+      if (values[18]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":326
+ *             bint tight_phrases=True,
+ *             # True to require use of double-binary alg, false otherwise
+ *             bint use_baeza_yates=True,             # <<<<<<<<<<<<<<
+ *             # True to enable used of precomputed collocations
+ *             bint use_collocations=True,
+ */
+        __pyx_v_use_baeza_yates = ((int)1);
+      }
+      if (values[19]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":328
+ *             bint use_baeza_yates=True,
+ *             # True to enable used of precomputed collocations
+ *             bint use_collocations=True,             # <<<<<<<<<<<<<<
+ *             # True to enable use of precomputed inverted indices
+ *             bint use_index=True):
+ */
+        __pyx_v_use_collocations = ((int)1);
+      }
+      if (values[20]) {
+      } else {
+
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":330
+ *             bint use_collocations=True,
+ *             # True to enable use of precomputed inverted indices
+ *             bint use_index=True):             # <<<<<<<<<<<<<<
+ *         '''Note: we make a distinction between the min_gap_size
+ *         and max_initial_size used in test and train.    The latter
+ */
+        __pyx_v_use_index = ((int)1);
       }
     } else {
       switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -39016,10 +38973,10 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
     }
     __pyx_v_alignment = ((struct __pyx_obj_3_sa_Alignment *)values[0]);
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":411
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+  __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":287
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":288
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":335
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":336
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-  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieTable)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieTable)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -39398,20 +39358,20 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":336
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":337
  *         them to be the same, therefore we don't either.'''
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  *         self.rules.root = ExtendedTrieNode(phrase_location=PhraseLocation())             # <<<<<<<<<<<<<<
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  *             raise Exception("Must specify an alignment object")
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-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__phrase_location), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -39420,7 +39380,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->rules->root = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":337
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":338
  *         self.rules = TrieTable(True) # cache
  *         self.rules.root = ExtendedTrieNode(phrase_location=PhraseLocation())
  *         if alignment is None:             # <<<<<<<<<<<<<<
@@ -39430,23 +39390,23 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_t_3 = (((PyObject *)__pyx_v_alignment) == Py_None);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":338
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":339
  *         self.rules.root = ExtendedTrieNode(phrase_location=PhraseLocation())
  *         if alignment is None:
  *             raise Exception("Must specify an alignment object")             # <<<<<<<<<<<<<<
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-    __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     goto __pyx_L3;
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":339
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":340
  *         if alignment is None:
  *             raise Exception("Must specify an alignment object")
  *         self.alignment = alignment             # <<<<<<<<<<<<<<
@@ -39459,7 +39419,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __Pyx_DECREF(((PyObject *)__pyx_v_self->alignment));
   __pyx_v_self->alignment = __pyx_v_alignment;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":343
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":344
  *         # grammar parameters and settings
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  *         self.max_length = max_length             # <<<<<<<<<<<<<<
@@ -39468,7 +39428,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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   __pyx_v_self->max_length = __pyx_v_max_length;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":344
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":345
  *         # NOTE: setting max_nonterminals > 2 is not currently supported in Hiero
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  *         self.max_nonterminals = max_nonterminals             # <<<<<<<<<<<<<<
@@ -39477,7 +39437,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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   __pyx_v_self->max_nonterminals = __pyx_v_max_nonterminals;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":345
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":346
  *         self.max_length = max_length
  *         self.max_nonterminals = max_nonterminals
  *         self.max_initial_size = max_initial_size             # <<<<<<<<<<<<<<
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  */
   __pyx_v_self->max_initial_size = __pyx_v_max_initial_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":346
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":347
  *         self.max_nonterminals = max_nonterminals
  *         self.max_initial_size = max_initial_size
  *         self.train_max_initial_size = train_max_initial_size             # <<<<<<<<<<<<<<
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   __pyx_v_self->train_max_initial_size = __pyx_v_train_max_initial_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":347
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":348
  *         self.max_initial_size = max_initial_size
  *         self.train_max_initial_size = train_max_initial_size
  *         self.min_gap_size = min_gap_size             # <<<<<<<<<<<<<<
@@ -39504,7 +39464,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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   __pyx_v_self->min_gap_size = __pyx_v_min_gap_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":348
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":349
  *         self.train_max_initial_size = train_max_initial_size
  *         self.min_gap_size = min_gap_size
  *         self.train_min_gap_size = train_min_gap_size             # <<<<<<<<<<<<<<
@@ -39513,7 +39473,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->train_min_gap_size = __pyx_v_train_min_gap_size;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":349
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":350
  *         self.min_gap_size = min_gap_size
  *         self.train_min_gap_size = train_min_gap_size
  *         self.category = sym_fromstring(category, False)             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":351
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":352
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  * 
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":352
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":353
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@@ -39544,19 +39504,19 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":354
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":355
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-    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_self->max_chunks = __pyx_t_4;
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":356
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":357
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  * 
  *         if max_target_chunks is None:             # <<<<<<<<<<<<<<
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   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":357
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":358
  * 
  *         if max_target_chunks is None:
  *             self.max_target_chunks = self.max_nonterminals + 1             # <<<<<<<<<<<<<<
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   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":359
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":360
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  *         else:
  *             self.max_target_chunks = max_target_chunks             # <<<<<<<<<<<<<<
  * 
  *         if max_target_length is None:
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-    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_self->max_target_chunks = __pyx_t_4;
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":361
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":362
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  * 
  *         if max_target_length is None:             # <<<<<<<<<<<<<<
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   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":362
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":363
  * 
  *         if max_target_length is None:
  *             self.max_target_length = max_initial_size             # <<<<<<<<<<<<<<
@@ -39612,26 +39572,26 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":364
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":365
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  *         else:
  *             self.max_target_length = max_target_length             # <<<<<<<<<<<<<<
  * 
  *         # algorithmic parameters and settings
  */
-    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_length); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_length); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __pyx_v_self->max_target_length = __pyx_t_4;
   }
   __pyx_L6:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":367
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":368
  * 
  *         # algorithmic parameters and settings
  *         self.precomputed_collocations = {}             # <<<<<<<<<<<<<<
  *         self.precomputed_index = {}
  *         self.use_index = use_index
  */
-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_2));
   __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->precomputed_collocations);
@@ -39639,14 +39599,14 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->precomputed_collocations = ((PyObject *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":368
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":369
  *         # algorithmic parameters and settings
  *         self.precomputed_collocations = {}
  *         self.precomputed_index = {}             # <<<<<<<<<<<<<<
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations
  */
-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_2));
   __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->precomputed_index);
@@ -39654,7 +39614,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->precomputed_index = ((PyObject *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":369
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":370
  *         self.precomputed_collocations = {}
  *         self.precomputed_index = {}
  *         self.use_index = use_index             # <<<<<<<<<<<<<<
@@ -39663,7 +39623,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_index = __pyx_v_use_index;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":370
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":371
  *         self.precomputed_index = {}
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations             # <<<<<<<<<<<<<<
@@ -39672,14 +39632,14 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_collocations = __pyx_v_use_collocations;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":371
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":372
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations
  *         self.max_rank = {}             # <<<<<<<<<<<<<<
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank
  */
-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_2));
   __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->max_rank);
@@ -39687,7 +39647,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->max_rank = ((PyObject *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":372
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":373
  *         self.use_collocations = use_collocations
  *         self.max_rank = {}
  *         self.precompute_file = precompute_file             # <<<<<<<<<<<<<<
@@ -39700,7 +39660,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __Pyx_DECREF(__pyx_v_self->precompute_file);
   __pyx_v_self->precompute_file = __pyx_v_precompute_file;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":373
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":374
  *         self.max_rank = {}
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank             # <<<<<<<<<<<<<<
@@ -39709,7 +39669,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->precompute_rank = __pyx_v_precompute_rank;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":374
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":375
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank             # <<<<<<<<<<<<<<
@@ -39718,7 +39678,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->precompute_secondary_rank = __pyx_v_precompute_secondary_rank;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":375
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":376
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.use_baeza_yates = use_baeza_yates             # <<<<<<<<<<<<<<
@@ -39727,7 +39687,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_baeza_yates = __pyx_v_use_baeza_yates;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":376
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":377
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.use_baeza_yates = use_baeza_yates
  *         self.by_slack_factor = by_slack_factor             # <<<<<<<<<<<<<<
@@ -39736,7 +39696,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->by_slack_factor = __pyx_v_by_slack_factor;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":377
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":378
  *         self.use_baeza_yates = use_baeza_yates
  *         self.by_slack_factor = by_slack_factor
  *         self.tight_phrases = tight_phrases             # <<<<<<<<<<<<<<
@@ -39745,7 +39705,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->tight_phrases = __pyx_v_tight_phrases;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":379
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":380
  *         self.tight_phrases = tight_phrases
  * 
  *         if require_aligned_chunks:             # <<<<<<<<<<<<<<
@@ -39754,7 +39714,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   if (__pyx_v_require_aligned_chunks) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":381
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":382
  *         if require_aligned_chunks:
  *             # one condition is a stronger version of the other.
  *             self.require_aligned_chunks = self.require_aligned_terminal = True             # <<<<<<<<<<<<<<
@@ -39766,7 +39726,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
     goto __pyx_L7;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":382
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":383
  *             # one condition is a stronger version of the other.
  *             self.require_aligned_chunks = self.require_aligned_terminal = True
  *         elif require_aligned_terminal:             # <<<<<<<<<<<<<<
@@ -39775,7 +39735,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   if (__pyx_v_require_aligned_terminal) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":383
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":384
  *             self.require_aligned_chunks = self.require_aligned_terminal = True
  *         elif require_aligned_terminal:
  *             self.require_aligned_chunks = False             # <<<<<<<<<<<<<<
@@ -39784,7 +39744,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
     __pyx_v_self->require_aligned_chunks = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":384
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":385
  *         elif require_aligned_terminal:
  *             self.require_aligned_chunks = False
  *             self.require_aligned_terminal = True             # <<<<<<<<<<<<<<
@@ -39796,7 +39756,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":386
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":387
  *             self.require_aligned_terminal = True
  *         else:
  *             self.require_aligned_chunks = self.require_aligned_terminal = False             # <<<<<<<<<<<<<<
@@ -39808,7 +39768,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   __pyx_L7:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":389
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":390
  * 
  *         # diagnostics
  *         self.prev_norm_prefix = ()             # <<<<<<<<<<<<<<
@@ -39821,17 +39781,17 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __Pyx_DECREF(__pyx_v_self->prev_norm_prefix);
   __pyx_v_self->prev_norm_prefix = ((PyObject *)__pyx_empty_tuple);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":391
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":392
  *         self.prev_norm_prefix = ()
  * 
  *         self.findexes = IntList(initial_len=10)             # <<<<<<<<<<<<<<
  *         self.findexes1 = IntList(initial_len=10)
  * 
  */
-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_2));
-  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_int_10) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_int_10) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
   __Pyx_GIVEREF(__pyx_t_1);
@@ -39840,17 +39800,17 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->findexes = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":392
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":393
  * 
  *         self.findexes = IntList(initial_len=10)
  *         self.findexes1 = IntList(initial_len=10)             # <<<<<<<<<<<<<<
  * 
  *         # Online stats
  */
-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
-  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_int_10) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_int_10) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
   __Pyx_GIVEREF(__pyx_t_2);
@@ -39859,7 +39819,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->findexes1 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":397
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":398
  * 
  *         # True after data is added
  *         self.online = False             # <<<<<<<<<<<<<<
@@ -39868,21 +39828,21 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->online = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":400
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":401
  * 
  *         # Keep track of everything that can be sampled:
  *         self.samples_f = defaultdict(int)             # <<<<<<<<<<<<<<
  * 
  *         # Phrase counts
  */
-  __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyInt_Type))));
   PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyInt_Type))));
   __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyInt_Type))));
-  __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -39892,21 +39852,21 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_v_self->samples_f = __pyx_t_5;
   __pyx_t_5 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":403
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":404
  * 
  *         # Phrase counts
  *         self.phrases_f = defaultdict(int)             # <<<<<<<<<<<<<<
  *         self.phrases_e = defaultdict(int)
  *         self.phrases_fe = defaultdict(lambda: defaultdict(int))
  */
-  __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
-  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyInt_Type))));
   PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyInt_Type))));
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-  __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":404
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":405
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":405
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":406
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":409
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":410
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+  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":411
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":418
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":419
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":420
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":421
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":422
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":422
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":423
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":424
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":425
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":427
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":431
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":432
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":433
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":434
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":435
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":436
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":439
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":441
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":442
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  *         result = ()             # <<<<<<<<<<<<<<
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   __pyx_v_result = __pyx_empty_tuple;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":442
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":443
  *         # pattern is a tuple, which we must convert to a hiero Phrase
  *         result = ()
  *         arity = 0             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":443
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":444
  *         result = ()
  *         arity = 0
  *         for word_id in pattern:             # <<<<<<<<<<<<<<
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-      #endif
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-      #endif
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-          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":444
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":445
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+    __pyx_t_4 = PyObject_RichCompare(__pyx_v_word_id, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_4);
+    __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":445
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  *             else:
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+      __pyx_t_4 = PyNumber_Add(__pyx_v_arity, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":446
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":447
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+      __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_v_arity); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":448
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":449
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-      __pyx_t_4 = PyObject_GetItem(__pyx_v_self->fda->id2word, __pyx_v_word_id); if (!__pyx_t_4) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":449
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+    __pyx_t_4 = PyInt_FromLong(__pyx_v_new_id); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyNumber_Add(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":450
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":451
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+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":452
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  * 
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":455
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+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":456
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":457
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  *         patterns = []
  *         result = ()             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":457
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  *         result = ()
  *         arity = 0             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":458
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":459
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  *         arity = 0
  *         for word_id in pattern:             # <<<<<<<<<<<<<<
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-      #endif
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-      #endif
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-          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":459
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":484
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":485
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":485
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":486
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":487
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  *             return PhraseLocation(arr=arr, arr_low=0, arr_high=len(arr), num_subpatterns=phrase.arity()+1)
  *         return None             # <<<<<<<<<<<<<<
@@ -41681,7 +41746,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_10get_precomputed_collo
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":508
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":509
  * 
  * 
  *     cdef int* baeza_yates_helper(self, int low1, int high1, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -41727,7 +41792,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("baeza_yates_helper", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":521
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":522
  *         cdef Matching loc1, loc2
  * 
  *         result = <int*> malloc(0*sizeof(int*))             # <<<<<<<<<<<<<<
@@ -41736,7 +41801,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = ((int *)malloc((0 * (sizeof(int *)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":523
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":524
  *         result = <int*> malloc(0*sizeof(int*))
  * 
  *         d_first = 0             # <<<<<<<<<<<<<<
@@ -41745,7 +41810,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_d_first = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":524
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":525
  * 
  *         d_first = 0
  *         if high1 - low1 > high2 - low2:             # <<<<<<<<<<<<<<
@@ -41755,7 +41820,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_1 = ((__pyx_v_high1 - __pyx_v_low1) > (__pyx_v_high2 - __pyx_v_low2));
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":525
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":526
  *         d_first = 0
  *         if high1 - low1 > high2 - low2:
  *             d_first = 1             # <<<<<<<<<<<<<<
@@ -41767,7 +41832,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":529
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":530
  *         # First, check to see if we are at any of the recursive base cases
  *         # Case 1: one of the sets is empty
  *         if low1 >= high1 or low2 >= high2:             # <<<<<<<<<<<<<<
@@ -41783,7 +41848,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":530
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":531
  *         # Case 1: one of the sets is empty
  *         if low1 >= high1 or low2 >= high2:
  *             return result             # <<<<<<<<<<<<<<
@@ -41796,7 +41861,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":533
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":534
  * 
  *         # Case 2: sets are non-overlapping
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -41805,7 +41870,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, (__pyx_v_high1 - __pyx_v_step1), __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":534
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":535
  *         # Case 2: sets are non-overlapping
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -41814,7 +41879,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_low2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":535
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":536
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == -1:             # <<<<<<<<<<<<<<
@@ -41824,7 +41889,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == -1);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":536
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":537
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == -1:
  *             return result             # <<<<<<<<<<<<<<
@@ -41837,7 +41902,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":538
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":539
  *             return result
  * 
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -41846,7 +41911,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_low1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":539
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":540
  * 
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -41855,7 +41920,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, (__pyx_v_high2 - __pyx_v_step2), __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":540
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":541
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:             # <<<<<<<<<<<<<<
@@ -41865,7 +41930,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == 1);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":541
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":542
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:
  *             return result             # <<<<<<<<<<<<<<
@@ -41878,7 +41943,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L6:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":545
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":546
  *         # Case 3: query set and data set do not meet size mismatch constraints;
  *         # We use mergesort instead in this case
  *         qsetsize = (high1-low1) / step1             # <<<<<<<<<<<<<<
@@ -41888,15 +41953,15 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_4 = (__pyx_v_high1 - __pyx_v_low1);
   if (unlikely(__pyx_v_step1 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_step1 == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_4))) {
     PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_v_qsetsize = __Pyx_div_int(__pyx_t_4, __pyx_v_step1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":546
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":547
  *         # We use mergesort instead in this case
  *         qsetsize = (high1-low1) / step1
  *         dsetsize = (high2-low2) / step2             # <<<<<<<<<<<<<<
@@ -41906,15 +41971,15 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_4 = (__pyx_v_high2 - __pyx_v_low2);
   if (unlikely(__pyx_v_step2 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_step2 == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_4))) {
     PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_v_dsetsize = __Pyx_div_int(__pyx_t_4, __pyx_v_step2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":547
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":548
  *         qsetsize = (high1-low1) / step1
  *         dsetsize = (high2-low2) / step2
  *         if d_first:             # <<<<<<<<<<<<<<
@@ -41923,7 +41988,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   if (__pyx_v_d_first) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":548
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":549
  *         dsetsize = (high2-low2) / step2
  *         if d_first:
  *             tmp = qsetsize             # <<<<<<<<<<<<<<
@@ -41932,7 +41997,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_tmp = __pyx_v_qsetsize;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":549
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":550
  *         if d_first:
  *             tmp = qsetsize
  *             qsetsize = dsetsize             # <<<<<<<<<<<<<<
@@ -41941,7 +42006,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_qsetsize = __pyx_v_dsetsize;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":550
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":551
  *             tmp = qsetsize
  *             qsetsize = dsetsize
  *             dsetsize = tmp             # <<<<<<<<<<<<<<
@@ -41953,7 +42018,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L7:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":552
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":553
  *             dsetsize = tmp
  * 
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:             # <<<<<<<<<<<<<<
@@ -41964,12 +42029,12 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_6 = log(2.0);
   if (unlikely(__pyx_t_6 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "float division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_t_3 = ((__pyx_t_5 / __pyx_t_6) > __pyx_v_dsetsize);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":553
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":554
  * 
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:
  *             free(result)             # <<<<<<<<<<<<<<
@@ -41978,7 +42043,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     free(__pyx_v_result);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":554
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":555
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:
  *             free(result)
  *             return self.merge_helper(low1, high1, arr1, step1, low2, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, result_len)             # <<<<<<<<<<<<<<
@@ -41991,7 +42056,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L8:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":558
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":559
  *         # binary search.    There are two flavors, depending on
  *         # whether the queryset or dataset is first
  *         if d_first:             # <<<<<<<<<<<<<<
@@ -42000,7 +42065,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   if (__pyx_v_d_first) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":559
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":560
  *         # whether the queryset or dataset is first
  *         if d_first:
  *             med2 = median(low2, high2, step2)             # <<<<<<<<<<<<<<
@@ -42009,7 +42074,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2 = __pyx_f_3_sa_median(__pyx_v_low2, __pyx_v_high2, __pyx_v_step2);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":560
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":561
  *         if d_first:
  *             med2 = median(low2, high2, step2)
  *             assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42018,7 +42083,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_med2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":562
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":563
  *             assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  * 
  *             search_low = low1             # <<<<<<<<<<<<<<
@@ -42027,7 +42092,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_low = __pyx_v_low1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":563
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":564
  * 
  *             search_low = low1
  *             search_high = high1             # <<<<<<<<<<<<<<
@@ -42036,7 +42101,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_high = __pyx_v_high1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":564
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":565
  *             search_low = low1
  *             search_high = high1
  *             while search_low < search_high:             # <<<<<<<<<<<<<<
@@ -42047,7 +42112,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_search_low < __pyx_v_search_high);
       if (!__pyx_t_3) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":565
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":566
  *             search_high = high1
  *             while search_low < search_high:
  *                 med1 = median(search_low, search_high, step1)             # <<<<<<<<<<<<<<
@@ -42056,7 +42121,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1 = __pyx_f_3_sa_median(__pyx_v_search_low, __pyx_v_search_high, __pyx_v_step1);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":566
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":567
  *             while search_low < search_high:
  *                 med1 = median(search_low, search_high, step1)
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)             # <<<<<<<<<<<<<<
@@ -42065,7 +42130,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_find_comparable_matchings(__pyx_v_low1, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med1, (&__pyx_v_med1_minus), (&__pyx_v_med1_plus));
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":567
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":568
  *                 med1 = median(search_low, search_high, step1)
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -42074,7 +42139,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings_set(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":570
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":571
  *                 if comparison == -1:
  *                     search_low = med1_plus
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -42083,7 +42148,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       switch (__pyx_v_comparison) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":568
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":569
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -42092,7 +42157,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case -1:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":569
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":570
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:
  *                     search_low = med1_plus             # <<<<<<<<<<<<<<
@@ -42102,7 +42167,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_v_search_low = __pyx_v_med1_plus;
         break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":570
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":571
  *                 if comparison == -1:
  *                     search_low = med1_plus
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -42111,7 +42176,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case 1:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":571
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":572
  *                     search_low = med1_plus
  *                 elif comparison == 1:
  *                     search_high = med1_minus             # <<<<<<<<<<<<<<
@@ -42122,7 +42187,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         break;
         default:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":573
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":574
  *                     search_high = med1_minus
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -42138,7 +42203,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":575
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":576
  *                     break
  *         else:
  *             med1 = median(low1, high1, step1)             # <<<<<<<<<<<<<<
@@ -42147,7 +42212,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med1 = __pyx_f_3_sa_median(__pyx_v_low1, __pyx_v_high1, __pyx_v_step1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":576
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":577
  *         else:
  *             med1 = median(low1, high1, step1)
  *             find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)             # <<<<<<<<<<<<<<
@@ -42156,7 +42221,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_f_3_sa_find_comparable_matchings(__pyx_v_low1, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med1, (&__pyx_v_med1_minus), (&__pyx_v_med1_plus));
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":578
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":579
  *             find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  * 
  *             search_low = low2             # <<<<<<<<<<<<<<
@@ -42165,7 +42230,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_low = __pyx_v_low2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":579
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":580
  * 
  *             search_low = low2
  *             search_high = high2             # <<<<<<<<<<<<<<
@@ -42174,7 +42239,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_high = __pyx_v_high2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":580
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":581
  *             search_low = low2
  *             search_high = high2
  *             while search_low < search_high:             # <<<<<<<<<<<<<<
@@ -42185,7 +42250,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_search_low < __pyx_v_search_high);
       if (!__pyx_t_3) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":581
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":582
  *             search_high = high2
  *             while search_low < search_high:
  *                 med2 = median(search_low, search_high, step2)             # <<<<<<<<<<<<<<
@@ -42194,7 +42259,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med2 = __pyx_f_3_sa_median(__pyx_v_search_low, __pyx_v_search_high, __pyx_v_step2);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":582
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":583
  *             while search_low < search_high:
  *                 med2 = median(search_low, search_high, step2)
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42203,7 +42268,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_med2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":583
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":584
  *                 med2 = median(search_low, search_high, step2)
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -42212,7 +42277,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings_set(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":586
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":587
  *                 if comparison == -1:
  *                     search_high = med2
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -42221,7 +42286,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       switch (__pyx_v_comparison) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":584
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":585
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -42230,7 +42295,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case -1:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":585
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":586
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:
  *                     search_high = med2             # <<<<<<<<<<<<<<
@@ -42240,7 +42305,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_v_search_high = __pyx_v_med2;
         break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":586
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":587
  *                 if comparison == -1:
  *                     search_high = med2
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -42249,7 +42314,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case 1:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":587
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":588
  *                     search_high = med2
  *                 elif comparison == 1:
  *                     search_low = med2 + step2             # <<<<<<<<<<<<<<
@@ -42260,7 +42325,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         break;
         default:
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":589
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":590
  *                     search_low = med2 + step2
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -42275,7 +42340,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L9:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":591
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":592
  *                     break
  * 
  *         med_result_len = 0             # <<<<<<<<<<<<<<
@@ -42284,7 +42349,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_med_result_len = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":592
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":593
  * 
  *         med_result_len = 0
  *         med_result = <int*> malloc(0*sizeof(int*))             # <<<<<<<<<<<<<<
@@ -42293,7 +42358,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_med_result = ((int *)malloc((0 * (sizeof(int *)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":593
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":594
  *         med_result_len = 0
  *         med_result = <int*> malloc(0*sizeof(int*))
  *         if search_high > search_low:             # <<<<<<<<<<<<<<
@@ -42303,7 +42368,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (__pyx_v_search_high > __pyx_v_search_low);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":599
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":600
  *             # want to store the bindings for all of those elements.    We can
  *             # subsequently throw all of them away.
  *             med2_minus = med2             # <<<<<<<<<<<<<<
@@ -42312,7 +42377,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_minus = __pyx_v_med2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":600
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":601
  *             # subsequently throw all of them away.
  *             med2_minus = med2
  *             med2_plus = med2 + step2             # <<<<<<<<<<<<<<
@@ -42321,7 +42386,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_plus = (__pyx_v_med2 + __pyx_v_step2);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":601
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":602
  *             med2_minus = med2
  *             med2_plus = med2 + step2
  *             i1 = med1_minus             # <<<<<<<<<<<<<<
@@ -42330,7 +42395,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_i1 = __pyx_v_med1_minus;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":602
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":603
  *             med2_plus = med2 + step2
  *             i1 = med1_minus
  *             while i1 < med1_plus:             # <<<<<<<<<<<<<<
@@ -42341,7 +42406,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_i1 < __pyx_v_med1_plus);
       if (!__pyx_t_3) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":603
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":604
  *             i1 = med1_minus
  *             while i1 < med1_plus:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42350,7 +42415,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":604
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":605
  *             while i1 < med1_plus:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 while med2_minus-step2 >= low2:             # <<<<<<<<<<<<<<
@@ -42361,7 +42426,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = ((__pyx_v_med2_minus - __pyx_v_step2) >= __pyx_v_low2);
         if (!__pyx_t_3) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":605
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":606
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 while med2_minus-step2 >= low2:
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42370,7 +42435,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, (__pyx_v_med2_minus - __pyx_v_step2), __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":606
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":607
  *                 while med2_minus-step2 >= low2:
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)
  *                     if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) < 1:             # <<<<<<<<<<<<<<
@@ -42380,7 +42445,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) < 1);
         if (__pyx_t_3) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":607
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":608
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)
  *                     if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) < 1:
  *                         med2_minus = med2_minus - step2             # <<<<<<<<<<<<<<
@@ -42392,7 +42457,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":609
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":610
  *                         med2_minus = med2_minus - step2
  *                     else:
  *                         break             # <<<<<<<<<<<<<<
@@ -42405,7 +42470,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L18_break:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":610
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":611
  *                     else:
  *                         break
  *                 i2 = med2_minus             # <<<<<<<<<<<<<<
@@ -42414,7 +42479,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_i2 = __pyx_v_med2_minus;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":611
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":612
  *                         break
  *                 i2 = med2_minus
  *                 while i2 < high2:             # <<<<<<<<<<<<<<
@@ -42425,7 +42490,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_i2 < __pyx_v_high2);
         if (!__pyx_t_3) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":612
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":613
  *                 i2 = med2_minus
  *                 while i2 < high2:
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42434,7 +42499,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_i2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":613
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":614
  *                 while i2 < high2:
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -42443,7 +42508,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":614
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":615
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:             # <<<<<<<<<<<<<<
@@ -42453,7 +42518,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_comparison == 0);
         if (__pyx_t_3) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":616
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":617
  *                     if comparison == 0:
  *                         pass
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)             # <<<<<<<<<<<<<<
@@ -42465,7 +42530,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         __pyx_L22:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":617
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":618
  *                         pass
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)
  *                     if comparison == -1:             # <<<<<<<<<<<<<<
@@ -42475,7 +42540,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_comparison == -1);
         if (__pyx_t_3) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":618
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":619
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)
  *                     if comparison == -1:
  *                         break             # <<<<<<<<<<<<<<
@@ -42487,7 +42552,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         __pyx_L23:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":619
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":620
  *                     if comparison == -1:
  *                         break
  *                     i2 = i2 + step2             # <<<<<<<<<<<<<<
@@ -42498,7 +42563,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L21_break:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":620
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":621
  *                         break
  *                     i2 = i2 + step2
  *                 if i2 > med2_plus:             # <<<<<<<<<<<<<<
@@ -42508,7 +42573,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_i2 > __pyx_v_med2_plus);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":621
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":622
  *                     i2 = i2 + step2
  *                 if i2 > med2_plus:
  *                     med2_plus = i2             # <<<<<<<<<<<<<<
@@ -42520,7 +42585,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L24:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":622
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":623
  *                 if i2 > med2_plus:
  *                     med2_plus = i2
  *                 i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -42530,7 +42595,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_v_i1 = (__pyx_v_i1 + __pyx_v_step1);
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":624
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":625
  *                 i1 = i1 + step1
  * 
  *             tmp = med1_minus             # <<<<<<<<<<<<<<
@@ -42539,7 +42604,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_tmp = __pyx_v_med1_minus;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":625
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":626
  * 
  *             tmp = med1_minus
  *             med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -42548,7 +42613,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med1_minus = __pyx_v_med1_plus;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":626
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":627
  *             tmp = med1_minus
  *             med1_minus = med1_plus
  *             med1_plus = tmp             # <<<<<<<<<<<<<<
@@ -42560,7 +42625,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":629
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":630
  *         else:
  *             # No match; need to figure out the point of division in D and Q
  *             med2_minus = med2             # <<<<<<<<<<<<<<
@@ -42569,7 +42634,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_minus = __pyx_v_med2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":630
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":631
  *             # No match; need to figure out the point of division in D and Q
  *             med2_minus = med2
  *             med2_plus = med2             # <<<<<<<<<<<<<<
@@ -42578,7 +42643,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_plus = __pyx_v_med2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":631
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":632
  *             med2_minus = med2
  *             med2_plus = med2
  *             if d_first:             # <<<<<<<<<<<<<<
@@ -42587,7 +42652,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     if (__pyx_v_d_first) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":632
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":633
  *             med2_plus = med2
  *             if d_first:
  *                 med2_minus = med2_minus + step2             # <<<<<<<<<<<<<<
@@ -42596,7 +42661,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med2_minus = (__pyx_v_med2_minus + __pyx_v_step2);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":633
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":634
  *             if d_first:
  *                 med2_minus = med2_minus + step2
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -42606,7 +42671,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == -1);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":634
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":635
  *                 med2_minus = med2_minus + step2
  *                 if comparison == -1:
  *                     med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -42618,7 +42683,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L26:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":635
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":636
  *                 if comparison == -1:
  *                     med1_minus = med1_plus
  *                 if comparison == 1:             # <<<<<<<<<<<<<<
@@ -42628,7 +42693,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == 1);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":636
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":637
  *                     med1_minus = med1_plus
  *                 if comparison == 1:
  *                     med1_plus = med1_minus             # <<<<<<<<<<<<<<
@@ -42643,7 +42708,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":638
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":639
  *                     med1_plus = med1_minus
  *             else:
  *                 tmp = med1_minus             # <<<<<<<<<<<<<<
@@ -42652,7 +42717,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_tmp = __pyx_v_med1_minus;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":639
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":640
  *             else:
  *                 tmp = med1_minus
  *                 med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -42661,7 +42726,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1_minus = __pyx_v_med1_plus;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":640
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":641
  *                 tmp = med1_minus
  *                 med1_minus = med1_plus
  *                 med1_plus = tmp             # <<<<<<<<<<<<<<
@@ -42670,7 +42735,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1_plus = __pyx_v_tmp;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":641
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":642
  *                 med1_minus = med1_plus
  *                 med1_plus = tmp
  *                 if comparison == 1:             # <<<<<<<<<<<<<<
@@ -42680,7 +42745,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == 1);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":642
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":643
  *                 med1_plus = tmp
  *                 if comparison == 1:
  *                     med2_minus = med2_minus + step2             # <<<<<<<<<<<<<<
@@ -42689,7 +42754,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_v_med2_minus = (__pyx_v_med2_minus + __pyx_v_step2);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":643
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":644
  *                 if comparison == 1:
  *                     med2_minus = med2_minus + step2
  *                     med2_plus = med2_plus + step2             # <<<<<<<<<<<<<<
@@ -42705,7 +42770,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L14:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":645
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":646
  *                     med2_plus = med2_plus + step2
  * 
  *         low_result_len = 0             # <<<<<<<<<<<<<<
@@ -42714,7 +42779,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_low_result_len = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":646
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":647
  * 
  *         low_result_len = 0
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)             # <<<<<<<<<<<<<<
@@ -42723,7 +42788,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_low_result = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->baeza_yates_helper(__pyx_v_self, __pyx_v_low1, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, __pyx_v_low2, __pyx_v_med2_plus, __pyx_v_arr2, __pyx_v_step2, __pyx_v_offset_by_one, __pyx_v_len_last, __pyx_v_num_subpatterns, (&__pyx_v_low_result_len));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":647
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":648
  *         low_result_len = 0
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)
  *         high_result_len = 0             # <<<<<<<<<<<<<<
@@ -42732,7 +42797,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_high_result_len = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":648
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":649
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)
  *         high_result_len = 0
  *         high_result = self.baeza_yates_helper(med1_minus, high1, arr1, step1, med2_minus, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, &high_result_len)             # <<<<<<<<<<<<<<
@@ -42741,7 +42806,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_high_result = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->baeza_yates_helper(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med2_minus, __pyx_v_high2, __pyx_v_arr2, __pyx_v_step2, __pyx_v_offset_by_one, __pyx_v_len_last, __pyx_v_num_subpatterns, (&__pyx_v_high_result_len));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":650
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":651
  *         high_result = self.baeza_yates_helper(med1_minus, high1, arr1, step1, med2_minus, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, &high_result_len)
  * 
  *         result = extend_arr(result, result_len, low_result, low_result_len)             # <<<<<<<<<<<<<<
@@ -42750,7 +42815,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_low_result, __pyx_v_low_result_len);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":651
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":652
  * 
  *         result = extend_arr(result, result_len, low_result, low_result_len)
  *         result = extend_arr(result, result_len, med_result, med_result_len)             # <<<<<<<<<<<<<<
@@ -42759,7 +42824,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_med_result, __pyx_v_med_result_len);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":652
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":653
  *         result = extend_arr(result, result_len, low_result, low_result_len)
  *         result = extend_arr(result, result_len, med_result, med_result_len)
  *         result = extend_arr(result, result_len, high_result, high_result_len)             # <<<<<<<<<<<<<<
@@ -42768,7 +42833,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_high_result, __pyx_v_high_result_len);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":653
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":654
  *         result = extend_arr(result, result_len, med_result, med_result_len)
  *         result = extend_arr(result, result_len, high_result, high_result_len)
  *         free(low_result)             # <<<<<<<<<<<<<<
@@ -42777,7 +42842,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_low_result);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":654
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":655
  *         result = extend_arr(result, result_len, high_result, high_result_len)
  *         free(low_result)
  *         free(med_result)             # <<<<<<<<<<<<<<
@@ -42786,7 +42851,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_med_result);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":655
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":656
  *         free(low_result)
  *         free(med_result)
  *         free(high_result)             # <<<<<<<<<<<<<<
@@ -42795,7 +42860,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_high_result);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":657
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":658
  *         free(high_result)
  * 
  *         return result             # <<<<<<<<<<<<<<
@@ -42815,7 +42880,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":661
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":662
  * 
  * 
  *     cdef long compare_matchings_set(self, int i1_minus, int i1_plus, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -42834,7 +42899,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("compare_matchings_set", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":672
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":673
  *         cdef Matching* loc1
  * 
  *         loc1 = &l1_stack             # <<<<<<<<<<<<<<
@@ -42843,7 +42908,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
   __pyx_v_loc1 = (&__pyx_v_l1_stack);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":674
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":675
  *         loc1 = &l1_stack
  * 
  *         i1 = i1_minus             # <<<<<<<<<<<<<<
@@ -42852,7 +42917,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
   __pyx_v_i1 = __pyx_v_i1_minus;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":675
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":676
  * 
  *         i1 = i1_minus
  *         while i1 < i1_plus:             # <<<<<<<<<<<<<<
@@ -42863,7 +42928,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_i1 < __pyx_v_i1_plus);
     if (!__pyx_t_1) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":676
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":677
  *         i1 = i1_minus
  *         while i1 < i1_plus:
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -42872,7 +42937,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
     __pyx_f_3_sa_assign_matching(__pyx_v_loc1, __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":677
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":678
  *         while i1 < i1_plus:
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -42881,7 +42946,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
     __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, __pyx_v_loc1, __pyx_v_loc2, __pyx_v_offset_by_one, __pyx_v_len_last);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":678
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":679
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)
  *             if comparison == 0:             # <<<<<<<<<<<<<<
@@ -42891,7 +42956,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_comparison == 0);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":679
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":680
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)
  *             if comparison == 0:
  *                 prev_comparison = 0             # <<<<<<<<<<<<<<
@@ -42900,7 +42965,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
       __pyx_v_prev_comparison = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":680
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":681
  *             if comparison == 0:
  *                 prev_comparison = 0
  *                 break             # <<<<<<<<<<<<<<
@@ -42911,7 +42976,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
       goto __pyx_L5;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":681
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":682
  *                 prev_comparison = 0
  *                 break
  *             elif i1 == i1_minus:             # <<<<<<<<<<<<<<
@@ -42921,7 +42986,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_i1 == __pyx_v_i1_minus);
     if (__pyx_t_1) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":682
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":683
  *                 break
  *             elif i1 == i1_minus:
  *                 prev_comparison = comparison             # <<<<<<<<<<<<<<
@@ -42933,7 +42998,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":684
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":685
  *                 prev_comparison = comparison
  *             else:
  *                 if comparison != prev_comparison:             # <<<<<<<<<<<<<<
@@ -42943,7 +43008,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
       __pyx_t_1 = (__pyx_v_comparison != __pyx_v_prev_comparison);
       if (__pyx_t_1) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":685
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":686
  *             else:
  *                 if comparison != prev_comparison:
  *                     prev_comparison = 0             # <<<<<<<<<<<<<<
@@ -42952,7 +43017,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
         __pyx_v_prev_comparison = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":686
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":687
  *                 if comparison != prev_comparison:
  *                     prev_comparison = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -42966,7 +43031,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     }
     __pyx_L5:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":687
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":688
  *                     prev_comparison = 0
  *                     break
  *             i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -42977,7 +43042,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   }
   __pyx_L4_break:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":688
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":689
  *                     break
  *             i1 = i1 + step1
  *         return prev_comparison             # <<<<<<<<<<<<<<
@@ -42993,7 +43058,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":691
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":692
  * 
  * 
  *     cdef long compare_matchings(self, Matching* loc1, Matching* loc2, int offset_by_one, int len_last):             # <<<<<<<<<<<<<<
@@ -43011,7 +43076,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("compare_matchings", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":694
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":695
  *         cdef int i
  * 
  *         if loc1.sent_id > loc2.sent_id:             # <<<<<<<<<<<<<<
@@ -43021,7 +43086,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_1 = (__pyx_v_loc1->sent_id > __pyx_v_loc2->sent_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":695
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":696
  * 
  *         if loc1.sent_id > loc2.sent_id:
  *             return 1             # <<<<<<<<<<<<<<
@@ -43034,7 +43099,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":696
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":697
  *         if loc1.sent_id > loc2.sent_id:
  *             return 1
  *         if loc2.sent_id > loc1.sent_id:             # <<<<<<<<<<<<<<
@@ -43044,7 +43109,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_1 = (__pyx_v_loc2->sent_id > __pyx_v_loc1->sent_id);
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":697
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":698
  *             return 1
  *         if loc2.sent_id > loc1.sent_id:
  *             return -1             # <<<<<<<<<<<<<<
@@ -43057,7 +43122,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":699
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":700
  *             return -1
  * 
  *         if loc1.size == 1 and loc2.size == 1:             # <<<<<<<<<<<<<<
@@ -43073,7 +43138,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":700
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":701
  * 
  *         if loc1.size == 1 and loc2.size == 1:
  *             if loc2.arr[loc2.start] - loc1.arr[loc1.start] <= self.train_min_gap_size:             # <<<<<<<<<<<<<<
@@ -43083,7 +43148,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc2->arr[__pyx_v_loc2->start]) - (__pyx_v_loc1->arr[__pyx_v_loc1->start])) <= __pyx_v_self->train_min_gap_size);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":701
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":702
  *         if loc1.size == 1 and loc2.size == 1:
  *             if loc2.arr[loc2.start] - loc1.arr[loc1.start] <= self.train_min_gap_size:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -43098,7 +43163,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     goto __pyx_L5;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":703
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":704
  *                 return 1
  * 
  *         elif offset_by_one:             # <<<<<<<<<<<<<<
@@ -43107,7 +43172,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
  */
   if (__pyx_v_offset_by_one) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":704
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":705
  * 
  *         elif offset_by_one:
  *             for i from 1 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -43117,7 +43182,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_4 = __pyx_v_loc1->size;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":705
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":706
  *         elif offset_by_one:
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:             # <<<<<<<<<<<<<<
@@ -43127,7 +43192,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) > (__pyx_v_loc2->arr[((__pyx_v_loc2->start + __pyx_v_i) - 1)]));
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":706
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":707
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:
  *                     return 1             # <<<<<<<<<<<<<<
@@ -43140,7 +43205,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       }
       __pyx_L9:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":707
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":708
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i-1]:             # <<<<<<<<<<<<<<
@@ -43150,7 +43215,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) < (__pyx_v_loc2->arr[((__pyx_v_loc2->start + __pyx_v_i) - 1)]));
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":708
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":709
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i-1]:
  *                     return -1             # <<<<<<<<<<<<<<
@@ -43167,7 +43232,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":711
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":712
  * 
  *         else:
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:             # <<<<<<<<<<<<<<
@@ -43177,7 +43242,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc1->arr[__pyx_v_loc1->start]) + 1) > (__pyx_v_loc2->arr[__pyx_v_loc2->start]));
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":712
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":713
  *         else:
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -43190,7 +43255,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     }
     __pyx_L11:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":713
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":714
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:
  *                 return 1
  *             if loc1.arr[loc1.start]+1 < loc2.arr[loc2.start]:             # <<<<<<<<<<<<<<
@@ -43200,7 +43265,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc1->arr[__pyx_v_loc1->start]) + 1) < (__pyx_v_loc2->arr[__pyx_v_loc2->start]));
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":714
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":715
  *                 return 1
  *             if loc1.arr[loc1.start]+1 < loc2.arr[loc2.start]:
  *                 return -1             # <<<<<<<<<<<<<<
@@ -43213,7 +43278,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     }
     __pyx_L12:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":716
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":717
  *                 return -1
  * 
  *             for i from 1 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -43223,7 +43288,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_4 = __pyx_v_loc1->size;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":717
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":718
  * 
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:             # <<<<<<<<<<<<<<
@@ -43233,7 +43298,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) > (__pyx_v_loc2->arr[(__pyx_v_loc2->start + __pyx_v_i)]));
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":718
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":719
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:
  *                     return 1             # <<<<<<<<<<<<<<
@@ -43246,7 +43311,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       }
       __pyx_L15:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":719
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":720
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i]:             # <<<<<<<<<<<<<<
@@ -43256,7 +43321,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) < (__pyx_v_loc2->arr[(__pyx_v_loc2->start + __pyx_v_i)]));
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":720
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":721
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i]:
  *                     return -1             # <<<<<<<<<<<<<<
@@ -43272,7 +43337,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L5:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":722
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":723
  *                     return -1
  * 
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -43282,7 +43347,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_3 = ((((__pyx_v_loc2->arr[(__pyx_v_loc2->end - 1)]) + __pyx_v_len_last) - (__pyx_v_loc1->arr[__pyx_v_loc1->start])) > __pyx_v_self->train_max_initial_size);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":723
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":724
  * 
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:
  *             return -1             # <<<<<<<<<<<<<<
@@ -43295,7 +43360,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L17:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":724
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":725
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:
  *             return -1
  *         return 0             # <<<<<<<<<<<<<<
@@ -43311,7 +43376,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":727
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":728
  * 
  * 
  *     cdef int* merge_helper(self, int low1, int high1, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -43335,7 +43400,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("merge_helper", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":735
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":736
  *         cdef Matching loc1, loc2
  * 
  *         result_len[0] = 0             # <<<<<<<<<<<<<<
@@ -43344,7 +43409,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   (__pyx_v_result_len[0]) = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":736
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":737
  * 
  *         result_len[0] = 0
  *         result = <int*> malloc(0*sizeof(int))             # <<<<<<<<<<<<<<
@@ -43353,7 +43418,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_result = ((int *)malloc((0 * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":738
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":739
  *         result = <int*> malloc(0*sizeof(int))
  * 
  *         i1 = low1             # <<<<<<<<<<<<<<
@@ -43362,7 +43427,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_i1 = __pyx_v_low1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":739
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":740
  * 
  *         i1 = low1
  *         i2 = low2             # <<<<<<<<<<<<<<
@@ -43371,7 +43436,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_i2 = __pyx_v_low2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":740
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":741
  *         i1 = low1
  *         i2 = low2
  *         while i1 < high1 and i2 < high2:             # <<<<<<<<<<<<<<
@@ -43388,7 +43453,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
     if (!__pyx_t_3) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":743
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":744
  * 
  *             # First, pop all unneeded loc2's off the stack
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -43397,7 +43462,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
     __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":744
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":745
  *             # First, pop all unneeded loc2's off the stack
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             while i2 < high2:             # <<<<<<<<<<<<<<
@@ -43408,7 +43473,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       __pyx_t_3 = (__pyx_v_i2 < __pyx_v_high2);
       if (!__pyx_t_3) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":745
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":746
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             while i2 < high2:
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -43417,7 +43482,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_i2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":746
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":747
  *             while i2 < high2:
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                 if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:             # <<<<<<<<<<<<<<
@@ -43427,7 +43492,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == 1);
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":747
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":748
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                 if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:
  *                     i2 = i2 + step2             # <<<<<<<<<<<<<<
@@ -43439,7 +43504,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":749
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":750
  *                     i2 = i2 + step2
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -43452,7 +43517,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
     __pyx_L6_break:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":752
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":753
  * 
  *             # Next: process all loc1's with the same starting val
  *             j1 = i1             # <<<<<<<<<<<<<<
@@ -43461,7 +43526,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
     __pyx_v_j1 = __pyx_v_i1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":753
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":754
  *             # Next: process all loc1's with the same starting val
  *             j1 = i1
  *             while i1 < high1 and arr1[j1] == arr1[i1]:             # <<<<<<<<<<<<<<
@@ -43478,7 +43543,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
       if (!__pyx_t_2) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":754
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":755
  *             j1 = i1
  *             while i1 < high1 and arr1[j1] == arr1[i1]:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -43487,7 +43552,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":755
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":756
  *             while i1 < high1 and arr1[j1] == arr1[i1]:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 j2 = i2             # <<<<<<<<<<<<<<
@@ -43496,7 +43561,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_v_j2 = __pyx_v_i2;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":756
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":757
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 j2 = i2
  *                 while j2 < high2:             # <<<<<<<<<<<<<<
@@ -43507,7 +43572,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         __pyx_t_2 = (__pyx_v_j2 < __pyx_v_high2);
         if (!__pyx_t_2) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":757
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":758
  *                 j2 = i2
  *                 while j2 < high2:
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -43516,7 +43581,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_j2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":758
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":759
  *                 while j2 < high2:
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -43525,7 +43590,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
         __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":759
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":760
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:             # <<<<<<<<<<<<<<
@@ -43535,7 +43600,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         __pyx_t_2 = (__pyx_v_comparison == 0);
         if (__pyx_t_2) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":760
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":761
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:
  *                         result = append_combined_matching(result, &loc1, &loc2, offset_by_one, num_subpatterns, result_len)             # <<<<<<<<<<<<<<
@@ -43547,7 +43612,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         __pyx_L12:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":761
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":762
  *                     if comparison == 0:
  *                         result = append_combined_matching(result, &loc1, &loc2, offset_by_one, num_subpatterns, result_len)
  *                     if comparison == 1:             # <<<<<<<<<<<<<<
@@ -43560,7 +43625,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         __pyx_L13:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":763
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":764
  *                     if comparison == 1:
  *                         pass
  *                     if comparison == -1:             # <<<<<<<<<<<<<<
@@ -43570,7 +43635,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         __pyx_t_2 = (__pyx_v_comparison == -1);
         if (__pyx_t_2) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":764
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":765
  *                         pass
  *                     if comparison == -1:
  *                         break             # <<<<<<<<<<<<<<
@@ -43582,7 +43647,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":766
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":767
  *                         break
  *                     else:
  *                         j2 = j2 + step2             # <<<<<<<<<<<<<<
@@ -43595,7 +43660,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
       __pyx_L11_break:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":767
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":768
  *                     else:
  *                         j2 = j2 + step2
  *                 i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -43606,7 +43671,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":768
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":769
  *                         j2 = j2 + step2
  *                 i1 = i1 + step1
  *         return result             # <<<<<<<<<<<<<<
@@ -43622,7 +43687,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":771
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":772
  * 
  * 
  *     cdef void sort_phrase_loc(self, IntList arr, PhraseLocation loc, Phrase phrase):             # <<<<<<<<<<<<<<
@@ -43644,26 +43709,26 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("sort_phrase_loc", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":776
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":777
  *         cdef IntList result
  * 
  *         if phrase in self.precomputed_index:             # <<<<<<<<<<<<<<
  *             loc.arr = self.precomputed_index[phrase]
  *         else:
  */
-  __pyx_t_1 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_v_phrase), __pyx_v_self->precomputed_index, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":777
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":778
  * 
  *         if phrase in self.precomputed_index:
  *             loc.arr = self.precomputed_index[phrase]             # <<<<<<<<<<<<<<
  *         else:
  *             loc.arr = IntList(initial_len=loc.sa_high-loc.sa_low)
  */
-    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_3_sa_IntList))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_3_sa_IntList))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GIVEREF(__pyx_t_2);
     __Pyx_GOTREF(__pyx_v_loc->arr);
     __Pyx_DECREF(((PyObject *)__pyx_v_loc->arr));
@@ -43673,20 +43738,20 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":779
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":780
  *             loc.arr = self.precomputed_index[phrase]
  *         else:
  *             loc.arr = IntList(initial_len=loc.sa_high-loc.sa_low)             # <<<<<<<<<<<<<<
  *             veb = VEB(arr.len)
  *             for i from loc.sa_low <= i < loc.sa_high:
  */
-    __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(((PyObject *)__pyx_t_2));
-    __pyx_t_3 = PyInt_FromLong((__pyx_v_loc->sa_high - __pyx_v_loc->sa_low)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong((__pyx_v_loc->sa_high - __pyx_v_loc->sa_low)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
-    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
     __Pyx_GIVEREF(__pyx_t_3);
@@ -43695,27 +43760,27 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
     __pyx_v_loc->arr = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_3);
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":780
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":781
  *         else:
  *             loc.arr = IntList(initial_len=loc.sa_high-loc.sa_low)
  *             veb = VEB(arr.len)             # <<<<<<<<<<<<<<
  *             for i from loc.sa_low <= i < loc.sa_high:
  *                 veb._insert(arr.arr[i])
  */
-    __pyx_t_3 = PyInt_FromLong(__pyx_v_arr->len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong(__pyx_v_arr->len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
-    __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
     __Pyx_GIVEREF(__pyx_t_3);
     __pyx_t_3 = 0;
-    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_VEB)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_VEB)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
     __pyx_v_veb = ((struct __pyx_obj_3_sa_VEB *)__pyx_t_3);
     __pyx_t_3 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":781
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":782
  *             loc.arr = IntList(initial_len=loc.sa_high-loc.sa_low)
  *             veb = VEB(arr.len)
  *             for i from loc.sa_low <= i < loc.sa_high:             # <<<<<<<<<<<<<<
@@ -43725,7 +43790,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
     __pyx_t_4 = __pyx_v_loc->sa_high;
     for (__pyx_v_i = __pyx_v_loc->sa_low; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":782
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":783
  *             veb = VEB(arr.len)
  *             for i from loc.sa_low <= i < loc.sa_high:
  *                 veb._insert(arr.arr[i])             # <<<<<<<<<<<<<<
@@ -43735,7 +43800,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":783
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":784
  *             for i from loc.sa_low <= i < loc.sa_high:
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  *             i = veb.veb.min_val             # <<<<<<<<<<<<<<
@@ -43744,7 +43809,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":784
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":785
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  *             for j from 0 <= j < loc.sa_high-loc.sa_low:             # <<<<<<<<<<<<<<
@@ -43754,7 +43819,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":785
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":786
  *             i = veb.veb.min_val
  *             for j from 0 <= j < loc.sa_high-loc.sa_low:
  *                 loc.arr.arr[j] = i             # <<<<<<<<<<<<<<
@@ -43763,7 +43828,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":786
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":787
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@@ -43775,7 +43840,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":787
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":788
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@@ -43784,7 +43849,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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   __pyx_v_loc->arr_low = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":788
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":789
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  *         loc.arr_high = loc.arr.len             # <<<<<<<<<<<<<<
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":791
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":792
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  * 
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":798
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":799
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@@ -43849,21 +43914,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_result_len = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":800
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":801
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-  __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_suffix), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_suffix), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":801
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":802
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  *         if sym_isvar(suffix[0]):
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@@ -43875,7 +43940,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":803
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":804
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@@ -43886,34 +43951,34 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":805
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":806
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-  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_suffix), __pyx_n_s__getchunk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_suffix), __pyx_n_s__getchunk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_suffix), __pyx_n_s__arity); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":807
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":808
  *         len_last = len(suffix.getchunk(suffix.arity()))
  * 
  *         if prefix_loc.arr is None:             # <<<<<<<<<<<<<<
@@ -43923,7 +43988,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __pyx_t_7 = (((PyObject *)__pyx_v_prefix_loc->arr) == Py_None);
   if (__pyx_t_7) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":808
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":809
  * 
  *         if prefix_loc.arr is None:
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@@ -43938,7 +44003,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   }
   __pyx_L4:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":809
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":810
  *         if prefix_loc.arr is None:
  *             self.sort_phrase_loc(self.fsa.sa, prefix_loc, prefix)
  *         arr1 = prefix_loc.arr             # <<<<<<<<<<<<<<
@@ -43948,7 +44013,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __Pyx_INCREF(((PyObject *)__pyx_v_prefix_loc->arr));
   __pyx_v_arr1 = __pyx_v_prefix_loc->arr;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":810
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":811
  *             self.sort_phrase_loc(self.fsa.sa, prefix_loc, prefix)
  *         arr1 = prefix_loc.arr
  *         low1 = prefix_loc.arr_low             # <<<<<<<<<<<<<<
@@ -43957,7 +44022,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
   __pyx_v_low1 = __pyx_v_prefix_loc->arr_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":811
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":812
  *         arr1 = prefix_loc.arr
  *         low1 = prefix_loc.arr_low
  *         high1 = prefix_loc.arr_high             # <<<<<<<<<<<<<<
@@ -43966,7 +44031,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
   __pyx_v_high1 = __pyx_v_prefix_loc->arr_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":812
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":813
  *         low1 = prefix_loc.arr_low
  *         high1 = prefix_loc.arr_high
  *         step1 = prefix_loc.num_subpatterns             # <<<<<<<<<<<<<<
@@ -43975,7 +44040,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
   __pyx_v_step1 = __pyx_v_prefix_loc->num_subpatterns;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":814
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":815
  *         step1 = prefix_loc.num_subpatterns
  * 
  *         if suffix_loc.arr is None:             # <<<<<<<<<<<<<<
@@ -43985,7 +44050,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __pyx_t_7 = (((PyObject *)__pyx_v_suffix_loc->arr) == Py_None);
   if (__pyx_t_7) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":815
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":816
  * 
  *         if suffix_loc.arr is None:
  *             self.sort_phrase_loc(self.fsa.sa, suffix_loc, suffix)             # <<<<<<<<<<<<<<
@@ -44000,7 +44065,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":816
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":817
  *         if suffix_loc.arr is None:
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  *         arr2 = suffix_loc.arr             # <<<<<<<<<<<<<<
@@ -44010,7 +44075,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __Pyx_INCREF(((PyObject *)__pyx_v_suffix_loc->arr));
   __pyx_v_arr2 = __pyx_v_suffix_loc->arr;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":817
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":818
  *             self.sort_phrase_loc(self.fsa.sa, suffix_loc, suffix)
  *         arr2 = suffix_loc.arr
  *         low2 = suffix_loc.arr_low             # <<<<<<<<<<<<<<
@@ -44019,7 +44084,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
   __pyx_v_low2 = __pyx_v_suffix_loc->arr_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":818
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":819
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  *         low2 = suffix_loc.arr_low
  *         high2 = suffix_loc.arr_high             # <<<<<<<<<<<<<<
@@ -44028,7 +44093,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_high2 = __pyx_v_suffix_loc->arr_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":819
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":820
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  *         high2 = suffix_loc.arr_high
  *         step2 = suffix_loc.num_subpatterns             # <<<<<<<<<<<<<<
@@ -44037,26 +44102,26 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_step2 = __pyx_v_suffix_loc->num_subpatterns;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":821
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":822
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  *         num_subpatterns = prefix.arity()+1             # <<<<<<<<<<<<<<
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-  __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_prefix), __pyx_n_s__arity); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_prefix), __pyx_n_s__arity); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_5 = PyNumber_Add(__pyx_t_4, __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_5); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_v_num_subpatterns = __pyx_t_3;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":823
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":824
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  *         if algorithm == MERGE:             # <<<<<<<<<<<<<<
@@ -44066,7 +44131,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":826
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":827
  *             result_ptr = self.merge_helper(low1, high1, arr1.arr, step1,
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@@ -44078,7 +44143,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":830
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":831
  *             result_ptr = self.baeza_yates_helper(low1, high1, arr1.arr, step1,
  *                                     low2, high2, arr2.arr, step2,
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@@ -44089,7 +44154,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":832
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":833
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@@ -44099,7 +44164,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":833
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":834
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  *         if result_len == 0:
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@@ -44108,7 +44173,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
     free(__pyx_v_result_ptr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":834
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":835
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@@ -44123,19 +44188,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   }
   /*else*/ {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":836
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":837
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-    __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":837
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":838
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  *             result = IntList()
  *             free(result.arr)             # <<<<<<<<<<<<<<
@@ -44144,7 +44209,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
     free(__pyx_v_result->arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":838
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":839
  *             result = IntList()
  *             free(result.arr)
  *             result.arr = result_ptr             # <<<<<<<<<<<<<<
@@ -44153,7 +44218,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
     __pyx_v_result->arr = __pyx_v_result_ptr;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":839
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":840
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  *             result.arr = result_ptr
  *             result.len = result_len             # <<<<<<<<<<<<<<
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     __pyx_v_result->len = __pyx_v_result_len;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":840
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":841
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  *             result.len = result_len
  *             result.size = result_len             # <<<<<<<<<<<<<<
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     __pyx_v_result->size = __pyx_v_result_len;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":841
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":842
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  *             result.size = result_len
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+    __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__arr_low), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyInt_FromLong(__pyx_v_result_len); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__arr_high), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyInt_FromLong(__pyx_v_num_subpatterns); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__arr), ((PyObject *)__pyx_v_result)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyInt_FromLong(__pyx_v_num_subpatterns); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__num_subpatterns), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__num_subpatterns), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -44217,7 +44282,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":843
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":844
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  *     cdef loc2str(self, PhraseLocation loc):             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":845
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":846
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   __pyx_v_result = ((PyObject *)__pyx_kp_s_116);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":846
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":847
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  *         i = 0             # <<<<<<<<<<<<<<
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  */
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":847
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":848
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  *         while i < loc.arr_high:             # <<<<<<<<<<<<<<
@@ -44270,20 +44335,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_loc2str(CYTHON_UNUSED st
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     if (!__pyx_t_1) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":848
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":849
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-    __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_117)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_117)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":849
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":850
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  *             for j from i <= j < i + loc.num_subpatterns:             # <<<<<<<<<<<<<<
@@ -44293,19 +44358,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_loc2str(CYTHON_UNUSED st
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":850
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":851
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+      __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_loc->arr), __pyx_v_j, sizeof(int), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -44313,20 +44378,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_loc2str(CYTHON_UNUSED st
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":851
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":852
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+    __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_59)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":852
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":853
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  *             i = i + loc.num_subpatterns             # <<<<<<<<<<<<<<
@@ -44336,20 +44401,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_loc2str(CYTHON_UNUSED st
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   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":853
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":854
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+  __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_118)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_v_result = __pyx_t_2;
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":854
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":855
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  *         result = result + "}"
  *         return result             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":856
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":857
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":860
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":861
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":861
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":862
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":862
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":863
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  *         suffix = suffix_node.phrase
  *         prefix_loc = prefix_node.phrase_location             # <<<<<<<<<<<<<<
  *         suffix_loc = suffix_node.phrase_location
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  */
-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":863
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":864
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":865
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":866
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+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_119); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":866
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":867
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   if (__pyx_t_4) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":867
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":868
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":869
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":870
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  * 
  *         if result is None:             # <<<<<<<<<<<<<<
@@ -44508,7 +44573,7 @@ static struct __pyx_obj_3_sa_PhraseLocation *__pyx_f_3_sa_23HieroCachingRuleFact
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":870
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":871
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  *         if result is None:
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     if (__pyx_v_self->use_baeza_yates) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":871
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":872
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+      __pyx_t_3 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->intersect_helper(__pyx_v_self, __pyx_v_prefix, __pyx_v_suffix, __pyx_v_prefix_loc, __pyx_v_suffix_loc, __pyx_v_3_sa_BAEZA_YATES); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":872
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":873
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@@ -44545,21 +44610,21 @@ static struct __pyx_obj_3_sa_PhraseLocation *__pyx_f_3_sa_23HieroCachingRuleFact
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":874
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":875
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+      __pyx_t_3 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->intersect_helper(__pyx_v_self, __pyx_v_prefix, __pyx_v_suffix, __pyx_v_prefix_loc, __pyx_v_suffix_loc, __pyx_v_3_sa_MERGE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":875
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":876
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":876
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":877
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       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__frontier)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__frontier);
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-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__res)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__res);
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+          __Pyx_RaiseArgtupleInvalid("advance", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords);
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-          __Pyx_RaiseArgtupleInvalid("advance", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("advance", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "advance") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("advance", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":878
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":880
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+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":881
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":882
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+    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_frontier); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      #endif
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-          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      #if CYTHON_COMPILING_IN_CPYTHON
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+          if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
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+          if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
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-      __pyx_t_8 = NULL;
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
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-      #if CYTHON_COMPILING_IN_CPYTHON
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+          else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
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       } else {
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+          if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
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-      __pyx_t_8 = NULL;
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+      if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":883
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+    __Pyx_GOTREF(__pyx_t_4);
+    __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":884
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+    __pyx_t_6 = PyNumber_Add(__pyx_v_i, __pyx_v_spanlen); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":886
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+    __pyx_t_13 = PyObject_Length(__pyx_v_fwords); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -44983,34 +45031,34 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_12advance(struct __pyx_
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":887
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":888
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+        __pyx_t_5 = PyNumber_Subtract(__pyx_v_toskip, __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_4 = PyNumber_Add(__pyx_v_pathlen, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":889
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-  __pyx_t_2 = PyList_GET_SIZE(((PyObject *)__pyx_v_nf)); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":890
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+    __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -45070,7 +45118,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_12advance(struct __pyx_
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+    __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":892
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":893
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-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__skip,&__pyx_n_s__i,&__pyx_n_s__spanlen,&__pyx_n_s__pathlen,&__pyx_n_s__fwords,&__pyx_n_s__next_states,&__pyx_n_s__reachable_buffer,0};
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@@ -45154,41 +45202,48 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_15get_all_nodes_isteps_
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       switch (pos_args) {
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-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__skip)) != 0)) kw_args--;
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+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
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-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__spanlen)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__spanlen);
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         else {
-          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
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-        if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pathlen)) != 0)) kw_args--;
+        values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pathlen);
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-          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 3); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 3); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  4:
-        if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords)) != 0)) kw_args--;
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         else {
-          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 4); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 4); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  5:
-        if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__next_states)) != 0)) kw_args--;
+        values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__next_states);
+        if (likely(values[5])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 5); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 5); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  6:
-        if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reachable_buffer)) != 0)) kw_args--;
+        values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reachable_buffer);
+        if (likely(values[6])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 6); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 6); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_all_nodes_isteps_away") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_all_nodes_isteps_away") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -45211,7 +45266,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_15get_all_nodes_isteps_
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-  __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-        #endif
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-            else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":908
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":909
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":909
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":910
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":912
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+        __pyx_t_4 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __pyx_t_11 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_11 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            #endif
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-            #endif
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-                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":913
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":914
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-            __pyx_t_13 = PyNumber_Add(__pyx_v_pathlen, __pyx_v_jump); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 914; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_13 = PyNumber_Add(__pyx_v_pathlen, __pyx_v_jump); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+            __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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             __pyx_t_10 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":915
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":916
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-            __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_v_newel), ((PyObject *)__pyx_v_frontier), Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(((PyObject *)__pyx_v_frontier), ((PyObject *)__pyx_v_newel)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":916
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":917
  *                             newel = (next_id,alt_id,pathlen+jump)
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-              __pyx_t_10 = PyNumber_Add(__pyx_v_pathlen, __pyx_v_jump); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_10 = PyNumber_Add(__pyx_v_pathlen, __pyx_v_jump); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              __pyx_t_13 = PyTuple_New(3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyTuple_New(3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              __pyx_t_14 = PyList_Append(__pyx_v_frontier, ((PyObject *)__pyx_t_13)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyList_Append(__pyx_v_frontier, ((PyObject *)__pyx_t_13)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -45727,7 +45762,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_14get_all_nodes_isteps_
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":917
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":918
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   PyObject *__pyx_v_dist = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fwords,&__pyx_n_s__ifrom,&__pyx_n_s__dist,0};
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@@ -45789,21 +45824,24 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_17reachable(PyObject *_
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       switch (pos_args) {
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-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords);
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-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ifrom)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ifrom);
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-          __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 919; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__dist)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__dist);
+        if (likely(values[2])) kw_args--;
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-          __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 919; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":920
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":921
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+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":921
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":922
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+  __pyx_t_2 = PyObject_Length(__pyx_v_fwords); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_t_1, Py_GE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_3);
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-  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":922
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":923
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+  __pyx_t_2 = PyObject_Length(__pyx_t_3); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -45935,24 +45974,16 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
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-      #if CYTHON_COMPILING_IN_CPYTHON
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-      #else
-      __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
     } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
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-      #if CYTHON_COMPILING_IN_CPYTHON
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-      #else
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-      #endif
+      __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
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       __pyx_t_3 = __pyx_t_5(__pyx_t_1);
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-          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -45962,53 +45993,54 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":924
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":925
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-            #endif
+            __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
           } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_6)) {
             if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
-            #if CYTHON_COMPILING_IN_CPYTHON
-            __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            #else
-            __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            #endif
+            __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
           } else {
             __pyx_t_3 = __pyx_t_11(__pyx_t_6);
             if (unlikely(!__pyx_t_3)) {
               if (PyErr_Occurred()) {
                 if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -46150,24 +46175,24 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
           __pyx_v_ifromchild = __pyx_t_3;
           __pyx_t_3 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":932
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":933
  *                 else:
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  *                         if (ifromchild not in ret):             # <<<<<<<<<<<<<<
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  */
-          __pyx_t_4 = (__Pyx_PySequence_Contains(__pyx_v_ifromchild, ((PyObject *)__pyx_v_ret), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_4 = (__Pyx_NegateNonNeg(PySequence_Contains(((PyObject *)__pyx_v_ret), __pyx_v_ifromchild))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           if (__pyx_t_4) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":933
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":934
  *                     for ifromchild in self.reachable(fwords,ifrom+fwords[ifrom][alt_id][2],dist-1):
  *                         if (ifromchild not in ret):
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  *         return ret
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+            __pyx_t_9 = PyList_Append(__pyx_v_ret, __pyx_v_ifromchild); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             goto __pyx_L11;
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@@ -46180,7 +46205,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":935
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":936
  *                             ret.append(ifromchild)
  * 
  *         return ret             # <<<<<<<<<<<<<<
@@ -46217,11 +46242,11 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_19shortest(PyObject *__
   PyObject *__pyx_v_fwords = 0;
   PyObject *__pyx_v_ifrom = 0;
   PyObject *__pyx_v_ito = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fwords,&__pyx_n_s__ifrom,&__pyx_n_s__ito,0};
   PyObject *__pyx_r = 0;
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   __Pyx_RefNannySetupContext("shortest (wrapper)", 0);
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-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fwords,&__pyx_n_s__ifrom,&__pyx_n_s__ito,0};
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@@ -46236,21 +46261,24 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_19shortest(PyObject *__
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwords);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ifrom)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ifrom);
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-          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ito)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ito);
+        if (likely(values[2])) kw_args--;
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-          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "shortest") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "shortest") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -46265,7 +46293,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_19shortest(PyObject *__
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-  __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":937
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":938
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":939
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":940
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@@ -46311,19 +46339,20 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_18shortest(struct __pyx
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   __pyx_v_min = __pyx_int_1000;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":940
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":941
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  *         if (ifrom > ito):             # <<<<<<<<<<<<<<
  *             return min
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-  __pyx_t_1 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_v_ito, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_v_ito, Py_GT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":941
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":942
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":942
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":943
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  *             return min
  *         if (ifrom == ito):             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_v_ito, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_v_ito, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":943
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":944
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  *         if (ifrom == ito):
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@@ -46365,41 +46395,41 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_18shortest(struct __pyx
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":944
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":945
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  *             return 0
  *         for alt_id in range(len(fwords[ifrom])):             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = PyObject_GetItem(__pyx_v_fwords, __pyx_v_ifrom); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetItem(__pyx_v_fwords, __pyx_v_ifrom); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":945
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-    __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__shortest); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__shortest); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_5 = PyObject_GetItem(__pyx_v_fwords, __pyx_v_ifrom); if (!__pyx_t_5) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_GetItem(__pyx_v_fwords, __pyx_v_ifrom); if (!__pyx_t_5) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_alt_id, sizeof(unsigned int)+1, PyLong_FromUnsignedLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
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+    __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_6, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_5);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-    __pyx_t_6 = PyNumber_Add(__pyx_v_ifrom, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PyNumber_Add(__pyx_v_ifrom, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
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-    __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_5);
     __Pyx_INCREF(__pyx_v_fwords);
     PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_fwords);
@@ -46410,7 +46440,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_18shortest(struct __pyx
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+    __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
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@@ -46418,38 +46448,39 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_18shortest(struct __pyx
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":946
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1039
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@@ -48323,36 +48364,36 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1040
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1041
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-        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-        if (__pyx_t_8) {
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+        __Pyx_GOTREF(__pyx_t_17);
+        __pyx_t_1 = PyObject_GetItem(__pyx_t_17, __pyx_cur_scope->__pyx_v_word_id); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(__pyx_t_1);
+        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1043
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@@ -48364,43 +48405,43 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1046
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-          __Pyx_GOTREF(__pyx_t_16);
-          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-          __Pyx_GIVEREF(__pyx_t_16);
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-          __pyx_t_16 = 0;
+          __Pyx_GIVEREF(__pyx_t_17);
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1048
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1050
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  *                     if node.suffix_link is None:             # <<<<<<<<<<<<<<
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-        __pyx_t_8 = (__pyx_t_16 == Py_None);
-        __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
-        if (__pyx_t_8) {
+        __pyx_t_17 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(__pyx_t_17);
+        __pyx_t_9 = (__pyx_t_17 == Py_None);
+        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1050
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1052
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  *                         # Current node is root; lookup required
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@@ -48412,54 +48453,54 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
         }
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1052
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-          __pyx_t_16 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __pyx_t_3 = PyObject_GetAttr(__pyx_t_16, __pyx_n_s__children); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          if (__pyx_t_8) {
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+          __Pyx_GOTREF(__pyx_t_1);
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+          __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1053
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-            __Pyx_GOTREF(__pyx_t_3);
-            __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
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-            __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-            if (__pyx_t_8) {
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+            __Pyx_GOTREF(__pyx_t_17);
+            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+            __Pyx_GOTREF(__pyx_t_1);
+            __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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+            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1055
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-              __Pyx_GOTREF(__pyx_t_3);
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-              __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+              __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__children); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __Pyx_GOTREF(__pyx_t_1);
+              if (PyObject_SetItem(__pyx_t_1, __pyx_cur_scope->__pyx_v_word_id, Py_None) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1056
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1058
  *                                 # Suffix link reports path is dead end
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@@ -48471,7 +48512,7 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
             }
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-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1059
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1061
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@@ -48485,18 +48526,18 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
           }
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1062
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1064
  *                         else:
  *                             #ERROR: We never get here
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-            __pyx_t_3 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            __Pyx_GOTREF(__pyx_t_3);
-            __Pyx_Raise(__pyx_t_3, 0, 0, 0);
-            __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-            {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_GOTREF(__pyx_t_1);
+            __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+            {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       }
       __pyx_L27:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1064
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1066
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       if (__pyx_cur_scope->__pyx_v_lookup_required) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1065
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1067
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         __pyx_cur_scope->__pyx_v_new_node = Py_None;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1066
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1068
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1080
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  *                             phrase_location = node.phrase_location
  *                             sa_range = self.fsa.lookup(sym_tostring(phrase[-1]), len(phrase)-1, phrase_location.sa_low, phrase_location.sa_high)
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  */
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-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1081
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             /*else*/ {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1083
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1088
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1085
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1086
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1088
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1093
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1090
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1095
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@@ -48799,95 +48895,95 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator4(__pyx_Gene
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1091
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1096
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1092
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-            __Pyx_GOTREF(__pyx_t_9);
-            __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
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+            __Pyx_GOTREF(__pyx_t_10);
+            __pyx_t_12 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__children); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+            __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+            __pyx_t_10 = PyObject_GetItem(__pyx_t_12, __pyx_cur_scope->__pyx_v_word_id); if (!__pyx_t_10) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_GOTREF(__pyx_t_10);
+            __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
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-            __Pyx_GIVEREF(__pyx_t_9);
-            __pyx_cur_scope->__pyx_v_suffix_link = __pyx_t_9;
-            __pyx_t_9 = 0;
+            __Pyx_GIVEREF(__pyx_t_10);
+            __pyx_cur_scope->__pyx_v_suffix_link = __pyx_t_10;
+            __pyx_t_10 = 0;
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1093
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1098
  *                         if node.suffix_link is not None:
  *                             suffix_link = node.suffix_link.children[word_id]
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-          __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(((PyObject *)__pyx_t_9));
-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase_location), ((PyObject *)__pyx_cur_scope->__pyx_v_phrase_location)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+          if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__phrase_location), ((PyObject *)__pyx_cur_scope->__pyx_v_phrase_location)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1094
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1099
  *                             suffix_link = node.suffix_link.children[word_id]
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  *                                 suffix_link=suffix_link,             # <<<<<<<<<<<<<<
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-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__suffix_link), __pyx_cur_scope->__pyx_v_suffix_link) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__suffix_link), __pyx_cur_scope->__pyx_v_suffix_link) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1095
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1100
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  *                                 suffix_link=suffix_link,
  *                                 phrase=hiero_phrase)             # <<<<<<<<<<<<<<
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-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase), ((PyObject *)__pyx_cur_scope->__pyx_v_hiero_phrase)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_11);
-          __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
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+          __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_12);
+          __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
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-          __Pyx_GIVEREF(__pyx_t_11);
-          __pyx_cur_scope->__pyx_v_new_node = __pyx_t_11;
-          __pyx_t_11 = 0;
+          __Pyx_GIVEREF(__pyx_t_12);
+          __pyx_cur_scope->__pyx_v_new_node = __pyx_t_12;
+          __pyx_t_12 = 0;
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1096
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1101
  *                                 suffix_link=suffix_link,
  *                                 phrase=hiero_phrase)
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-        __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
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+        __Pyx_GOTREF(__pyx_t_12);
+        if (PyObject_SetItem(__pyx_t_12, __pyx_cur_scope->__pyx_v_word_id, __pyx_cur_scope->__pyx_v_new_node) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1097
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1102
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1102
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1107
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-        __pyx_t_8 = (__pyx_cur_scope->__pyx_v_arity < __pyx_cur_scope->__pyx_v_self->max_nonterminals);
-        if (__pyx_t_8) {
+        __pyx_t_9 = (__pyx_cur_scope->__pyx_v_arity < __pyx_cur_scope->__pyx_v_self->max_nonterminals);
+        if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1103
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1108
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  *                         xcat_index = arity+1             # <<<<<<<<<<<<<<
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-          __pyx_t_11 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_arity + 1)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_11);
+          __pyx_t_12 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_arity + 1)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_12);
           __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_xcat_index);
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-          __pyx_cur_scope->__pyx_v_xcat_index = __pyx_t_11;
-          __pyx_t_11 = 0;
+          __Pyx_GIVEREF(__pyx_t_12);
+          __pyx_cur_scope->__pyx_v_xcat_index = __pyx_t_12;
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1104
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1109
  *                     if arity < self.max_nonterminals:
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  *                         xcat = sym_setindex(self.category, xcat_index)             # <<<<<<<<<<<<<<
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-          __pyx_cur_scope->__pyx_v_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_19);
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+          __pyx_cur_scope->__pyx_v_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_20);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1105
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1110
  *                         xcat_index = arity+1
  *                         xcat = sym_setindex(self.category, xcat_index)
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1106
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-          __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_is_shadow_path); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          if (__pyx_t_8) {
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1107
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1112
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-            __pyx_t_11 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_xcat_index, __pyx_int_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            __Pyx_GOTREF(__pyx_t_11);
+            __pyx_t_12 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_xcat_index, __pyx_int_1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_GOTREF(__pyx_t_12);
             __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_suffix_link_xcat_index);
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-            __pyx_t_11 = 0;
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+            __pyx_cur_scope->__pyx_v_suffix_link_xcat_index = __pyx_t_12;
+            __pyx_t_12 = 0;
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           __pyx_L39:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1108
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1113
  *                         if is_shadow_path:
  *                             suffix_link_xcat_index = xcat_index-1
  *                         suffix_link_xcat = sym_setindex(self.category, suffix_link_xcat_index)             # <<<<<<<<<<<<<<
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-          __pyx_t_19 = __Pyx_PyInt_AsInt(__pyx_cur_scope->__pyx_v_suffix_link_xcat_index); if (unlikely((__pyx_t_19 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __pyx_cur_scope->__pyx_v_suffix_link_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_19);
+          __pyx_t_20 = __Pyx_PyInt_AsInt(__pyx_cur_scope->__pyx_v_suffix_link_xcat_index); if (unlikely((__pyx_t_20 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_cur_scope->__pyx_v_suffix_link_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_20);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1109
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1114
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-          __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
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+          __Pyx_GOTREF(((PyObject *)__pyx_t_12));
+          __pyx_t_10 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_10);
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+          __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1110
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1115
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  *                         node.children[xcat] = ExtendedTrieNode(phrase_location=node.phrase_location,
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1119
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1120
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1121
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1122
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1123
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1126
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1127
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1128
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1161
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1162
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1163
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-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1165
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-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1173
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-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1208
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1214
  * 
  * 
  *     cdef int find_fixpoint(self,             # <<<<<<<<<<<<<<
@@ -51266,7 +51437,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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   __Pyx_RefNannySetupContext("find_fixpoint", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1223
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1229
  *         cdef int e_low_prev, e_high_prev, f_low_prev, f_high_prev, new_x, new_low_x, new_high_x
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  *         e_low[0] = e_in_low             # <<<<<<<<<<<<<<
@@ -51275,7 +51446,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   (__pyx_v_e_low[0]) = __pyx_v_e_in_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1224
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1230
  * 
  *         e_low[0] = e_in_low
  *         e_high[0] = e_in_high             # <<<<<<<<<<<<<<
@@ -51284,19 +51455,19 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   (__pyx_v_e_high[0]) = __pyx_v_e_in_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1225
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1231
  *         e_low[0] = e_in_low
  *         e_high[0] = e_in_high
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1226
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1232
  *         e_high[0] = e_in_high
  *         self.find_projection(f_low, f_high, f_links_low, f_links_high, e_low, e_high)
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@@ -51306,7 +51477,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   __pyx_t_3 = ((__pyx_v_e_low[0]) == -1);
   if (__pyx_t_3) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1232
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1238
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     goto __pyx_L3;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1233
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1239
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@@ -51334,7 +51505,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   }
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1234
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1240
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1235
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1241
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@@ -51353,7 +51524,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1236
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1242
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       if (__pyx_t_5) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1237
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1243
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@@ -51382,7 +51553,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1239
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1245
  *                     return 0
  * 
  *         if e_high[0] - e_low[0] > max_e_len:             # <<<<<<<<<<<<<<
@@ -51392,7 +51563,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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   if (__pyx_t_5) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1240
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1246
  * 
  *         if e_high[0] - e_low[0] > max_e_len:
  *             return 0             # <<<<<<<<<<<<<<
@@ -51404,7 +51575,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     goto __pyx_L6;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1241
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1247
  *         if e_high[0] - e_low[0] > max_e_len:
  *             return 0
  *         elif e_in_high != -1 and e_high[0] != e_in_high:             # <<<<<<<<<<<<<<
@@ -51420,7 +51591,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   }
   if (__pyx_t_4) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1242
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1248
  *             return 0
  *         elif e_in_high != -1 and e_high[0] != e_in_high:
  *             if e_high[0] - e_in_high < min_ex_size:             # <<<<<<<<<<<<<<
@@ -51430,7 +51601,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1243
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1249
  *         elif e_in_high != -1 and e_high[0] != e_in_high:
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  *                 e_high[0] = e_in_high + min_ex_size             # <<<<<<<<<<<<<<
@@ -51439,7 +51610,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
       (__pyx_v_e_high[0]) = (__pyx_v_e_in_high + __pyx_v_min_ex_size);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1244
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1250
  *             if e_high[0] - e_in_high < min_ex_size:
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  *                 if e_high[0] > e_sent_len:             # <<<<<<<<<<<<<<
@@ -51449,7 +51620,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1245
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1251
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   }
   __pyx_L6:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1247
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1253
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  */
   (__pyx_v_f_back_low[0]) = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1248
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1254
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  *         f_back_high[0] = -1             # <<<<<<<<<<<<<<
@@ -51486,7 +51657,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   (__pyx_v_f_back_high[0]) = -1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1249
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1255
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  *         f_back_high[0] = -1
  *         f_low_prev = f_low             # <<<<<<<<<<<<<<
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1250
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1256
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1251
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1257
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  *         f_high_prev = f_high
  *         new_x = 0             # <<<<<<<<<<<<<<
@@ -51514,7 +51685,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_x = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1252
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1258
  *         f_high_prev = f_high
  *         new_x = 0
  *         new_low_x = 0             # <<<<<<<<<<<<<<
@@ -51523,7 +51694,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_low_x = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1253
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1259
  *         new_x = 0
  *         new_low_x = 0
  *         new_high_x = 0             # <<<<<<<<<<<<<<
@@ -51532,7 +51703,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_high_x = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1255
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1261
  *         new_high_x = 0
  * 
  *         while True:             # <<<<<<<<<<<<<<
@@ -51542,7 +51713,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   while (1) {
     if (!1) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1257
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1263
  *         while True:
  * 
  *             if f_back_low[0] == -1:             # <<<<<<<<<<<<<<
@@ -51552,45 +51723,45 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = ((__pyx_v_f_back_low[0]) == -1);
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1258
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1264
  * 
  *             if f_back_low[0] == -1:
  *                 self.find_projection(e_low[0], e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       goto __pyx_L11;
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1260
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1266
  *                 self.find_projection(e_low[0], e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  * 
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), __pyx_v_e_low_prev, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), __pyx_v_e_low_prev, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1261
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1267
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  * 
  *             if f_back_low[0] > f_low:
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_e_high_prev, (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_e_high_prev, (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     }
     __pyx_L11:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1263
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1269
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  * 
  *             if f_back_low[0] > f_low:             # <<<<<<<<<<<<<<
@@ -51600,7 +51771,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = ((__pyx_v_f_back_low[0]) > __pyx_v_f_low);
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1264
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1270
  * 
  *             if f_back_low[0] > f_low:
  *                 f_back_low[0] = f_low             # <<<<<<<<<<<<<<
@@ -51612,35 +51783,36 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L12:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1266
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1272
  *                 f_back_low[0] = f_low
  * 
  *             if f_back_high[0] < f_high:             # <<<<<<<<<<<<<<
  *                 f_back_high[0] = f_high
  * 
  */
-    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_v_f_high, Py_LT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_v_f_high, Py_LT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1267
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1273
  * 
  *             if f_back_high[0] < f_high:
  *                 f_back_high[0] = f_high             # <<<<<<<<<<<<<<
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:
  */
-      __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       (__pyx_v_f_back_high[0]) = __pyx_t_1;
       goto __pyx_L13;
     }
     __pyx_L13:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1269
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1275
  *                 f_back_high[0] = f_high
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:             # <<<<<<<<<<<<<<
@@ -51656,7 +51828,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1270
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1276
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -51669,7 +51841,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L14:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1272
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1278
  *                 return 1
  * 
  *             if allow_low_x == 0 and f_back_low[0] < f_low:             # <<<<<<<<<<<<<<
@@ -51685,7 +51857,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1274
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1280
  *             if allow_low_x == 0 and f_back_low[0] < f_low:
  *                 # FAIL: f phrase is not tight
  *                 return 0             # <<<<<<<<<<<<<<
@@ -51698,7 +51870,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L15:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1276
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1282
  *                 return 0
  * 
  *             if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -51708,7 +51880,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_5 = (((__pyx_v_f_back_high[0]) - (__pyx_v_f_back_low[0])) > __pyx_v_max_f_len);
     if (__pyx_t_5) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1278
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1284
  *             if f_back_high[0] - f_back_low[0] > max_f_len:
  *                 # FAIL: f back projection is too wide
  *                 return 0             # <<<<<<<<<<<<<<
@@ -51721,7 +51893,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L16:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1280
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1286
  *                 return 0
  * 
  *             if allow_high_x == 0 and f_back_high[0] > f_high:             # <<<<<<<<<<<<<<
@@ -51730,11 +51902,12 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_t_5 = (__pyx_v_allow_high_x == 0);
     if (__pyx_t_5) {
-      __pyx_t_6 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
-      __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_v_f_high, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_v_f_high, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-      __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       __pyx_t_4 = __pyx_t_3;
     } else {
@@ -51742,7 +51915,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1282
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1288
  *             if allow_high_x == 0 and f_back_high[0] > f_high:
  *                 # FAIL: extension on high side not allowed
  *                 return 0             # <<<<<<<<<<<<<<
@@ -51755,7 +51928,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L17:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1284
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1290
  *                 return 0
  * 
  *             if f_low != f_back_low[0]:             # <<<<<<<<<<<<<<
@@ -51765,7 +51938,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = (__pyx_v_f_low != (__pyx_v_f_back_low[0]));
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1285
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1291
  * 
  *             if f_low != f_back_low[0]:
  *                 if new_low_x == 0:             # <<<<<<<<<<<<<<
@@ -51775,7 +51948,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       __pyx_t_4 = (__pyx_v_new_low_x == 0);
       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1286
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1292
  *             if f_low != f_back_low[0]:
  *                 if new_low_x == 0:
  *                     if new_x >= max_new_x:             # <<<<<<<<<<<<<<
@@ -51785,7 +51958,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = (__pyx_v_new_x >= __pyx_v_max_new_x);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1288
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1294
  *                     if new_x >= max_new_x:
  *                         # FAIL: extension required on low side violates max # of gaps
  *                         return 0             # <<<<<<<<<<<<<<
@@ -51798,7 +51971,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1290
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1296
  *                         return 0
  *                     else:
  *                         new_x = new_x + 1             # <<<<<<<<<<<<<<
@@ -51807,7 +51980,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
           __pyx_v_new_x = (__pyx_v_new_x + 1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1291
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1297
  *                     else:
  *                         new_x = new_x + 1
  *                         new_low_x = 1             # <<<<<<<<<<<<<<
@@ -51821,7 +51994,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       }
       __pyx_L19:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1292
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1298
  *                         new_x = new_x + 1
  *                         new_low_x = 1
  *                 if f_low - f_back_low[0] < min_fx_size:             # <<<<<<<<<<<<<<
@@ -51831,7 +52004,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       __pyx_t_4 = ((__pyx_v_f_low - (__pyx_v_f_back_low[0])) < __pyx_v_min_fx_size);
       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1293
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1299
  *                         new_low_x = 1
  *                 if f_low - f_back_low[0] < min_fx_size:
  *                     f_back_low[0] = f_low - min_fx_size             # <<<<<<<<<<<<<<
@@ -51840,7 +52013,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
         (__pyx_v_f_back_low[0]) = (__pyx_v_f_low - __pyx_v_min_fx_size);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1294
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1300
  *                 if f_low - f_back_low[0] < min_fx_size:
  *                     f_back_low[0] = f_low - min_fx_size
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -51850,7 +52023,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = (((__pyx_v_f_back_high[0]) - (__pyx_v_f_back_low[0])) > __pyx_v_max_f_len);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1296
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1302
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  *                         # FAIL: extension required on low side violates max initial length
  *                         return 0             # <<<<<<<<<<<<<<
@@ -51863,7 +52036,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         }
         __pyx_L22:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1297
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1303
  *                         # FAIL: extension required on low side violates max initial length
  *                         return 0
  *                     if f_back_low[0] < 0:             # <<<<<<<<<<<<<<
@@ -51873,7 +52046,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = ((__pyx_v_f_back_low[0]) < 0);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1299
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1305
  *                     if f_back_low[0] < 0:
  *                         # FAIL: extension required on low side violates sentence boundary
  *                         return 0             # <<<<<<<<<<<<<<
@@ -51892,22 +52065,23 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L18:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1301
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1307
  *                         return 0
  * 
  *             if f_high != f_back_high[0]:             # <<<<<<<<<<<<<<
  *                 if new_high_x == 0:
  *                     if new_x >= max_new_x:
  */
-    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_6 = PyObject_RichCompare(__pyx_v_f_high, __pyx_t_2, Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PyObject_RichCompare(__pyx_v_f_high, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     if (__pyx_t_4) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1302
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1308
  * 
  *             if f_high != f_back_high[0]:
  *                 if new_high_x == 0:             # <<<<<<<<<<<<<<
@@ -51917,7 +52091,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       __pyx_t_4 = (__pyx_v_new_high_x == 0);
       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1303
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1309
  *             if f_high != f_back_high[0]:
  *                 if new_high_x == 0:
  *                     if new_x >= max_new_x:             # <<<<<<<<<<<<<<
@@ -51927,7 +52101,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = (__pyx_v_new_x >= __pyx_v_max_new_x);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1305
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1311
  *                     if new_x >= max_new_x:
  *                         # FAIL: extension required on high side violates max # of gaps
  *                         return 0             # <<<<<<<<<<<<<<
@@ -51940,7 +52114,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         }
         /*else*/ {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1307
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1313
  *                         return 0
  *                     else:
  *                         new_x = new_x + 1             # <<<<<<<<<<<<<<
@@ -51949,7 +52123,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
           __pyx_v_new_x = (__pyx_v_new_x + 1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1308
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1314
  *                     else:
  *                         new_x = new_x + 1
  *                         new_high_x = 1             # <<<<<<<<<<<<<<
@@ -51963,44 +52137,45 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       }
       __pyx_L25:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1309
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1315
  *                         new_x = new_x + 1
  *                         new_high_x = 1
  *                 if f_back_high[0] - f_high < min_fx_size:             # <<<<<<<<<<<<<<
  *                     f_back_high[0] = f_high + min_fx_size
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  */
-      __pyx_t_6 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
-      __pyx_t_2 = PyNumber_Subtract(__pyx_t_6, __pyx_v_f_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyNumber_Subtract(__pyx_t_6, __pyx_v_f_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-      __pyx_t_6 = PyInt_FromLong(__pyx_v_min_fx_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyInt_FromLong(__pyx_v_min_fx_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
-      __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_7);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-      __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1310
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1316
  *                         new_high_x = 1
  *                 if f_back_high[0] - f_high < min_fx_size:
  *                     f_back_high[0] = f_high + min_fx_size             # <<<<<<<<<<<<<<
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  *                         # FAIL: extension required on high side violates max initial length
  */
-        __pyx_t_7 = PyInt_FromLong(__pyx_v_min_fx_size); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_7 = PyInt_FromLong(__pyx_v_min_fx_size); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_7);
-        __pyx_t_6 = PyNumber_Add(__pyx_v_f_high, __pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PyNumber_Add(__pyx_v_f_high, __pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_6);
         __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
-        __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
         (__pyx_v_f_back_high[0]) = __pyx_t_1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1311
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1317
  *                 if f_back_high[0] - f_high < min_fx_size:
  *                     f_back_high[0] = f_high + min_fx_size
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -52010,7 +52185,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = (((__pyx_v_f_back_high[0]) - (__pyx_v_f_back_low[0])) > __pyx_v_max_f_len);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1313
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1319
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  *                         # FAIL: extension required on high side violates max initial length
  *                         return 0             # <<<<<<<<<<<<<<
@@ -52023,7 +52198,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         }
         __pyx_L28:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1314
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1320
  *                         # FAIL: extension required on high side violates max initial length
  *                         return 0
  *                     if f_back_high[0] > f_sent_len:             # <<<<<<<<<<<<<<
@@ -52033,7 +52208,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = ((__pyx_v_f_back_high[0]) > __pyx_v_f_sent_len);
         if (__pyx_t_4) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1316
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1322
  *                     if f_back_high[0] > f_sent_len:
  *                         # FAIL: extension required on high side violates sentence boundary
  *                         return 0             # <<<<<<<<<<<<<<
@@ -52052,7 +52227,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L24:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1318
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1324
  *                         return 0
  * 
  *             e_low_prev = e_low[0]             # <<<<<<<<<<<<<<
@@ -52061,7 +52236,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_e_low_prev = (__pyx_v_e_low[0]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1319
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1325
  * 
  *             e_low_prev = e_low[0]
  *             e_high_prev = e_high[0]             # <<<<<<<<<<<<<<
@@ -52070,29 +52245,29 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_e_high_prev = (__pyx_v_e_high[0]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1321
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1327
  *             e_high_prev = e_high[0]
  * 
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  */
-    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_f_back_low[0]), __pyx_v_f_low_prev, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_f_back_low[0]), __pyx_v_f_low_prev, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1322
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1328
  * 
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1
  */
-    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_f_high_prev, (__pyx_v_f_back_high[0]), __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_f_high_prev, (__pyx_v_f_back_high[0]), __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1323
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1329
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:             # <<<<<<<<<<<<<<
@@ -52108,7 +52283,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1324
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1330
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -52121,7 +52296,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L30:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1325
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1331
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1
  *             if allow_arbitrary_x == 0:             # <<<<<<<<<<<<<<
@@ -52131,7 +52306,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_3 = (__pyx_v_allow_arbitrary_x == 0);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1327
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1333
  *             if allow_arbitrary_x == 0:
  *                 # FAIL: arbitrary expansion not permitted
  *                 return 0             # <<<<<<<<<<<<<<
@@ -52144,7 +52319,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L31:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1328
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1334
  *                 # FAIL: arbitrary expansion not permitted
  *                 return 0
  *             if e_high[0] - e_low[0] > max_e_len:             # <<<<<<<<<<<<<<
@@ -52154,7 +52329,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_3 = (((__pyx_v_e_high[0]) - (__pyx_v_e_low[0])) > __pyx_v_max_e_len);
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1330
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1336
  *             if e_high[0] - e_low[0] > max_e_len:
  *                 # FAIL: re-projection violates sentence max phrase length
  *                 return 0             # <<<<<<<<<<<<<<
@@ -52167,7 +52342,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L32:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1331
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1337
  *                 # FAIL: re-projection violates sentence max phrase length
  *                 return 0
  *             f_low_prev = f_back_low[0]             # <<<<<<<<<<<<<<
@@ -52176,7 +52351,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_f_low_prev = (__pyx_v_f_back_low[0]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1332
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1338
  *                 return 0
  *             f_low_prev = f_back_low[0]
  *             f_high_prev = f_back_high[0]             # <<<<<<<<<<<<<<
@@ -52199,7 +52374,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1335
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1341
  * 
  * 
  *     cdef find_projection(self, int in_low, int in_high, int* in_links_low, int* in_links_high,             # <<<<<<<<<<<<<<
@@ -52217,7 +52392,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("find_projection", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1338
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1344
  *                         int* out_low, int* out_high):
  *         cdef int i
  *         for i from in_low <= i < in_high:             # <<<<<<<<<<<<<<
@@ -52227,7 +52402,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   __pyx_t_1 = __pyx_v_in_high;
   for (__pyx_v_i = __pyx_v_in_low; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1339
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1345
  *         cdef int i
  *         for i from in_low <= i < in_high:
  *             if in_links_low[i] != -1:             # <<<<<<<<<<<<<<
@@ -52237,7 +52412,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
     __pyx_t_2 = ((__pyx_v_in_links_low[__pyx_v_i]) != -1);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1340
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1346
  *         for i from in_low <= i < in_high:
  *             if in_links_low[i] != -1:
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:             # <<<<<<<<<<<<<<
@@ -52253,7 +52428,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       if (__pyx_t_4) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1341
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1347
  *             if in_links_low[i] != -1:
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:
  *                     out_low[0] = in_links_low[i]             # <<<<<<<<<<<<<<
@@ -52265,7 +52440,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       __pyx_L6:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1342
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1348
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:
  *                     out_low[0] = in_links_low[i]
  *                 if out_high[0] == -1 or in_links_high[i] > out_high[0]:             # <<<<<<<<<<<<<<
@@ -52281,7 +52456,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       if (__pyx_t_3) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1343
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1349
  *                     out_low[0] = in_links_low[i]
  *                 if out_high[0] == -1 or in_links_high[i] > out_high[0]:
  *                     out_high[0] = in_links_high[i]             # <<<<<<<<<<<<<<
@@ -52303,7 +52478,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1346
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1352
  * 
  * 
  *     cdef int* int_arr_extend(self, int* arr, int* arr_len, int* data, int data_len):             # <<<<<<<<<<<<<<
@@ -52317,7 +52492,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("int_arr_extend", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1348
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1354
  *     cdef int* int_arr_extend(self, int* arr, int* arr_len, int* data, int data_len):
  *         cdef int new_len
  *         new_len = arr_len[0] + data_len             # <<<<<<<<<<<<<<
@@ -52326,7 +52501,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   __pyx_v_new_len = ((__pyx_v_arr_len[0]) + __pyx_v_data_len);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1349
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1355
  *         cdef int new_len
  *         new_len = arr_len[0] + data_len
  *         arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -52335,7 +52510,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1350
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1356
  *         new_len = arr_len[0] + data_len
  *         arr = <int*> realloc(arr, new_len*sizeof(int))
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -52344,7 +52519,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   memcpy((__pyx_v_arr + (__pyx_v_arr_len[0])), __pyx_v_data, (__pyx_v_data_len * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1351
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1357
  *         arr = <int*> realloc(arr, new_len*sizeof(int))
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))
  *         arr_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -52353,7 +52528,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   (__pyx_v_arr_len[0]) = __pyx_v_new_len;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1352
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1358
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))
  *         arr_len[0] = new_len
  *         return arr             # <<<<<<<<<<<<<<
@@ -52369,7 +52544,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1355
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1361
  * 
  * 
  *     cdef extract_phrases(self, int e_low, int e_high, int* e_gap_low, int* e_gap_high, int* e_links_low, int num_gaps,             # <<<<<<<<<<<<<<
@@ -52415,19 +52590,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("extract_phrases", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1363
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1369
  *         cdef result
  * 
  *         result = []             # <<<<<<<<<<<<<<
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)
  */
-  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_v_result = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1364
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1370
  * 
  *         result = []
  *         len1 = 0             # <<<<<<<<<<<<<<
@@ -52436,7 +52611,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1365
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1371
  *         result = []
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -52445,19 +52620,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps1 = ((int *)malloc(0));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1366
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1372
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)
  *         ephr_arr = IntList()             # <<<<<<<<<<<<<<
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  */
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_v_ephr_arr = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1368
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1374
  *         ephr_arr = IntList()
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))             # <<<<<<<<<<<<<<
@@ -52466,7 +52641,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gap_order = ((int *)malloc((__pyx_v_num_gaps * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1369
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1375
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  *         if num_gaps > 0:             # <<<<<<<<<<<<<<
@@ -52476,7 +52651,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_2 = (__pyx_v_num_gaps > 0);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1370
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1376
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  *         if num_gaps > 0:
  *             e_gap_order[0] = 0             # <<<<<<<<<<<<<<
@@ -52485,7 +52660,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     (__pyx_v_e_gap_order[0]) = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1371
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1377
  *         if num_gaps > 0:
  *             e_gap_order[0] = 0
  *             for i from 1 <= i < num_gaps:             # <<<<<<<<<<<<<<
@@ -52495,7 +52670,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_3 = __pyx_v_num_gaps;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1372
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1378
  *             e_gap_order[0] = 0
  *             for i from 1 <= i < num_gaps:
  *                 for j from 0 <= j < i:             # <<<<<<<<<<<<<<
@@ -52505,7 +52680,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_4 = __pyx_v_i;
       for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_4; __pyx_v_j++) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1373
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1379
  *             for i from 1 <= i < num_gaps:
  *                 for j from 0 <= j < i:
  *                     if e_gap_low[i] < e_gap_low[j]:             # <<<<<<<<<<<<<<
@@ -52515,7 +52690,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_t_2 = ((__pyx_v_e_gap_low[__pyx_v_i]) < (__pyx_v_e_gap_low[__pyx_v_j]));
         if (__pyx_t_2) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1374
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1380
  *                 for j from 0 <= j < i:
  *                     if e_gap_low[i] < e_gap_low[j]:
  *                         for k from j <= k < i:             # <<<<<<<<<<<<<<
@@ -52525,7 +52700,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
           __pyx_t_5 = __pyx_v_i;
           for (__pyx_v_k = __pyx_v_j; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1375
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1381
  *                     if e_gap_low[i] < e_gap_low[j]:
  *                         for k from j <= k < i:
  *                             e_gap_order[k+1] = e_gap_order[k]             # <<<<<<<<<<<<<<
@@ -52535,7 +52710,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
             (__pyx_v_e_gap_order[(__pyx_v_k + 1)]) = (__pyx_v_e_gap_order[__pyx_v_k]);
           }
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1376
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1382
  *                         for k from j <= k < i:
  *                             e_gap_order[k+1] = e_gap_order[k]
  *                         e_gap_order[j] = i             # <<<<<<<<<<<<<<
@@ -52544,7 +52719,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
           (__pyx_v_e_gap_order[__pyx_v_j]) = __pyx_v_i;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1377
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1383
  *                             e_gap_order[k+1] = e_gap_order[k]
  *                         e_gap_order[j] = i
  *                         break             # <<<<<<<<<<<<<<
@@ -52558,7 +52733,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1379
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1385
  *                         break
  *                 else:
  *                     e_gap_order[i] = i             # <<<<<<<<<<<<<<
@@ -52573,7 +52748,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   }
   __pyx_L3:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1381
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1387
  *                     e_gap_order[i] = i
  * 
  *         e_x_low = e_low             # <<<<<<<<<<<<<<
@@ -52582,7 +52757,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_x_low = __pyx_v_e_low;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1382
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1388
  * 
  *         e_x_low = e_low
  *         e_x_high = e_high             # <<<<<<<<<<<<<<
@@ -52591,7 +52766,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_x_high = __pyx_v_e_high;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1383
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1389
  *         e_x_low = e_low
  *         e_x_high = e_high
  *         if not self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -52601,7 +52776,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_2 = (!__pyx_v_self->tight_phrases);
   if (__pyx_t_2) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1384
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1390
  *         e_x_high = e_high
  *         if not self.tight_phrases:
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -52624,7 +52799,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (!__pyx_t_6) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1385
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1391
  *         if not self.tight_phrases:
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:
  *                 e_x_low = e_x_low - 1             # <<<<<<<<<<<<<<
@@ -52634,7 +52809,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_v_e_x_low = (__pyx_v_e_x_low - 1);
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1386
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1392
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:
  *                 e_x_low = e_x_low - 1
  *             while e_x_high < e_sent_len and e_x_high - e_low < self.train_max_initial_size and e_links_low[e_x_high] == -1:             # <<<<<<<<<<<<<<
@@ -52657,7 +52832,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (!__pyx_t_2) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1387
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1393
  *                 e_x_low = e_x_low - 1
  *             while e_x_high < e_sent_len and e_x_high - e_low < self.train_max_initial_size and e_links_low[e_x_high] == -1:
  *                 e_x_high = e_x_high + 1             # <<<<<<<<<<<<<<
@@ -52670,7 +52845,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   }
   __pyx_L11:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1389
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1395
  *                 e_x_high = e_x_high + 1
  * 
  *         for i from e_x_low <= i <= e_low:             # <<<<<<<<<<<<<<
@@ -52680,7 +52855,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_e_low;
   for (__pyx_v_i = __pyx_v_e_x_low; __pyx_v_i <= __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1390
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1396
  * 
  *         for i from e_x_low <= i <= e_low:
  *             e_gaps1 = self.int_arr_extend(e_gaps1, &len1, &i, 1)             # <<<<<<<<<<<<<<
@@ -52690,7 +52865,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_v_e_gaps1 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps1, (&__pyx_v_len1), (&__pyx_v_i), 1);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1392
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1398
  *             e_gaps1 = self.int_arr_extend(e_gaps1, &len1, &i, 1)
  * 
  *         for i from 0 <= i < num_gaps:             # <<<<<<<<<<<<<<
@@ -52700,7 +52875,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_num_gaps;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1393
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1399
  * 
  *         for i from 0 <= i < num_gaps:
  *             e_gaps2 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -52709,7 +52884,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_gaps2 = ((int *)malloc(0));
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1394
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1400
  *         for i from 0 <= i < num_gaps:
  *             e_gaps2 = <int*> malloc(0)
  *             len2 = 0             # <<<<<<<<<<<<<<
@@ -52718,7 +52893,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_len2 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1396
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1402
  *             len2 = 0
  * 
  *             j = e_gap_order[i]             # <<<<<<<<<<<<<<
@@ -52727,7 +52902,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_j = (__pyx_v_e_gap_order[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1397
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1403
  * 
  *             j = e_gap_order[i]
  *             e_x_gap_low = e_gap_low[j]             # <<<<<<<<<<<<<<
@@ -52736,7 +52911,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_x_gap_low = (__pyx_v_e_gap_low[__pyx_v_j]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1398
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1404
  *             j = e_gap_order[i]
  *             e_x_gap_low = e_gap_low[j]
  *             e_x_gap_high = e_gap_high[j]             # <<<<<<<<<<<<<<
@@ -52745,7 +52920,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_x_gap_high = (__pyx_v_e_gap_high[__pyx_v_j]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1399
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1405
  *             e_x_gap_low = e_gap_low[j]
  *             e_x_gap_high = e_gap_high[j]
  *             if not self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -52755,7 +52930,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_2 = (!__pyx_v_self->tight_phrases);
     if (__pyx_t_2) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1400
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1406
  *             e_x_gap_high = e_gap_high[j]
  *             if not self.tight_phrases:
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -52772,7 +52947,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         }
         if (!__pyx_t_7) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1401
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1407
  *             if not self.tight_phrases:
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:
  *                     e_x_gap_low = e_x_gap_low - 1             # <<<<<<<<<<<<<<
@@ -52782,7 +52957,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_v_e_x_gap_low = (__pyx_v_e_x_gap_low - 1);
       }
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1402
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1408
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:
  *                     e_x_gap_low = e_x_gap_low - 1
  *                 while e_x_gap_high < e_x_high and e_links_low[e_x_gap_high] == -1:             # <<<<<<<<<<<<<<
@@ -52799,7 +52974,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         }
         if (!__pyx_t_6) break;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1403
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1409
  *                     e_x_gap_low = e_x_gap_low - 1
  *                 while e_x_gap_high < e_x_high and e_links_low[e_x_gap_high] == -1:
  *                     e_x_gap_high = e_x_gap_high + 1             # <<<<<<<<<<<<<<
@@ -52812,7 +52987,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     }
     __pyx_L20:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1405
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1411
  *                     e_x_gap_high = e_x_gap_high + 1
  * 
  *             k = 0             # <<<<<<<<<<<<<<
@@ -52821,7 +52996,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_k = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1406
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1412
  * 
  *             k = 0
  *             step = 1+(i*2)             # <<<<<<<<<<<<<<
@@ -52830,7 +53005,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_step = (1 + (__pyx_v_i * 2));
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1407
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1413
  *             k = 0
  *             step = 1+(i*2)
  *             while k < len1:             # <<<<<<<<<<<<<<
@@ -52841,7 +53016,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_6 = (__pyx_v_k < __pyx_v_len1);
       if (!__pyx_t_6) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1408
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1414
  *             step = 1+(i*2)
  *             while k < len1:
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:             # <<<<<<<<<<<<<<
@@ -52851,7 +53026,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_4 = (__pyx_v_e_gap_low[__pyx_v_j]);
       for (__pyx_v_m = __pyx_v_e_x_gap_low; __pyx_v_m <= __pyx_t_4; __pyx_v_m++) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1409
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1415
  *             while k < len1:
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:
  *                     if m >= e_gaps1[k+step-1]:             # <<<<<<<<<<<<<<
@@ -52861,7 +53036,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_t_6 = (__pyx_v_m >= (__pyx_v_e_gaps1[((__pyx_v_k + __pyx_v_step) - 1)]));
         if (__pyx_t_6) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1410
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1416
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:
  *                     if m >= e_gaps1[k+step-1]:
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:             # <<<<<<<<<<<<<<
@@ -52871,7 +53046,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
           __pyx_t_5 = __pyx_v_e_x_gap_high;
           for (__pyx_v_n = (__pyx_v_e_gap_high[__pyx_v_j]); __pyx_v_n <= __pyx_t_5; __pyx_v_n++) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1411
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1417
  *                     if m >= e_gaps1[k+step-1]:
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length             # <<<<<<<<<<<<<<
@@ -52881,7 +53056,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
             __pyx_t_6 = ((__pyx_v_n - __pyx_v_m) >= 1);
             if (__pyx_t_6) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1412
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1418
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)             # <<<<<<<<<<<<<<
@@ -52890,7 +53065,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
               __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (__pyx_v_e_gaps1 + __pyx_v_k), __pyx_v_step);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1413
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1419
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)             # <<<<<<<<<<<<<<
@@ -52899,7 +53074,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
               __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (&__pyx_v_m), 1);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1414
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1420
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)             # <<<<<<<<<<<<<<
@@ -52916,7 +53091,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_L29:;
       }
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1415
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1421
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)
  *                 k = k + step             # <<<<<<<<<<<<<<
@@ -52926,7 +53101,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_v_k = (__pyx_v_k + __pyx_v_step);
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1416
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1422
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)
  *                 k = k + step
  *             free(e_gaps1)             # <<<<<<<<<<<<<<
@@ -52935,7 +53110,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     free(__pyx_v_e_gaps1);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1417
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1423
  *                 k = k + step
  *             free(e_gaps1)
  *             e_gaps1 = e_gaps2             # <<<<<<<<<<<<<<
@@ -52944,7 +53119,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_gaps1 = __pyx_v_e_gaps2;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1418
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1424
  *             free(e_gaps1)
  *             e_gaps1 = e_gaps2
  *             len1 = len2             # <<<<<<<<<<<<<<
@@ -52954,7 +53129,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_v_len1 = __pyx_v_len2;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1420
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1426
  *             len1 = len2
  * 
  *         step = 1+(num_gaps*2)             # <<<<<<<<<<<<<<
@@ -52963,7 +53138,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_step = (1 + (__pyx_v_num_gaps * 2));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1421
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1427
  * 
  *         step = 1+(num_gaps*2)
  *         e_gaps2 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -52972,7 +53147,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps2 = ((int *)malloc(0));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1422
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1428
  *         step = 1+(num_gaps*2)
  *         e_gaps2 = <int*> malloc(0)
  *         len2 = 0             # <<<<<<<<<<<<<<
@@ -52981,7 +53156,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1423
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1429
  *         e_gaps2 = <int*> malloc(0)
  *         len2 = 0
  *         for i from e_high <= i <= e_x_high:             # <<<<<<<<<<<<<<
@@ -52991,7 +53166,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_e_x_high;
   for (__pyx_v_i = __pyx_v_e_high; __pyx_v_i <= __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1424
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1430
  *         len2 = 0
  *         for i from e_high <= i <= e_x_high:
  *             j = 0             # <<<<<<<<<<<<<<
@@ -53000,7 +53175,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_j = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1425
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1431
  *         for i from e_high <= i <= e_x_high:
  *             j = 0
  *             while j < len1:             # <<<<<<<<<<<<<<
@@ -53011,7 +53186,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_6 = (__pyx_v_j < __pyx_v_len1);
       if (!__pyx_t_6) break;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1426
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1432
  *             j = 0
  *             while j < len1:
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:             # <<<<<<<<<<<<<<
@@ -53027,7 +53202,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (__pyx_t_2) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1427
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1433
  *             while j < len1:
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)             # <<<<<<<<<<<<<<
@@ -53036,7 +53211,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
         __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (__pyx_v_e_gaps1 + __pyx_v_j), __pyx_v_step);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1428
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1434
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)             # <<<<<<<<<<<<<<
@@ -53048,7 +53223,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       __pyx_L37:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1429
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1435
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)
  *                 j = j + step             # <<<<<<<<<<<<<<
@@ -53059,7 +53234,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     }
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1430
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1436
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)
  *                 j = j + step
  *         free(e_gaps1)             # <<<<<<<<<<<<<<
@@ -53068,7 +53243,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   free(__pyx_v_e_gaps1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1431
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1437
  *                 j = j + step
  *         free(e_gaps1)
  *         e_gaps1 = e_gaps2             # <<<<<<<<<<<<<<
@@ -53077,7 +53252,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps1 = __pyx_v_e_gaps2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1432
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1438
  *         free(e_gaps1)
  *         e_gaps1 = e_gaps2
  *         len1 = len2             # <<<<<<<<<<<<<<
@@ -53086,7 +53261,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len1 = __pyx_v_len2;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1434
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1440
  *         len1 = len2
  * 
  *         step = (num_gaps+1)*2             # <<<<<<<<<<<<<<
@@ -53095,7 +53270,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_step = ((__pyx_v_num_gaps + 1) * 2);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1435
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1441
  * 
  *         step = (num_gaps+1)*2
  *         i = 0             # <<<<<<<<<<<<<<
@@ -53104,7 +53279,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_i = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1437
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1443
  *         i = 0
  * 
  *         while i < len1:             # <<<<<<<<<<<<<<
@@ -53115,7 +53290,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_2 = (__pyx_v_i < __pyx_v_len1);
     if (!__pyx_t_2) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1438
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1444
  * 
  *         while i < len1:
  *             ephr_arr._clear()             # <<<<<<<<<<<<<<
@@ -53124,7 +53299,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_ephr_arr->__pyx_vtab)->_clear(__pyx_v_ephr_arr);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1439
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1445
  *         while i < len1:
  *             ephr_arr._clear()
  *             num_chunks = 0             # <<<<<<<<<<<<<<
@@ -53133,20 +53308,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_num_chunks = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1440
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1446
  *             ephr_arr._clear()
  *             num_chunks = 0
  *             indexes = []             # <<<<<<<<<<<<<<
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  */
-    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
     __Pyx_XDECREF(((PyObject *)__pyx_v_indexes));
     __pyx_v_indexes = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1441
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1447
  *             num_chunks = 0
  *             indexes = []
  *             for j from 0 <= j < num_gaps+1:             # <<<<<<<<<<<<<<
@@ -53156,7 +53331,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_9 = (__pyx_v_num_gaps + 1);
     for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_9; __pyx_v_j++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1442
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1448
  *             indexes = []
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:             # <<<<<<<<<<<<<<
@@ -53166,7 +53341,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_2 = ((__pyx_v_e_gaps1[(__pyx_v_i + (2 * __pyx_v_j))]) < (__pyx_v_e_gaps1[((__pyx_v_i + (2 * __pyx_v_j)) + 1)]));
       if (__pyx_t_2) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1443
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1449
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  *                     num_chunks = num_chunks + 1             # <<<<<<<<<<<<<<
@@ -53178,7 +53353,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       __pyx_L42:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1444
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1450
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  *                     num_chunks = num_chunks + 1
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:             # <<<<<<<<<<<<<<
@@ -53188,19 +53363,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_3 = (__pyx_v_e_gaps1[((__pyx_v_i + (2 * __pyx_v_j)) + 1)]);
       for (__pyx_v_k = (__pyx_v_e_gaps1[(__pyx_v_i + (2 * __pyx_v_j))]); __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1445
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1451
  *                     num_chunks = num_chunks + 1
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:
  *                     indexes.append(k)             # <<<<<<<<<<<<<<
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:
  */
-        __pyx_t_1 = PyInt_FromLong(__pyx_v_k); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyInt_FromLong(__pyx_v_k); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1446
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1452
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:
  *                     indexes.append(k)
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])             # <<<<<<<<<<<<<<
@@ -53208,14 +53383,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))
  */
         __pyx_t_4 = (__pyx_v_self->eda->data->arr[(__pyx_v_e_sent_start + __pyx_v_k)]);
-        __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->eid2symid), __pyx_t_4, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->eid2symid), __pyx_t_4, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_ephr_arr->__pyx_vtab)->_append(__pyx_v_ephr_arr, __pyx_t_4);
       }
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1447
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1453
  *                     indexes.append(k)
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:             # <<<<<<<<<<<<<<
@@ -53225,19 +53400,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_2 = (__pyx_v_j < __pyx_v_num_gaps);
       if (__pyx_t_2) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1448
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1454
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))             # <<<<<<<<<<<<<<
  *                     ephr_arr._append(sym_setindex(self.category, e_gap_order[j]+1))
  *             i = i + step
  */
-        __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, ((__pyx_v_e_gap_order[__pyx_v_j]) + 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, ((__pyx_v_e_gap_order[__pyx_v_j]) + 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1449
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1455
  *                 if j < num_gaps:
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))
  *                     ephr_arr._append(sym_setindex(self.category, e_gap_order[j]+1))             # <<<<<<<<<<<<<<
@@ -53250,7 +53425,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_L45:;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1450
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1456
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))
  *                     ephr_arr._append(sym_setindex(self.category, e_gap_order[j]+1))
  *             i = i + step             # <<<<<<<<<<<<<<
@@ -53259,7 +53434,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_i = (__pyx_v_i + __pyx_v_step);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1451
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1457
  *                     ephr_arr._append(sym_setindex(self.category, e_gap_order[j]+1))
  *             i = i + step
  *             if ephr_arr.len <= self.max_target_length and num_chunks <= self.max_target_chunks:             # <<<<<<<<<<<<<<
@@ -53275,22 +53450,22 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     }
     if (__pyx_t_7) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1452
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1458
  *             i = i + step
  *             if ephr_arr.len <= self.max_target_length and num_chunks <= self.max_target_chunks:
  *                 result.append((Phrase(ephr_arr),indexes))             # <<<<<<<<<<<<<<
  * 
  *         free(e_gaps1)
  */
-      __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_INCREF(((PyObject *)__pyx_v_ephr_arr));
       PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_ephr_arr));
       __Pyx_GIVEREF(((PyObject *)__pyx_v_ephr_arr));
-      __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_11);
       __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-      __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_11);
       __Pyx_GIVEREF(__pyx_t_11);
@@ -53298,7 +53473,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_v_indexes));
       __Pyx_GIVEREF(((PyObject *)__pyx_v_indexes));
       __pyx_t_11 = 0;
-      __pyx_t_11 = __Pyx_PyObject_Append(__pyx_v_result, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_11 = __Pyx_PyObject_Append(__pyx_v_result, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_11);
       __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
       __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
@@ -53307,7 +53482,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_L46:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1454
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1460
  *                 result.append((Phrase(ephr_arr),indexes))
  * 
  *         free(e_gaps1)             # <<<<<<<<<<<<<<
@@ -53316,7 +53491,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   free(__pyx_v_e_gaps1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1455
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1461
  * 
  *         free(e_gaps1)
  *         free(e_gap_order)             # <<<<<<<<<<<<<<
@@ -53325,7 +53500,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   free(__pyx_v_e_gap_order);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1456
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1462
  *         free(e_gaps1)
  *         free(e_gap_order)
  *         return result             # <<<<<<<<<<<<<<
@@ -53353,7 +53528,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1458
+/* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1464
  *         return result
  * 
  *     cdef IntList create_alignments(self, int* sent_links, int num_links, findexes, eindexes):             # <<<<<<<<<<<<<<
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1469
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1470
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  *         phrase_len = phrase.n
  *         extracts = []             # <<<<<<<<<<<<<<
  *         sent_links = self.alignment._get_sent_links(matching.sent_id, &num_links)
  * 
  */
-  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_v_extracts = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1489
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1495
  *         phrase_len = phrase.n
  *         extracts = []
  *         sent_links = self.alignment._get_sent_links(matching.sent_id, &num_links)             # <<<<<<<<<<<<<<
@@ -53714,7 +53892,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_sent_links = ((struct __pyx_vtabstruct_3_sa_Alignment *)__pyx_v_self->alignment->__pyx_vtab)->_get_sent_links(__pyx_v_self->alignment, __pyx_v_matching->sent_id, (&__pyx_v_num_links));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1491
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1497
  *         sent_links = self.alignment._get_sent_links(matching.sent_id, &num_links)
  * 
  *         e_sent_start = self.eda.sent_index.arr[matching.sent_id]             # <<<<<<<<<<<<<<
@@ -53723,7 +53901,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_sent_start = (__pyx_v_self->eda->sent_index->arr[__pyx_v_matching->sent_id]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1492
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1498
  * 
  *         e_sent_start = self.eda.sent_index.arr[matching.sent_id]
  *         e_sent_end = self.eda.sent_index.arr[matching.sent_id+1]             # <<<<<<<<<<<<<<
@@ -53732,7 +53910,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_sent_end = (__pyx_v_self->eda->sent_index->arr[(__pyx_v_matching->sent_id + 1)]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1493
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1499
  *         e_sent_start = self.eda.sent_index.arr[matching.sent_id]
  *         e_sent_end = self.eda.sent_index.arr[matching.sent_id+1]
  *         e_sent_len = e_sent_end - e_sent_start - 1             # <<<<<<<<<<<<<<
@@ -53741,7 +53919,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_sent_len = ((__pyx_v_e_sent_end - __pyx_v_e_sent_start) - 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1494
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1500
  *         e_sent_end = self.eda.sent_index.arr[matching.sent_id+1]
  *         e_sent_len = e_sent_end - e_sent_start - 1
  *         f_sent_start = self.fda.sent_index.arr[matching.sent_id]             # <<<<<<<<<<<<<<
@@ -53750,7 +53928,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_sent_start = (__pyx_v_self->fda->sent_index->arr[__pyx_v_matching->sent_id]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1495
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1501
  *         e_sent_len = e_sent_end - e_sent_start - 1
  *         f_sent_start = self.fda.sent_index.arr[matching.sent_id]
  *         f_sent_end = self.fda.sent_index.arr[matching.sent_id+1]             # <<<<<<<<<<<<<<
@@ -53759,7 +53937,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_sent_end = (__pyx_v_self->fda->sent_index->arr[(__pyx_v_matching->sent_id + 1)]);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1496
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1502
  *         f_sent_start = self.fda.sent_index.arr[matching.sent_id]
  *         f_sent_end = self.fda.sent_index.arr[matching.sent_id+1]
  *         f_sent_len = f_sent_end - f_sent_start - 1             # <<<<<<<<<<<<<<
@@ -53768,21 +53946,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_sent_len = ((__pyx_v_f_sent_end - __pyx_v_f_sent_start) - 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1498
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1504
  *         f_sent_len = f_sent_end - f_sent_start - 1
  * 
  *         self.findexes1.reset()             # <<<<<<<<<<<<<<
  *         sofar = 0
  *         for i in range(num_chunks):
  */
-  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes1), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes1), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1499
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1505
  * 
  *         self.findexes1.reset()
  *         sofar = 0             # <<<<<<<<<<<<<<
@@ -53792,7 +53970,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __Pyx_INCREF(__pyx_int_0);
   __pyx_v_sofar = __pyx_int_0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1500
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1506
  *         self.findexes1.reset()
  *         sofar = 0
  *         for i in range(num_chunks):             # <<<<<<<<<<<<<<
@@ -53803,7 +53981,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
     __pyx_v_i = __pyx_t_4;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1501
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1507
  *         sofar = 0
  *         for i in range(num_chunks):
  *             for j in range(chunklen[i]):             # <<<<<<<<<<<<<<
@@ -53814,35 +53992,35 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
       __pyx_v_j = __pyx_t_6;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1502
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1508
  *         for i in range(num_chunks):
  *             for j in range(chunklen[i]):
  *                 self.findexes1.append(matching.arr[matching.start+i]+j-f_sent_start);             # <<<<<<<<<<<<<<
  *                 sofar += 1
  *             if (i+1<num_chunks):
  */
-      __pyx_t_2 = PyInt_FromLong((((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyInt_FromLong((((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
-      __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1503
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1509
  *             for j in range(chunklen[i]):
  *                 self.findexes1.append(matching.arr[matching.start+i]+j-f_sent_start);
  *                 sofar += 1             # <<<<<<<<<<<<<<
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])
  */
-      __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_v_sofar);
       __pyx_v_sofar = __pyx_t_1;
       __pyx_t_1 = 0;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1504
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1510
  *                 self.findexes1.append(matching.arr[matching.start+i]+j-f_sent_start);
  *                 sofar += 1
  *             if (i+1<num_chunks):             # <<<<<<<<<<<<<<
@@ -53852,28 +54030,28 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_7 = ((__pyx_v_i + 1) < __pyx_v_num_chunks);
     if (__pyx_t_7) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1505
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1511
  *                 sofar += 1
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])             # <<<<<<<<<<<<<<
  *                 sofar += 1
  * 
  */
-      __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_phrase), __pyx_v_sofar); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_phrase), __pyx_v_sofar); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
-      __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1506
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1512
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])
  *                 sofar += 1             # <<<<<<<<<<<<<<
  * 
  * 
  */
-      __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_v_sofar);
       __pyx_v_sofar = __pyx_t_2;
@@ -53883,7 +54061,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_L7:;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1509
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1515
  * 
  * 
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53892,7 +54070,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_links_low = ((int *)malloc((__pyx_v_e_sent_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1510
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1516
  * 
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53901,7 +54079,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_links_high = ((int *)malloc((__pyx_v_e_sent_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1511
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1517
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53910,7 +54088,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_links_low = ((int *)malloc((__pyx_v_f_sent_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1512
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1518
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53919,7 +54097,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_links_high = ((int *)malloc((__pyx_v_f_sent_len * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1513
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1519
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53928,7 +54106,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_gap_low = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1514
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1520
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53937,7 +54115,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_gap_high = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1515
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1521
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53946,7 +54124,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_gap_low = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1516
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1522
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53955,7 +54133,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_gap_high = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1517
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1523
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53964,7 +54142,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_f_gap_low, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1518
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1524
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53973,7 +54151,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_f_gap_high, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1519
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1525
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_low, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53982,7 +54160,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_e_gap_low, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1520
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1526
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_high, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -53991,7 +54169,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_e_gap_high, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1522
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1528
  *         memset(e_gap_high, 0, (num_chunks+1)*sizeof(int))
  * 
  *         reason_for_failure = ""             # <<<<<<<<<<<<<<
@@ -54001,7 +54179,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
   __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_45);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1524
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1530
  *         reason_for_failure = ""
  * 
  *         for i from 0 <= i < e_sent_len:             # <<<<<<<<<<<<<<
@@ -54011,7 +54189,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __pyx_t_3 = __pyx_v_e_sent_len;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1525
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1531
  * 
  *         for i from 0 <= i < e_sent_len:
  *             e_links_low[i] = -1             # <<<<<<<<<<<<<<
@@ -54020,7 +54198,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     (__pyx_v_e_links_low[__pyx_v_i]) = -1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1526
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1532
  *         for i from 0 <= i < e_sent_len:
  *             e_links_low[i] = -1
  *             e_links_high[i] = -1             # <<<<<<<<<<<<<<
@@ -54030,7 +54208,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     (__pyx_v_e_links_high[__pyx_v_i]) = -1;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1527
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1533
  *             e_links_low[i] = -1
  *             e_links_high[i] = -1
  *         for i from 0 <= i < f_sent_len:             # <<<<<<<<<<<<<<
@@ -54040,7 +54218,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __pyx_t_3 = __pyx_v_f_sent_len;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1528
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1534
  *             e_links_high[i] = -1
  *         for i from 0 <= i < f_sent_len:
  *             f_links_low[i] = -1             # <<<<<<<<<<<<<<
@@ -54049,7 +54227,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     (__pyx_v_f_links_low[__pyx_v_i]) = -1;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1529
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1535
  *         for i from 0 <= i < f_sent_len:
  *             f_links_low[i] = -1
  *             f_links_high[i] = -1             # <<<<<<<<<<<<<<
@@ -54059,7 +54237,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     (__pyx_v_f_links_high[__pyx_v_i]) = -1;
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1535
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1541
  *         # links that we care about (but then how to look up
  *         # when we want to check something on the e side?)
  *         i = 0             # <<<<<<<<<<<<<<
@@ -54068,7 +54246,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_i = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1536
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1542
  *         # when we want to check something on the e side?)
  *         i = 0
  *         while i < num_links*2:             # <<<<<<<<<<<<<<
@@ -54079,7 +54257,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_7 = (__pyx_v_i < (__pyx_v_num_links * 2));
     if (!__pyx_t_7) break;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1537
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1543
  *         i = 0
  *         while i < num_links*2:
  *             f_i = sent_links[i]             # <<<<<<<<<<<<<<
@@ -54088,7 +54266,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_f_i = (__pyx_v_sent_links[__pyx_v_i]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1538
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1544
  *         while i < num_links*2:
  *             f_i = sent_links[i]
  *             e_i = sent_links[i+1]             # <<<<<<<<<<<<<<
@@ -54097,7 +54275,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_e_i = (__pyx_v_sent_links[(__pyx_v_i + 1)]);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1539
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1545
  *             f_i = sent_links[i]
  *             e_i = sent_links[i+1]
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:             # <<<<<<<<<<<<<<
@@ -54113,7 +54291,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_9) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1540
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1546
  *             e_i = sent_links[i+1]
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:
  *                 f_links_low[f_i] = e_i             # <<<<<<<<<<<<<<
@@ -54125,7 +54303,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L14:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1541
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1547
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:
  *                 f_links_low[f_i] = e_i
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:             # <<<<<<<<<<<<<<
@@ -54141,7 +54319,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_8) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1542
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1548
  *                 f_links_low[f_i] = e_i
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:
  *                 f_links_high[f_i] = e_i + 1             # <<<<<<<<<<<<<<
@@ -54153,7 +54331,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L15:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1543
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1549
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:
  *                 f_links_high[f_i] = e_i + 1
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:             # <<<<<<<<<<<<<<
@@ -54169,7 +54347,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_7) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1544
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1550
  *                 f_links_high[f_i] = e_i + 1
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:
  *                 e_links_low[e_i] = f_i             # <<<<<<<<<<<<<<
@@ -54181,7 +54359,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L16:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1545
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1551
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:
  *                 e_links_low[e_i] = f_i
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:             # <<<<<<<<<<<<<<
@@ -54197,7 +54375,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_9) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1546
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1552
  *                 e_links_low[e_i] = f_i
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:
  *                 e_links_high[e_i] = f_i + 1             # <<<<<<<<<<<<<<
@@ -54209,7 +54387,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L17:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1547
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1553
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:
  *                 e_links_high[e_i] = f_i + 1
  *             i = i + 2             # <<<<<<<<<<<<<<
@@ -54219,19 +54397,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_v_i = (__pyx_v_i + 2);
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1549
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1555
  *             i = i + 2
  * 
  *         als = []             # <<<<<<<<<<<<<<
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])
  */
-  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __pyx_v_als = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1550
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1556
  * 
  *         als = []
  *         for x in range(matching.start,matching.end):             # <<<<<<<<<<<<<<
@@ -54242,18 +54420,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   for (__pyx_t_4 = __pyx_v_matching->start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
     __pyx_v_x = __pyx_t_4;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1551
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1557
  *         als = []
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])             # <<<<<<<<<<<<<<
  *             als.append(al)
  *         # check all source-side alignment constraints
  */
-    __pyx_t_2 = PyInt_FromLong(((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong(((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_1 = PyInt_FromLong((__pyx_v_f_links_low[((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyInt_FromLong((__pyx_v_f_links_low[((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
-    __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_10);
     PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
     __Pyx_GIVEREF(__pyx_t_2);
@@ -54265,17 +54443,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_v_al = __pyx_t_10;
     __pyx_t_10 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1552
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1558
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])
  *             als.append(al)             # <<<<<<<<<<<<<<
  *         # check all source-side alignment constraints
  *         met_constraints = 1
  */
-    __pyx_t_11 = PyList_Append(__pyx_v_als, ((PyObject *)__pyx_v_al)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_11 = PyList_Append(__pyx_v_als, ((PyObject *)__pyx_v_al)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1554
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1560
  *             als.append(al)
  *         # check all source-side alignment constraints
  *         met_constraints = 1             # <<<<<<<<<<<<<<
@@ -54284,7 +54462,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_met_constraints = 1;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1555
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1561
  *         # check all source-side alignment constraints
  *         met_constraints = 1
  *         if self.require_aligned_terminal:             # <<<<<<<<<<<<<<
@@ -54293,7 +54471,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   if (__pyx_v_self->require_aligned_terminal) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1556
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1562
  *         met_constraints = 1
  *         if self.require_aligned_terminal:
  *             num_aligned_chunks = 0             # <<<<<<<<<<<<<<
@@ -54302,7 +54480,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_num_aligned_chunks = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1557
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1563
  *         if self.require_aligned_terminal:
  *             num_aligned_chunks = 0
  *             for i from 0 <= i < num_chunks:             # <<<<<<<<<<<<<<
@@ -54312,7 +54490,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_3 = __pyx_v_num_chunks;
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1558
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1564
  *             num_aligned_chunks = 0
  *             for i from 0 <= i < num_chunks:
  *                 for j from 0 <= j < chunklen[i]:             # <<<<<<<<<<<<<<
@@ -54322,7 +54500,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_4 = (__pyx_v_chunklen[__pyx_v_i]);
       for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_4; __pyx_v_j++) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1559
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1565
  *             for i from 0 <= i < num_chunks:
  *                 for j from 0 <= j < chunklen[i]:
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:             # <<<<<<<<<<<<<<
@@ -54332,7 +54510,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)]) > -1);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1560
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1566
  *                 for j from 0 <= j < chunklen[i]:
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:
  *                         num_aligned_chunks = num_aligned_chunks + 1             # <<<<<<<<<<<<<<
@@ -54341,7 +54519,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           __pyx_v_num_aligned_chunks = (__pyx_v_num_aligned_chunks + 1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1561
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1567
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:
  *                         num_aligned_chunks = num_aligned_chunks + 1
  *                         break             # <<<<<<<<<<<<<<
@@ -54356,7 +54534,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_L24_break:;
     }
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1562
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1568
  *                         num_aligned_chunks = num_aligned_chunks + 1
  *                         break
  *             if num_aligned_chunks == 0:             # <<<<<<<<<<<<<<
@@ -54366,18 +54544,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_9 = (__pyx_v_num_aligned_chunks == 0);
     if (__pyx_t_9) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1563
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1569
  *                         break
  *             if num_aligned_chunks == 0:
  *                 reason_for_failure = "No aligned terminals"             # <<<<<<<<<<<<<<
  *                 met_constraints = 0
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:
  */
-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_126));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_127));
       __Pyx_DECREF(__pyx_v_reason_for_failure);
-      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_126);
+      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_127);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1564
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1570
  *             if num_aligned_chunks == 0:
  *                 reason_for_failure = "No aligned terminals"
  *                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54389,7 +54567,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L26:;
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1565
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1571
  *                 reason_for_failure = "No aligned terminals"
  *                 met_constraints = 0
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:             # <<<<<<<<<<<<<<
@@ -54404,18 +54582,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_7) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1566
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1572
  *                 met_constraints = 0
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:
  *                 reason_for_failure = "Unaligned chunk"             # <<<<<<<<<<<<<<
  *                 met_constraints = 0
  * 
  */
-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_127));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_128));
       __Pyx_DECREF(__pyx_v_reason_for_failure);
-      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_127);
+      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_128);
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1567
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1573
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:
  *                 reason_for_failure = "Unaligned chunk"
  *                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54430,7 +54608,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   __pyx_L20:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1569
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1575
  *                 met_constraints = 0
  * 
  *         if met_constraints and self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -54445,7 +54623,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   if (__pyx_t_9) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1571
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1577
  *         if met_constraints and self.tight_phrases:
  *             # outside edge constraints are checked later
  *             for i from 0 <= i < num_chunks-1:             # <<<<<<<<<<<<<<
@@ -54455,7 +54633,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_12 = (__pyx_v_num_chunks - 1);
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_12; __pyx_v_i++) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1572
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1578
  *             # outside edge constraints are checked later
  *             for i from 0 <= i < num_chunks-1:
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:             # <<<<<<<<<<<<<<
@@ -54465,18 +54643,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + (__pyx_v_chunklen[__pyx_v_i])) - __pyx_v_f_sent_start)]) == -1);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1573
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1579
  *             for i from 0 <= i < num_chunks-1:
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"             # <<<<<<<<<<<<<<
  *                     met_constraints = 0
  *                     break
  */
-        __Pyx_INCREF(((PyObject *)__pyx_kp_s_128));
+        __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
         __Pyx_DECREF(__pyx_v_reason_for_failure);
-        __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_128);
+        __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_129);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1574
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1580
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54485,7 +54663,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_met_constraints = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1575
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1581
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -54497,7 +54675,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L31:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1576
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1582
  *                     met_constraints = 0
  *                     break
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:             # <<<<<<<<<<<<<<
@@ -54507,18 +54685,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_i) + 1)]) - 1) - __pyx_v_f_sent_start)]) == -1);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1577
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1583
  *                     break
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"             # <<<<<<<<<<<<<<
  *                     met_constraints = 0
  *                     break
  */
-        __Pyx_INCREF(((PyObject *)__pyx_kp_s_128));
+        __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
         __Pyx_DECREF(__pyx_v_reason_for_failure);
-        __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_128);
+        __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_129);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1578
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1584
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54527,7 +54705,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_met_constraints = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1579
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1585
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -54544,7 +54722,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   __pyx_L28:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1581
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1587
  *                     break
  * 
  *         f_low = matching.arr[matching.start] - f_sent_start             # <<<<<<<<<<<<<<
@@ -54553,7 +54731,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_low = ((__pyx_v_matching->arr[__pyx_v_matching->start]) - __pyx_v_f_sent_start);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1582
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1588
  * 
  *         f_low = matching.arr[matching.start] - f_sent_start
  *         f_high = matching.arr[matching.start + matching.size - 1] + chunklen[num_chunks-1] - f_sent_start             # <<<<<<<<<<<<<<
@@ -54562,7 +54740,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_high = (((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_matching->size) - 1)]) + (__pyx_v_chunklen[(__pyx_v_num_chunks - 1)])) - __pyx_v_f_sent_start);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1583
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1589
  *         f_low = matching.arr[matching.start] - f_sent_start
  *         f_high = matching.arr[matching.start + matching.size - 1] + chunklen[num_chunks-1] - f_sent_start
  *         if met_constraints:             # <<<<<<<<<<<<<<
@@ -54571,17 +54749,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   if (__pyx_v_met_constraints) {
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1585
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1591
  *         if met_constraints:
  * 
  *             if self.find_fixpoint(f_low, f_high, f_links_low, f_links_high, e_links_low, e_links_high,             # <<<<<<<<<<<<<<
  *                                 -1, -1, &e_low, &e_high, &f_back_low, &f_back_high, f_sent_len, e_sent_len,
  *                                 self.train_max_initial_size, self.train_max_initial_size,
  */
-    __pyx_t_10 = PyInt_FromLong(__pyx_v_f_high); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_10 = PyInt_FromLong(__pyx_v_f_high); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_10);
 
-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1589
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1595
  *                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                 self.train_min_gap_size, 0,
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):             # <<<<<<<<<<<<<<
@@ -54592,7 +54770,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
     if (__pyx_t_3) {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1590
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1596
  *                                 self.train_min_gap_size, 0,
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):
  *                 gap_error = 0             # <<<<<<<<<<<<<<
@@ -54601,7 +54779,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
       __pyx_v_gap_error = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1591
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1597
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):
  *                 gap_error = 0
  *                 num_gaps = 0             # <<<<<<<<<<<<<<
@@ -54610,7 +54788,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
       __pyx_v_num_gaps = 0;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1593
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1599
  *                 num_gaps = 0
  * 
  *                 if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -54620,7 +54798,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = (__pyx_v_f_back_low < __pyx_v_f_low);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1594
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1600
  * 
  *                 if f_back_low < f_low:
  *                     f_gap_low[0] = f_back_low             # <<<<<<<<<<<<<<
@@ -54629,7 +54807,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[0]) = __pyx_v_f_back_low;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1595
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1601
  *                 if f_back_low < f_low:
  *                     f_gap_low[0] = f_back_low
  *                     f_gap_high[0] = f_low             # <<<<<<<<<<<<<<
@@ -54638,7 +54816,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[0]) = __pyx_v_f_low;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1596
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1602
  *                     f_gap_low[0] = f_back_low
  *                     f_gap_high[0] = f_low
  *                     num_gaps = 1             # <<<<<<<<<<<<<<
@@ -54647,7 +54825,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_num_gaps = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1597
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1603
  *                     f_gap_high[0] = f_low
  *                     num_gaps = 1
  *                     gap_start = 0             # <<<<<<<<<<<<<<
@@ -54656,7 +54834,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_gap_start = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1598
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1604
  *                     num_gaps = 1
  *                     gap_start = 0
  *                     phrase_len = phrase_len+1             # <<<<<<<<<<<<<<
@@ -54665,7 +54843,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_phrase_len = (__pyx_v_phrase_len + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1599
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1605
  *                     gap_start = 0
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:             # <<<<<<<<<<<<<<
@@ -54675,7 +54853,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = (__pyx_v_phrase_len > __pyx_v_self->max_length);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1600
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1606
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1             # <<<<<<<<<<<<<<
@@ -54687,7 +54865,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L36:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1601
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1607
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1
  *                     if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -54696,7 +54874,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_self->tight_phrases) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1602
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1608
  *                         gap_error = 1
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -54712,7 +54890,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_8) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1603
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1609
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -54721,16 +54899,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1604
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1610
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:
  *                             gap_error = 1
  *                             reason_for_failure = "Inside edges of preceding subphrase are not tight"             # <<<<<<<<<<<<<<
  *                 else:
  *                     gap_start = 1
  */
-            __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
+            __Pyx_INCREF(((PyObject *)__pyx_kp_s_130));
             __Pyx_DECREF(__pyx_v_reason_for_failure);
-            __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_129);
+            __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_130);
             goto __pyx_L38;
           }
           __pyx_L38:;
@@ -54741,7 +54919,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1606
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1612
  *                             reason_for_failure = "Inside edges of preceding subphrase are not tight"
  *                 else:
  *                     gap_start = 1             # <<<<<<<<<<<<<<
@@ -54750,7 +54928,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_gap_start = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1607
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1613
  *                 else:
  *                     gap_start = 1
  *                     if self.tight_phrases and f_links_low[f_low] == -1:             # <<<<<<<<<<<<<<
@@ -54765,7 +54943,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1610
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1616
  *                         # this is not a hard error.    we can't extract this phrase
  *                         # but we still might be able to extract a superphrase
  *                         met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54779,7 +54957,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L35:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1612
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1618
  *                         met_constraints = 0
  * 
  *                 for i from 0 <= i < matching.size - 1:             # <<<<<<<<<<<<<<
@@ -54789,7 +54967,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_12 = (__pyx_v_matching->size - 1);
       for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_12; __pyx_v_i++) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1613
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1619
  * 
  *                 for i from 0 <= i < matching.size - 1:
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start             # <<<<<<<<<<<<<<
@@ -54798,7 +54976,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[(1 + __pyx_v_i)]) = (((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + (__pyx_v_chunklen[__pyx_v_i])) - __pyx_v_f_sent_start);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1614
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1620
  *                 for i from 0 <= i < matching.size - 1:
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start
  *                     f_gap_high[1+i] = matching.arr[matching.start+i+1] - f_sent_start             # <<<<<<<<<<<<<<
@@ -54807,7 +54985,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[(1 + __pyx_v_i)]) = ((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_i) + 1)]) - __pyx_v_f_sent_start);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1615
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1621
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start
  *                     f_gap_high[1+i] = matching.arr[matching.start+i+1] - f_sent_start
  *                     num_gaps = num_gaps + 1             # <<<<<<<<<<<<<<
@@ -54817,7 +54995,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_v_num_gaps = (__pyx_v_num_gaps + 1);
       }
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1617
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1623
  *                     num_gaps = num_gaps + 1
  * 
  *                 if f_high < f_back_high:             # <<<<<<<<<<<<<<
@@ -54827,7 +55005,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = (__pyx_v_f_high < __pyx_v_f_back_high);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1618
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1624
  * 
  *                 if f_high < f_back_high:
  *                     f_gap_low[gap_start+num_gaps] = f_high             # <<<<<<<<<<<<<<
@@ -54836,7 +55014,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_num_gaps)]) = __pyx_v_f_high;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1619
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1625
  *                 if f_high < f_back_high:
  *                     f_gap_low[gap_start+num_gaps] = f_high
  *                     f_gap_high[gap_start+num_gaps] = f_back_high             # <<<<<<<<<<<<<<
@@ -54845,7 +55023,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_num_gaps)]) = __pyx_v_f_back_high;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1620
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1626
  *                     f_gap_low[gap_start+num_gaps] = f_high
  *                     f_gap_high[gap_start+num_gaps] = f_back_high
  *                     num_gaps = num_gaps + 1             # <<<<<<<<<<<<<<
@@ -54854,7 +55032,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_num_gaps = (__pyx_v_num_gaps + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1621
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1627
  *                     f_gap_high[gap_start+num_gaps] = f_back_high
  *                     num_gaps = num_gaps + 1
  *                     phrase_len = phrase_len+1             # <<<<<<<<<<<<<<
@@ -54863,7 +55041,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_phrase_len = (__pyx_v_phrase_len + 1);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1622
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1628
  *                     num_gaps = num_gaps + 1
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:             # <<<<<<<<<<<<<<
@@ -54873,7 +55051,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = (__pyx_v_phrase_len > __pyx_v_self->max_length);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1623
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1629
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1             # <<<<<<<<<<<<<<
@@ -54885,7 +55063,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L43:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1624
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1630
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1
  *                     if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -54894,7 +55072,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_self->tight_phrases) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1625
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1631
  *                         gap_error = 1
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:             # <<<<<<<<<<<<<<
@@ -54910,7 +55088,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1626
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1632
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -54919,16 +55097,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1627
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1633
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:
  *                             gap_error = 1
  *                             reason_for_failure = "Inside edges of following subphrase are not tight"             # <<<<<<<<<<<<<<
  *                 else:
  *                     if self.tight_phrases and f_links_low[f_high-1] == -1:
  */
-            __Pyx_INCREF(((PyObject *)__pyx_kp_s_130));
+            __Pyx_INCREF(((PyObject *)__pyx_kp_s_131));
             __Pyx_DECREF(__pyx_v_reason_for_failure);
-            __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_130);
+            __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_131);
             goto __pyx_L45;
           }
           __pyx_L45:;
@@ -54939,7 +55117,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1629
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1635
  *                             reason_for_failure = "Inside edges of following subphrase are not tight"
  *                 else:
  *                     if self.tight_phrases and f_links_low[f_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -54954,7 +55132,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1630
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1636
  *                 else:
  *                     if self.tight_phrases and f_links_low[f_high-1] == -1:
  *                         met_constraints = 0             # <<<<<<<<<<<<<<
@@ -54968,7 +55146,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L42:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1632
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1638
  *                         met_constraints = 0
  * 
  *                 if gap_error == 0:             # <<<<<<<<<<<<<<
@@ -54978,7 +55156,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = (__pyx_v_gap_error == 0);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1633
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1639
  * 
  *                 if gap_error == 0:
  *                     e_word_count = e_high - e_low             # <<<<<<<<<<<<<<
@@ -54987,7 +55165,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_e_word_count = (__pyx_v_e_high - __pyx_v_e_low);
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1634
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1640
  *                 if gap_error == 0:
  *                     e_word_count = e_high - e_low
  *                     for i from 0 <= i < num_gaps: # check integrity of subphrases             # <<<<<<<<<<<<<<
@@ -54997,17 +55175,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_3 = __pyx_v_num_gaps;
         for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1635
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1641
  *                     e_word_count = e_high - e_low
  *                     for i from 0 <= i < num_gaps: # check integrity of subphrases
  *                         if self.find_fixpoint(f_gap_low[gap_start+i], f_gap_high[gap_start+i],             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low+gap_start+i, e_gap_high+gap_start+i,
  */
-          __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1640
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1646
  *                                             f_gap_low+gap_start+i, f_gap_high+gap_start+i,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -55018,7 +55196,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
           if (__pyx_t_9) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1642
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1648
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0) == 0:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -55027,18 +55205,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1643
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1649
  *                                             0, 0, 0, 0, 0, 0, 0) == 0:
  *                             gap_error = 1
  *                             reason_for_failure = "Subphrase [%d, %d] failed integrity check" % (f_gap_low[gap_start+i], f_gap_high[gap_start+i])             # <<<<<<<<<<<<<<
  *                             break
  * 
  */
-            __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_10);
-            __pyx_t_1 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
-            __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
             PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
             __Pyx_GIVEREF(__pyx_t_10);
@@ -55046,14 +55224,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __Pyx_GIVEREF(__pyx_t_1);
             __pyx_t_10 = 0;
             __pyx_t_1 = 0;
-            __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_131), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_132), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(((PyObject *)__pyx_t_1));
             __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
             __Pyx_DECREF(__pyx_v_reason_for_failure);
             __pyx_v_reason_for_failure = ((PyObject *)__pyx_t_1);
             __pyx_t_1 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1644
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1650
  *                             gap_error = 1
  *                             reason_for_failure = "Subphrase [%d, %d] failed integrity check" % (f_gap_low[gap_start+i], f_gap_high[gap_start+i])
  *                             break             # <<<<<<<<<<<<<<
@@ -55070,7 +55248,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L47:;
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1646
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1652
  *                             break
  * 
  *                 if gap_error == 0:             # <<<<<<<<<<<<<<
@@ -55080,7 +55258,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_9 = (__pyx_v_gap_error == 0);
       if (__pyx_t_9) {
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1647
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1653
  * 
  *                 if gap_error == 0:
  *                     i = 1             # <<<<<<<<<<<<<<
@@ -55089,21 +55267,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_i = 1;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1648
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1654
  *                 if gap_error == 0:
  *                     i = 1
  *                     self.findexes.reset()             # <<<<<<<<<<<<<<
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  */
-        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1649
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1655
  *                     i = 1
  *                     self.findexes.reset()
  *                     if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -55113,7 +55291,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = (__pyx_v_f_back_low < __pyx_v_f_low);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1650
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1656
  *                     self.findexes.reset()
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55122,7 +55300,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1651
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1657
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         i = i+1             # <<<<<<<<<<<<<<
@@ -55131,16 +55309,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           __pyx_v_i = (__pyx_v_i + 1);
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1652
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1658
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         i = i+1
  *                         self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:
  */
-          __pyx_t_2 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_2 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_2);
-          __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_1);
           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -55148,27 +55326,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L52:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1653
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1659
  *                         i = i+1
  *                         self.findexes.append(sym_setindex(self.category, i))
  *                     self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):
  */
-        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
         PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->findexes1));
         __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-        __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_10);
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
         __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1654
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1660
  *                         self.findexes.append(sym_setindex(self.category, i))
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -55178,7 +55356,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_3 = __pyx_v_phrase->n;
         for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1655
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1661
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -55188,7 +55366,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
           if (__pyx_t_4) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1656
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1662
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):
  *                             fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55197,7 +55375,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1657
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1663
  *                         if sym_isvar(phrase.syms[j]):
  *                             fphr_arr._append(sym_setindex(self.category, i))
  *                             i = i + 1             # <<<<<<<<<<<<<<
@@ -55209,7 +55387,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           /*else*/ {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1659
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1665
  *                             i = i + 1
  *                         else:
  *                             fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -55221,7 +55399,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_L55:;
         }
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1660
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1666
  *                         else:
  *                             fphr_arr._append(phrase.syms[j])
  *                     if f_back_high > f_high:             # <<<<<<<<<<<<<<
@@ -55231,7 +55409,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = (__pyx_v_f_back_high > __pyx_v_f_high);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1661
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1667
  *                             fphr_arr._append(phrase.syms[j])
  *                     if f_back_high > f_high:
  *                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55240,16 +55418,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1662
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1668
  *                     if f_back_high > f_high:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  * 
  *                     fphr = Phrase(fphr_arr)
  */
-          __pyx_t_10 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
-          __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_10); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_10); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_2);
           __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -55257,25 +55435,25 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L56:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1664
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1670
  *                         self.findexes.append(sym_setindex(self.category, i))
  * 
  *                     fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                     if met_constraints:
  *                         phrase_list = self.extract_phrases(e_low, e_high, e_gap_low + gap_start, e_gap_high + gap_start, e_links_low, num_gaps,
  */
-        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
         PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_fphr_arr));
         __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-        __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_10);
         __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
         __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_10);
         __pyx_t_10 = 0;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1665
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1671
  * 
  *                     fphr = Phrase(fphr_arr)
  *                     if met_constraints:             # <<<<<<<<<<<<<<
@@ -55284,47 +55462,47 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_met_constraints) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1668
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1674
  *                         phrase_list = self.extract_phrases(e_low, e_high, e_gap_low + gap_start, e_gap_high + gap_start, e_links_low, num_gaps,
  *                                             f_back_low, f_back_high, f_gap_low + gap_start, f_gap_high + gap_start, f_links_low,
  *                                             matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                         if len(phrase_list) > 0:
  *                             pair_count = 1.0 / len(phrase_list)
  */
-          __pyx_t_10 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_low, __pyx_v_e_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, __pyx_v_num_gaps, __pyx_v_f_back_low, __pyx_v_f_back_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_low, __pyx_v_e_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, __pyx_v_num_gaps, __pyx_v_f_back_low, __pyx_v_f_back_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
           __pyx_v_phrase_list = __pyx_t_10;
           __pyx_t_10 = 0;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1669
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1675
  *                                             f_back_low, f_back_high, f_gap_low + gap_start, f_gap_high + gap_start, f_links_low,
  *                                             matching.sent_id, e_sent_len, e_sent_start)
  *                         if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                             pair_count = 1.0 / len(phrase_list)
  *                         else:
  */
-          __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __pyx_t_9 = (__pyx_t_13 > 0);
           if (__pyx_t_9) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1670
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1676
  *                                             matching.sent_id, e_sent_len, e_sent_start)
  *                         if len(phrase_list) > 0:
  *                             pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                         else:
  *                             pair_count = 0
  */
-            __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             if (unlikely(__pyx_t_13 == 0)) {
               PyErr_Format(PyExc_ZeroDivisionError, "float division");
-              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             }
             __pyx_v_pair_count = (1.0 / __pyx_t_13);
             goto __pyx_L58;
           }
           /*else*/ {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1672
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1678
  *                             pair_count = 1.0 / len(phrase_list)
  *                         else:
  *                             pair_count = 0             # <<<<<<<<<<<<<<
@@ -55333,22 +55511,22 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_pair_count = 0.0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1673
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1679
  *                         else:
  *                             pair_count = 0
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  */
-            __pyx_t_10 = PyInt_FromLong(__pyx_v_f_back_low); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_10 = PyInt_FromLong(__pyx_v_f_back_low); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_10);
-            __pyx_t_2 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
-            __pyx_t_1 = PyInt_FromLong(__pyx_v_e_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyInt_FromLong(__pyx_v_e_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
-            __pyx_t_14 = PyInt_FromLong(__pyx_v_e_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_14 = PyInt_FromLong(__pyx_v_e_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_14);
-            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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             PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_t_10);
             __Pyx_GIVEREF(__pyx_t_10);
@@ -55362,7 +55540,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_2 = 0;
             __pyx_t_1 = 0;
             __pyx_t_14 = 0;
-            __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_132), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_133), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
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@@ -55371,7 +55549,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L58:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1674
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1680
  *                             pair_count = 0
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)
  *                         for (phrase2,eindexes) in phrase_list:             # <<<<<<<<<<<<<<
@@ -55382,31 +55560,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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             __pyx_t_16 = NULL;
           } else {
-            __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_14);
             __pyx_t_16 = Py_TYPE(__pyx_t_14)->tp_iternext;
           }
           for (;;) {
             if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_14)) {
               if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_14)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              #else
-              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              #endif
+              __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
             } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_14)) {
               if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              #else
-              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              #endif
+              __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
             } else {
               __pyx_t_15 = __pyx_t_16(__pyx_t_14);
               if (unlikely(!__pyx_t_15)) {
                 if (PyErr_Occurred()) {
                   if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                  else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 break;
               }
@@ -55414,35 +55584,29 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if ((likely(PyTuple_CheckExact(__pyx_t_15))) || (PyList_CheckExact(__pyx_t_15))) {
               PyObject* sequence = __pyx_t_15;
-              #if CYTHON_COMPILING_IN_CPYTHON
-              Py_ssize_t size = Py_SIZE(sequence);
-              #else
-              Py_ssize_t size = PySequence_Size(sequence);
-              #endif
-              if (unlikely(size != 2)) {
-                if (size > 2) __Pyx_RaiseTooManyValuesError(2);
-                else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              }
-              #if CYTHON_COMPILING_IN_CPYTHON
               if (likely(PyTuple_CheckExact(sequence))) {
+                if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+                  if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                  else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                }
                 __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
                 __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
               } else {
+                if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+                  if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                  else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                }
                 __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
                 __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
               }
               __Pyx_INCREF(__pyx_t_1);
               __Pyx_INCREF(__pyx_t_2);
-              #else
-              __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              #endif
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
-            } else
-            {
+            } else {
               Py_ssize_t index = -1;
-              __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_10);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __pyx_t_17 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -55450,15 +55614,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __Pyx_GOTREF(__pyx_t_1);
               index = 1; __pyx_t_2 = __pyx_t_17(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L61_unpacking_failed;
               __Pyx_GOTREF(__pyx_t_2);
-              if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              __pyx_t_17 = NULL;
+              if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
               goto __pyx_L62_unpacking_done;
               __pyx_L61_unpacking_failed:;
               __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
-              __pyx_t_17 = NULL;
-              if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+              if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_L62_unpacking_done:;
             }
             __Pyx_XDECREF(__pyx_v_phrase2);
@@ -55468,40 +55631,40 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_v_eindexes = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1675
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1681
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)             # <<<<<<<<<<<<<<
  *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))
- * 
+ *                     if (num_gaps < self.max_nonterminals and
  */
             __pyx_t_15 = ((PyObject *)__pyx_v_self->findexes);
             __Pyx_INCREF(__pyx_t_15);
-            __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
             __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
             __Pyx_XDECREF(((PyObject *)__pyx_v_als1));
             __pyx_v_als1 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
             __pyx_t_2 = 0;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1676
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1682
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))             # <<<<<<<<<<<<<<
- * 
  *                     if (num_gaps < self.max_nonterminals and
+ *                         phrase_len < self.max_length and
  */
-            __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
-            __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_15);
             __Pyx_INCREF(((PyObject *)__pyx_v_als1));
             PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_als1));
             __Pyx_GIVEREF(((PyObject *)__pyx_v_als1));
-            __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
-            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_15);
             __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
             PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_fphr));
@@ -55515,7 +55678,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __Pyx_GIVEREF(__pyx_t_1);
             __pyx_t_2 = 0;
             __pyx_t_1 = 0;
-            __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
             __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -55525,9 +55688,9 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L57:;
 
-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1678
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1683
+ *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))
- * 
  *                     if (num_gaps < self.max_nonterminals and             # <<<<<<<<<<<<<<
  *                         phrase_len < self.max_length and
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
@@ -55535,8 +55698,8 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = (__pyx_v_num_gaps < __pyx_v_self->max_nonterminals);
         if (__pyx_t_9) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1679
- * 
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1684
+ *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))
  *                     if (num_gaps < self.max_nonterminals and
  *                         phrase_len < self.max_length and             # <<<<<<<<<<<<<<
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
@@ -55545,7 +55708,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_7 = (__pyx_v_phrase_len < __pyx_v_self->max_length);
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1680
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1685
  *                     if (num_gaps < self.max_nonterminals and
  *                         phrase_len < self.max_length and
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):             # <<<<<<<<<<<<<<
@@ -55563,7 +55726,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_7) {
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1681
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1686
  *                         phrase_len < self.max_length and
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
  *                         if (f_back_low == f_low and             # <<<<<<<<<<<<<<
@@ -55573,7 +55736,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_7 = (__pyx_v_f_back_low == __pyx_v_f_low);
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1682
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1687
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
  *                         if (f_back_low == f_low and
  *                                 f_low >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -55583,7 +55746,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_9 = (__pyx_v_f_low >= __pyx_v_self->train_min_gap_size);
             if (__pyx_t_9) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1683
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1688
  *                         if (f_back_low == f_low and
  *                                 f_low >= self.train_min_gap_size and
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):             # <<<<<<<<<<<<<<
@@ -55613,7 +55776,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_9) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1684
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1689
  *                                 f_low >= self.train_min_gap_size and
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):
  *                             f_x_low = f_low-self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -55622,7 +55785,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_low = (__pyx_v_f_low - __pyx_v_self->train_min_gap_size);
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1685
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1690
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -55631,7 +55794,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1686
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1691
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             met_constraints = 1
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -55640,7 +55803,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1687
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1692
  *                             met_constraints = 1
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:             # <<<<<<<<<<<<<<
@@ -55657,7 +55820,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1688
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1693
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1             # <<<<<<<<<<<<<<
@@ -55670,7 +55833,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L65:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1689
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1694
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0 or f_back_high - f_x_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -55686,7 +55849,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_7) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1690
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1695
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0 or f_back_high - f_x_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -55698,85 +55861,85 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L68:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1692
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1697
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
- *                                 self.find_fixpoint(f_x_low, f_back_high,
+ *                                 (self.find_fixpoint(f_x_low, f_back_high,
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1693
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1698
  * 
  *                             if (met_constraints and
- *                                 self.find_fixpoint(f_x_low, f_back_high,             # <<<<<<<<<<<<<<
+ *                                 (self.find_fixpoint(f_x_low, f_back_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_14 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1697
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1702
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
- *                                             1, 1, 1, 1, 0, 1, 0) and
+ *                                             1, 1, 1, 1, 0, 1, 0) == 1) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and
  */
-              if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 1, 0, 1, 0)) {
-                __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+              __pyx_t_7 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 1, 0, 1, 0) == 1);
+              __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+              if (__pyx_t_7) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1699
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1704
  *                                             self.train_max_initial_size, self.train_max_initial_size,
- *                                             1, 1, 1, 1, 0, 1, 0) and
+ *                                             1, 1, 1, 1, 0, 1, 0) == 1) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and             # <<<<<<<<<<<<<<
  *                                 self.find_fixpoint(f_x_low, f_low,    # check integrity of new subphrase
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  */
-                __pyx_t_7 = (!__pyx_v_self->tight_phrases);
-                if (!__pyx_t_7) {
-                  __pyx_t_18 = ((__pyx_v_f_links_low[__pyx_v_f_x_low]) != -1);
-                  __pyx_t_9 = __pyx_t_18;
+                __pyx_t_18 = (!__pyx_v_self->tight_phrases);
+                if (!__pyx_t_18) {
+                  __pyx_t_9 = ((__pyx_v_f_links_low[__pyx_v_f_x_low]) != -1);
+                  __pyx_t_8 = __pyx_t_9;
                 } else {
-                  __pyx_t_9 = __pyx_t_7;
+                  __pyx_t_8 = __pyx_t_18;
                 }
-                if (__pyx_t_9) {
+                if (__pyx_t_8) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1700
- *                                             1, 1, 1, 1, 0, 1, 0) and
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1705
+ *                                             1, 1, 1, 1, 0, 1, 0) == 1) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and
  *                                 self.find_fixpoint(f_x_low, f_low,    # check integrity of new subphrase             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  */
-                  __pyx_t_1 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __Pyx_GOTREF(__pyx_t_1);
+                  __pyx_t_14 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __Pyx_GOTREF(__pyx_t_14);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1704
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1709
  *                                             -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  */
-                  __pyx_t_7 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
-                  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+                  __pyx_t_18 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
+                  __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                 } else {
-                  __pyx_t_7 = __pyx_t_9;
+                  __pyx_t_18 = __pyx_t_8;
                 }
-                __pyx_t_9 = __pyx_t_7;
+                __pyx_t_8 = __pyx_t_18;
               } else {
-                __pyx_t_9 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 1, 0, 1, 0);
-                __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+                __pyx_t_8 = __pyx_t_7;
               }
-              __pyx_t_7 = __pyx_t_9;
+              __pyx_t_7 = __pyx_t_8;
             } else {
               __pyx_t_7 = __pyx_v_met_constraints;
             }
             if (__pyx_t_7) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1706
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1711
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -55785,7 +55948,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1707
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1712
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -55794,35 +55957,35 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1708
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1713
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1709
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1714
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1710
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1715
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55831,7 +55994,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1711
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1716
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1             # <<<<<<<<<<<<<<
@@ -55840,27 +56003,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = (__pyx_v_i + 1);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1712
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1717
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_15 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1713
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1718
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -55870,7 +56033,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1714
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1719
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -55880,7 +56043,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1715
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1720
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55889,7 +56052,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1716
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1721
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -55901,7 +56064,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1718
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1723
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -55913,7 +56076,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L72:;
               }
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1719
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1724
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 if f_back_high > f_high:             # <<<<<<<<<<<<<<
@@ -55923,7 +56086,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_7 = (__pyx_v_f_back_high > __pyx_v_f_high);
               if (__pyx_t_7) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1720
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1725
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 if f_back_high > f_high:
  *                                     fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -55932,16 +56095,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1721
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1726
  *                                 if f_back_high > f_high:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  */
-                __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
-                __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -55949,67 +56112,67 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L73:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1722
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1727
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  */
-              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_15);
               __pyx_t_15 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1725
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1730
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  *                                                     e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
-              __pyx_t_15 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_15;
               __pyx_t_15 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1726
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1731
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  *                                                     e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_7 = (__pyx_t_13 > 0);
               if (__pyx_t_7) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1727
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1732
  *                                                     e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L74;
               }
               /*else*/ {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1729
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1734
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -56020,7 +56183,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L74:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1730
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1735
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2,eindexes in phrase_list:             # <<<<<<<<<<<<<<
@@ -56031,31 +56194,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_15 = __pyx_v_phrase_list; __Pyx_INCREF(__pyx_t_15); __pyx_t_13 = 0;
                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_15 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_15 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __pyx_t_16 = Py_TYPE(__pyx_t_15)->tp_iternext;
               }
               for (;;) {
                 if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_15)) {
                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_15)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_1 = PyList_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_1 = PyList_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++;
                 } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_15)) {
                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_15)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++;
                 } else {
                   __pyx_t_1 = __pyx_t_16(__pyx_t_15);
                   if (unlikely(!__pyx_t_1)) {
                     if (PyErr_Occurred()) {
                       if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                     }
                     break;
                   }
@@ -56063,35 +56218,29 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
                   PyObject* sequence = __pyx_t_1;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  Py_ssize_t size = Py_SIZE(sequence);
-                  #else
-                  Py_ssize_t size = PySequence_Size(sequence);
-                  #endif
-                  if (unlikely(size != 2)) {
-                    if (size > 2) __Pyx_RaiseTooManyValuesError(2);
-                    else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  }
-                  #if CYTHON_COMPILING_IN_CPYTHON
                   if (likely(PyTuple_CheckExact(sequence))) {
+                    if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+                      if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_14 = PyTuple_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
                   } else {
+                    if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+                      if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_14 = PyList_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
                   }
                   __Pyx_INCREF(__pyx_t_14);
                   __Pyx_INCREF(__pyx_t_2);
-                  #else
-                  __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
                   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-                } else
-                {
+                } else {
                   Py_ssize_t index = -1;
-                  __pyx_t_10 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_10 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_10);
                   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                   __pyx_t_17 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -56099,15 +56248,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_GOTREF(__pyx_t_14);
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                   __Pyx_GOTREF(__pyx_t_2);
-                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_17 = NULL;
+                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
                   goto __pyx_L78_unpacking_done;
                   __pyx_L77_unpacking_failed:;
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
-                  __pyx_t_17 = NULL;
-                  if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+                  if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __pyx_L78_unpacking_done:;
                 }
                 __Pyx_XDECREF(__pyx_v_phrase2);
@@ -56117,7 +56265,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_v_eindexes = __pyx_t_2;
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1731
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1736
  *                                     pair_count = 0
  *                                 for phrase2,eindexes in phrase_list:
  *                                     als2 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)             # <<<<<<<<<<<<<<
@@ -56126,31 +56274,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_t_1 = ((PyObject *)__pyx_v_self->findexes);
                 __Pyx_INCREF(__pyx_t_1);
-                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_1, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_1, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                 __Pyx_XDECREF(((PyObject *)__pyx_v_als2));
                 __pyx_v_als2 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1732
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1737
  *                                 for phrase2,eindexes in phrase_list:
  *                                     als2 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als2)))             # <<<<<<<<<<<<<<
  * 
  *                         if (f_back_high == f_high and
  */
-                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
-                __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_INCREF(((PyObject *)__pyx_v_als2));
                 PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_als2));
                 __Pyx_GIVEREF(((PyObject *)__pyx_v_als2));
-                __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-                __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
                 PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fphr));
@@ -56164,7 +56312,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __Pyx_GIVEREF(__pyx_t_14);
                 __pyx_t_2 = 0;
                 __pyx_t_14 = 0;
-                __pyx_t_14 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
@@ -56177,7 +56325,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L64:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1734
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1739
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als2)))
  * 
  *                         if (f_back_high == f_high and             # <<<<<<<<<<<<<<
@@ -56187,17 +56335,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_7 = (__pyx_v_f_back_high == __pyx_v_f_high);
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1735
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1740
  * 
  *                         if (f_back_high == f_high and
  *                             f_sent_len - f_high >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):
  *                             f_x_high = f_high+self.train_min_gap_size
  */
-            __pyx_t_9 = ((__pyx_v_f_sent_len - __pyx_v_f_high) >= __pyx_v_self->train_min_gap_size);
-            if (__pyx_t_9) {
+            __pyx_t_8 = ((__pyx_v_f_sent_len - __pyx_v_f_high) >= __pyx_v_self->train_min_gap_size);
+            if (__pyx_t_8) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1736
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1741
  *                         if (f_back_high == f_high and
  *                             f_sent_len - f_high >= self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):             # <<<<<<<<<<<<<<
@@ -56206,28 +56354,28 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_t_18 = (!__pyx_v_self->tight_phrases);
               if (!__pyx_t_18) {
-                __pyx_t_8 = ((__pyx_v_f_links_low[__pyx_v_f_high]) != -1);
-                if (__pyx_t_8) {
+                __pyx_t_9 = ((__pyx_v_f_links_low[__pyx_v_f_high]) != -1);
+                if (__pyx_t_9) {
                   __pyx_t_20 = ((__pyx_v_f_links_low[__pyx_v_f_back_low]) != -1);
                   __pyx_t_19 = __pyx_t_20;
                 } else {
-                  __pyx_t_19 = __pyx_t_8;
+                  __pyx_t_19 = __pyx_t_9;
                 }
-                __pyx_t_8 = __pyx_t_19;
+                __pyx_t_9 = __pyx_t_19;
               } else {
-                __pyx_t_8 = __pyx_t_18;
+                __pyx_t_9 = __pyx_t_18;
               }
-              __pyx_t_18 = __pyx_t_8;
-            } else {
               __pyx_t_18 = __pyx_t_9;
+            } else {
+              __pyx_t_18 = __pyx_t_8;
             }
-            __pyx_t_9 = __pyx_t_18;
+            __pyx_t_8 = __pyx_t_18;
           } else {
-            __pyx_t_9 = __pyx_t_7;
+            __pyx_t_8 = __pyx_t_7;
           }
-          if (__pyx_t_9) {
+          if (__pyx_t_8) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1737
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1742
  *                             f_sent_len - f_high >= self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):
  *                             f_x_high = f_high+self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -56236,7 +56384,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_high = (__pyx_v_f_high + __pyx_v_self->train_min_gap_size);
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1738
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1743
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -56245,7 +56393,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1739
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1744
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             met_constraints = 1
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -56254,7 +56402,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1740
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1745
  *                             met_constraints = 1
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -56262,16 +56410,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  *                             if f_x_high > f_sent_len or f_x_high - f_back_low > self.train_max_initial_size:
  */
               while (1) {
-                __pyx_t_9 = (__pyx_v_f_x_high <= __pyx_v_f_sent_len);
-                if (__pyx_t_9) {
+                __pyx_t_8 = (__pyx_v_f_x_high <= __pyx_v_f_sent_len);
+                if (__pyx_t_8) {
                   __pyx_t_7 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) == -1);
                   __pyx_t_18 = __pyx_t_7;
                 } else {
-                  __pyx_t_18 = __pyx_t_9;
+                  __pyx_t_18 = __pyx_t_8;
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1741
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1746
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1             # <<<<<<<<<<<<<<
@@ -56284,7 +56432,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L80:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1742
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1747
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_back_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -56293,14 +56441,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_t_18 = (__pyx_v_f_x_high > __pyx_v_f_sent_len);
             if (!__pyx_t_18) {
-              __pyx_t_9 = ((__pyx_v_f_x_high - __pyx_v_f_back_low) > __pyx_v_self->train_max_initial_size);
-              __pyx_t_7 = __pyx_t_9;
+              __pyx_t_8 = ((__pyx_v_f_x_high - __pyx_v_f_back_low) > __pyx_v_self->train_max_initial_size);
+              __pyx_t_7 = __pyx_t_8;
             } else {
               __pyx_t_7 = __pyx_t_18;
             }
             if (__pyx_t_7) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1743
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1748
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_back_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -56312,7 +56460,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L83:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1745
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1750
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
@@ -56321,17 +56469,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1746
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1751
  * 
  *                             if (met_constraints and
  *                                 self.find_fixpoint(f_back_low, f_x_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1750
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1755
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -56341,7 +56489,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_back_low, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 0, 1, 1, 0)) {
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1752
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1757
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             1, 1, 1, 0, 1, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_high-1] != -1) and             # <<<<<<<<<<<<<<
@@ -56351,23 +56499,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_7 = (!__pyx_v_self->tight_phrases);
                 if (!__pyx_t_7) {
                   __pyx_t_18 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) != -1);
-                  __pyx_t_9 = __pyx_t_18;
+                  __pyx_t_8 = __pyx_t_18;
                 } else {
-                  __pyx_t_9 = __pyx_t_7;
+                  __pyx_t_8 = __pyx_t_7;
                 }
-                if (__pyx_t_9) {
+                if (__pyx_t_8) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1753
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1758
  *                                             1, 1, 1, 0, 1, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_high-1] != -1) and
  *                                 self.find_fixpoint(f_high, f_x_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low+gap_start+num_gaps, e_gap_high+gap_start+num_gaps,
  */
-                  __pyx_t_14 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_14 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_14);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1758
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1763
  *                                             f_gap_low+gap_start+num_gaps, f_gap_high+gap_start+num_gaps,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -56377,20 +56525,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __pyx_t_7 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_high, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, ((__pyx_v_e_gap_low + __pyx_v_gap_start) + __pyx_v_num_gaps), ((__pyx_v_e_gap_high + __pyx_v_gap_start) + __pyx_v_num_gaps), ((__pyx_v_f_gap_low + __pyx_v_gap_start) + __pyx_v_num_gaps), ((__pyx_v_f_gap_high + __pyx_v_gap_start) + __pyx_v_num_gaps), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
                   __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                 } else {
-                  __pyx_t_7 = __pyx_t_9;
+                  __pyx_t_7 = __pyx_t_8;
                 }
-                __pyx_t_9 = __pyx_t_7;
+                __pyx_t_8 = __pyx_t_7;
               } else {
-                __pyx_t_9 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_back_low, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 0, 1, 1, 0);
+                __pyx_t_8 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_back_low, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 0, 1, 1, 0);
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               }
-              __pyx_t_7 = __pyx_t_9;
+              __pyx_t_7 = __pyx_t_8;
             } else {
               __pyx_t_7 = __pyx_v_met_constraints;
             }
             if (__pyx_t_7) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1760
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1765
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -56399,7 +56547,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1761
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1766
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -56408,21 +56556,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1762
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1767
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1763
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1768
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -56432,7 +56580,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_7 = (__pyx_v_f_back_low < __pyx_v_f_low);
               if (__pyx_t_7) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1764
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1769
  *                                 self.findexes.reset()
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -56441,7 +56589,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1765
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1770
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     i = i+1             # <<<<<<<<<<<<<<
@@ -56450,16 +56598,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_v_i = (__pyx_v_i + 1);
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1766
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1771
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     i = i+1
  *                                     self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  */
-                __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
-                __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
@@ -56467,27 +56615,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L85:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1767
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1772
  *                                     i = i+1
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_1 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1768
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1773
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -56497,7 +56645,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1769
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1774
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -56507,7 +56655,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1770
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1775
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -56516,7 +56664,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1771
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1776
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -56528,7 +56676,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1773
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1778
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -56540,7 +56688,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L88:;
               }
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1774
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1779
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -56549,81 +56697,81 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1775
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1780
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1776
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1781
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  */
-              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_1);
               __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1779
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1784
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
-              __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_1;
               __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1780
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1785
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_7 = (__pyx_t_13 > 0);
               if (__pyx_t_7) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1781
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1786
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L89;
               }
               /*else*/ {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1783
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1788
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -56634,7 +56782,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L89:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1784
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1789
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:             # <<<<<<<<<<<<<<
@@ -56645,31 +56793,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_1 = __pyx_v_phrase_list; __Pyx_INCREF(__pyx_t_1); __pyx_t_13 = 0;
                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __pyx_t_16 = Py_TYPE(__pyx_t_1)->tp_iternext;
               }
               for (;;) {
                 if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_1)) {
                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_1)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_14 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_14 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++;
                 } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_1)) {
                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_14 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_14 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++;
                 } else {
                   __pyx_t_14 = __pyx_t_16(__pyx_t_1);
                   if (unlikely(!__pyx_t_14)) {
                     if (PyErr_Occurred()) {
                       if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                     }
                     break;
                   }
@@ -56677,35 +56817,29 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if ((likely(PyTuple_CheckExact(__pyx_t_14))) || (PyList_CheckExact(__pyx_t_14))) {
                   PyObject* sequence = __pyx_t_14;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  Py_ssize_t size = Py_SIZE(sequence);
-                  #else
-                  Py_ssize_t size = PySequence_Size(sequence);
-                  #endif
-                  if (unlikely(size != 2)) {
-                    if (size > 2) __Pyx_RaiseTooManyValuesError(2);
-                    else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  }
-                  #if CYTHON_COMPILING_IN_CPYTHON
                   if (likely(PyTuple_CheckExact(sequence))) {
+                    if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+                      if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_15 = PyTuple_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
                   } else {
+                    if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+                      if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_15 = PyList_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
                   }
                   __Pyx_INCREF(__pyx_t_15);
                   __Pyx_INCREF(__pyx_t_2);
-                  #else
-                  __pyx_t_15 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
                   __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
-                } else
-                {
+                } else {
                   Py_ssize_t index = -1;
-                  __pyx_t_10 = PyObject_GetIter(__pyx_t_14); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_10 = PyObject_GetIter(__pyx_t_14); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_10);
                   __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                   __pyx_t_17 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -56713,15 +56847,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_GOTREF(__pyx_t_15);
                   index = 1; __pyx_t_2 = __pyx_t_17(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L92_unpacking_failed;
                   __Pyx_GOTREF(__pyx_t_2);
-                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_17 = NULL;
+                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
                   goto __pyx_L93_unpacking_done;
                   __pyx_L92_unpacking_failed:;
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
-                  __pyx_t_17 = NULL;
-                  if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+                  if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __pyx_L93_unpacking_done:;
                 }
                 __Pyx_XDECREF(__pyx_v_phrase2);
@@ -56731,7 +56864,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_v_eindexes = __pyx_t_2;
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1785
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1790
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:
  *                                     als3 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)             # <<<<<<<<<<<<<<
@@ -56740,31 +56873,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_t_14 = ((PyObject *)__pyx_v_self->findexes);
                 __Pyx_INCREF(__pyx_t_14);
-                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_14, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_14, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                 __Pyx_XDECREF(((PyObject *)__pyx_v_als3));
                 __pyx_v_als3 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1786
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1791
  *                                 for phrase2, eindexes in phrase_list:
  *                                     als3 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))             # <<<<<<<<<<<<<<
  *                         if (num_gaps < self.max_nonterminals - 1 and
  *                             phrase_len+1 < self.max_length and
  */
-                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
-                __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_INCREF(((PyObject *)__pyx_v_als3));
                 PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_als3));
                 __Pyx_GIVEREF(((PyObject *)__pyx_v_als3));
-                __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
-                __pyx_t_14 = PyTuple_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyTuple_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
                 PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_fphr));
@@ -56778,7 +56911,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __Pyx_GIVEREF(__pyx_t_15);
                 __pyx_t_2 = 0;
                 __pyx_t_15 = 0;
-                __pyx_t_15 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
@@ -56791,7 +56924,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L79:;
 
-          /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1787
+          /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1792
  *                                     als3 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))
  *                         if (num_gaps < self.max_nonterminals - 1 and             # <<<<<<<<<<<<<<
@@ -56801,17 +56934,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_7 = (__pyx_v_num_gaps < (__pyx_v_self->max_nonterminals - 1));
           if (__pyx_t_7) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1788
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1793
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))
  *                         if (num_gaps < self.max_nonterminals - 1 and
  *                             phrase_len+1 < self.max_length and             # <<<<<<<<<<<<<<
  *                             f_back_high == f_high and
  *                             f_back_low == f_low and
  */
-            __pyx_t_9 = ((__pyx_v_phrase_len + 1) < __pyx_v_self->max_length);
-            if (__pyx_t_9) {
+            __pyx_t_8 = ((__pyx_v_phrase_len + 1) < __pyx_v_self->max_length);
+            if (__pyx_t_8) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1789
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1794
  *                         if (num_gaps < self.max_nonterminals - 1 and
  *                             phrase_len+1 < self.max_length and
  *                             f_back_high == f_high and             # <<<<<<<<<<<<<<
@@ -56821,17 +56954,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_18 = (__pyx_v_f_back_high == __pyx_v_f_high);
               if (__pyx_t_18) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1790
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1795
  *                             phrase_len+1 < self.max_length and
  *                             f_back_high == f_high and
  *                             f_back_low == f_low and             # <<<<<<<<<<<<<<
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and
  *                             f_low >= self.train_min_gap_size and
  */
-                __pyx_t_8 = (__pyx_v_f_back_low == __pyx_v_f_low);
-                if (__pyx_t_8) {
+                __pyx_t_9 = (__pyx_v_f_back_low == __pyx_v_f_low);
+                if (__pyx_t_9) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1791
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1796
  *                             f_back_high == f_high and
  *                             f_back_low == f_low and
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
@@ -56841,7 +56974,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __pyx_t_19 = (((__pyx_v_f_back_high - __pyx_v_f_back_low) + (2 * __pyx_v_self->train_min_gap_size)) <= __pyx_v_self->train_max_initial_size);
                   if (__pyx_t_19) {
 
-                    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1792
+                    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1797
  *                             f_back_low == f_low and
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and
  *                             f_low >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -56851,7 +56984,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                     __pyx_t_20 = (__pyx_v_f_low >= __pyx_v_self->train_min_gap_size);
                     if (__pyx_t_20) {
 
-                      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1793
+                      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1798
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and
  *                             f_low >= self.train_min_gap_size and
  *                             f_high <= f_sent_len - self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -56861,7 +56994,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                       __pyx_t_21 = (__pyx_v_f_high <= (__pyx_v_f_sent_len - __pyx_v_self->train_min_gap_size));
                       if (__pyx_t_21) {
 
-                        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1794
+                        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1799
  *                             f_low >= self.train_min_gap_size and
  *                             f_high <= f_sent_len - self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_high] != -1))):             # <<<<<<<<<<<<<<
@@ -56895,23 +57028,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   }
                   __pyx_t_19 = __pyx_t_20;
                 } else {
-                  __pyx_t_19 = __pyx_t_8;
+                  __pyx_t_19 = __pyx_t_9;
                 }
-                __pyx_t_8 = __pyx_t_19;
+                __pyx_t_9 = __pyx_t_19;
               } else {
-                __pyx_t_8 = __pyx_t_18;
+                __pyx_t_9 = __pyx_t_18;
               }
-              __pyx_t_18 = __pyx_t_8;
-            } else {
               __pyx_t_18 = __pyx_t_9;
+            } else {
+              __pyx_t_18 = __pyx_t_8;
             }
-            __pyx_t_9 = __pyx_t_18;
+            __pyx_t_8 = __pyx_t_18;
           } else {
-            __pyx_t_9 = __pyx_t_7;
+            __pyx_t_8 = __pyx_t_7;
           }
-          if (__pyx_t_9) {
+          if (__pyx_t_8) {
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1796
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1801
  *                             ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_high] != -1))):
  * 
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -56920,7 +57053,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1797
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1802
  * 
  *                             met_constraints = 1
  *                             f_x_low = f_low-self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -56929,7 +57062,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_low = (__pyx_v_f_low - __pyx_v_self->train_min_gap_size);
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1798
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1803
  *                             met_constraints = 1
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -56938,7 +57071,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1799
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1804
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:             # <<<<<<<<<<<<<<
@@ -56946,16 +57079,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  *                             if f_x_low < 0:
  */
               while (1) {
-                __pyx_t_9 = (__pyx_v_f_x_low >= 0);
-                if (__pyx_t_9) {
+                __pyx_t_8 = (__pyx_v_f_x_low >= 0);
+                if (__pyx_t_8) {
                   __pyx_t_7 = ((__pyx_v_f_links_low[__pyx_v_f_x_low]) == -1);
                   __pyx_t_18 = __pyx_t_7;
                 } else {
-                  __pyx_t_18 = __pyx_t_9;
+                  __pyx_t_18 = __pyx_t_8;
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1800
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1805
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1             # <<<<<<<<<<<<<<
@@ -56968,7 +57101,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L95:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1801
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1806
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0:             # <<<<<<<<<<<<<<
@@ -56978,7 +57111,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_18 = (__pyx_v_f_x_low < 0);
             if (__pyx_t_18) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1802
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1807
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -56990,7 +57123,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L98:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1804
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1809
  *                                 met_constraints = 0
  * 
  *                             f_x_high = f_high+self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -56999,7 +57132,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_high = (__pyx_v_f_high + __pyx_v_self->train_min_gap_size);
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1805
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1810
  * 
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -57008,7 +57141,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1806
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1811
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -57018,14 +57151,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               while (1) {
                 __pyx_t_18 = (__pyx_v_f_x_high <= __pyx_v_f_sent_len);
                 if (__pyx_t_18) {
-                  __pyx_t_9 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) == -1);
-                  __pyx_t_7 = __pyx_t_9;
+                  __pyx_t_8 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) == -1);
+                  __pyx_t_7 = __pyx_t_8;
                 } else {
                   __pyx_t_7 = __pyx_t_18;
                 }
                 if (!__pyx_t_7) break;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1807
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1812
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1             # <<<<<<<<<<<<<<
@@ -57038,7 +57171,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L99:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1808
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1813
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_x_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -57048,13 +57181,13 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_7 = (__pyx_v_f_x_high > __pyx_v_f_sent_len);
             if (!__pyx_t_7) {
               __pyx_t_18 = ((__pyx_v_f_x_high - __pyx_v_f_x_low) > __pyx_v_self->train_max_initial_size);
-              __pyx_t_9 = __pyx_t_18;
+              __pyx_t_8 = __pyx_t_18;
             } else {
-              __pyx_t_9 = __pyx_t_7;
+              __pyx_t_8 = __pyx_t_7;
             }
-            if (__pyx_t_9) {
+            if (__pyx_t_8) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1809
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1814
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_x_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -57066,117 +57199,117 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L102:;
 
-            /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1811
+            /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1816
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
- *                                 self.find_fixpoint(f_x_low, f_x_high,
+ *                                 (self.find_fixpoint(f_x_low, f_x_high,
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1812
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1817
  * 
  *                             if (met_constraints and
- *                                 self.find_fixpoint(f_x_low, f_x_high,             # <<<<<<<<<<<<<<
+ *                                 (self.find_fixpoint(f_x_low, f_x_high,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1816
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1821
  *                                                 e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
- *                                                 1, 1, 2, 1, 1, 1, 1) and
+ *                                                 1, 1, 2, 1, 1, 1, 1) == 1) and
  *                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and
  */
-              if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 2, 1, 1, 1, 1)) {
-                __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+              __pyx_t_8 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 2, 1, 1, 1, 1) == 1);
+              __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+              if (__pyx_t_8) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1818
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1823
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
- *                                                 1, 1, 2, 1, 1, 1, 1) and
+ *                                                 1, 1, 2, 1, 1, 1, 1) == 1) and
  *                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and             # <<<<<<<<<<<<<<
  *                                 self.find_fixpoint(f_x_low, f_low,
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  */
-                __pyx_t_9 = (!__pyx_v_self->tight_phrases);
-                if (!__pyx_t_9) {
-                  __pyx_t_7 = ((__pyx_v_f_links_low[__pyx_v_f_x_low]) != -1);
-                  if (__pyx_t_7) {
-                    __pyx_t_18 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) != -1);
-                    __pyx_t_8 = __pyx_t_18;
+                __pyx_t_7 = (!__pyx_v_self->tight_phrases);
+                if (!__pyx_t_7) {
+                  __pyx_t_18 = ((__pyx_v_f_links_low[__pyx_v_f_x_low]) != -1);
+                  if (__pyx_t_18) {
+                    __pyx_t_9 = ((__pyx_v_f_links_low[(__pyx_v_f_x_high - 1)]) != -1);
+                    __pyx_t_19 = __pyx_t_9;
                   } else {
-                    __pyx_t_8 = __pyx_t_7;
+                    __pyx_t_19 = __pyx_t_18;
                   }
-                  __pyx_t_7 = __pyx_t_8;
+                  __pyx_t_18 = __pyx_t_19;
                 } else {
-                  __pyx_t_7 = __pyx_t_9;
+                  __pyx_t_18 = __pyx_t_7;
                 }
-                if (__pyx_t_7) {
+                if (__pyx_t_18) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1819
- *                                                 1, 1, 2, 1, 1, 1, 1) and
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1824
+ *                                                 1, 1, 2, 1, 1, 1, 1) == 1) and
  *                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and
  *                                 self.find_fixpoint(f_x_low, f_low,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  */
-                  __pyx_t_15 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __Pyx_GOTREF(__pyx_t_15);
+                  __pyx_t_1 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __Pyx_GOTREF(__pyx_t_1);
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1823
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1828
  *                                                 -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
  *                                                 0, 0, 0, 0, 0, 0, 0) and
  *                                 self.find_fixpoint(f_high, f_x_high,
  */
-                  __pyx_t_3 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
-                  __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+                  __pyx_t_3 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
+                  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                   if (__pyx_t_3) {
 
-                    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1825
+                    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1830
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                                 0, 0, 0, 0, 0, 0, 0) and
  *                                 self.find_fixpoint(f_high, f_x_high,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 -1, -1, e_gap_low+1+num_gaps, e_gap_high+1+num_gaps,
  */
-                    __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                    __Pyx_GOTREF(__pyx_t_15);
+                    __pyx_t_1 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    __Pyx_GOTREF(__pyx_t_1);
 
-                    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1830
+                    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1835
  *                                                 f_gap_low+1+num_gaps, f_gap_high+1+num_gaps,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
  *                                                 0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  */
-                    __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_high, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, ((__pyx_v_e_gap_low + 1) + __pyx_v_num_gaps), ((__pyx_v_e_gap_high + 1) + __pyx_v_num_gaps), ((__pyx_v_f_gap_low + 1) + __pyx_v_num_gaps), ((__pyx_v_f_gap_high + 1) + __pyx_v_num_gaps), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
-                    __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
-                    __pyx_t_9 = __pyx_t_4;
+                    __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_high, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, -1, -1, ((__pyx_v_e_gap_low + 1) + __pyx_v_num_gaps), ((__pyx_v_e_gap_high + 1) + __pyx_v_num_gaps), ((__pyx_v_f_gap_low + 1) + __pyx_v_num_gaps), ((__pyx_v_f_gap_high + 1) + __pyx_v_num_gaps), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 0, 0, 0, 0, 0, 0, 0);
+                    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+                    __pyx_t_7 = __pyx_t_4;
                   } else {
-                    __pyx_t_9 = __pyx_t_3;
+                    __pyx_t_7 = __pyx_t_3;
                   }
-                  __pyx_t_8 = __pyx_t_9;
+                  __pyx_t_19 = __pyx_t_7;
                 } else {
-                  __pyx_t_8 = __pyx_t_7;
+                  __pyx_t_19 = __pyx_t_18;
                 }
-                __pyx_t_7 = __pyx_t_8;
+                __pyx_t_18 = __pyx_t_19;
               } else {
-                __pyx_t_7 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 2, 1, 1, 1, 1);
-                __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+                __pyx_t_18 = __pyx_t_8;
               }
-              __pyx_t_8 = __pyx_t_7;
+              __pyx_t_8 = __pyx_t_18;
             } else {
               __pyx_t_8 = __pyx_v_met_constraints;
             }
             if (__pyx_t_8) {
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1832
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1837
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                                 0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -57185,7 +57318,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1833
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1838
  *                                                 0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -57194,35 +57327,35 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1834
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1839
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1835
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1840
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  */
-              __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1836
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1841
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -57231,7 +57364,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1837
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1842
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1             # <<<<<<<<<<<<<<
@@ -57240,27 +57373,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = (__pyx_v_i + 1);
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1838
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1843
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1839
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1844
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -57270,7 +57403,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1840
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1845
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -57280,7 +57413,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1841
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1846
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -57289,7 +57422,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1842
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1847
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -57301,7 +57434,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1844
+                  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1849
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -57313,7 +57446,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L106:;
               }
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1845
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1850
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -57322,81 +57455,81 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1846
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1851
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  */
-              __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1847
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1852
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  */
-              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_14);
               __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1850
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1855
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
-              __pyx_t_14 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 2), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 2), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_14;
               __pyx_t_14 = 0;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1851
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1856
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_8 = (__pyx_t_13 > 0);
               if (__pyx_t_8) {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1852
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1857
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L107;
               }
               /*else*/ {
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1854
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1859
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -57407,7 +57540,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L107:;
 
-              /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1855
+              /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1860
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:             # <<<<<<<<<<<<<<
@@ -57418,31 +57551,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_14 = __pyx_v_phrase_list; __Pyx_INCREF(__pyx_t_14); __pyx_t_13 = 0;
                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __pyx_t_16 = Py_TYPE(__pyx_t_14)->tp_iternext;
               }
               for (;;) {
                 if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_14)) {
                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_14)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
                 } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_14)) {
                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #else
-                  __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
+                  __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
                 } else {
                   __pyx_t_15 = __pyx_t_16(__pyx_t_14);
                   if (unlikely(!__pyx_t_15)) {
                     if (PyErr_Occurred()) {
                       if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -57450,35 +57575,29 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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                 if ((likely(PyTuple_CheckExact(__pyx_t_15))) || (PyList_CheckExact(__pyx_t_15))) {
                   PyObject* sequence = __pyx_t_15;
-                  #if CYTHON_COMPILING_IN_CPYTHON
-                  Py_ssize_t size = Py_SIZE(sequence);
-                  #else
-                  Py_ssize_t size = PySequence_Size(sequence);
-                  #endif
-                  if (unlikely(size != 2)) {
-                    if (size > 2) __Pyx_RaiseTooManyValuesError(2);
-                    else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  }
-                  #if CYTHON_COMPILING_IN_CPYTHON
                   if (likely(PyTuple_CheckExact(sequence))) {
+                    if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+                      if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
                   } else {
+                    if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+                      if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+                      else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+                      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    }
                     __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
                     __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
                   }
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                   __Pyx_INCREF(__pyx_t_2);
-                  #else
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-                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  #endif
                   __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
-                } else
-                {
+                } else {
                   Py_ssize_t index = -1;
-                  __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_10);
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@@ -57486,15 +57605,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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                   __Pyx_GOTREF(__pyx_t_2);
-                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_17 = NULL;
+                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
                   goto __pyx_L111_unpacking_done;
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                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
-                  __pyx_t_17 = NULL;
-                  if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+                  if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 __Pyx_XDECREF(__pyx_v_phrase2);
@@ -57504,7 +57622,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_v_eindexes = __pyx_t_2;
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1856
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1861
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:
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@@ -57513,31 +57631,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_t_15 = ((PyObject *)__pyx_v_self->findexes);
                 __Pyx_INCREF(__pyx_t_15);
-                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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                 __pyx_v_als4 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
                 __pyx_t_2 = 0;
 
-                /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1857
+                /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1862
  *                                 for phrase2, eindexes in phrase_list:
  *                                     als4 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
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  *                 reason_for_failure = "Unable to extract basic phrase"
  */
-                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
-                __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 __Pyx_INCREF(((PyObject *)__pyx_v_als4));
                 PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_als4));
                 __Pyx_GIVEREF(((PyObject *)__pyx_v_als4));
-                __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
-                __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
                 PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_fphr));
@@ -57551,7 +57669,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __Pyx_GIVEREF(__pyx_t_1);
                 __pyx_t_2 = 0;
                 __pyx_t_1 = 0;
-                __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -57573,23 +57691,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     /*else*/ {
 
-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1859
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1864
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als4)))
  *             else:
  *                 reason_for_failure = "Unable to extract basic phrase"             # <<<<<<<<<<<<<<
  * 
  *         free(sent_links)
  */
-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_133));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_134));
       __Pyx_DECREF(__pyx_v_reason_for_failure);
-      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_133);
+      __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_134);
     }
     __pyx_L34:;
     goto __pyx_L33;
   }
   __pyx_L33:;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1861
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1866
  *                 reason_for_failure = "Unable to extract basic phrase"
  * 
  *         free(sent_links)             # <<<<<<<<<<<<<<
@@ -57598,7 +57716,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_sent_links);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1862
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1867
  * 
  *         free(sent_links)
  *         free(f_links_low)             # <<<<<<<<<<<<<<
@@ -57607,7 +57725,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_f_links_low);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1863
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1868
  *         free(sent_links)
  *         free(f_links_low)
  *         free(f_links_high)             # <<<<<<<<<<<<<<
@@ -57616,7 +57734,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_f_links_high);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1864
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1869
  *         free(f_links_low)
  *         free(f_links_high)
  *         free(e_links_low)             # <<<<<<<<<<<<<<
@@ -57625,7 +57743,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_e_links_low);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1865
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1870
  *         free(f_links_high)
  *         free(e_links_low)
  *         free(e_links_high)             # <<<<<<<<<<<<<<
@@ -57634,7 +57752,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_e_links_high);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1866
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1871
  *         free(e_links_low)
  *         free(e_links_high)
  *         free(f_gap_low)             # <<<<<<<<<<<<<<
@@ -57643,7 +57761,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_f_gap_low);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1867
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1872
  *         free(e_links_high)
  *         free(f_gap_low)
  *         free(f_gap_high)             # <<<<<<<<<<<<<<
@@ -57652,7 +57770,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_f_gap_high);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1868
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1873
  *         free(f_gap_low)
  *         free(f_gap_high)
  *         free(e_gap_low)             # <<<<<<<<<<<<<<
@@ -57661,7 +57779,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_e_gap_low);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1869
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1874
  *         free(f_gap_high)
  *         free(e_gap_low)
  *         free(e_gap_high)             # <<<<<<<<<<<<<<
@@ -57670,7 +57788,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   free(__pyx_v_e_gap_high);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1871
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1876
  *         free(e_gap_high)
  * 
  *         return extracts             # <<<<<<<<<<<<<<
@@ -57718,11 +57836,11 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_26add_instance(PyObject
   PyObject *__pyx_v_f_words = 0;
   PyObject *__pyx_v_e_words = 0;
   PyObject *__pyx_v_alignment = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__f_words,&__pyx_n_s__e_words,&__pyx_n_s__alignment,0};
   PyObject *__pyx_r = 0;
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-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__f_words,&__pyx_n_s__e_words,&__pyx_n_s__alignment,0};
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       Py_ssize_t kw_args;
@@ -57737,21 +57855,24 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_26add_instance(PyObject
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_words)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_words);
+        if (likely(values[0])) kw_args--;
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         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_words)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_words);
+        if (likely(values[1])) kw_args--;
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-          __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alignment)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alignment);
+        if (likely(values[2])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       }
       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add_instance") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add_instance") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       goto __pyx_L5_argtuple_error;
@@ -57766,7 +57887,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_26add_instance(PyObject
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   goto __pyx_L4_argument_unpacking_done;
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-  __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1879; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("add_instance", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
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@@ -57790,11 +57911,12 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_12add_instance_1extract
   PyObject *__pyx_v_links = 0;
   PyObject *__pyx_v_nt = 0;
   PyObject *__pyx_v_nt_open = 0;
+  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__f_i,&__pyx_n_s__f_j,&__pyx_n_s__e_i,&__pyx_n_s__e_j,&__pyx_n_s__min_bound,&__pyx_n_s__wc,&__pyx_n_s__links,&__pyx_n_s__nt,&__pyx_n_s__nt_open,0};
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("extract (wrapper)", 0);
+  __pyx_self = __pyx_self;
   {
-    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__f_i,&__pyx_n_s__f_j,&__pyx_n_s__e_i,&__pyx_n_s__e_j,&__pyx_n_s__min_bound,&__pyx_n_s__wc,&__pyx_n_s__links,&__pyx_n_s__nt,&__pyx_n_s__nt_open,0};
     PyObject* values[9] = {0,0,0,0,0,0,0,0,0};
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       Py_ssize_t kw_args;
@@ -57815,51 +57937,60 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_12add_instance_1extract
       kw_args = PyDict_Size(__pyx_kwds);
       switch (pos_args) {
         case  0:
-        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_i)) != 0)) kw_args--;
+        values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_i);
+        if (likely(values[0])) kw_args--;
         else goto __pyx_L5_argtuple_error;
         case  1:
-        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_j)) != 0)) kw_args--;
+        values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__f_j);
+        if (likely(values[1])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
-        if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_i)) != 0)) kw_args--;
+        values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_i);
+        if (likely(values[2])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  3:
-        if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_j)) != 0)) kw_args--;
+        values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__e_j);
+        if (likely(values[3])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 3); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 3); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  4:
-        if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__min_bound)) != 0)) kw_args--;
+        values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__min_bound);
+        if (likely(values[4])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 4); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 4); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  5:
-        if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__wc)) != 0)) kw_args--;
+        values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__wc);
+        if (likely(values[5])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 5); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 5); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  6:
-        if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__links)) != 0)) kw_args--;
+        values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__links);
+        if (likely(values[6])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 6); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 6); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  7:
-        if (likely((values[7] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__nt)) != 0)) kw_args--;
+        values[7] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__nt);
+        if (likely(values[7])) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 7); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 7); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  8:
-        if (likely((values[8] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__nt_open)) != 0)) kw_args--;
+        values[8] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__nt_open);
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-          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 8); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, 8); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
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       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "extract") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "extract") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -57886,7 +58017,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_12add_instance_1extract
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-  __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1913; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("extract", 1, 9, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -57897,7 +58028,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_12add_instance_1extract
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 }
 
-/* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1913
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1915
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1920
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-  if (unlikely(!__pyx_cur_scope->__pyx_v_f_len)) { __Pyx_RaiseClosureNameError("f_len"); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
-  __pyx_t_1 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_f_len, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_cur_scope->__pyx_v_f_len)) { __Pyx_RaiseClosureNameError("f_len"); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1920; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+  __pyx_t_1 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_f_len, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyObject_RichCompare(__pyx_v_f_j, __pyx_t_1, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_RichCompare(__pyx_v_f_j, __pyx_t_1, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_2);
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+  __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1951
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1952
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+      __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1949
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1954
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1954
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-  __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_nt_open); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_nt_open); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1955
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1960
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1956
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1961
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+      __pyx_t_7 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        #endif
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-        #endif
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-            else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1957
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+      __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1958
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1961
+    /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1966
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+      __pyx_t_2 = PyInt_FromLong(__pyx_cur_scope->__pyx_v_self->max_length); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyObject_RichCompare(__pyx_v_wc, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_4);
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-      __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1962
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+      __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1963
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+        __pyx_t_7 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          #endif
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-              else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1964
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1969
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+        __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1965
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+        if (unlikely(!__pyx_cur_scope->__pyx_v_cover)) { __Pyx_RaiseClosureNameError("cover"); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
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+        if (PyObject_SetItem(__pyx_cur_scope->__pyx_v_cover, __pyx_t_4, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1966
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1971
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+      __pyx_t_2 = __Pyx_PyObject_Append(__pyx_v_links, ((PyObject *)__pyx_v_plus_links)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1967
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1968
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1969
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1970
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1971
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-          #endif
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-          #if CYTHON_COMPILING_IN_CPYTHON
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-          #endif
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-              else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1972
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1977
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-        __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_t_15, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        if (unlikely(!__pyx_cur_scope->__pyx_v_cover)) { __Pyx_RaiseClosureNameError("cover"); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1974
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+  __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_nt); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_4, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyNumber_Subtract(__pyx_v_f_j, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1976
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+    __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_nt, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = __Pyx_PySequence_GetSlice(__pyx_t_8, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1977
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+    __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_nt, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1980
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1981
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1982
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+      __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_nt, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1983
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+      __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1984
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1985
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1987
+        /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1992
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-        /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1988
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1989
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1990
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1991
+      /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1996
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1992
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1994
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2001
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+      if (unlikely(!__pyx_cur_scope->__pyx_v_e_nt_cover)) { __Pyx_RaiseClosureNameError("e_nt_cover"); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2006; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2012
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2013
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2016
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1890
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-      __pyx_t_8 = NULL;
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2029
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2032
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2033
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-      #if CYTHON_COMPILING_IN_CPYTHON
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+          {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_8 = NULL;
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2034
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2092
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-      /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2094
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2100
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-    /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2155
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2164
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2194
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-    #if CYTHON_COMPILING_IN_CPYTHON
-    __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    #else
-    __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    #endif
+    __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++;
     __Pyx_XDECREF(__pyx_v_model);
     __pyx_v_model = __pyx_t_4;
     __pyx_t_4 = 0;
@@ -66760,7 +66725,7 @@ static int __pyx_pf_3_sa_6Scorer___init__(struct __pyx_obj_3_sa_Scorer *__pyx_v_
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
     __pyx_t_4 = PyInt_FromLong(((struct __pyx_vtabstruct_3_sa_StringMap *)__pyx_v_3_sa_FD->__pyx_vtab)->index(__pyx_v_3_sa_FD, ((char *)__pyx_t_5))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
-    if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   }
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -66768,7 +66733,7 @@ static int __pyx_pf_3_sa_6Scorer___init__(struct __pyx_obj_3_sa_Scorer *__pyx_v_
   __pyx_v_names = __pyx_t_1;
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":27
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":27
  *     def __init__(self, *models):
  *         names = [FD.index(<char *>model.__name__) for model in models]
  *         self.models = zip(names, models)             # <<<<<<<<<<<<<<
@@ -66807,7 +66772,7 @@ static int __pyx_pf_3_sa_6Scorer___init__(struct __pyx_obj_3_sa_Scorer *__pyx_v_
   return __pyx_r;
 }
 
-/* "/home/m/workspace/cdec/python/src/sa/features.pxi":29
+/* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":29
  *         self.models = zip(names, models)
  * 
  *     cdef FeatureVector score(self, ctx):             # <<<<<<<<<<<<<<
@@ -66834,7 +66799,7 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("score", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":30
  * 
  *     cdef FeatureVector score(self, ctx):
  *         cdef FeatureVector scores = FeatureVector()             # <<<<<<<<<<<<<<
@@ -66846,7 +66811,7 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
   __pyx_v_scores = ((struct __pyx_obj_3_sa_FeatureVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":31
  *     cdef FeatureVector score(self, ctx):
  *         cdef FeatureVector scores = FeatureVector()
  *         for name, model in self.models:             # <<<<<<<<<<<<<<
@@ -66864,18 +66829,10 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
   for (;;) {
     if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
       if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
     } else {
       __pyx_t_4 = __pyx_t_3(__pyx_t_1);
       if (unlikely(!__pyx_t_4)) {
@@ -66889,33 +66846,27 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
     }
     if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
       PyObject* sequence = __pyx_t_4;
-      #if CYTHON_COMPILING_IN_CPYTHON
-      Py_ssize_t size = Py_SIZE(sequence);
-      #else
-      Py_ssize_t size = PySequence_Size(sequence);
-      #endif
-      if (unlikely(size != 2)) {
-        if (size > 2) __Pyx_RaiseTooManyValuesError(2);
-        else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-        {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      }
-      #if CYTHON_COMPILING_IN_CPYTHON
       if (likely(PyTuple_CheckExact(sequence))) {
+        if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+          if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+          else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+          {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        }
         __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); 
         __pyx_t_6 = PyTuple_GET_ITEM(sequence, 1); 
       } else {
+        if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+          if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+          else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+          {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        }
         __pyx_t_5 = PyList_GET_ITEM(sequence, 0); 
         __pyx_t_6 = PyList_GET_ITEM(sequence, 1); 
       }
       __Pyx_INCREF(__pyx_t_5);
       __Pyx_INCREF(__pyx_t_6);
-      #else
-      __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      #endif
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-    } else
-    {
+    } else {
       Py_ssize_t index = -1;
       __pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_7);
@@ -66926,13 +66877,12 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
       index = 1; __pyx_t_6 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_6)) goto __pyx_L5_unpacking_failed;
       __Pyx_GOTREF(__pyx_t_6);
       if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_8 = NULL;
       __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
       goto __pyx_L6_unpacking_done;
       __pyx_L5_unpacking_failed:;
       __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
-      __pyx_t_8 = NULL;
-      if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+      if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+      if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
       {__pyx_filename = __pyx_f[13]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_L6_unpacking_done:;
     }
@@ -66943,7 +66893,7 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
     __pyx_v_model = __pyx_t_6;
     __pyx_t_6 = 0;
 
-    /* "/home/m/workspace/cdec/python/src/sa/features.pxi":32
+    /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":32
  *         cdef FeatureVector scores = FeatureVector()
  *         for name, model in self.models:
  *             scores.set(name, model(ctx))             # <<<<<<<<<<<<<<
@@ -66975,7 +66925,7 @@ static struct __pyx_obj_3_sa_FeatureVector *__pyx_f_3_sa_6Scorer_score(struct __
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":33
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":33
  *         for name, model in self.models:
  *             scores.set(name, model(ctx))
  *         return scores             # <<<<<<<<<<<<<<
@@ -67421,7 +67371,7 @@ static PyTypeObject __pyx_type_3_sa_IntList = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa_FeatureVector(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_FeatureVector(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa_FeatureVector *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -67436,8 +67386,8 @@ static PyObject *__pyx_tp_new_3_sa_FeatureVector(PyTypeObject *t, CYTHON_UNUSED
 
 static void __pyx_tp_dealloc_3_sa_FeatureVector(PyObject *o) {
   struct __pyx_obj_3_sa_FeatureVector *p = (struct __pyx_obj_3_sa_FeatureVector *)o;
-  Py_CLEAR(p->names);
-  Py_CLEAR(p->values);
+  Py_XDECREF(((PyObject *)p->names));
+  Py_XDECREF(((PyObject *)p->values));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -67657,7 +67607,7 @@ static PyObject *__pyx_sq_item_3_sa_Phrase(PyObject *o, Py_ssize_t i) {
   return r;
 }
 
-static PyObject *__pyx_getprop_3_sa_6Phrase_words(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_6Phrase_words(PyObject *o, void *x) {
   return __pyx_pw_3_sa_6Phrase_5words_1__get__(o);
 }
 
@@ -67849,10 +67799,10 @@ static PyObject *__pyx_tp_new_3_sa_Rule(PyTypeObject *t, PyObject *a, PyObject *
 
 static void __pyx_tp_dealloc_3_sa_Rule(PyObject *o) {
   struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
-  Py_CLEAR(p->f);
-  Py_CLEAR(p->e);
-  Py_CLEAR(p->scores);
-  Py_CLEAR(p->word_alignments);
+  Py_XDECREF(((PyObject *)p->f));
+  Py_XDECREF(((PyObject *)p->e));
+  Py_XDECREF(((PyObject *)p->scores));
+  Py_XDECREF(p->word_alignments);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -67892,11 +67842,11 @@ static int __pyx_tp_clear_3_sa_Rule(PyObject *o) {
   return 0;
 }
 
-static PyObject *__pyx_getprop_3_sa_4Rule_f(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_4Rule_f(PyObject *o, void *x) {
   return __pyx_pw_3_sa_4Rule_1f_1__get__(o);
 }
 
-static PyObject *__pyx_getprop_3_sa_4Rule_e(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_4Rule_e(PyObject *o, void *x) {
   return __pyx_pw_3_sa_4Rule_1e_1__get__(o);
 }
 
@@ -68068,7 +68018,7 @@ static PyTypeObject __pyx_type_3_sa_Rule = {
 };
 static struct __pyx_vtabstruct_3_sa_StringMap __pyx_vtable_3_sa_StringMap;
 
-static PyObject *__pyx_tp_new_3_sa_StringMap(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_StringMap(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa_StringMap *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -68271,11 +68221,11 @@ static PyObject *__pyx_tp_new_3_sa_DataArray(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_DataArray(PyObject *o) {
   struct __pyx_obj_3_sa_DataArray *p = (struct __pyx_obj_3_sa_DataArray *)o;
-  Py_CLEAR(p->word2id);
-  Py_CLEAR(p->id2word);
-  Py_CLEAR(p->data);
-  Py_CLEAR(p->sent_id);
-  Py_CLEAR(p->sent_index);
+  Py_XDECREF(p->word2id);
+  Py_XDECREF(p->id2word);
+  Py_XDECREF(((PyObject *)p->data));
+  Py_XDECREF(((PyObject *)p->sent_id));
+  Py_XDECREF(((PyObject *)p->sent_index));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -68328,11 +68278,11 @@ static PyObject *__pyx_sq_item_3_sa_DataArray(PyObject *o, Py_ssize_t i) {
   return r;
 }
 
-static PyObject *__pyx_getprop_3_sa_9DataArray_word2id(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9DataArray_word2id(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9DataArray_7word2id_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9DataArray_word2id(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9DataArray_word2id(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9DataArray_7word2id_3__set__(o, v);
   }
@@ -68341,11 +68291,11 @@ static int __pyx_setprop_3_sa_9DataArray_word2id(PyObject *o, PyObject *v, CYTHO
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9DataArray_id2word(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9DataArray_id2word(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9DataArray_7id2word_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9DataArray_id2word(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9DataArray_id2word(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9DataArray_7id2word_3__set__(o, v);
   }
@@ -68354,11 +68304,11 @@ static int __pyx_setprop_3_sa_9DataArray_id2word(PyObject *o, PyObject *v, CYTHO
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9DataArray_data(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9DataArray_data(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9DataArray_4data_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9DataArray_data(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9DataArray_data(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9DataArray_4data_3__set__(o, v);
   }
@@ -68367,11 +68317,11 @@ static int __pyx_setprop_3_sa_9DataArray_data(PyObject *o, PyObject *v, CYTHON_U
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9DataArray_sent_id(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9DataArray_sent_id(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9DataArray_7sent_id_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9DataArray_sent_id(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9DataArray_sent_id(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9DataArray_7sent_id_3__set__(o, v);
   }
@@ -68380,11 +68330,11 @@ static int __pyx_setprop_3_sa_9DataArray_sent_id(PyObject *o, PyObject *v, CYTHO
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9DataArray_sent_index(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9DataArray_sent_index(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9DataArray_10sent_index_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9DataArray_sent_index(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9DataArray_sent_index(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9DataArray_10sent_index_3__set__(o, v);
   }
@@ -68589,8 +68539,8 @@ static PyObject *__pyx_tp_new_3_sa_Alignment(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_Alignment(PyObject *o) {
   struct __pyx_obj_3_sa_Alignment *p = (struct __pyx_obj_3_sa_Alignment *)o;
-  Py_CLEAR(p->links);
-  Py_CLEAR(p->sent_index);
+  Py_XDECREF(((PyObject *)p->links));
+  Py_XDECREF(((PyObject *)p->sent_index));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -68807,14 +68757,14 @@ static PyObject *__pyx_tp_new_3_sa_BiLex(PyTypeObject *t, PyObject *a, PyObject
 
 static void __pyx_tp_dealloc_3_sa_BiLex(PyObject *o) {
   struct __pyx_obj_3_sa_BiLex *p = (struct __pyx_obj_3_sa_BiLex *)o;
-  Py_CLEAR(p->col1);
-  Py_CLEAR(p->col2);
-  Py_CLEAR(p->f_index);
-  Py_CLEAR(p->e_index);
-  Py_CLEAR(p->id2eword);
-  Py_CLEAR(p->id2fword);
-  Py_CLEAR(p->eword2id);
-  Py_CLEAR(p->fword2id);
+  Py_XDECREF(((PyObject *)p->col1));
+  Py_XDECREF(((PyObject *)p->col2));
+  Py_XDECREF(((PyObject *)p->f_index));
+  Py_XDECREF(((PyObject *)p->e_index));
+  Py_XDECREF(p->id2eword);
+  Py_XDECREF(p->id2fword);
+  Py_XDECREF(p->eword2id);
+  Py_XDECREF(p->fword2id);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -69044,7 +68994,7 @@ static PyTypeObject __pyx_type_3_sa_BiLex = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa_BitSetIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_BitSetIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
   return o;
@@ -69213,7 +69163,7 @@ static PyTypeObject __pyx_type_3_sa_BitSetIterator = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa_BitSet(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_BitSet(PyTypeObject *t, PyObject *a, PyObject *k) {
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
   if (__pyx_pw_3_sa_6BitSet_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
@@ -69397,7 +69347,7 @@ static PyTypeObject __pyx_type_3_sa_BitSet = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa_VEBIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_VEBIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
   return o;
@@ -69767,8 +69717,8 @@ static PyObject *__pyx_tp_new_3_sa_LCP(PyTypeObject *t, PyObject *a, PyObject *k
 
 static void __pyx_tp_dealloc_3_sa_LCP(PyObject *o) {
   struct __pyx_obj_3_sa_LCP *p = (struct __pyx_obj_3_sa_LCP *)o;
-  Py_CLEAR(p->sa);
-  Py_CLEAR(p->lcp);
+  Py_XDECREF(((PyObject *)p->sa));
+  Py_XDECREF(((PyObject *)p->lcp));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -69956,7 +69906,7 @@ static PyTypeObject __pyx_type_3_sa_LCP = {
 };
 static struct __pyx_vtabstruct_3_sa_Alphabet __pyx_vtable_3_sa_Alphabet;
 
-static PyObject *__pyx_tp_new_3_sa_Alphabet(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_Alphabet(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa_Alphabet *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -69982,9 +69932,9 @@ static void __pyx_tp_dealloc_3_sa_Alphabet(PyObject *o) {
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
   }
-  Py_CLEAR(p->terminals);
-  Py_CLEAR(p->nonterminals);
-  Py_CLEAR(p->id2sym);
+  Py_XDECREF(((PyObject *)p->terminals));
+  Py_XDECREF(((PyObject *)p->nonterminals));
+  Py_XDECREF(((PyObject *)p->id2sym));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -70018,11 +69968,11 @@ static int __pyx_tp_clear_3_sa_Alphabet(PyObject *o) {
   return 0;
 }
 
-static PyObject *__pyx_getprop_3_sa_8Alphabet_terminals(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_8Alphabet_terminals(PyObject *o, void *x) {
   return __pyx_pw_3_sa_8Alphabet_9terminals_1__get__(o);
 }
 
-static PyObject *__pyx_getprop_3_sa_8Alphabet_nonterminals(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_8Alphabet_nonterminals(PyObject *o, void *x) {
   return __pyx_pw_3_sa_8Alphabet_12nonterminals_1__get__(o);
 }
 
@@ -70394,8 +70344,8 @@ static PyObject *__pyx_tp_new_3_sa_Precomputation(PyTypeObject *t, PyObject *a,
 
 static void __pyx_tp_dealloc_3_sa_Precomputation(PyObject *o) {
   struct __pyx_obj_3_sa_Precomputation *p = (struct __pyx_obj_3_sa_Precomputation *)o;
-  Py_CLEAR(p->precomputed_index);
-  Py_CLEAR(p->precomputed_collocations);
+  Py_XDECREF(p->precomputed_index);
+  Py_XDECREF(p->precomputed_collocations);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -70602,9 +70552,9 @@ static PyObject *__pyx_tp_new_3_sa_SuffixArray(PyTypeObject *t, PyObject *a, PyO
 
 static void __pyx_tp_dealloc_3_sa_SuffixArray(PyObject *o) {
   struct __pyx_obj_3_sa_SuffixArray *p = (struct __pyx_obj_3_sa_SuffixArray *)o;
-  Py_CLEAR(p->darray);
-  Py_CLEAR(p->sa);
-  Py_CLEAR(p->ha);
+  Py_XDECREF(((PyObject *)p->darray));
+  Py_XDECREF(((PyObject *)p->sa));
+  Py_XDECREF(((PyObject *)p->ha));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -70810,7 +70760,7 @@ static PyTypeObject __pyx_type_3_sa_SuffixArray = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa_TrieNode(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_TrieNode(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa_TrieNode *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -70824,7 +70774,7 @@ static PyObject *__pyx_tp_new_3_sa_TrieNode(PyTypeObject *t, CYTHON_UNUSED PyObj
 
 static void __pyx_tp_dealloc_3_sa_TrieNode(PyObject *o) {
   struct __pyx_obj_3_sa_TrieNode *p = (struct __pyx_obj_3_sa_TrieNode *)o;
-  Py_CLEAR(p->children);
+  Py_XDECREF(p->children);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -70846,11 +70796,11 @@ static int __pyx_tp_clear_3_sa_TrieNode(PyObject *o) {
   return 0;
 }
 
-static PyObject *__pyx_getprop_3_sa_8TrieNode_children(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_8TrieNode_children(PyObject *o, void *x) {
   return __pyx_pw_3_sa_8TrieNode_8children_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_8TrieNode_children(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_8TrieNode_children(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_8TrieNode_8children_3__set__(o, v);
   }
@@ -71038,9 +70988,9 @@ static PyObject *__pyx_tp_new_3_sa_ExtendedTrieNode(PyTypeObject *t, PyObject *a
 
 static void __pyx_tp_dealloc_3_sa_ExtendedTrieNode(PyObject *o) {
   struct __pyx_obj_3_sa_ExtendedTrieNode *p = (struct __pyx_obj_3_sa_ExtendedTrieNode *)o;
-  Py_CLEAR(p->phrase);
-  Py_CLEAR(p->phrase_location);
-  Py_CLEAR(p->suffix_link);
+  Py_XDECREF(p->phrase);
+  Py_XDECREF(p->phrase_location);
+  Py_XDECREF(p->suffix_link);
   __pyx_tp_dealloc_3_sa_TrieNode(o);
 }
 
@@ -71076,11 +71026,11 @@ static int __pyx_tp_clear_3_sa_ExtendedTrieNode(PyObject *o) {
   return 0;
 }
 
-static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_phrase(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_phrase(PyObject *o, void *x) {
   return __pyx_pw_3_sa_16ExtendedTrieNode_6phrase_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_16ExtendedTrieNode_6phrase_3__set__(o, v);
   }
@@ -71089,11 +71039,11 @@ static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase(PyObject *o, PyObject *v
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_phrase_location(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_phrase_location(PyObject *o, void *x) {
   return __pyx_pw_3_sa_16ExtendedTrieNode_15phrase_location_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase_location(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase_location(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_16ExtendedTrieNode_15phrase_location_3__set__(o, v);
   }
@@ -71102,11 +71052,11 @@ static int __pyx_setprop_3_sa_16ExtendedTrieNode_phrase_location(PyObject *o, Py
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_suffix_link(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_16ExtendedTrieNode_suffix_link(PyObject *o, void *x) {
   return __pyx_pw_3_sa_16ExtendedTrieNode_11suffix_link_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_16ExtendedTrieNode_suffix_link(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_16ExtendedTrieNode_suffix_link(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_16ExtendedTrieNode_11suffix_link_3__set__(o, v);
   }
@@ -71294,7 +71244,7 @@ static PyObject *__pyx_tp_new_3_sa_TrieTable(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_TrieTable(PyObject *o) {
   struct __pyx_obj_3_sa_TrieTable *p = (struct __pyx_obj_3_sa_TrieTable *)o;
-  Py_CLEAR(p->root);
+  Py_XDECREF(p->root);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -71316,11 +71266,11 @@ static int __pyx_tp_clear_3_sa_TrieTable(PyObject *o) {
   return 0;
 }
 
-static PyObject *__pyx_getprop_3_sa_9TrieTable_extended(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9TrieTable_extended(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9TrieTable_8extended_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9TrieTable_extended(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9TrieTable_extended(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9TrieTable_8extended_3__set__(o, v);
   }
@@ -71330,11 +71280,11 @@ static int __pyx_setprop_3_sa_9TrieTable_extended(PyObject *o, PyObject *v, CYTH
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9TrieTable_count(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9TrieTable_count(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9TrieTable_5count_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9TrieTable_count(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9TrieTable_count(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9TrieTable_5count_3__set__(o, v);
   }
@@ -71344,11 +71294,11 @@ static int __pyx_setprop_3_sa_9TrieTable_count(PyObject *o, PyObject *v, CYTHON_
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_9TrieTable_root(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_3_sa_9TrieTable_root(PyObject *o, void *x) {
   return __pyx_pw_3_sa_9TrieTable_4root_1__get__(o);
 }
 
-static int __pyx_setprop_3_sa_9TrieTable_root(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_3_sa_9TrieTable_root(PyObject *o, PyObject *v, void *x) {
   if (v) {
     return __pyx_pw_3_sa_9TrieTable_4root_3__set__(o, v);
   }
@@ -71538,7 +71488,7 @@ static PyObject *__pyx_tp_new_3_sa_PhraseLocation(PyTypeObject *t, PyObject *a,
 
 static void __pyx_tp_dealloc_3_sa_PhraseLocation(PyObject *o) {
   struct __pyx_obj_3_sa_PhraseLocation *p = (struct __pyx_obj_3_sa_PhraseLocation *)o;
-  Py_CLEAR(p->arr);
+  Py_XDECREF(((PyObject *)p->arr));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -71732,7 +71682,7 @@ static PyObject *__pyx_tp_new_3_sa_Sampler(PyTypeObject *t, PyObject *a, PyObjec
 
 static void __pyx_tp_dealloc_3_sa_Sampler(PyObject *o) {
   struct __pyx_obj_3_sa_Sampler *p = (struct __pyx_obj_3_sa_Sampler *)o;
-  Py_CLEAR(p->sa);
+  Py_XDECREF(((PyObject *)p->sa));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -71952,30 +71902,30 @@ static PyObject *__pyx_tp_new_3_sa_HieroCachingRuleFactory(PyTypeObject *t, PyOb
 
 static void __pyx_tp_dealloc_3_sa_HieroCachingRuleFactory(PyObject *o) {
   struct __pyx_obj_3_sa_HieroCachingRuleFactory *p = (struct __pyx_obj_3_sa_HieroCachingRuleFactory *)o;
-  Py_CLEAR(p->rules);
-  Py_CLEAR(p->sampler);
-  Py_CLEAR(p->scorer);
-  Py_CLEAR(p->precomputed_index);
-  Py_CLEAR(p->precomputed_collocations);
-  Py_CLEAR(p->precompute_file);
-  Py_CLEAR(p->max_rank);
-  Py_CLEAR(p->prev_norm_prefix);
-  Py_CLEAR(p->fsa);
-  Py_CLEAR(p->fda);
-  Py_CLEAR(p->eda);
-  Py_CLEAR(p->alignment);
-  Py_CLEAR(p->eid2symid);
-  Py_CLEAR(p->fid2symid);
-  Py_CLEAR(p->findexes);
-  Py_CLEAR(p->findexes1);
-  Py_CLEAR(p->samples_f);
-  Py_CLEAR(p->phrases_f);
-  Py_CLEAR(p->phrases_e);
-  Py_CLEAR(p->phrases_fe);
-  Py_CLEAR(p->phrases_al);
-  Py_CLEAR(p->bilex_f);
-  Py_CLEAR(p->bilex_e);
-  Py_CLEAR(p->bilex_fe);
+  Py_XDECREF(((PyObject *)p->rules));
+  Py_XDECREF(((PyObject *)p->sampler));
+  Py_XDECREF(((PyObject *)p->scorer));
+  Py_XDECREF(p->precomputed_index);
+  Py_XDECREF(p->precomputed_collocations);
+  Py_XDECREF(p->precompute_file);
+  Py_XDECREF(p->max_rank);
+  Py_XDECREF(p->prev_norm_prefix);
+  Py_XDECREF(((PyObject *)p->fsa));
+  Py_XDECREF(((PyObject *)p->fda));
+  Py_XDECREF(((PyObject *)p->eda));
+  Py_XDECREF(((PyObject *)p->alignment));
+  Py_XDECREF(((PyObject *)p->eid2symid));
+  Py_XDECREF(((PyObject *)p->fid2symid));
+  Py_XDECREF(((PyObject *)p->findexes));
+  Py_XDECREF(((PyObject *)p->findexes1));
+  Py_XDECREF(p->samples_f);
+  Py_XDECREF(p->phrases_f);
+  Py_XDECREF(p->phrases_e);
+  Py_XDECREF(p->phrases_fe);
+  Py_XDECREF(p->phrases_al);
+  Py_XDECREF(p->bilex_f);
+  Py_XDECREF(p->bilex_e);
+  Py_XDECREF(p->bilex_fe);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -72312,7 +72262,7 @@ static PyTypeObject __pyx_type_3_sa_HieroCachingRuleFactory = {
 };
 static struct __pyx_vtabstruct_3_sa_Scorer __pyx_vtable_3_sa_Scorer;
 
-static PyObject *__pyx_tp_new_3_sa_Scorer(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa_Scorer(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa_Scorer *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -72324,7 +72274,7 @@ static PyObject *__pyx_tp_new_3_sa_Scorer(PyTypeObject *t, CYTHON_UNUSED PyObjec
 
 static void __pyx_tp_dealloc_3_sa_Scorer(PyObject *o) {
   struct __pyx_obj_3_sa_Scorer *p = (struct __pyx_obj_3_sa_Scorer *)o;
-  Py_CLEAR(p->models);
+  Py_XDECREF(p->models);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -72504,7 +72454,7 @@ static PyTypeObject __pyx_type_3_sa_Scorer = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct____iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -72515,7 +72465,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct____iter__(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct____iter__(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *)o;
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -72695,7 +72645,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct____iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_1_read_bitext(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_1_read_bitext(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -72706,7 +72656,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_1_read_bitext(PyTypeObject
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_1_read_bitext(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)o;
-  Py_CLEAR(p->__pyx_v_fp);
+  Py_XDECREF(p->__pyx_v_fp);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -72886,7 +72836,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_read_bitext = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -72899,9 +72849,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_genexpr(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_2_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_line);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_line);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -73093,7 +73043,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_3_compute_stats(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_3_compute_stats(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -73109,12 +73059,12 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_3_compute_stats(PyTypeObje
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_3_compute_stats(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)o;
-  Py_CLEAR(p->__pyx_v_ngram);
-  Py_CLEAR(p->__pyx_v_ngram_start);
-  Py_CLEAR(p->__pyx_v_ngram_starts);
-  Py_CLEAR(p->__pyx_v_run_start);
-  Py_CLEAR(p->__pyx_v_self);
-  Py_CLEAR(p->__pyx_v_veb);
+  Py_XDECREF(((PyObject *)p->__pyx_v_ngram));
+  Py_XDECREF(((PyObject *)p->__pyx_v_ngram_start));
+  Py_XDECREF(((PyObject *)p->__pyx_v_ngram_starts));
+  Py_XDECREF(((PyObject *)p->__pyx_v_run_start));
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_XDECREF(((PyObject *)p->__pyx_v_veb));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -73324,7 +73274,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3_compute_stats = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_make_lattice(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_make_lattice(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -73336,8 +73286,8 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_make_lattice(PyTypeObjec
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_4_make_lattice(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)o;
-  Py_CLEAR(p->__pyx_v_word_ids);
-  Py_CLEAR(p->__pyx_v_words);
+  Py_XDECREF(p->__pyx_v_word_ids);
+  Py_XDECREF(p->__pyx_v_words);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -73523,7 +73473,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_4_make_lattice = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_5_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_5_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -73536,9 +73486,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_5_genexpr(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_5_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_word);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_word);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -73730,7 +73680,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_5_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_6_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_6_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -73743,9 +73693,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_6_genexpr(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_6_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_word);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_word);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -73937,7 +73887,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_6_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_7_decode_lattice(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_7_decode_lattice(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -73948,7 +73898,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_7_decode_lattice(PyTypeObj
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_7_decode_lattice(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)o;
-  Py_CLEAR(p->__pyx_v_lattice);
+  Py_XDECREF(p->__pyx_v_lattice);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -74128,7 +74078,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_7_decode_lattice = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_8_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_8_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -74147,15 +74097,15 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_8_genexpr(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_8_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_arc);
-  Py_CLEAR(p->__pyx_v_dist);
-  Py_CLEAR(p->__pyx_v_node);
-  Py_CLEAR(p->__pyx_v_sym);
-  Py_CLEAR(p->__pyx_v_weight);
-  Py_CLEAR(p->__pyx_t_0);
-  Py_CLEAR(p->__pyx_t_3);
-  Py_CLEAR(p->__pyx_t_4);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_arc);
+  Py_XDECREF(p->__pyx_v_dist);
+  Py_XDECREF(p->__pyx_v_node);
+  Py_XDECREF(p->__pyx_v_sym);
+  Py_XDECREF(p->__pyx_v_weight);
+  Py_XDECREF(p->__pyx_t_0);
+  Py_XDECREF(p->__pyx_t_3);
+  Py_XDECREF(p->__pyx_t_4);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -74383,7 +74333,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_8_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_9_decode_sentence(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_9_decode_sentence(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -74394,7 +74344,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_9_decode_sentence(PyTypeOb
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_9_decode_sentence(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p = (struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)o;
-  Py_CLEAR(p->__pyx_v_lattice);
+  Py_XDECREF(p->__pyx_v_lattice);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -74574,7 +74524,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_9_decode_sentence = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_10_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_10_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -74588,10 +74538,10 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_10_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_10_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v__);
-  Py_CLEAR(p->__pyx_v_sym);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v__);
+  Py_XDECREF(p->__pyx_v_sym);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -74789,7 +74739,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_10_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_11_encode_words(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_11_encode_words(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_11_encode_words *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -74800,7 +74750,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_11_encode_words(PyTypeObje
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_11_encode_words(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_11_encode_words *p = (struct __pyx_obj_3_sa___pyx_scope_struct_11_encode_words *)o;
-  Py_CLEAR(p->__pyx_v_words);
+  Py_XDECREF(p->__pyx_v_words);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -74980,7 +74930,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_11_encode_words = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_12_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_12_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_12_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -74993,9 +74943,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_12_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_12_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_12_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_12_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_word);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_word);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -75187,7 +75137,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_12_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_13_decode_words(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_13_decode_words(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_13_decode_words *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -75198,7 +75148,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_13_decode_words(PyTypeObje
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_13_decode_words(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_13_decode_words *p = (struct __pyx_obj_3_sa___pyx_scope_struct_13_decode_words *)o;
-  Py_CLEAR(p->__pyx_v_syms);
+  Py_XDECREF(p->__pyx_v_syms);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -75378,7 +75328,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_13_decode_words = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_14_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_14_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_14_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -75391,9 +75341,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_14_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_14_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_14_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_14_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_sym);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_sym);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -75585,7 +75535,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_14_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_15___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_15___iter__(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_15___iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -75596,7 +75546,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_15___iter__(PyTypeObject *
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_15___iter__(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_15___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_15___iter__ *)o;
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -75776,7 +75726,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_15___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_16___str__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_16___str__(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_16___str__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -75787,7 +75737,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_16___str__(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_16___str__(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_16___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_16___str__ *)o;
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -75967,7 +75917,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_16___str__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_17_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_17_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_17_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -75980,9 +75930,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_17_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_17_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_17_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_17_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_a);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_a);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -76174,7 +76124,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_17_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_18_alignments(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_18_alignments(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_18_alignments *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -76187,9 +76137,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_18_alignments(PyTypeObject
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_18_alignments(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_18_alignments *p = (struct __pyx_obj_3_sa___pyx_scope_struct_18_alignments *)o;
-  Py_CLEAR(p->__pyx_v_point);
-  Py_CLEAR(p->__pyx_v_self);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(p->__pyx_v_point);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -76381,7 +76331,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_18_alignments = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_19_input(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_19_input(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_19_input *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -76407,6 +76357,8 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_19_input(PyTypeObject *t,
   p->__pyx_v_genexpr = 0;
   p->__pyx_v_hiero_phrase = 0;
   p->__pyx_v_input_match = 0;
+  p->__pyx_v_intersect_start_time = 0;
+  p->__pyx_v_intersect_stop_time = 0;
   p->__pyx_v_is_shadow_path = 0;
   p->__pyx_v_key = 0;
   p->__pyx_v_lex_i = 0;
@@ -76438,69 +76390,71 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_19_input(PyTypeObject *t,
   p->__pyx_v_xcat_index = 0;
   p->__pyx_v_xnode = 0;
   p->__pyx_v_xroot = 0;
-  p->__pyx_t_1 = 0;
+  p->__pyx_t_2 = 0;
+  p->__pyx_t_3 = 0;
   p->__pyx_t_4 = 0;
-  p->__pyx_t_5 = 0;
   return o;
 }
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_19_input(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_19_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_19_input *)o;
-  Py_CLEAR(p->__pyx_v_alignment);
-  Py_CLEAR(p->__pyx_v_als);
-  Py_CLEAR(p->__pyx_v_alslist);
-  Py_CLEAR(p->__pyx_v_chunklen);
-  Py_CLEAR(p->__pyx_v_count);
-  Py_CLEAR(p->__pyx_v_e);
-  Py_CLEAR(p->__pyx_v_elist);
-  Py_CLEAR(p->__pyx_v_extract);
-  Py_CLEAR(p->__pyx_v_extract_start);
-  Py_CLEAR(p->__pyx_v_extract_stop);
-  Py_CLEAR(p->__pyx_v_extracts);
-  Py_CLEAR(p->__pyx_v_f);
-  Py_CLEAR(p->__pyx_v_f_syms);
-  Py_CLEAR(p->__pyx_v_fcount);
-  Py_CLEAR(p->__pyx_v_fphrases);
-  Py_CLEAR(p->__pyx_v_frontier);
-  Py_CLEAR(p->__pyx_v_frontier_nodes);
-  Py_CLEAR(p->__pyx_v_fwords);
-  Py_CLEAR(p->__pyx_v_genexpr);
-  Py_CLEAR(p->__pyx_v_hiero_phrase);
-  Py_CLEAR(p->__pyx_v_input_match);
-  Py_CLEAR(p->__pyx_v_is_shadow_path);
-  Py_CLEAR(p->__pyx_v_key);
-  Py_CLEAR(p->__pyx_v_lex_i);
-  Py_CLEAR(p->__pyx_v_lex_j);
-  Py_CLEAR(p->__pyx_v_loc);
-  Py_CLEAR(p->__pyx_v_locs);
-  Py_CLEAR(p->__pyx_v_max_locs);
-  Py_CLEAR(p->__pyx_v_meta);
-  Py_CLEAR(p->__pyx_v_new_frontier);
-  Py_CLEAR(p->__pyx_v_new_node);
-  Py_CLEAR(p->__pyx_v_next_states);
-  Py_CLEAR(p->__pyx_v_node);
-  Py_CLEAR(p->__pyx_v_nodes_isteps_away_buffer);
-  Py_CLEAR(p->__pyx_v_pathlen);
-  Py_CLEAR(p->__pyx_v_phrase);
-  Py_CLEAR(p->__pyx_v_phrase_location);
-  Py_CLEAR(p->__pyx_v_prefix);
-  Py_CLEAR(p->__pyx_v_reachable_buffer);
-  Py_CLEAR(p->__pyx_v_sa_range);
-  Py_CLEAR(p->__pyx_v_sample);
-  Py_CLEAR(p->__pyx_v_scores);
-  Py_CLEAR(p->__pyx_v_seen_phrases);
-  Py_CLEAR(p->__pyx_v_self);
-  Py_CLEAR(p->__pyx_v_spanlen);
-  Py_CLEAR(p->__pyx_v_stop_time);
-  Py_CLEAR(p->__pyx_v_suffix_link);
-  Py_CLEAR(p->__pyx_v_suffix_link_xcat_index);
-  Py_CLEAR(p->__pyx_v_word_id);
-  Py_CLEAR(p->__pyx_v_xcat_index);
-  Py_CLEAR(p->__pyx_v_xnode);
-  Py_CLEAR(p->__pyx_v_xroot);
-  Py_CLEAR(p->__pyx_t_1);
-  Py_CLEAR(p->__pyx_t_4);
-  Py_CLEAR(p->__pyx_t_5);
+  Py_XDECREF(p->__pyx_v_alignment);
+  Py_XDECREF(p->__pyx_v_als);
+  Py_XDECREF(p->__pyx_v_alslist);
+  Py_XDECREF(((PyObject *)p->__pyx_v_chunklen));
+  Py_XDECREF(p->__pyx_v_count);
+  Py_XDECREF(p->__pyx_v_e);
+  Py_XDECREF(p->__pyx_v_elist);
+  Py_XDECREF(p->__pyx_v_extract);
+  Py_XDECREF(p->__pyx_v_extract_start);
+  Py_XDECREF(p->__pyx_v_extract_stop);
+  Py_XDECREF(((PyObject *)p->__pyx_v_extracts));
+  Py_XDECREF(p->__pyx_v_f);
+  Py_XDECREF(((PyObject *)p->__pyx_v_f_syms));
+  Py_XDECREF(p->__pyx_v_fcount);
+  Py_XDECREF(p->__pyx_v_fphrases);
+  Py_XDECREF(((PyObject *)p->__pyx_v_frontier));
+  Py_XDECREF(p->__pyx_v_frontier_nodes);
+  Py_XDECREF(p->__pyx_v_fwords);
+  Py_XDECREF(p->__pyx_v_genexpr);
+  Py_XDECREF(((PyObject *)p->__pyx_v_hiero_phrase));
+  Py_XDECREF(p->__pyx_v_input_match);
+  Py_XDECREF(p->__pyx_v_intersect_start_time);
+  Py_XDECREF(p->__pyx_v_intersect_stop_time);
+  Py_XDECREF(p->__pyx_v_is_shadow_path);
+  Py_XDECREF(((PyObject *)p->__pyx_v_key));
+  Py_XDECREF(p->__pyx_v_lex_i);
+  Py_XDECREF(p->__pyx_v_lex_j);
+  Py_XDECREF(p->__pyx_v_loc);
+  Py_XDECREF(((PyObject *)p->__pyx_v_locs));
+  Py_XDECREF(p->__pyx_v_max_locs);
+  Py_XDECREF(p->__pyx_v_meta);
+  Py_XDECREF(((PyObject *)p->__pyx_v_new_frontier));
+  Py_XDECREF(p->__pyx_v_new_node);
+  Py_XDECREF(((PyObject *)p->__pyx_v_next_states));
+  Py_XDECREF(p->__pyx_v_node);
+  Py_XDECREF(((PyObject *)p->__pyx_v_nodes_isteps_away_buffer));
+  Py_XDECREF(p->__pyx_v_pathlen);
+  Py_XDECREF(p->__pyx_v_phrase);
+  Py_XDECREF(((PyObject *)p->__pyx_v_phrase_location));
+  Py_XDECREF(p->__pyx_v_prefix);
+  Py_XDECREF(((PyObject *)p->__pyx_v_reachable_buffer));
+  Py_XDECREF(p->__pyx_v_sa_range);
+  Py_XDECREF(((PyObject *)p->__pyx_v_sample));
+  Py_XDECREF(((PyObject *)p->__pyx_v_scores));
+  Py_XDECREF(((PyObject *)p->__pyx_v_seen_phrases));
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_XDECREF(p->__pyx_v_spanlen);
+  Py_XDECREF(p->__pyx_v_stop_time);
+  Py_XDECREF(p->__pyx_v_suffix_link);
+  Py_XDECREF(p->__pyx_v_suffix_link_xcat_index);
+  Py_XDECREF(p->__pyx_v_word_id);
+  Py_XDECREF(p->__pyx_v_xcat_index);
+  Py_XDECREF(p->__pyx_v_xnode);
+  Py_XDECREF(p->__pyx_v_xroot);
+  Py_XDECREF(p->__pyx_t_2);
+  Py_XDECREF(p->__pyx_t_3);
+  Py_XDECREF(p->__pyx_t_4);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -76570,6 +76524,12 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_19_input(PyObject *o, visit
   if (p->__pyx_v_input_match) {
     e = (*v)(p->__pyx_v_input_match, a); if (e) return e;
   }
+  if (p->__pyx_v_intersect_start_time) {
+    e = (*v)(p->__pyx_v_intersect_start_time, a); if (e) return e;
+  }
+  if (p->__pyx_v_intersect_stop_time) {
+    e = (*v)(p->__pyx_v_intersect_stop_time, a); if (e) return e;
+  }
   if (p->__pyx_v_is_shadow_path) {
     e = (*v)(p->__pyx_v_is_shadow_path, a); if (e) return e;
   }
@@ -76663,15 +76623,15 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_19_input(PyObject *o, visit
   if (p->__pyx_v_xroot) {
     e = (*v)(p->__pyx_v_xroot, a); if (e) return e;
   }
-  if (p->__pyx_t_1) {
-    e = (*v)(p->__pyx_t_1, a); if (e) return e;
+  if (p->__pyx_t_2) {
+    e = (*v)(p->__pyx_t_2, a); if (e) return e;
+  }
+  if (p->__pyx_t_3) {
+    e = (*v)(p->__pyx_t_3, a); if (e) return e;
   }
   if (p->__pyx_t_4) {
     e = (*v)(p->__pyx_t_4, a); if (e) return e;
   }
-  if (p->__pyx_t_5) {
-    e = (*v)(p->__pyx_t_5, a); if (e) return e;
-  }
   return 0;
 }
 
@@ -76741,6 +76701,12 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_19_input(PyObject *o) {
   tmp = ((PyObject*)p->__pyx_v_input_match);
   p->__pyx_v_input_match = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_intersect_start_time);
+  p->__pyx_v_intersect_start_time = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_intersect_stop_time);
+  p->__pyx_v_intersect_stop_time = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_is_shadow_path);
   p->__pyx_v_is_shadow_path = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
@@ -76834,15 +76800,15 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_19_input(PyObject *o) {
   tmp = ((PyObject*)p->__pyx_v_xroot);
   p->__pyx_v_xroot = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_t_1);
-  p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
+  tmp = ((PyObject*)p->__pyx_t_2);
+  p->__pyx_t_2 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_3);
+  p->__pyx_t_3 = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_t_4);
   p->__pyx_t_4 = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_t_5);
-  p->__pyx_t_5 = Py_None; Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
   return 0;
 }
 
@@ -77004,7 +76970,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_19_input = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_20_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_20_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_20_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -77017,9 +76983,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_20_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_20_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_20_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_20_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_word);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_word);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -77211,7 +77177,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_20_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_21_add_instance(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_21_add_instance(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_21_add_instance *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -77232,17 +77198,17 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_21_add_instance(PyTypeObje
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_21_add_instance(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_21_add_instance *p = (struct __pyx_obj_3_sa___pyx_scope_struct_21_add_instance *)o;
-  Py_CLEAR(p->__pyx_v_al);
-  Py_CLEAR(p->__pyx_v_cover);
-  Py_CLEAR(p->__pyx_v_e_nt_cover);
-  Py_CLEAR(p->__pyx_v_e_words);
-  Py_CLEAR(p->__pyx_v_ef_span);
-  Py_CLEAR(p->__pyx_v_extract);
-  Py_CLEAR(p->__pyx_v_f_len);
-  Py_CLEAR(p->__pyx_v_f_words);
-  Py_CLEAR(p->__pyx_v_fe_span);
-  Py_CLEAR(p->__pyx_v_rules);
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(p->__pyx_v_al);
+  Py_XDECREF(p->__pyx_v_cover);
+  Py_XDECREF(p->__pyx_v_e_nt_cover);
+  Py_XDECREF(p->__pyx_v_e_words);
+  Py_XDECREF(p->__pyx_v_ef_span);
+  Py_XDECREF(p->__pyx_v_extract);
+  Py_XDECREF(p->__pyx_v_f_len);
+  Py_XDECREF(p->__pyx_v_f_words);
+  Py_XDECREF(p->__pyx_v_fe_span);
+  Py_XDECREF(p->__pyx_v_rules);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -77482,7 +77448,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_21_add_instance = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_22_form_rule(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_22_form_rule(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_22_form_rule *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -77494,8 +77460,8 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_22_form_rule(PyTypeObject
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_22_form_rule(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_22_form_rule *p = (struct __pyx_obj_3_sa___pyx_scope_struct_22_form_rule *)o;
-  Py_CLEAR(p->__pyx_v_links);
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(p->__pyx_v_links);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -77681,7 +77647,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_22_form_rule = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_23_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_23_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_23_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -77695,10 +77661,10 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_23_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_23_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_23_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_23_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_i);
-  Py_CLEAR(p->__pyx_v_j);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_i);
+  Py_XDECREF(p->__pyx_v_j);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -77896,7 +77862,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_23_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_24_fmt_rule(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_24_fmt_rule(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_24_fmt_rule *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -77908,8 +77874,8 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_24_fmt_rule(PyTypeObject *
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_24_fmt_rule(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_24_fmt_rule *p = (struct __pyx_obj_3_sa___pyx_scope_struct_24_fmt_rule *)o;
-  Py_CLEAR(p->__pyx_v_a);
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(p->__pyx_v_a);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -78095,7 +78061,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_24_fmt_rule = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_25_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_25_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_25_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -78108,9 +78074,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_25_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_25_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_25_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_25_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_packed);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_packed);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -78302,7 +78268,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_25_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_26_get_f_phrases(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_26_get_f_phrases(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_26_get_f_phrases *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -78317,11 +78283,11 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_26_get_f_phrases(PyTypeObj
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_26_get_f_phrases(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_26_get_f_phrases *p = (struct __pyx_obj_3_sa___pyx_scope_struct_26_get_f_phrases *)o;
-  Py_CLEAR(p->__pyx_v_extract);
-  Py_CLEAR(p->__pyx_v_f_len);
-  Py_CLEAR(p->__pyx_v_f_words);
-  Py_CLEAR(p->__pyx_v_phrases);
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(p->__pyx_v_extract);
+  Py_XDECREF(p->__pyx_v_f_len);
+  Py_XDECREF(p->__pyx_v_f_words);
+  Py_XDECREF(p->__pyx_v_phrases);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -78525,7 +78491,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_26_get_f_phrases = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_27___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_27___iter__(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_27___iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -78536,7 +78502,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_27___iter__(PyTypeObject *
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_27___iter__(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_27___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_27___iter__ *)o;
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -78716,7 +78682,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_27___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_28___str__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_28___str__(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_28___str__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -78727,7 +78693,7 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_28___str__(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_28___str__(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_28___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_28___str__ *)o;
-  Py_CLEAR(p->__pyx_v_self);
+  Py_XDECREF(((PyObject *)p->__pyx_v_self));
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -78907,7 +78873,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_28___str__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_29_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_29_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
   struct __pyx_obj_3_sa___pyx_scope_struct_29_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
@@ -78920,9 +78886,9 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_29_genexpr(PyTypeObject *t
 
 static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_29_genexpr(PyObject *o) {
   struct __pyx_obj_3_sa___pyx_scope_struct_29_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_29_genexpr *)o;
-  Py_CLEAR(p->__pyx_outer_scope);
-  Py_CLEAR(p->__pyx_v_feat);
-  Py_CLEAR(p->__pyx_t_0);
+  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+  Py_XDECREF(p->__pyx_v_feat);
+  Py_XDECREF(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -79165,18 +79131,19 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_kp_s_131, __pyx_k_131, sizeof(__pyx_k_131), 0, 0, 1, 0},
   {&__pyx_kp_s_132, __pyx_k_132, sizeof(__pyx_k_132), 0, 0, 1, 0},
   {&__pyx_kp_s_133, __pyx_k_133, sizeof(__pyx_k_133), 0, 0, 1, 0},
-  {&__pyx_kp_s_136, __pyx_k_136, sizeof(__pyx_k_136), 0, 0, 1, 0},
+  {&__pyx_kp_s_134, __pyx_k_134, sizeof(__pyx_k_134), 0, 0, 1, 0},
   {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
   {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
   {&__pyx_kp_s_139, __pyx_k_139, sizeof(__pyx_k_139), 0, 0, 1, 0},
   {&__pyx_kp_s_14, __pyx_k_14, sizeof(__pyx_k_14), 0, 0, 1, 0},
-  {&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
-  {&__pyx_kp_s_145, __pyx_k_145, sizeof(__pyx_k_145), 0, 0, 1, 0},
-  {&__pyx_n_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 1},
-  {&__pyx_kp_s_154, __pyx_k_154, sizeof(__pyx_k_154), 0, 0, 1, 0},
+  {&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0},
+  {&__pyx_kp_s_142, __pyx_k_142, sizeof(__pyx_k_142), 0, 0, 1, 0},
+  {&__pyx_kp_s_146, __pyx_k_146, sizeof(__pyx_k_146), 0, 0, 1, 0},
+  {&__pyx_n_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 1},
+  {&__pyx_kp_s_155, __pyx_k_155, sizeof(__pyx_k_155), 0, 0, 1, 0},
   {&__pyx_kp_s_157, __pyx_k_157, sizeof(__pyx_k_157), 0, 0, 1, 0},
-  {&__pyx_kp_s_158, __pyx_k_158, sizeof(__pyx_k_158), 0, 0, 1, 0},
-  {&__pyx_kp_s_162, __pyx_k_162, sizeof(__pyx_k_162), 0, 0, 1, 0},
+  {&__pyx_kp_s_160, __pyx_k_160, sizeof(__pyx_k_160), 0, 0, 1, 0},
+  {&__pyx_kp_s_164, __pyx_k_164, sizeof(__pyx_k_164), 0, 0, 1, 0},
   {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
   {&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
   {&__pyx_kp_s_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 1, 0},
@@ -79383,6 +79350,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__min_bound, __pyx_k__min_bound, sizeof(__pyx_k__min_bound), 0, 0, 1, 1},
   {&__pyx_n_s__min_dist, __pyx_k__min_dist, sizeof(__pyx_k__min_dist), 0, 0, 1, 1},
   {&__pyx_n_s__min_gap_size, __pyx_k__min_gap_size, sizeof(__pyx_k__min_gap_size), 0, 0, 1, 1},
+  {&__pyx_n_s__monitor_cpu, __pyx_k__monitor_cpu, sizeof(__pyx_k__monitor_cpu), 0, 0, 1, 1},
   {&__pyx_n_s__name, __pyx_k__name, sizeof(__pyx_k__name), 0, 0, 1, 1},
   {&__pyx_n_s__namedtuple, __pyx_k__namedtuple, sizeof(__pyx_k__namedtuple), 0, 0, 1, 1},
   {&__pyx_n_s__new_e_i, __pyx_k__new_e_i, sizeof(__pyx_k__new_e_i), 0, 0, 1, 1},
@@ -79492,8 +79460,8 @@ static int __Pyx_InitCachedBuiltins(void) {
   __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[6]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_cmp = __Pyx_GetName(__pyx_b, __pyx_n_s__cmp); if (!__pyx_builtin_cmp) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   return 0;
   __pyx_L1_error:;
   return -1;
@@ -79503,7 +79471,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":20
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":20
  *         self.word2id = {"END_OF_FILE":0, "END_OF_LINE":1}
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
  *         self.data = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -79520,7 +79488,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_1000);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":21
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":21
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -79537,7 +79505,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_1000);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":22
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":22
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -79554,7 +79522,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_1000);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":66
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":66
  *                     f.write("%s " % self.get_word(w_id))
  *                 if w_id == 1:
  *                     f.write("\n")             # <<<<<<<<<<<<<<
@@ -79568,7 +79536,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":61
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":61
  * 
  *     def write_text(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -79588,7 +79556,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":69
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":69
  * 
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as fp:             # <<<<<<<<<<<<<<
@@ -79608,7 +79576,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":74
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":74
  *     def read_bitext(self, char* filename, int side):
  *         with gzip_or_text(filename) as fp:
  *             data = (line.split(' ||| ')[side] for line in fp)             # <<<<<<<<<<<<<<
@@ -79622,7 +79590,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_18));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":73
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":73
  * 
  *     def read_bitext(self, char* filename, int side):
  *         with gzip_or_text(filename) as fp:             # <<<<<<<<<<<<<<
@@ -79642,7 +79610,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":144
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":144
  *         for i in self.data:
  *             f.write("%d " %i)
  *         f.write("\n")             # <<<<<<<<<<<<<<
@@ -79656,7 +79624,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":147
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":147
  *         for i in self.sent_index:
  *             f.write("%d " %i)
  *         f.write("\n")             # <<<<<<<<<<<<<<
@@ -79670,7 +79638,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":150
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":150
  *         for i in self.sent_id:
  *             f.write("%d " %i)
  *         f.write("\n")             # <<<<<<<<<<<<<<
@@ -79684,7 +79652,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":153
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":153
  *         for word in self.id2word:
  *             f.write("%s %d " % (word, self.word2id[word]))
  *         f.write("\n")             # <<<<<<<<<<<<<<
@@ -79698,7 +79666,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
 
-  /* "/home/m/workspace/cdec/python/src/sa/data_array.pxi":156
+  /* "/home/paulb/workspace/cdec/python/src/sa/data_array.pxi":156
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -79717,7 +79685,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":46
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":46
  * 
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -79734,7 +79702,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_1000);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":47
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":47
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -79751,7 +79719,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_1000);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_30));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":59
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":59
  *                 pairs = line.split()
  *                 for pair in pairs:
  *                     (i, j) = map(int, pair.split('-'))             # <<<<<<<<<<<<<<
@@ -79765,7 +79733,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_31));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_32));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":54
  * 
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -79785,7 +79753,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":75
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":75
  *             for i, link in enumerate(self.links):
  *                 while i >= self.sent_index[sent_num]:
  *                     f.write("\n")             # <<<<<<<<<<<<<<
@@ -79799,7 +79767,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_34));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":78
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":78
  *                     sent_num = sent_num + 1
  *                 f.write("%d-%d " % self.unlink(link))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79813,7 +79781,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_36));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":71
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":71
  * 
  *     def write_text(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -79833,7 +79801,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":92
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":92
  *             for link in self.links:
  *                 f.write("%d " % link)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79847,7 +79815,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":95
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":95
  *             for i in self.sent_index:
  *                 f.write("%d " % i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79861,7 +79829,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
 
-  /* "/home/m/workspace/cdec/python/src/sa/alignment.pxi":88
+  /* "/home/paulb/workspace/cdec/python/src/sa/alignment.pxi":88
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -79881,7 +79849,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":297
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":297
  * 
  *             # Re-read file, placing words into buckets
  *             f.seek(0)             # <<<<<<<<<<<<<<
@@ -79895,7 +79863,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_0);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":273
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":273
  * 
  *         fcount = IntList()
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -79915,7 +79883,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":339
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":339
  * 
  *         if i > j:
  *             raise Exception("Sort error in CLex")             # <<<<<<<<<<<<<<
@@ -79929,7 +79897,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_46));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":362
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":362
  *             for i in self.f_index:
  *                 f.write("%d " % i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79943,7 +79911,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":365
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":365
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
  *                 f.write("%d %f %f " % (i, s1, s2))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79957,7 +79925,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":368
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":368
  *             for i, w in enumerate(self.id2fword):
  *                 f.write("%d %s " % (i, w))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79971,7 +79939,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":371
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":371
  *             for i, w in enumerate(self.id2eword):
  *                 f.write("%d %s " % (i, w))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -79985,7 +79953,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_54));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":359
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":359
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -80005,7 +79973,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
 
-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":404
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":404
  *         cdef i, N, e_id, f_id
  * 
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -80025,7 +79993,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":13
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":13
  *         cdef IntList rank
  * 
  *         logger.info("Constructing LCP array")             # <<<<<<<<<<<<<<
@@ -80039,7 +80007,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
 
-  /* "/home/m/workspace/cdec/python/src/sa/lcp.pxi":34
+  /* "/home/paulb/workspace/cdec/python/src/sa/lcp.pxi":34
  *             if h > 0:
  *                 h = h-1
  *         logger.info("LCP array completed")             # <<<<<<<<<<<<<<
@@ -80053,7 +80021,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":297
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":297
  *         pattern_rank = {}
  * 
  *         logger.info("Precomputing frequent intersections")             # <<<<<<<<<<<<<<
@@ -80067,7 +80035,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_72));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":314
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":314
  *         queue = IntList(increment=1000)
  * 
  *         logger.info("    Computing inverted indexes...")             # <<<<<<<<<<<<<<
@@ -80081,7 +80049,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_74));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":329
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":329
  *                     trie_node_data_append(node, i)
  * 
  *         logger.info("    Computing collocations...")             # <<<<<<<<<<<<<<
@@ -80095,7 +80063,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":393
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":393
  *             for pattern2 in J_set:
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2             # <<<<<<<<<<<<<<
@@ -80109,7 +80077,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_neg_1);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_79));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":400
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":400
  *                 x = x+1
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2             # <<<<<<<<<<<<<<
@@ -80123,7 +80091,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_neg_1);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":407
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":407
  *                 x = x+2
  *                 if len(pattern1) + len(pattern2) + 1<= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2             # <<<<<<<<<<<<<<
@@ -80137,7 +80105,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_neg_1);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
 
-  /* "/home/m/workspace/cdec/python/src/sa/precomputation.pxi":409
+  /* "/home/paulb/workspace/cdec/python/src/sa/precomputation.pxi":409
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  *                     IJ_set.add(combined_pattern)
  *                     combined_pattern = pattern2 + (-1,) + pattern1             # <<<<<<<<<<<<<<
@@ -80151,7 +80119,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_int_neg_1);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82));
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":94
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":94
  * 
  *         '''Step 3: read off suffix array from inverse suffix array'''
  *         logger.info("    Finalizing sort...")             # <<<<<<<<<<<<<<
@@ -80165,7 +80133,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":193
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":193
  *             for a_i in self.sa:
  *                 f.write("%d " % a_i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -80179,7 +80147,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":196
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":196
  *             for w_i in self.ha:
  *                 f.write("%d " % w_i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -80193,7 +80161,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
 
-  /* "/home/m/workspace/cdec/python/src/sa/suffix_array.pxi":189
+  /* "/home/paulb/workspace/cdec/python/src/sa/suffix_array.pxi":189
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -80213,7 +80181,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":119
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":119
  *             logger.info("Sampling strategy: uniform, max sample size = %d", sample_size)
  *         else:
  *             logger.info("Sampling strategy: no sampling")             # <<<<<<<<<<<<<<
@@ -80227,270 +80195,279 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_101));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_102));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":338
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":339
  *         self.rules.root = ExtendedTrieNode(phrase_location=PhraseLocation())
  *         if alignment is None:
  *             raise Exception("Must specify an alignment object")             # <<<<<<<<<<<<<<
  *         self.alignment = alignment
  * 
  */
-  __pyx_k_tuple_107 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_107)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_107 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_107)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   PyTuple_SET_ITEM(__pyx_k_tuple_107, 0, ((PyObject *)__pyx_kp_s_106));
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_106));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_107));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1062
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1064
  *                         else:
  *                             #ERROR: We never get here
  *                             raise Exception("Keyword trie error")             # <<<<<<<<<<<<<<
  *                 # checking whether lookup_required
  *                 if lookup_required:
  */
-  __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":1913
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":1918
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2120
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2125
  *     # Debugging
  *     def dump_online_stats(self):
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-  __pyx_k_tuple_140 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_140)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_139));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_140));
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+  __Pyx_GOTREF(__pyx_k_tuple_141);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_140));
+  PyTuple_SET_ITEM(__pyx_k_tuple_141, 0, ((PyObject *)__pyx_kp_s_140));
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+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_141));
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2121
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2126
  *     def dump_online_stats(self):
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  *         logger.info('         Online Stats         ')             # <<<<<<<<<<<<<<
  *         logger.info('------------------------------')
  *         logger.info('f')
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2122
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2127
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-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_139));
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2123
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2128
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2126
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2129
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2133
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+
+  /* "_sa.pyx":5
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@@ -80517,209 +80494,209 @@ static int __Pyx_InitCachedConstants(void) {
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-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_159));
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+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_161));
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":107
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":107
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-  #if CYTHON_COMPILING_IN_PYPY
-  Py_INCREF(__pyx_b);
+  if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  #if PY_MAJOR_VERSION < 3
+  Py_INCREF(__pyx_m);
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+  __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+  if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_26_get_f_phrases) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  * import gzip             # <<<<<<<<<<<<<<
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- * cdef float monitor_cpu():
+ * def monitor_cpu():
  */
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
+  /* "_sa.pyx":5
+ * import gzip
+ * 
+ * def monitor_cpu():             # <<<<<<<<<<<<<<
+ *     return (resource.getrusage(resource.RUSAGE_SELF).ru_utime+
+ *             resource.getrusage(resource.RUSAGE_SELF).ru_stime)
+ */
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+  __Pyx_GOTREF(__pyx_t_1);
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__monitor_cpu, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
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  *             resource.getrusage(resource.RUSAGE_SELF).ru_stime)
  * 
@@ -81090,7 +81080,7 @@ PyMODINIT_FUNC PyInit__sa(void)
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+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_3gzip_or_text, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_161), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/bilex.pxi":54
+  /* "/home/paulb/workspace/cdec/python/src/sa/bilex.pxi":54
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   __Pyx_GIVEREF(__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":17
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":17
  * from libc.string cimport memset
  * 
  * cdef int MIN_BOTTOM_SIZE = 32             # <<<<<<<<<<<<<<
@@ -81135,7 +81125,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_MIN_BOTTOM_SIZE = 32;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":18
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":18
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  * cdef int MIN_BOTTOM_SIZE = 32
  * cdef int MIN_BOTTOM_BITS = 5             # <<<<<<<<<<<<<<
@@ -81144,7 +81134,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_MIN_BOTTOM_BITS = 5;
 
-  /* "/home/m/workspace/cdec/python/src/sa/veb.pxi":28
+  /* "/home/paulb/workspace/cdec/python/src/sa/veb.pxi":28
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@@ -81153,7 +81143,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":4
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":4
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  * 
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  */
   __pyx_v_3_sa_INDEX_SHIFT = 3;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":5
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":5
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":87
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":87
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  * 
  * cdef Alphabet ALPHABET = Alphabet()             # <<<<<<<<<<<<<<
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   __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":107
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":107
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  * 
  * def isvar(sym):             # <<<<<<<<<<<<<<
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+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_5isvar, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":110
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":110
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-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_5make_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_7make_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":114
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":114
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-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_7decode_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_9decode_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":118
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":118
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-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_9decode_sentence, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_11decode_sentence, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":121
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":121
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-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_11encode_words, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_13encode_words, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/sym.pxi":124
+  /* "/home/paulb/workspace/cdec/python/src/sa/sym.pxi":124
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-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_13decode_words, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_15decode_words, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":5
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":5
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":6
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":6
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":12
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":12
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":14
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":14
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@@ -81338,7 +81328,7 @@ PyMODINIT_FUNC PyInit__sa(void)
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":15
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":15
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":30
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":30
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@@ -81411,7 +81401,7 @@ PyMODINIT_FUNC PyInit__sa(void)
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   __Pyx_GOTREF(__pyx_t_1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":31
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":31
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@@ -81440,9 +81430,9 @@ PyMODINIT_FUNC PyInit__sa(void)
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-  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s_151));
-  __Pyx_GIVEREF(((PyObject *)__pyx_n_s_151));
+  __Pyx_INCREF(((PyObject *)__pyx_n_s_152));
+  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s_152));
+  __Pyx_GIVEREF(((PyObject *)__pyx_n_s_152));
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-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_151, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_152, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":39
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":39
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":40
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":40
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":41
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":41
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":44
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":44
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-  __pyx_v_3_sa_EPSILON = __pyx_f_3_sa_sym_fromstring(__pyx_k_173, 1);
+  __pyx_v_3_sa_EPSILON = __pyx_f_3_sa_sym_fromstring(__pyx_k_175, 1);
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":67
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":67
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2200
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2205
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  * def span_check(vec, i, j):             # <<<<<<<<<<<<<<
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-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_15span_check, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_17span_check, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_check, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_check, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2208
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2213
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  * 
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-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_17span_inc, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_19span_inc, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_inc, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_inc, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/rulefactory.pxi":2214
+  /* "/home/paulb/workspace/cdec/python/src/sa/rulefactory.pxi":2219
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  * 
  * def span_dec(vec, i, j):             # <<<<<<<<<<<<<<
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  *     while k <= j:
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-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_19span_dec, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_3_sa_21span_dec, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_dec, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__span_dec, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":1
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":1
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-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":3
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":3
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  * 
  * INITIAL_CAPACITY = 7 # default number of features             # <<<<<<<<<<<<<<
@@ -81560,7 +81550,7 @@ PyMODINIT_FUNC PyInit__sa(void)
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-  /* "/home/m/workspace/cdec/python/src/sa/features.pxi":4
+  /* "/home/paulb/workspace/cdec/python/src/sa/features.pxi":4
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         #else
         "%s() got multiple values for keyword argument '%s'", func_name,
-        PyString_AsString(kw_name));
+        PyString_AS_STRING(kw_name));
         #endif
 }
 
@@ -81663,72 +81653,48 @@ static int __Pyx_ParseOptionalKeywords(
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-        name = first_kw_arg;
-        #if PY_MAJOR_VERSION < 3
-        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
-            while (*name) {
-                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
-                        && _PyString_Eq(**name, key)) {
-                    values[name-argnames] = value;
-                    break;
-                }
-                name++;
-            }
-            if (*name) continue;
-            else {
-                PyObject*** argname = argnames;
-                while (argname != first_kw_arg) {
-                    if ((**argname == key) || (
-                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
-                             && _PyString_Eq(**argname, key))) {
-                        goto arg_passed_twice;
-                    }
-                    argname++;
+        } else {
+            #if PY_MAJOR_VERSION < 3
+            if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+            #else
+            if (unlikely(!PyUnicode_Check(key))) {
+            #endif
+                goto invalid_keyword_type;
+            } else {
+                for (name = first_kw_arg; *name; name++) {
+                    #if PY_MAJOR_VERSION >= 3
+                    if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+                        PyUnicode_Compare(**name, key) == 0) break;
+                    #else
+                    if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+                        _PyString_Eq(**name, key)) break;
+                    #endif
                 }
-            }
-        } else
-        #endif
-        if (likely(PyUnicode_Check(key))) {
-            while (*name) {
-                int cmp = (**name == key) ? 0 :
-                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
-                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
-                #endif
-                    PyUnicode_Compare(**name, key);
-                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
-                if (cmp == 0) {
+                if (*name) {
                     values[name-argnames] = value;
-                    break;
-                }
-                name++;
-            }
-            if (*name) continue;
-            else {
-                PyObject*** argname = argnames;
-                while (argname != first_kw_arg) {
-                    int cmp = (**argname == key) ? 0 :
-                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
-                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
-                    #endif
-                        PyUnicode_Compare(**argname, key);
-                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
-                    if (cmp == 0) goto arg_passed_twice;
-                    argname++;
+                } else {
+                    for (name=argnames; name != first_kw_arg; name++) {
+                        if (**name == key) goto arg_passed_twice;
+                        #if PY_MAJOR_VERSION >= 3
+                        if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+                            PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+                        #else
+                        if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+                            _PyString_Eq(**name, key)) goto arg_passed_twice;
+                        #endif
+                    }
+                    if (kwds2) {
+                        if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+                    } else {
+                        goto invalid_keyword;
+                    }
                 }
             }
-        } else
-            goto invalid_keyword_type;
-        if (kwds2) {
-            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
-        } else {
-            goto invalid_keyword;
         }
     }
     return 0;
 arg_passed_twice:
-    __Pyx_RaiseDoubleKeywordsError(function_name, key);
+    __Pyx_RaiseDoubleKeywordsError(function_name, **name);
     goto bad;
 invalid_keyword_type:
     PyErr_Format(PyExc_TypeError,
@@ -81767,7 +81733,7 @@ static void __Pyx_RaiseArgtupleInvalid(
         more_or_less = "exactly";
     }
     PyErr_Format(PyExc_TypeError,
-                 "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+                 "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
                  func_name, more_or_less, num_expected,
                  (num_expected == 1) ? "" : "s", num_found);
 }
@@ -81807,38 +81773,33 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                         CYTHON_UNUSED PyObject *cause) {
     Py_XINCREF(type);
-    if (!value || value == Py_None)
-        value = NULL;
-    else
+    Py_XINCREF(value);
+    Py_XINCREF(tb);
+    if (tb == Py_None) {
+        Py_DECREF(tb);
+        tb = 0;
+    }
+    else if (tb != NULL && !PyTraceBack_Check(tb)) {
+        PyErr_SetString(PyExc_TypeError,
+            "raise: arg 3 must be a traceback or None");
+        goto raise_error;
+    }
+    if (value == NULL) {
+        value = Py_None;
         Py_INCREF(value);
-    if (!tb || tb == Py_None)
-        tb = NULL;
-    else {
-        Py_INCREF(tb);
-        if (!PyTraceBack_Check(tb)) {
-            PyErr_SetString(PyExc_TypeError,
-                "raise: arg 3 must be a traceback or None");
-            goto raise_error;
-        }
     }
     #if PY_VERSION_HEX < 0x02050000
-    if (PyClass_Check(type)) {
+    if (!PyClass_Check(type))
     #else
-    if (PyType_Check(type)) {
+    if (!PyType_Check(type))
     #endif
-#if CYTHON_COMPILING_IN_PYPY
-        if (!value) {
-            Py_INCREF(Py_None);
-            value = Py_None;
-        }
-#endif
-        PyErr_NormalizeException(&type, &value, &tb);
-    } else {
-        if (value) {
+    {
+        if (value != Py_None) {
             PyErr_SetString(PyExc_TypeError,
                 "instance exception may not have a separate value");
             goto raise_error;
         }
+        Py_DECREF(value);
         value = type;
         #if PY_VERSION_HEX < 0x02050000
             if (PyInstance_Check(type)) {
@@ -81871,7 +81832,6 @@ raise_error:
 }
 #else /* Python 3+ */
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
-    PyObject* owned_instance = NULL;
     if (tb == Py_None) {
         tb = 0;
     } else if (tb && !PyTraceBack_Check(tb)) {
@@ -81889,36 +81849,12 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
         value = type;
         type = (PyObject*) Py_TYPE(value);
-    } else if (PyExceptionClass_Check(type)) {
-        PyObject *args;
-        if (!value)
-            args = PyTuple_New(0);
-        else if (PyTuple_Check(value)) {
-            Py_INCREF(value);
-            args = value;
-        }
-        else
-            args = PyTuple_Pack(1, value);
-        if (!args)
-            goto bad;
-        owned_instance = PyEval_CallObject(type, args);
-        Py_DECREF(args);
-        if (!owned_instance)
-            goto bad;
-        value = owned_instance;
-        if (!PyExceptionInstance_Check(value)) {
-            PyErr_Format(PyExc_TypeError,
-                         "calling %R should have returned an instance of "
-                         "BaseException, not %R",
-                         type, Py_TYPE(value));
-            goto bad;
-        }
-    } else {
+    } else if (!PyExceptionClass_Check(type)) {
         PyErr_SetString(PyExc_TypeError,
             "raise: exception class must be a subclass of BaseException");
         goto bad;
     }
-    if (cause && cause != Py_None) {
+    if (cause) {
         PyObject *fixed_cause;
         if (PyExceptionClass_Check(cause)) {
             fixed_cause = PyObject_CallObject(cause, NULL);
@@ -81935,6 +81871,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
                             "BaseException");
             goto bad;
         }
+        if (!value) {
+            value = PyObject_CallObject(type, NULL);
+        }
         PyException_SetCause(value, fixed_cause);
     }
     PyErr_SetObject(type, value);
@@ -81948,7 +81887,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
     }
 bad:
-    Py_XDECREF(owned_instance);
     return;
 }
 #endif
@@ -81972,17 +81910,13 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
 {
     PyObject* key = 0;
     Py_ssize_t pos = 0;
-#if CPYTHON_COMPILING_IN_PYPY
-    if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
-        goto invalid_keyword;
-    return 1;
-#else
     while (PyDict_Next(kwdict, &pos, &key, 0)) {
         #if PY_MAJOR_VERSION < 3
         if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
+        #else
+        if (unlikely(!PyUnicode_Check(key)))
         #endif
-            if (unlikely(!PyUnicode_Check(key)))
-                goto invalid_keyword_type;
+            goto invalid_keyword_type;
     }
     if ((!kw_allowed) && unlikely(key))
         goto invalid_keyword;
@@ -81991,7 +81925,6 @@ invalid_keyword_type:
     PyErr_Format(PyExc_TypeError,
         "%s() keywords must be strings", function_name);
     return 0;
-#endif
 invalid_keyword:
     PyErr_Format(PyExc_TypeError,
     #if PY_MAJOR_VERSION < 3
@@ -82004,9 +81937,10 @@ invalid_keyword:
     return 0;
 }
 
+
+
 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
     PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
     PyObject *tmp_type, *tmp_value, *tmp_tb;
     PyThreadState *tstate = PyThreadState_GET();
     local_type = tstate->curexc_type;
@@ -82015,27 +81949,19 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
     tstate->curexc_type = 0;
     tstate->curexc_value = 0;
     tstate->curexc_traceback = 0;
-#else
-    PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
     PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
     if (unlikely(tstate->curexc_type))
-#else
-    if (unlikely(PyErr_Occurred()))
-#endif
         goto bad;
     #if PY_MAJOR_VERSION >= 3
     if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
         goto bad;
     #endif
-    Py_INCREF(local_type);
-    Py_INCREF(local_value);
-    Py_INCREF(local_tb);
     *type = local_type;
     *value = local_value;
     *tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+    Py_INCREF(local_type);
+    Py_INCREF(local_value);
+    Py_INCREF(local_tb);
     tmp_type = tstate->exc_type;
     tmp_value = tstate->exc_value;
     tmp_tb = tstate->exc_traceback;
@@ -82043,13 +81969,10 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
     tstate->exc_value = local_value;
     tstate->exc_traceback = local_tb;
     /* Make sure tstate is in a consistent state when we XDECREF
-       these objects (DECREF may run arbitrary code). */
+       these objects (XDECREF may run arbitrary code). */
     Py_XDECREF(tmp_type);
     Py_XDECREF(tmp_value);
     Py_XDECREF(tmp_tb);
-#else
-    PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
     return 0;
 bad:
     *type = 0;
@@ -82078,40 +82001,23 @@ static CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
     return r;
 }
 
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
     PyErr_Format(PyExc_ValueError,
-                 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+                 "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+                 index, (index == 1) ? "" : "s");
 }
 
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
     PyErr_Format(PyExc_ValueError,
-                 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
-                 index, (index == 1) ? "" : "s");
+                 "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
 }
 
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
-    PyThreadState *tstate = PyThreadState_GET();
-    PyObject* exc_type = tstate->curexc_type;
-    if (unlikely(exc_type)) {
-        if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
-            PyObject *exc_value, *exc_tb;
-            exc_value = tstate->curexc_value;
-            exc_tb = tstate->curexc_traceback;
-            tstate->curexc_type = 0;
-            tstate->curexc_value = 0;
-            tstate->curexc_traceback = 0;
-            Py_DECREF(exc_type);
-            Py_XDECREF(exc_value);
-            Py_XDECREF(exc_tb);
-            return 0;
-        } else {
-            return -1;
-        }
-    }
-    return 0;
-#else
-    if (unlikely(PyErr_Occurred())) {
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+    if (unlikely(retval)) {
+        Py_DECREF(retval);
+        __Pyx_RaiseTooManyValuesError(expected);
+        return -1;
+    } else if (PyErr_Occurred()) {
         if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
             PyErr_Clear();
             return 0;
@@ -82120,25 +82026,12 @@ static CYTHON_INLINE int __Pyx_IterFinish(void) {
         }
     }
     return 0;
-#endif
 }
 
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
-    if (unlikely(retval)) {
-        Py_DECREF(retval);
-        __Pyx_RaiseTooManyValuesError(expected);
-        return -1;
-    } else {
-        return __Pyx_IterFinish();
-    }
-    return 0;
-}
+
 
 static double __Pyx__PyObject_AsDouble(PyObject* obj) {
     PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
-    float_value = PyNumber_Float(obj);
-#else
     if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
         return PyFloat_AsDouble(obj);
     } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
@@ -82155,7 +82048,6 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) {
         PyTuple_SET_ITEM(args, 0, 0);
         Py_DECREF(args);
     }
-#endif
     if (likely(float_value)) {
         double value = PyFloat_AS_DOUBLE(float_value);
         Py_DECREF(float_value);
@@ -82189,158 +82081,8 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
     return 0;
 }
 
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
-    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
-    if (t == Py_None) {
-      __Pyx_RaiseNoneNotIterableError();
-    } else if (PyTuple_GET_SIZE(t) < index) {
-      __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
-    } else {
-      __Pyx_RaiseTooManyValuesError(index);
-    }
-}
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
-                                             int is_tuple, int has_known_size, int decref_tuple) {
-    Py_ssize_t index;
-    PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
-    if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
-        iternextfunc iternext;
-        iter = PyObject_GetIter(tuple);
-        if (unlikely(!iter)) goto bad;
-        if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
-        iternext = Py_TYPE(iter)->tp_iternext;
-        value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
-        value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
-        if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
-        Py_DECREF(iter);
-    } else {
-        if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
-            __Pyx_UnpackTupleError(tuple, 2);
-            goto bad;
-        }
-#if CYTHON_COMPILING_IN_PYPY
-        value1 = PySequence_ITEM(tuple, 0);
-        if (unlikely(!value1)) goto bad;
-        value2 = PySequence_ITEM(tuple, 1);
-        if (unlikely(!value2)) goto bad;
-#else
-        value1 = PyTuple_GET_ITEM(tuple, 0);
-        value2 = PyTuple_GET_ITEM(tuple, 1);
-        Py_INCREF(value1);
-        Py_INCREF(value2);
-#endif
-        if (decref_tuple) { Py_DECREF(tuple); }
-    }
-    *pvalue1 = value1;
-    *pvalue2 = value2;
-    return 0;
-unpacking_failed:
-    if (!has_known_size && __Pyx_IterFinish() == 0)
-        __Pyx_RaiseNeedMoreValuesError(index);
-bad:
-    Py_XDECREF(iter);
-    Py_XDECREF(value1);
-    Py_XDECREF(value2);
-    if (decref_tuple) { Py_XDECREF(tuple); }
-    return -1;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
-                                                   Py_ssize_t* p_orig_length, int* p_source_is_dict) {
-    is_dict = is_dict || likely(PyDict_CheckExact(iterable));
-    *p_source_is_dict = is_dict;
-#if !CYTHON_COMPILING_IN_PYPY
-    if (is_dict) {
-        *p_orig_length = PyDict_Size(iterable);
-        Py_INCREF(iterable);
-        return iterable;
-    }
-#endif
-    *p_orig_length = 0;
-    if (method_name) {
-        PyObject* iter;
-        iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
-        if (!iterable)
-            return NULL;
-#if !CYTHON_COMPILING_IN_PYPY
-        if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
-            return iterable;
-#endif
-        iter = PyObject_GetIter(iterable);
-        Py_DECREF(iterable);
-        return iter;
-    }
-    return PyObject_GetIter(iterable);
-}
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
-                                              PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
-    PyObject* next_item;
-#if !CYTHON_COMPILING_IN_PYPY
-    if (source_is_dict) {
-        PyObject *key, *value;
-        if (unlikely(orig_length != PyDict_Size(iter_obj))) {
-            PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
-            return -1;
-        }
-        if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
-            return 0;
-        }
-        if (pitem) {
-            PyObject* tuple = PyTuple_New(2);
-            if (unlikely(!tuple)) {
-                return -1;
-            }
-            Py_INCREF(key);
-            Py_INCREF(value);
-            PyTuple_SET_ITEM(tuple, 0, key);
-            PyTuple_SET_ITEM(tuple, 1, value);
-            *pitem = tuple;
-        } else {
-            if (pkey) {
-                Py_INCREF(key);
-                *pkey = key;
-            }
-            if (pvalue) {
-                Py_INCREF(value);
-                *pvalue = value;
-            }
-        }
-        return 1;
-    } else if (PyTuple_CheckExact(iter_obj)) {
-        Py_ssize_t pos = *ppos;
-        if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
-        *ppos = pos + 1;
-        next_item = PyTuple_GET_ITEM(iter_obj, pos);
-        Py_INCREF(next_item);
-    } else if (PyList_CheckExact(iter_obj)) {
-        Py_ssize_t pos = *ppos;
-        if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
-        *ppos = pos + 1;
-        next_item = PyList_GET_ITEM(iter_obj, pos);
-        Py_INCREF(next_item);
-    } else
-#endif
-    {
-        next_item = PyIter_Next(iter_obj);
-        if (unlikely(!next_item)) {
-            return __Pyx_IterFinish();
-        }
-    }
-    if (pitem) {
-        *pitem = next_item;
-    } else if (pkey && pvalue) {
-        if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
-            return -1;
-    } else if (pkey) {
-        *pkey = next_item;
-    } else {
-        *pvalue = next_item;
-    }
-    return 1;
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+    PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
 }
 
 static CYTHON_INLINE int __Pyx_div_int(int a, int b) {
@@ -82351,7 +82093,6 @@ static CYTHON_INLINE int __Pyx_div_int(int a, int b) {
 }
 
 static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
     PyThreadState *tstate = PyThreadState_GET();
     *type = tstate->exc_type;
     *value = tstate->exc_value;
@@ -82359,12 +82100,8 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
     Py_XINCREF(*type);
     Py_XINCREF(*value);
     Py_XINCREF(*tb);
-#else
-    PyErr_GetExcInfo(type, value, tb);
-#endif
 }
 static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
     PyObject *tmp_type, *tmp_value, *tmp_tb;
     PyThreadState *tstate = PyThreadState_GET();
     tmp_type = tstate->exc_type;
@@ -82376,9 +82113,6 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
     Py_XDECREF(tmp_type);
     Py_XDECREF(tmp_value);
     Py_XDECREF(tmp_tb);
-#else
-    PyErr_SetExcInfo(type, value, tb);
-#endif
 }
 
 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -82459,6 +82193,78 @@ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
 #endif
 }
 
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+    if (s1 == s2) {
+        return (equals == Py_EQ);
+    } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+        if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+            return (equals == Py_NE);
+        } else if (PyBytes_GET_SIZE(s1) == 1) {
+            if (equals == Py_EQ)
+                return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+            else
+                return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+        } else {
+            int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+            return (equals == Py_EQ) ? (result == 0) : (result != 0);
+        }
+    } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+        return (equals == Py_NE);
+    } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+        return (equals == Py_NE);
+    } else {
+        int result;
+        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+        if (!py_result)
+            return -1;
+        result = __Pyx_PyObject_IsTrue(py_result);
+        Py_DECREF(py_result);
+        return result;
+    }
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+    if (s1 == s2) {
+        return (equals == Py_EQ);
+    } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+        #if CYTHON_PEP393_ENABLED
+        if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
+            return -1;
+        if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
+            return (equals == Py_NE);
+        } else if (PyUnicode_GET_LENGTH(s1) == 1) {
+            Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
+            Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
+            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+        #else
+        if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+            return (equals == Py_NE);
+        } else if (PyUnicode_GET_SIZE(s1) == 1) {
+            Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
+            Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
+            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+        #endif
+        } else {
+            int result = PyUnicode_Compare(s1, s2);
+            if ((result == -1) && unlikely(PyErr_Occurred()))
+                return -1;
+            return (equals == Py_EQ) ? (result == 0) : (result != 0);
+        }
+    } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+        return (equals == Py_NE);
+    } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+        return (equals == Py_NE);
+    } else {
+        int result;
+        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+        if (!py_result)
+            return -1;
+        result = __Pyx_PyObject_IsTrue(py_result);
+        Py_DECREF(py_result);
+        return result;
+    }
+}
+
 static PyObject *
 __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
 {
@@ -82739,56 +82545,6 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
                                PyString_AsString(func_name), (void *)op);
 #endif
 }
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
-    PyCFunctionObject* f = (PyCFunctionObject*)func;
-    PyCFunction meth = PyCFunction_GET_FUNCTION(func);
-    PyObject *self = PyCFunction_GET_SELF(func);
-    Py_ssize_t size;
-    switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
-    case METH_VARARGS:
-        if (likely(kw == NULL) || PyDict_Size(kw) == 0)
-            return (*meth)(self, arg);
-        break;
-    case METH_VARARGS | METH_KEYWORDS:
-        return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
-    case METH_NOARGS:
-        if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
-            size = PyTuple_GET_SIZE(arg);
-            if (size == 0)
-                return (*meth)(self, NULL);
-            PyErr_Format(PyExc_TypeError,
-                "%.200s() takes no arguments (%zd given)",
-                f->m_ml->ml_name, size);
-            return NULL;
-        }
-        break;
-    case METH_O:
-        if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
-            size = PyTuple_GET_SIZE(arg);
-            if (size == 1)
-                return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
-            PyErr_Format(PyExc_TypeError,
-                "%.200s() takes exactly one argument (%zd given)",
-                f->m_ml->ml_name, size);
-            return NULL;
-        }
-        break;
-    default:
-        PyErr_SetString(PyExc_SystemError, "Bad call flags in "
-                        "__Pyx_CyFunction_Call. METH_OLDARGS is no "
-                        "longer supported!");
-        return NULL;
-    }
-    PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
-                 f->m_ml->ml_name);
-    return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
-	return PyCFunction_Call(func, arg, kw);
-}
-#endif
 static PyTypeObject __pyx_CyFunctionType_type = {
     PyVarObject_HEAD_INIT(0, 0)
     __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -82808,7 +82564,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
     0,                                  /*tp_as_sequence*/
     0,                                  /*tp_as_mapping*/
     0,                                  /*tp_hash*/
-    __Pyx_CyFunction_Call,              /*tp_call*/
+    __Pyx_PyCFunction_Call,             /*tp_call*/
     0,                                  /*tp_str*/
     0,                                  /*tp_getattro*/
     0,                                  /*tp_setattro*/
@@ -82844,16 +82600,15 @@ static PyTypeObject __pyx_CyFunctionType_type = {
     0,                                  /*tp_version_tag*/
 #endif
 };
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
-    __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
+static int __Pyx_CyFunction_init(void)
+{
     if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
         return -1;
     __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
     return 0;
 }
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
+{
     __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
     m->defaults = PyMem_Malloc(size);
     if (!m->defaults)
@@ -82862,7 +82617,8 @@ static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t
     m->defaults_pyobjects = pyobjects;
     return m->defaults;
 }
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
+{
     __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
     m->defaults_tuple = tuple;
     Py_INCREF(tuple);
@@ -83268,8 +83024,8 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
     }
 }
 
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
-                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+                                  int lineno, const char *filename) {
     PyObject *old_exc, *old_val, *old_tb;
     PyObject *ctx;
     __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
@@ -83289,7 +83045,6 @@ static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
 
 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
     PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
     PyThreadState *tstate = PyThreadState_GET();
     tmp_type = tstate->exc_type;
     tmp_value = tstate->exc_value;
@@ -83297,10 +83052,6 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
     tstate->exc_type = *type;
     tstate->exc_value = *value;
     tstate->exc_traceback = *tb;
-#else
-    PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
-    PyErr_SetExcInfo(*type, *value, *tb);
-#endif
     *type = tmp_type;
     *value = tmp_value;
     *tb = tmp_tb;
@@ -83310,70 +83061,9 @@ static PyObject *__Pyx_Generator_Next(PyObject *self);
 static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
 static PyObject *__Pyx_Generator_Close(PyObject *self);
 static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static PyTypeObject *__pyx_GeneratorType = 0;
-#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
-#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
-    PyObject *et, *ev, *tb;
-    PyObject *value = NULL;
-    __Pyx_ErrFetch(&et, &ev, &tb);
-    if (!et) {
-        Py_XDECREF(tb);
-        Py_XDECREF(ev);
-        Py_INCREF(Py_None);
-        *pvalue = Py_None;
-        return 0;
-    }
-    if (unlikely(et != PyExc_StopIteration) &&
-            unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
-        __Pyx_ErrRestore(et, ev, tb);
-        return -1;
-    }
-    if (likely(et == PyExc_StopIteration)) {
-        if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
-            if (!ev) {
-                Py_INCREF(Py_None);
-                ev = Py_None;
-            }
-            Py_XDECREF(tb);
-            Py_DECREF(et);
-            *pvalue = ev;
-            return 0;
-        }
-    }
-    PyErr_NormalizeException(&et, &ev, &tb);
-    if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
-        __Pyx_ErrRestore(et, ev, tb);
-        return -1;
-    }
-    Py_XDECREF(tb);
-    Py_DECREF(et);
-#if PY_VERSION_HEX >= 0x030300A0
-    value = ((PyStopIterationObject *)ev)->value;
-    Py_INCREF(value);
-    Py_DECREF(ev);
-#else
-    {
-        PyObject* args = PyObject_GetAttrString(ev, "args");
-        Py_DECREF(ev);
-        if (likely(args)) {
-            value = PyObject_GetItem(args, 0);
-            Py_DECREF(args);
-        }
-        if (unlikely(!value)) {
-            __Pyx_ErrRestore(NULL, NULL, NULL);
-            Py_INCREF(Py_None);
-            value = Py_None;
-        }
-    }
-#endif
-    *pvalue = value;
-    return 0;
-}
-#endif
 static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+{
     PyObject *exc_type = self->exc_type;
     PyObject *exc_value = self->exc_value;
     PyObject *exc_traceback = self->exc_traceback;
@@ -83385,18 +83075,14 @@ void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
     Py_XDECREF(exc_traceback);
 }
 static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
-    if (unlikely(gen->is_running)) {
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+{
+    PyObject *retval;
+    if (unlikely(self->is_running)) {
         PyErr_SetString(PyExc_ValueError,
                         "generator already executing");
-        return 1;
+        return NULL;
     }
-    return 0;
-}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
-    PyObject *retval;
-    assert(!self->is_running);
     if (unlikely(self->resume_label == 0)) {
         if (unlikely(value && value != Py_None)) {
             PyErr_SetString(PyExc_TypeError,
@@ -83409,240 +83095,81 @@ PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
         PyErr_SetNone(PyExc_StopIteration);
         return NULL;
     }
-    if (value) {
-#if CYTHON_COMPILING_IN_PYPY
-#else
-        /* Generators always return to their most recent caller, not
-         * necessarily their creator. */
-        if (self->exc_traceback) {
-            PyThreadState *tstate = PyThreadState_GET();
-            PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
-            PyFrameObject *f = tb->tb_frame;
-            Py_XINCREF(tstate->frame);
-            assert(f->f_back == NULL);
-            f->f_back = tstate->frame;
-        }
-#endif
-        __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
-                            &self->exc_traceback);
-    } else {
+    if (value)
+        __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+    else
         __Pyx_Generator_ExceptionClear(self);
-    }
     self->is_running = 1;
     retval = self->body((PyObject *) self, value);
     self->is_running = 0;
-    if (retval) {
-        __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
-                            &self->exc_traceback);
-#if CYTHON_COMPILING_IN_PYPY
-#else
-        /* Don't keep the reference to f_back any longer than necessary.  It
-         * may keep a chain of frames alive or it could create a reference
-         * cycle. */
-        if (self->exc_traceback) {
-            PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
-            PyFrameObject *f = tb->tb_frame;
-            Py_CLEAR(f->f_back);
-        }
-#endif
-    } else {
+    if (retval)
+        __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+    else
         __Pyx_Generator_ExceptionClear(self);
-    }
     return retval;
 }
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
-    PyObject *ret;
-    PyObject *val = NULL;
-    __Pyx_Generator_Undelegate(gen);
-    __Pyx_PyGen_FetchStopIterationValue(&val);
-    ret = __Pyx_Generator_SendEx(gen, val);
-    Py_XDECREF(val);
-    return ret;
-}
-static PyObject *__Pyx_Generator_Next(PyObject *self) {
-    __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
-    PyObject *yf = gen->yieldfrom;
-    if (unlikely(__Pyx_Generator_CheckRunning(gen)))
-        return NULL;
-    if (yf) {
-        PyObject *ret;
-        gen->is_running = 1;
-        ret = Py_TYPE(yf)->tp_iternext(yf);
-        gen->is_running = 0;
-        if (likely(ret)) {
-            return ret;
-        }
-        return __Pyx_Generator_FinishDelegation(gen);
-    }
-    return __Pyx_Generator_SendEx(gen, Py_None);
-}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
-    __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
-    PyObject *yf = gen->yieldfrom;
-    if (unlikely(__Pyx_Generator_CheckRunning(gen)))
-        return NULL;
-    if (yf) {
-        PyObject *ret;
-        gen->is_running = 1;
-        if (__Pyx_Generator_CheckExact(yf)) {
-            ret = __Pyx_Generator_Send(yf, value);
-        } else {
-            if (value == Py_None)
-                ret = PyIter_Next(yf);
-            else
-                ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
-        }
-        gen->is_running = 0;
-        if (likely(ret)) {
-            return ret;
-        }
-        return __Pyx_Generator_FinishDelegation(gen);
-    }
-    return __Pyx_Generator_SendEx(gen, value);
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+    return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
 }
-static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
-    PyObject *retval = NULL;
-    int err = 0;
-    if (__Pyx_Generator_CheckExact(yf)) {
-        retval = __Pyx_Generator_Close(yf);
-        if (!retval)
-            return -1;
-    } else {
-        PyObject *meth;
-        gen->is_running = 1;
-        meth = PyObject_GetAttrString(yf, "close");
-        if (unlikely(!meth)) {
-            if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
-                PyErr_WriteUnraisable(yf);
-            }
-            PyErr_Clear();
-        } else {
-            retval = PyObject_CallFunction(meth, NULL);
-            Py_DECREF(meth);
-            if (!retval)
-                err = -1;
-        }
-        gen->is_running = 0;
-    }
-    Py_XDECREF(retval);
-    return err;
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+    return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
 }
-static PyObject *__Pyx_Generator_Close(PyObject *self) {
-    __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
-    PyObject *retval, *raised_exception;
-    PyObject *yf = gen->yieldfrom;
-    int err = 0;
-    if (unlikely(__Pyx_Generator_CheckRunning(gen)))
-        return NULL;
-    if (yf) {
-        Py_INCREF(yf);
-        err = __Pyx_Generator_CloseIter(gen, yf);
-        __Pyx_Generator_Undelegate(gen);
-        Py_DECREF(yf);
-    }
-    if (err == 0)
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+    __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+    PyObject *retval;
 #if PY_VERSION_HEX < 0x02050000
-        PyErr_SetNone(PyExc_StopIteration);
+    PyErr_SetNone(PyExc_StopIteration);
 #else
-        PyErr_SetNone(PyExc_GeneratorExit);
+    PyErr_SetNone(PyExc_GeneratorExit);
 #endif
-    retval = __Pyx_Generator_SendEx(gen, NULL);
+    retval = __Pyx_Generator_SendEx(generator, NULL);
     if (retval) {
         Py_DECREF(retval);
         PyErr_SetString(PyExc_RuntimeError,
                         "generator ignored GeneratorExit");
         return NULL;
     }
-    raised_exception = PyErr_Occurred();
-    if (!raised_exception
-        || raised_exception == PyExc_StopIteration
-#if PY_VERSION_HEX >= 0x02050000
-        || raised_exception == PyExc_GeneratorExit
-        || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
+#if PY_VERSION_HEX < 0x02050000
+    if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+    if (PyErr_ExceptionMatches(PyExc_StopIteration)
+        || PyErr_ExceptionMatches(PyExc_GeneratorExit))
 #endif
-        || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
     {
-        if (raised_exception) PyErr_Clear();      /* ignore these errors */
+        PyErr_Clear();          /* ignore these errors */
         Py_INCREF(Py_None);
         return Py_None;
     }
     return NULL;
 }
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
-    __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+{
+    __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
     PyObject *typ;
     PyObject *tb = NULL;
     PyObject *val = NULL;
-    PyObject *yf = gen->yieldfrom;
     if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
         return NULL;
-    if (unlikely(__Pyx_Generator_CheckRunning(gen)))
-        return NULL;
-    if (yf) {
-        PyObject *ret;
-        Py_INCREF(yf);
-#if PY_VERSION_HEX >= 0x02050000
-        if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
-            int err = __Pyx_Generator_CloseIter(gen, yf);
-            Py_DECREF(yf);
-            __Pyx_Generator_Undelegate(gen);
-            if (err < 0)
-                return __Pyx_Generator_SendEx(gen, NULL);
-            goto throw_here;
-        }
-#endif
-        gen->is_running = 1;
-        if (__Pyx_Generator_CheckExact(yf)) {
-            ret = __Pyx_Generator_Throw(yf, args);
-        } else {
-            PyObject *meth = PyObject_GetAttrString(yf, "throw");
-            if (unlikely(!meth)) {
-                Py_DECREF(yf);
-                if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
-                    gen->is_running = 0;
-                    return NULL;
-                }
-                PyErr_Clear();
-                __Pyx_Generator_Undelegate(gen);
-                gen->is_running = 0;
-                goto throw_here;
-            }
-            ret = PyObject_CallObject(meth, args);
-            Py_DECREF(meth);
-        }
-        gen->is_running = 0;
-        Py_DECREF(yf);
-        if (!ret) {
-            ret = __Pyx_Generator_FinishDelegation(gen);
-        }
-        return ret;
-    }
-throw_here:
     __Pyx_Raise(typ, val, tb, NULL);
-    return __Pyx_Generator_SendEx(gen, NULL);
+    return __Pyx_Generator_SendEx(generator, NULL);
 }
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
+static int
+__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
+{
     __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
     Py_VISIT(gen->closure);
     Py_VISIT(gen->classobj);
-    Py_VISIT(gen->yieldfrom);
     Py_VISIT(gen->exc_type);
     Py_VISIT(gen->exc_value);
     Py_VISIT(gen->exc_traceback);
     return 0;
 }
-static int __Pyx_Generator_clear(PyObject *self) {
-    __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
-    Py_CLEAR(gen->closure);
-    Py_CLEAR(gen->classobj);
-    Py_CLEAR(gen->yieldfrom);
-    Py_CLEAR(gen->exc_type);
-    Py_CLEAR(gen->exc_value);
-    Py_CLEAR(gen->exc_traceback);
-    return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
+static void
+__Pyx_Generator_dealloc(PyObject *self)
+{
     __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
     PyObject_GC_UnTrack(gen);
     if (gen->gi_weakreflist != NULL)
@@ -83654,10 +83181,16 @@ static void __Pyx_Generator_dealloc(PyObject *self) {
             return;                     /* resurrected.  :( */
     }
     PyObject_GC_UnTrack(self);
-    __Pyx_Generator_clear(self);
+    Py_CLEAR(gen->closure);
+    Py_CLEAR(gen->classobj);
+    Py_CLEAR(gen->exc_type);
+    Py_CLEAR(gen->exc_value);
+    Py_CLEAR(gen->exc_traceback);
     PyObject_GC_Del(gen);
 }
-static void __Pyx_Generator_del(PyObject *self) {
+static void
+__Pyx_Generator_del(PyObject *self)
+{
     PyObject *res;
     PyObject *error_type, *error_value, *error_traceback;
     __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
@@ -83686,13 +83219,11 @@ static void __Pyx_Generator_del(PyObject *self) {
         _Py_NewReference(self);
         self->ob_refcnt = refcnt;
     }
-#if CYTHON_COMPILING_FOR_CPYTHON
     assert(PyType_IS_GC(self->ob_type) &&
            _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
     /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
      * we need to undo that. */
     _Py_DEC_REFTOTAL;
-#endif
     /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
      * chain, so no more to do there.
      * If COUNT_ALLOCS, the original decref bumped tp_frees, and
@@ -83700,17 +83231,13 @@ static void __Pyx_Generator_del(PyObject *self) {
      * undone.
      */
 #ifdef COUNT_ALLOCS
-    --Py_TYPE(self)->tp_frees;
-    --Py_TYPE(self)->tp_allocs;
+    --self->ob_type->tp_frees;
+    --self->ob_type->tp_allocs;
 #endif
 }
 static PyMemberDef __pyx_Generator_memberlist[] = {
     {(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
-     T_BOOL,
-#else
-     T_BYTE,
-#endif
+     T_INT,
      offsetof(__pyx_GeneratorObject, is_running),
      READONLY,
      NULL},
@@ -83722,7 +83249,7 @@ static PyMethodDef __pyx_Generator_methods[] = {
     {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
     {0, 0, 0, 0}
 };
-static PyTypeObject __pyx_GeneratorType_type = {
+static PyTypeObject __pyx_GeneratorType = {
     PyVarObject_HEAD_INIT(0, 0)
     __Pyx_NAMESTR("generator"),         /*tp_name*/
     sizeof(__pyx_GeneratorObject),      /*tp_basicsize*/
@@ -83743,7 +83270,7 @@ static PyTypeObject __pyx_GeneratorType_type = {
     0,                                  /*tp_hash*/
     0,                                  /*tp_call*/
     0,                                  /*tp_str*/
-    0,                                  /*tp_getattro*/
+    PyObject_GenericGetAttr,            /*tp_getattro*/
     0,                                  /*tp_setattro*/
     0,                                  /*tp_as_buffer*/
     Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
@@ -83752,7 +83279,7 @@ static PyTypeObject __pyx_GeneratorType_type = {
     0,                                  /*tp_clear*/
     0,                                  /*tp_richcompare*/
     offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
-    0,                                  /*tp_iter*/
+    PyObject_SelfIter,                  /*tp_iter*/
     (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
     __pyx_Generator_methods,            /*tp_methods*/
     __pyx_Generator_memberlist,         /*tp_members*/
@@ -83777,10 +83304,12 @@ static PyTypeObject __pyx_GeneratorType_type = {
     0,                                  /*tp_version_tag*/
 #endif
 };
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
-                                                  PyObject *closure) {
+static
+__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+                                           PyObject *closure)
+{
     __pyx_GeneratorObject *gen =
-        PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
+        PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
     if (gen == NULL)
         return NULL;
     gen->body = body;
@@ -83789,7 +83318,6 @@ static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
     gen->is_running = 0;
     gen->resume_label = 0;
     gen->classobj = NULL;
-    gen->yieldfrom = NULL;
     gen->exc_type = NULL;
     gen->exc_value = NULL;
     gen->exc_traceback = NULL;
@@ -83797,14 +83325,9 @@ static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
     PyObject_GC_Track(gen);
     return gen;
 }
-static int __pyx_Generator_init(void) {
-    __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
-    __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
-    if (PyType_Ready(&__pyx_GeneratorType_type)) {
-        return -1;
-    }
-    __pyx_GeneratorType = &__pyx_GeneratorType_type;
-    return 0;
+static int __pyx_Generator_init(void)
+{
+    return PyType_Ready(&__pyx_GeneratorType);
 }
 
 static int __Pyx_check_binary_version(void) {
diff --git a/python/src/sa/_sa.pyx b/python/src/sa/_sa.pyx
index 50da4235..4716d174 100644
--- a/python/src/sa/_sa.pyx
+++ b/python/src/sa/_sa.pyx
@@ -2,7 +2,7 @@ import logging
 import resource
 import gzip
 
-cdef float monitor_cpu():
+def monitor_cpu():
     return (resource.getrusage(resource.RUSAGE_SELF).ru_utime+
             resource.getrusage(resource.RUSAGE_SELF).ru_stime)
 
diff --git a/python/src/sa/rulefactory.pxi b/python/src/sa/rulefactory.pxi
index 7063c2da..559e8396 100644
--- a/python/src/sa/rulefactory.pxi
+++ b/python/src/sa/rulefactory.pxi
@@ -260,6 +260,7 @@ cdef class HieroCachingRuleFactory:
 
     cdef prev_norm_prefix
     cdef float extract_time
+    cdef float intersect_time
     cdef SuffixArray fsa
     cdef DataArray fda
     cdef DataArray eda
@@ -979,10 +980,11 @@ cdef class HieroCachingRuleFactory:
         cdef IntList sample, chunklen
         cdef Matching matching
         cdef Phrase hiero_phrase
-        
+
         flen = len(fwords)
         start_time = monitor_cpu()
         self.extract_time = 0.0
+        self.intersect_time = 0.0
         nodes_isteps_away_buffer = {}
         hit = 0
         reachable_buffer = {}
@@ -1072,7 +1074,10 @@ cdef class HieroCachingRuleFactory:
                     else:
                         if arity > 0:
                             # Intersecting because of arity > 0
+                            intersect_start_time = monitor_cpu()
                             phrase_location = self.intersect(node, node.suffix_link.children[word_id], hiero_phrase)
+                            intersect_stop_time = monitor_cpu()
+                            self.intersect_time += intersect_stop_time - intersect_start_time
                         else:
                             # Suffix array search
                             phrase_location = node.phrase_location
@@ -1203,6 +1208,7 @@ cdef class HieroCachingRuleFactory:
         logger.info("Total time for rule lookup, extraction, and scoring = %f seconds", (stop_time - start_time))
         gc.collect()
         logger.info("    Extract time = %f seconds", self.extract_time)
+        logger.info("    Intersect time = %f seconds", self.intersect_time)
 
 
     cdef int find_fixpoint(self, 
@@ -1674,7 +1680,6 @@ cdef class HieroCachingRuleFactory:
                         for (phrase2,eindexes) in phrase_list:
                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)        
                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))
-
                     if (num_gaps < self.max_nonterminals and
                         phrase_len < self.max_length and
                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
@@ -1690,12 +1695,12 @@ cdef class HieroCachingRuleFactory:
                                 met_constraints = 0
 
                             if (met_constraints and
-                                self.find_fixpoint(f_x_low, f_back_high,
+                                (self.find_fixpoint(f_x_low, f_back_high,
                                             f_links_low, f_links_high, e_links_low, e_links_high, 
                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high, 
                                             f_sent_len, e_sent_len, 
                                             self.train_max_initial_size, self.train_max_initial_size, 
-                                            1, 1, 1, 1, 0, 1, 0) and
+                                            1, 1, 1, 1, 0, 1, 0) == 1) and
                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and
                                 self.find_fixpoint(f_x_low, f_low,    # check integrity of new subphrase
                                             f_links_low, f_links_high, e_links_low, e_links_high,
@@ -1809,12 +1814,12 @@ cdef class HieroCachingRuleFactory:
                                 met_constraints = 0
 
                             if (met_constraints and
-                                self.find_fixpoint(f_x_low, f_x_high,
+                                (self.find_fixpoint(f_x_low, f_x_high,
                                                 f_links_low, f_links_high, e_links_low, e_links_high,
                                                 e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high, 
                                                 f_sent_len, e_sent_len,
                                                 self.train_max_initial_size, self.train_max_initial_size, 
-                                                1, 1, 2, 1, 1, 1, 1) and
+                                                1, 1, 2, 1, 1, 1, 1) == 1) and
                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and
                                 self.find_fixpoint(f_x_low, f_low,
                                                 f_links_low, f_links_high, e_links_low, e_links_high,
diff --git a/training/Makefile.am b/training/Makefile.am
index e95e045f..8ef3c939 100644
--- a/training/Makefile.am
+++ b/training/Makefile.am
@@ -6,6 +6,7 @@ SUBDIRS = \
   dpmert \
   pro \
   dtrain \
+  latent_svm \
   mira \
   rampion
 
diff --git a/training/latent_svm/Makefile.am b/training/latent_svm/Makefile.am
new file mode 100644
index 00000000..65c5e038
--- /dev/null
+++ b/training/latent_svm/Makefile.am
@@ -0,0 +1,6 @@
+bin_PROGRAMS = latent_svm
+
+latent_svm_SOURCES = latent_svm.cc
+latent_svm_LDADD = ../..//decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
+
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/latent_svm/latent_svm.cc b/training/latent_svm/latent_svm.cc
new file mode 100644
index 00000000..ab9c1d5d
--- /dev/null
+++ b/training/latent_svm/latent_svm.cc
@@ -0,0 +1,412 @@
+/*
+Points to note regarding variable names:
+total_loss and prev_loss actually refer not to loss, but the metric (usually BLEU)
+*/
+#include <sstream>
+#include <iostream>
+#include <vector>
+#include <cassert>
+#include <cmath>
+
+//boost libraries
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+//cdec libraries
+#include "config.h"
+#include "hg_sampler.h"
+#include "sentence_metadata.h"
+#include "scorer.h"
+#include "verbose.h"
+#include "viterbi.h"
+#include "hg.h"
+#include "prob.h"
+#include "kbest.h"
+#include "ff_register.h"
+#include "decoder.h"
+#include "filelib.h"
+#include "fdict.h"
+#include "weights.h"
+#include "sparse_vector.h"
+#include "sampler.h"
+
+using namespace std;
+using boost::shared_ptr;
+namespace po = boost::program_options;
+
+bool invert_score; 
+boost::shared_ptr<MT19937> rng; //random seed ptr
+
+void RandomPermutation(int len, vector<int>* p_ids) {
+  vector<int>& ids = *p_ids;
+  ids.resize(len);
+  for (int i = 0; i < len; ++i) ids[i] = i;
+  for (int i = len; i > 0; --i) {
+    int j = rng->next() * i;
+    if (j == i) i--;
+    swap(ids[i-1], ids[j]);
+  }  
+}
+
+bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+        ("weights,w",po::value<string>(),"[REQD] Input feature weights file")
+        ("input,i",po::value<string>(),"[REQD] Input source file for development set")
+        ("passes,p", po::value<int>()->default_value(15), "Number of passes through the training data")
+        ("weights_write_interval,n", po::value<int>()->default_value(1000), "Number of lines between writing out weights")
+        ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation(s) (tokenized text file)")
+        ("mt_metric,m",po::value<string>()->default_value("ibm_bleu"), "Scoring metric (ibm_bleu, nist_bleu, koehn_bleu, ter, combi)")
+        ("regularizer_strength,C", po::value<double>()->default_value(0.01), "regularization strength")
+        ("mt_metric_scale,s", po::value<double>()->default_value(1.0), "Cost function is -mt_metric_scale*BLEU")
+        ("costaug_log_bleu,l", "Flag converts BLEU to log space. Cost function is thus -mt_metric_scale*log(BLEU). Not on by default")
+        ("average,A", "Average the weights (this is a weighted average due to the scaling factor)")
+        ("mu,u", po::value<double>()->default_value(0.0), "weight (between 0 and 1) to scale model score by for oracle selection")
+        ("stepsize_param,a", po::value<double>()->default_value(0.01), "Stepsize parameter, during optimization")
+        ("stepsize_reduce,t", "Divide step size by sqrt(number of examples seen so far), as per Ratliff et al., 2007")
+	("metric_threshold,T", po::value<double>()->default_value(0.0), "Threshold for diff between oracle BLEU and cost-aug BLEU for updating the weights")
+	("check_positive,P", "Check that the loss is positive before updating")
+        ("k_best_size,k", po::value<int>()->default_value(250), "Size of hypothesis list to search for oracles")
+        ("best_ever,b", "Keep track of the best hypothesis we've ever seen (metric score), and use that as the reference")
+        ("random_seed,S", po::value<uint32_t>(), "Random seed (if not specified, /dev/random will be used)")
+        ("decoder_config,c",po::value<string>(),"Decoder configuration file");
+  po::options_description clo("Command line options");
+  clo.add_options()
+        ("config", po::value<string>(), "Configuration file")
+        ("help,h", "Print this help message and exit");
+  po::options_description dconfig_options, dcmdline_options;
+  dconfig_options.add(opts);
+  dcmdline_options.add(opts).add(clo);
+  
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  if (conf->count("config")) {
+    ifstream config((*conf)["config"].as<string>().c_str());
+    po::store(po::parse_config_file(config, dconfig_options), *conf);
+  }
+  po::notify(*conf);
+
+  if (conf->count("help") || !conf->count("weights") || !conf->count("input") || !conf->count("decoder_config") || !conf->count("reference")) {
+    cerr << dcmdline_options << endl;
+    return false;
+  }
+  return true;
+}
+
+double scaling_trick = 1; // see http://blog.smola.org/post/940672544/fast-quadratic-regularization-for-online-learning
+/*computes and returns cost augmented score for negative example selection*/
+double cost_augmented_score(const LogVal<double> model_score, const double mt_metric_score, const double mt_metric_scale, const bool logbleu) {
+  if(logbleu) {
+    if(mt_metric_score != 0)
+      // NOTE: log(model_score) is just the model score feature weights * features
+      return log(model_score) * scaling_trick + (- mt_metric_scale * log(mt_metric_score));
+    else
+      return -1000000;
+  }
+  // NOTE: log(model_score) is just the model score feature weights * features
+  return log(model_score) * scaling_trick + (- mt_metric_scale * mt_metric_score);
+}
+
+/*computes and returns mu score, for oracle selection*/
+double muscore(const vector<weight_t>& feature_weights, const SparseVector<double>& feature_values, const double mt_metric_score, const double mu, const bool logbleu) {
+  if(logbleu) {
+    if(mt_metric_score != 0)
+      return feature_values.dot(feature_weights) * mu + (1 - mu) * log(mt_metric_score);
+    else
+      return feature_values.dot(feature_weights) * mu + (1 - mu) * (-1000000);  // log(0) is -inf
+  }
+  return feature_values.dot(feature_weights) * mu + (1 - mu) * mt_metric_score;
+}
+
+static const double kMINUS_EPSILON = -1e-6;
+
+struct HypothesisInfo {
+  SparseVector<double> features;
+  double mt_metric_score;
+  // The model score changes when the feature weights change, so it is not stored here
+  // It must be recomputed every time
+};
+
+struct GoodOracle {
+  shared_ptr<HypothesisInfo> good;
+};
+
+struct TrainingObserver : public DecoderObserver {
+  TrainingObserver(const int k,
+                   const DocScorer& d,
+                   vector<GoodOracle>* o,
+                   const vector<weight_t>& feat_weights,
+                   const double metric_scale,
+                   const double Mu,
+                   const bool bestever,
+                   const bool LogBleu) : ds(d), feature_weights(feat_weights), oracles(*o), kbest_size(k), mt_metric_scale(metric_scale), mu(Mu), best_ever(bestever), log_bleu(LogBleu) {}
+  const DocScorer& ds;
+  const vector<weight_t>& feature_weights;
+  vector<GoodOracle>& oracles;
+  shared_ptr<HypothesisInfo> cur_best;
+  shared_ptr<HypothesisInfo> cur_costaug_best;
+  shared_ptr<HypothesisInfo> cur_ref; 
+  const int kbest_size;
+  const double mt_metric_scale;
+  const double mu;
+  const bool best_ever;
+  const bool log_bleu;
+
+  const HypothesisInfo& GetCurrentBestHypothesis() const {
+    return *cur_best;
+  }
+
+  const HypothesisInfo& GetCurrentCostAugmentedHypothesis() const {
+    return *cur_costaug_best;
+  }
+
+  const HypothesisInfo& GetCurrentReference() const {
+    return *cur_ref; 
+  }
+
+  virtual void NotifyTranslationForest(const SentenceMetadata& smeta, Hypergraph* hg) {
+    UpdateOracles(smeta.GetSentenceID(), *hg);
+  }
+
+  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double metric) {
+    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+    h->features = feats;
+    h->mt_metric_score = metric;
+    return h;
+  }
+
+  void UpdateOracles(int sent_id, const Hypergraph& forest) {
+    //shared_ptr<HypothesisInfo>& cur_ref = oracles[sent_id].good;
+    cur_ref = oracles[sent_id].good; 
+    if(!best_ever)
+      cur_ref.reset();
+
+    KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(forest, kbest_size);
+    double costaug_best_score = 0;
+
+    for (int i = 0; i < kbest_size; ++i) {
+      const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+      double mt_metric_score = ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore(); //this might need to change!!
+      const SparseVector<double>& feature_vals = d->feature_values; 
+      double costaugmented_score = cost_augmented_score(d->score, mt_metric_score, mt_metric_scale, log_bleu); //note that d->score, i.e., model score, is passed in
+      if (i == 0) { //i.e., setting up cur_best to be model score highest, and initializing costaug_best
+        cur_best = MakeHypothesisInfo(feature_vals, mt_metric_score);
+        cur_costaug_best = cur_best;
+        costaug_best_score = costaugmented_score; 
+      }
+      if (costaugmented_score > costaug_best_score) {   // kbest_mira's cur_bad, i.e., "fear" derivation
+        cur_costaug_best = MakeHypothesisInfo(feature_vals, mt_metric_score);
+        costaug_best_score = costaugmented_score;
+      }
+      double cur_muscore = mt_metric_score;
+      if (!cur_ref)   // kbest_mira's cur_good, i.e., "hope" derivation
+        cur_ref =  MakeHypothesisInfo(feature_vals, cur_muscore);
+      else {
+          double cur_ref_muscore = cur_ref->mt_metric_score;
+          if(mu > 0) { //select oracle with mixture of model score and BLEU
+              cur_ref_muscore =  muscore(feature_weights, cur_ref->features, cur_ref->mt_metric_score, mu, log_bleu);
+              cur_muscore = muscore(feature_weights, d->feature_values, mt_metric_score, mu, log_bleu);
+          }
+          if (cur_muscore > cur_ref_muscore) //replace oracle
+            cur_ref = MakeHypothesisInfo(feature_vals, mt_metric_score);
+      }
+    }
+  }
+};
+
+void ReadTrainingCorpus(const string& fname, vector<string>* c) {
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  string line;
+  while(in) {
+    getline(in, line);
+    if (!in) break;
+    c->push_back(line);
+  }
+}
+
+bool ApproxEqual(double a, double b) {
+  if (a == b) return true;
+  return (fabs(a-b)/fabs(b)) < 0.000001;
+}
+
+int main(int argc, char** argv) {
+  register_feature_functions();
+  SetSilent(true);  // turn off verbose decoder output
+
+  po::variables_map conf;
+  if (!InitCommandLine(argc, argv, &conf)) return 1;
+
+  if (conf.count("random_seed"))
+    rng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
+  else
+    rng.reset(new MT19937);
+
+  const bool best_ever = conf.count("best_ever") > 0;
+  vector<string> corpus;
+  ReadTrainingCorpus(conf["input"].as<string>(), &corpus);
+
+  const string metric_name = conf["mt_metric"].as<string>(); //set up scoring; this may need to be changed!!
+  
+  ScoreType type = ScoreTypeFromString(metric_name);
+  if (type == TER) {
+    invert_score = true;
+  } else {
+    invert_score = false;
+  } 
+  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  if (ds.size() != corpus.size()) {
+    cerr << "Mismatched number of references (" << ds.size() << ") and sources (" << corpus.size() << ")\n";
+    return 1;
+  }
+
+  ReadFile ini_rf(conf["decoder_config"].as<string>());
+  Decoder decoder(ini_rf.stream());
+
+  // load initial weights
+  vector<weight_t>& decoder_weights = decoder.CurrentWeightVector(); //equivalent to "dense_weights" vector in kbest_mira.cc
+  SparseVector<weight_t> sparse_weights; //equivaelnt to  kbest_mira.cc "lambdas"
+  Weights::InitFromFile(conf["weights"].as<string>(), &decoder_weights);
+  Weights::InitSparseVector(decoder_weights, &sparse_weights);
+
+  //initializing other algorithm and output parameters
+  const double c = conf["regularizer_strength"].as<double>();
+  const int weights_write_interval = conf["weights_write_interval"].as<int>();
+  const double mt_metric_scale = conf["mt_metric_scale"].as<double>();
+  const double mu = conf["mu"].as<double>();
+  const double metric_threshold = conf["metric_threshold"].as<double>();
+  const double stepsize_param = conf["stepsize_param"].as<double>(); //step size in structured SGD optimization step
+  const bool stepsize_reduce = conf.count("stepsize_reduce") > 0; 
+  const bool costaug_log_bleu = conf.count("costaug_log_bleu") > 0;
+  const bool average = conf.count("average") > 0;
+  const bool checkpositive = conf.count("check_positive") > 0;
+
+  assert(corpus.size() > 0);
+  vector<GoodOracle> oracles(corpus.size());
+  TrainingObserver observer(conf["k_best_size"].as<int>(),  // kbest size
+                            ds,                             // doc scorer
+                            &oracles,
+                            decoder_weights,
+                            mt_metric_scale,
+                            mu,
+                            best_ever,
+                            costaug_log_bleu);
+  int cur_sent = 0;
+  int line_count = 0;
+  int normalizer = 0; 
+  double total_loss = 0;
+  double prev_loss = 0;
+  int dots = 0;             // progess bar
+  int cur_pass = 0;
+  SparseVector<double> tot;
+  tot += sparse_weights; //add initial weights to total
+  normalizer++; //add 1 to normalizer
+  int max_iteration = conf["passes"].as<int>();
+  string msg = "# LatentSVM tuned weights";
+  vector<int> order;
+  int interval_counter = 0;
+  RandomPermutation(corpus.size(), &order); //shuffle corpus
+  while (line_count <= max_iteration * corpus.size()) { //loop over all (passes * num sentences) examples
+    //if ((interval_counter * 40 / weights_write_interval) > dots) { ++dots; cerr << '.'; } //check this
+    if ((cur_sent * 40 / corpus.size()) > dots) { ++dots; cerr << '.';}
+    if (interval_counter == weights_write_interval) { //i.e., we need to write out weights
+      sparse_weights *= scaling_trick;
+      tot *= scaling_trick;
+      scaling_trick = 1;
+      cerr << " [SENTENCE NUMBER= " << cur_sent << "\n";
+      cerr << " [AVG METRIC LAST INTERVAL =" << ((total_loss - prev_loss) / weights_write_interval) << "]\n";
+      cerr << " [AVG METRIC THIS PASS THUS FAR =" << (total_loss / cur_sent) << "]\n";
+      cerr << " [TOTAL LOSS: =" << total_loss << "\n";
+      Weights::ShowLargestFeatures(decoder_weights);
+      //dots = 0;
+      interval_counter = 0;
+      prev_loss = total_loss;
+      if (average){
+	SparseVector<double> x = tot;
+	x /= normalizer;
+	ostringstream sa;
+	sa << "weights.latentsvm-" << line_count/weights_write_interval << "-avg.gz";
+	x.init_vector(&decoder_weights);
+	Weights::WriteToFile(sa.str(), decoder_weights, true, &msg); 
+      }
+      else {
+	ostringstream os;
+	os << "weights.latentsvm-" << line_count/weights_write_interval << ".gz";
+	sparse_weights.init_vector(&decoder_weights);
+	Weights::WriteToFile(os.str(), decoder_weights, true, &msg);
+      }
+    }
+    if (corpus.size() == cur_sent) { //i.e., finished a pass
+      //cerr << " [AVG METRIC LAST PASS=" << (document_metric_score / corpus.size()) << "]\n";
+      cerr << " [AVG METRIC LAST PASS=" << (total_loss / corpus.size()) << "]\n";
+      cerr << " TOTAL LOSS: " << total_loss << "\n";
+      Weights::ShowLargestFeatures(decoder_weights);
+      cur_sent = 0;
+      total_loss = 0;
+      dots = 0;
+      if(average) {
+        SparseVector<double> x = tot; 
+        x /= normalizer;
+        ostringstream sa;
+        sa << "weights.latentsvm-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "-avg.gz";
+        x.init_vector(&decoder_weights);
+        Weights::WriteToFile(sa.str(), decoder_weights, true, &msg);
+      }
+      else {
+	ostringstream os;
+	os << "weights.latentsvm-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << ".gz";
+	Weights::WriteToFile(os.str(), decoder_weights, true, &msg);	
+      }
+      cur_pass++;
+      RandomPermutation(corpus.size(), &order);
+    }
+    if (cur_sent == 0) { //i.e., starting a new pass
+      cerr << "PASS " << (line_count / corpus.size() + 1) << endl;
+    }
+    sparse_weights.init_vector(&decoder_weights);   // copy sparse_weights to the decoder weights
+    decoder.SetId(order[cur_sent]); //assign current sentence
+    decoder.Decode(corpus[order[cur_sent]], &observer);  // decode/update oracles
+
+    const HypothesisInfo& cur_best = observer.GetCurrentBestHypothesis(); //model score best
+    const HypothesisInfo& cur_costaug = observer.GetCurrentCostAugmentedHypothesis(); //(model + cost) best; cost = -metric_scale*log(BLEU) or -metric_scale*BLEU
+    //const HypothesisInfo& cur_ref = *oracles[order[cur_sent]].good; //this oracle-best line only picks based on BLEU
+    const HypothesisInfo& cur_ref = observer.GetCurrentReference();  //if mu > 0, this mu-mixed oracle will be picked; otherwise, only on BLEU
+    total_loss += cur_best.mt_metric_score; 
+
+    double step_size = stepsize_param;
+    if (stepsize_reduce){       // w_{t+1} = w_t - stepsize_t * grad(Loss) 
+        step_size  /= (sqrt(cur_sent+1.0)); 
+    }
+    //actual update step - compute gradient, and modify sparse_weights
+    if(cur_ref.mt_metric_score - cur_costaug.mt_metric_score > metric_threshold) {
+      const double loss = (cur_costaug.features.dot(decoder_weights) - cur_ref.features.dot(decoder_weights)) * scaling_trick + mt_metric_scale * (cur_ref.mt_metric_score - cur_costaug.mt_metric_score);
+      if (!checkpositive || loss > 0.0) { //can update either all the time if check positive is off, or only when loss > 0 if it's on
+	sparse_weights -= cur_costaug.features * step_size / ((1.0-2.0*step_size*c)*scaling_trick);    // cost augmented hyp orig -
+	sparse_weights += cur_ref.features * step_size / ((1.0-2.0*step_size*c)*scaling_trick);        // ref orig +
+      }
+    }
+    scaling_trick *= (1.0 - 2.0 * step_size * c);
+
+    tot += sparse_weights; //for averaging purposes
+    normalizer++; //for averaging purposes
+    line_count++;
+    interval_counter++;
+    cur_sent++;
+  }
+  cerr << endl;
+  if(average) {
+    tot /= normalizer;
+    tot.init_vector(decoder_weights);
+    msg = "# Latent SSVM tuned weights (averaged vector)";
+    Weights::WriteToFile("weights.latentsvm-final-avg.gz", decoder_weights, true, &msg); 
+    cerr << "Optimization complete.\n" << "AVERAGED WEIGHTS: weights.latentsvm-final-avg.gz\n";
+  } else {
+    Weights::WriteToFile("weights.latentsvm-final.gz", decoder_weights, true, &msg);    
+    cerr << "Optimization complete.\n";
+  }
+  return 0;
+}
+
diff --git a/training/mira/Makefile.am b/training/mira/Makefile.am
index fa4fb22d..8cddc2d7 100644
--- a/training/mira/Makefile.am
+++ b/training/mira/Makefile.am
@@ -1,6 +1,11 @@
-bin_PROGRAMS = kbest_mira
+bin_PROGRAMS = kbest_mira \
+		kbest_cut_mira 
 
 kbest_mira_SOURCES = kbest_mira.cc
 kbest_mira_LDADD = ../../decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
 
+
+kbest_cut_mira_SOURCES = kbest_cut_mira.cc
+kbest_cut_mira_LDADD = ../../decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
+
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/mira/kbest_cut_mira.cc b/training/mira/kbest_cut_mira.cc
new file mode 100644
index 00000000..7df9a18f
--- /dev/null
+++ b/training/mira/kbest_cut_mira.cc
@@ -0,0 +1,954 @@
+#include <sstream>
+#include <iostream>
+#include <vector>
+#include <cassert>
+#include <cmath>
+#include <algorithm>
+
+#include "config.h"
+
+
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "sentence_metadata.h"
+#include "scorer.h"
+#include "verbose.h"
+#include "viterbi.h"
+#include "hg.h"
+#include "prob.h"
+#include "kbest.h"
+#include "ff_register.h"
+#include "decoder.h"
+#include "filelib.h"
+#include "fdict.h"
+#include "time.h"
+#include "sampler.h"
+
+#include "weights.h"
+#include "sparse_vector.h"
+
+using namespace std;
+using boost::shared_ptr;
+namespace po = boost::program_options;
+
+bool invert_score;
+boost::shared_ptr<MT19937> rng;
+bool approx_score;
+bool no_reweight;
+bool no_select;
+bool unique_kbest;
+int update_list_size;
+vector<weight_t> dense_w_local;
+double mt_metric_scale;
+int optimizer;
+int fear_select;
+int hope_select;
+bool pseudo_doc;
+bool sent_approx;
+bool checkloss;
+
+void SanityCheck(const vector<double>& w) {
+  for (int i = 0; i < w.size(); ++i) {
+    assert(!isnan(w[i]));
+    assert(!isinf(w[i]));
+  }
+}
+
+struct FComp {
+  const vector<double>& w_;
+  FComp(const vector<double>& w) : w_(w) {}
+  bool operator()(int a, int b) const {
+    return fabs(w_[a]) > fabs(w_[b]);
+  }
+};
+
+void ShowLargestFeatures(const vector<double>& w) {
+  vector<int> fnums(w.size());
+  for (int i = 0; i < w.size(); ++i)
+    fnums[i] = i;
+  vector<int>::iterator mid = fnums.begin();
+  mid += (w.size() > 10 ? 10 : w.size());
+  partial_sort(fnums.begin(), mid, fnums.end(), FComp(w));
+  cerr << "TOP FEATURES:";
+  for (vector<int>::iterator i = fnums.begin(); i != mid; ++i) {
+    cerr << ' ' << FD::Convert(*i) << '=' << w[*i];
+  }
+  cerr << endl;
+}
+
+bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+    ("input_weights,w",po::value<string>(),"Input feature weights file")
+    ("source,i",po::value<string>(),"Source file for development set")
+    ("pass,p", po::value<int>()->default_value(15), "Current pass through the training data")
+    ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation(s) (tokenized text file)")
+    ("mt_metric,m",po::value<string>()->default_value("ibm_bleu"), "Scoring metric (ibm_bleu, nist_bleu, koehn_bleu, ter, combi)")
+    ("optimizer,o",po::value<int>()->default_value(1), "Optimizer (SGD=1, PA MIRA w/Delta=2, Cutting Plane MIRA=3, PA MIRA=4, Triple nbest list MIRA=5)")
+    ("fear,f",po::value<int>()->default_value(1), "Fear selection (model-cost=1, maxcost=2, maxscore=3)")
+    ("hope,h",po::value<int>()->default_value(1), "Hope selection (model+cost=1, mincost=2)")
+    ("max_step_size,C", po::value<double>()->default_value(0.01), "regularization strength (C)")
+    ("random_seed,S", po::value<uint32_t>(), "Random seed (if not specified, /dev/random will be used)")
+    ("mt_metric_scale,s", po::value<double>()->default_value(1.0), "Amount to scale MT loss function by")
+    ("sent_approx,a", "Use smoothed sentence-level BLEU score for approximate scoring")
+    ("pseudo_doc,e", "Use pseudo-document BLEU score for approximate scoring")
+    ("no_reweight,d","Do not reweight forest for cutting plane")
+    ("no_select,n", "Do not use selection heuristic")
+    ("k_best_size,k", po::value<int>()->default_value(250), "Size of hypothesis list to search for oracles")
+    ("update_k_best,b", po::value<int>()->default_value(1), "Size of good, bad lists to perform update with")
+    ("unique_k_best,u", "Unique k-best translation list")
+    ("weights_output,O",po::value<string>(),"Directory to write weights to")
+    ("output_dir,D",po::value<string>(),"Directory to place output in")
+    ("decoder_config,c",po::value<string>(),"Decoder configuration file");
+  po::options_description clo("Command line options");
+  clo.add_options()
+    ("config", po::value<string>(), "Configuration file")
+    ("help,H", "Print this help message and exit");
+  po::options_description dconfig_options, dcmdline_options;
+  dconfig_options.add(opts);
+  dcmdline_options.add(opts).add(clo);
+  
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  if (conf->count("config")) {
+    ifstream config((*conf)["config"].as<string>().c_str());
+    po::store(po::parse_config_file(config, dconfig_options), *conf);
+  }
+  po::notify(*conf);
+
+  if (conf->count("help") || !conf->count("input_weights") || !conf->count("decoder_config") || !conf->count("reference")) {
+    cerr << dcmdline_options << endl;
+    return false;
+  }
+  return true;
+}
+
+//load previous translation, store array of each sentences score, subtract it from current sentence and replace with new translation score
+
+
+static const double kMINUS_EPSILON = -1e-6;
+static const double EPSILON = 0.000001;
+static const double SMO_EPSILON = 0.0001;
+static const double PSEUDO_SCALE = 0.95;
+static const int MAX_SMO = 10;
+int cur_pass;
+
+struct HypothesisInfo {
+  SparseVector<double> features;
+  vector<WordID> hyp;
+  double mt_metric;
+  double hope;
+  double fear;
+  double alpha;
+  double oracle_loss;
+  SparseVector<double> oracle_feat_diff;
+  shared_ptr<HypothesisInfo> oracleN;
+};
+
+bool ApproxEqual(double a, double b) {
+  if (a == b) return true;
+  return (fabs(a-b)/fabs(b)) < EPSILON;
+}
+
+typedef shared_ptr<HypothesisInfo> HI;
+bool HypothesisCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->mt_metric > h2->mt_metric;
+};
+
+
+bool HopeCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->hope > h2->hope;
+};
+
+bool FearCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->fear > h2->fear;
+};
+
+bool FearComparePred(const HI& h1, const HI& h2 ) 
+{
+  return h1->features.dot(dense_w_local) > h2->features.dot(dense_w_local);
+};
+
+bool HypothesisCompareG(const HI& h1, const HI& h2 ) 
+{
+  return h1->mt_metric < h2->mt_metric;
+};
+
+
+void CuttingPlane(vector<shared_ptr<HypothesisInfo> >* cur_c, bool* again, vector<shared_ptr<HypothesisInfo> >& all_hyp, vector<weight_t> dense_weights)
+{
+  bool DEBUG_CUT = false;
+  shared_ptr<HypothesisInfo> max_fear, max_fear_in_set;
+  vector<shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
+
+  if(no_reweight)
+    {
+      //find new hope hypothesis
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_weights);
+	  all_hyp[u]->hope = 1 * all_hyp[u]->mt_metric + t_score;
+	}
+      
+      //sort hyps by hope score
+      sort(all_hyp.begin(),all_hyp.end(),HopeCompareB);    
+      
+      double hope_score = all_hyp[0]->features.dot(dense_weights);
+      if(DEBUG_CUT) cerr << "New hope derivation score " << hope_score << endl;
+     
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_weights);
+	  all_hyp[u]->fear = -1*all_hyp[u]->mt_metric + 1*all_hyp[0]->mt_metric - hope_score + t_score; //relative loss
+	}
+    
+      sort(all_hyp.begin(),all_hyp.end(),FearCompareB);
+      
+    }
+  //assign maximum fear derivation from all derivations
+  max_fear = all_hyp[0];
+  
+  if(DEBUG_CUT) cerr <<"Cutting Plane Max Fear "<<max_fear->fear ;
+  for(int i=0; i < cur_constraint.size();i++) //select maximal violator already in constraint set
+    {
+      if (!max_fear_in_set || cur_constraint[i]->fear > max_fear_in_set->fear)
+	max_fear_in_set = cur_constraint[i];
+    }
+  if(DEBUG_CUT) cerr << "Max Fear in constraint set " << max_fear_in_set->fear << endl;
+  
+  if(max_fear->fear > max_fear_in_set->fear + SMO_EPSILON)
+    {
+      cur_constraint.push_back(max_fear);
+      *again = true;
+      if(DEBUG_CUT) cerr << "Optimize Again " << *again << endl;
+    }
+}
+
+
+double ComputeDelta(vector<shared_ptr<HypothesisInfo> >* cur_p, double max_step_size,vector<weight_t> dense_weights )
+{
+  vector<shared_ptr<HypothesisInfo> >& cur_pair = *cur_p;
+   double loss = cur_pair[0]->oracle_loss - cur_pair[1]->oracle_loss;
+
+   double margin = -(cur_pair[0]->oracleN->features.dot(dense_weights)- cur_pair[0]->features.dot(dense_weights)) + (cur_pair[1]->oracleN->features.dot(dense_weights) - cur_pair[1]->features.dot(dense_weights));
+   const double num = margin +  loss;
+   cerr << "LOSS: " << num << " Margin:" << margin << " BLEUL:" << loss << " " << cur_pair[1]->features.dot(dense_weights) << " " << cur_pair[0]->features.dot(dense_weights) <<endl;
+   
+
+  SparseVector<double> diff = cur_pair[0]->features;
+  diff -= cur_pair[1]->features;
+  double diffsqnorm = diff.l2norm_sq();
+  double delta;
+  if (diffsqnorm > 0)
+    delta = num / (diffsqnorm * max_step_size);
+  else
+    delta = 0;
+  cerr << " D1:" << delta;
+  //clip delta (enforce margin constraints)
+  delta = max(-cur_pair[0]->alpha, min(delta, cur_pair[1]->alpha));
+  cerr << " D2:" << delta;
+  return delta;
+}
+
+
+vector<shared_ptr<HypothesisInfo> > SelectPair(vector<shared_ptr<HypothesisInfo> >* cur_c)
+{
+  bool DEBUG_SELECT= false;
+  vector<shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
+  
+  vector<shared_ptr<HypothesisInfo> > pair;
+
+  if (no_select || optimizer == 2){ //skip heuristic search and return oracle and fear for pa-mira
+
+      pair.push_back(cur_constraint[0]);
+      pair.push_back(cur_constraint[1]);
+      return pair;
+
+    }
+  
+  for(int u=0;u != cur_constraint.size();u++)	
+    {
+      shared_ptr<HypothesisInfo> max_fear;
+      
+      if(DEBUG_SELECT) cerr<< "cur alpha " << u  << " " << cur_constraint[u]->alpha;
+      for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	{
+	  if(i != u)
+	    if (!max_fear || cur_constraint[i]->fear > max_fear->fear)
+	      max_fear = cur_constraint[i];
+	}
+      if(!max_fear) return pair; //
+      
+      
+      if ((cur_constraint[u]->alpha == 0) && (cur_constraint[u]->fear > max_fear->fear + SMO_EPSILON))
+	{
+	  for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	    {
+	      if(i != u)
+		if (cur_constraint[i]->alpha > 0)
+		  {
+		    pair.push_back(cur_constraint[u]);
+		    pair.push_back(cur_constraint[i]);		    
+		    return pair;
+		  }
+	    }
+	}	       
+      if ((cur_constraint[u]->alpha > 0) && (cur_constraint[u]->fear < max_fear->fear - SMO_EPSILON))
+	{
+	  for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	    {
+	      if(i != u)	
+		if (cur_constraint[i]->fear > cur_constraint[u]->fear)
+		  {
+		    pair.push_back(cur_constraint[u]);
+		    pair.push_back(cur_constraint[i]);
+		    return pair;
+		  }
+	    }  
+	}
+    
+    } 
+  return pair; //no more constraints to optimize, we're done here
+
+}
+
+struct GoodBadOracle {
+  vector<shared_ptr<HypothesisInfo> > good;
+  vector<shared_ptr<HypothesisInfo> > bad;
+};
+
+struct TrainingObserver : public DecoderObserver {
+  TrainingObserver(const int k, const DocScorer& d, vector<GoodBadOracle>* o, vector<ScoreP>* cbs) : ds(d), oracles(*o), corpus_bleu_sent_stats(*cbs), kbest_size(k) {
+    
+
+    if(!pseudo_doc && !sent_approx)
+    if(cur_pass > 0)     //calculate corpus bleu score from previous iterations 1-best for BLEU gain
+      {
+	ScoreP acc;
+	for (int ii = 0; ii < corpus_bleu_sent_stats.size(); ii++) {
+	  if (!acc) { acc = corpus_bleu_sent_stats[ii]->GetZero(); }
+	  acc->PlusEquals(*corpus_bleu_sent_stats[ii]);
+	  
+	}
+	corpus_bleu_stats = acc;
+	corpus_bleu_score = acc->ComputeScore();
+      }
+
+}
+  const DocScorer& ds;
+  vector<ScoreP>& corpus_bleu_sent_stats;
+  vector<GoodBadOracle>& oracles;
+  vector<shared_ptr<HypothesisInfo> > cur_best;
+  shared_ptr<HypothesisInfo> cur_oracle;
+  const int kbest_size;
+  Hypergraph forest;
+  int cur_sent;
+  ScoreP corpus_bleu_stats;
+  float corpus_bleu_score;
+
+  float corpus_src_length;
+  float curr_src_length;
+
+  const int GetCurrentSent() const {
+    return cur_sent;
+  }
+
+  const HypothesisInfo& GetCurrentBestHypothesis() const {
+    return *cur_best[0];
+  }
+
+  const vector<shared_ptr<HypothesisInfo> > GetCurrentBest() const {
+    return cur_best;
+  }
+  
+ const HypothesisInfo& GetCurrentOracle() const {
+    return *cur_oracle;
+  }
+  
+  const Hypergraph& GetCurrentForest() const {
+    return forest;
+  }
+  
+
+  virtual void NotifyTranslationForest(const SentenceMetadata& smeta, Hypergraph* hg) {
+    cur_sent = smeta.GetSentenceID();
+    curr_src_length = (float) smeta.GetSourceLength();
+
+    if(unique_kbest)
+      UpdateOracles<KBest::FilterUnique>(smeta.GetSentenceID(), *hg);
+    else
+      UpdateOracles<KBest::NoFilter<std::vector<WordID> > >(smeta.GetSentenceID(), *hg);
+    forest = *hg;
+    
+  }
+
+  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score, const vector<WordID>& hyp) {
+    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+    h->features = feats;
+    h->mt_metric = score;
+    h->hyp = hyp;
+    return h;
+  }
+
+  template <class Filter>  
+  void UpdateOracles(int sent_id, const Hypergraph& forest) {
+
+    bool PRINT_LIST= false;    
+    vector<shared_ptr<HypothesisInfo> >& cur_good = oracles[sent_id].good;
+    vector<shared_ptr<HypothesisInfo> >& cur_bad = oracles[sent_id].bad;
+    //TODO: look at keeping previous iterations hypothesis lists around
+    cur_best.clear();
+    cur_good.clear();
+    cur_bad.clear();
+
+    vector<shared_ptr<HypothesisInfo> > all_hyp;
+
+    typedef KBest::KBestDerivations<vector<WordID>, ESentenceTraversal,Filter> K;
+    K kbest(forest,kbest_size);
+    
+    for (int i = 0; i < kbest_size; ++i) {
+
+      typename K::Derivation *d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+
+      float sentscore;
+	  if(cur_pass > 0 && !pseudo_doc && !sent_approx)
+	    {
+	      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(d->yield);
+	      ScoreP corpus_no_best = corpus_bleu_stats->GetZero();
+
+	      corpus_bleu_stats->Subtract(*corpus_bleu_sent_stats[sent_id], &*corpus_no_best);
+	      sent_stats->PlusEquals(*corpus_no_best, 0.5);
+	      
+	      //compute gain from new sentence in 1-best corpus
+	      sentscore = mt_metric_scale * (sent_stats->ComputeScore() - corpus_no_best->ComputeScore());// - corpus_bleu_score);
+	    }
+	  else if(pseudo_doc)   //pseudo-corpus smoothing 
+	    {
+	      float src_scale = corpus_src_length + curr_src_length;
+	      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(d->yield);
+	      if(!corpus_bleu_stats){ corpus_bleu_stats = sent_stats->GetZero();}
+	      
+	      sent_stats->PlusEquals(*corpus_bleu_stats);
+	      sentscore =  mt_metric_scale  * src_scale * sent_stats->ComputeScore();
+
+	    }
+	  else //use sentence-level smoothing ( used when cur_pass=0 if not pseudo_doc)
+	    {
+	     
+	      sentscore = mt_metric_scale * (ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore());
+	    }
+	
+      if (invert_score) sentscore *= -1.0;
+      
+      if (i < update_list_size){ 
+	if(PRINT_LIST)cerr << TD::GetString(d->yield) << " ||| " << d->score << " ||| " << sentscore << endl; 
+	cur_best.push_back( MakeHypothesisInfo(d->feature_values, sentscore, d->yield));
+      }
+      
+      all_hyp.push_back(MakeHypothesisInfo(d->feature_values, sentscore,d->yield));   //store all hyp to extract hope and fear         
+    }
+    
+    if(pseudo_doc){
+    //update psuedo-doc stats
+      string details, details2;     
+      corpus_bleu_stats->ScoreDetails(&details2);   
+      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(cur_best[0]->hyp);
+      corpus_bleu_stats->PlusEquals(*sent_stats);
+      
+      sent_stats->ScoreDetails(&details);
+      sent_stats = corpus_bleu_stats;
+      corpus_bleu_stats = sent_stats->GetZero();
+      corpus_bleu_stats->PlusEquals(*sent_stats, PSEUDO_SCALE);
+            
+      corpus_src_length = PSEUDO_SCALE * (corpus_src_length + curr_src_length);
+      cerr << "ps corpus size: " << corpus_src_length << " " << curr_src_length << "\n" << details << "\n" << details2 << endl;
+    }
+
+    //figure out how many hyps we can keep maximum
+    int temp_update_size = update_list_size;
+    if (all_hyp.size() < update_list_size){ temp_update_size = all_hyp.size();}
+
+    //sort all hyps by sentscore (eg. bleu)
+    sort(all_hyp.begin(),all_hyp.end(),HypothesisCompareB);
+    
+    if(PRINT_LIST){  cerr << "Sorting " << endl; for(int u=0;u!=all_hyp.size();u++)  
+						   cerr << all_hyp[u]->mt_metric << " " << all_hyp[u]->features.dot(dense_w_local) << endl; }
+    
+    if(hope_select == 1)
+      {
+	//find hope hypothesis using model + bleu
+	if (PRINT_LIST) cerr << "HOPE " << endl;
+	for(int u=0;u!=all_hyp.size();u++)	
+	  { 
+	    double t_score = all_hyp[u]->features.dot(dense_w_local);
+	    all_hyp[u]->hope = all_hyp[u]->mt_metric + t_score;
+	    if (PRINT_LIST) cerr << all_hyp[u]->mt_metric << " H:" << all_hyp[u]->hope << " S:" << t_score << endl; 
+	    
+	  }
+	
+	//sort hyps by hope score
+	sort(all_hyp.begin(),all_hyp.end(),HopeCompareB);
+      }        
+
+    //assign cur_good the sorted list
+    cur_good.insert(cur_good.begin(), all_hyp.begin(), all_hyp.begin()+temp_update_size);    
+    if(PRINT_LIST) { cerr << "GOOD" << endl;  for(int u=0;u!=cur_good.size();u++) cerr << cur_good[u]->mt_metric << " " << cur_good[u]->hope << endl;}     
+
+    //use hope for fear selection
+    shared_ptr<HypothesisInfo>& oracleN = cur_good[0];
+
+    if(fear_select == 1){   //compute fear hyps with model - bleu
+      if (PRINT_LIST) cerr << "FEAR " << endl;
+      double hope_score = oracleN->features.dot(dense_w_local);
+
+      if (PRINT_LIST) cerr << "hope score " << hope_score << endl;
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_w_local);
+
+	  all_hyp[u]->fear = -1*all_hyp[u]->mt_metric + 1*oracleN->mt_metric - hope_score + t_score; //relative loss
+	  all_hyp[u]->oracle_loss = -1*all_hyp[u]->mt_metric + 1*oracleN->mt_metric;
+	  all_hyp[u]->oracle_feat_diff = oracleN->features - all_hyp[u]->features;
+	  all_hyp[u]->oracleN=oracleN;
+	  if (PRINT_LIST) cerr << all_hyp[u]->mt_metric << " H:" << all_hyp[u]->hope << " F:" << all_hyp[u]->fear << endl; 
+	  
+	}
+      
+      sort(all_hyp.begin(),all_hyp.end(),FearCompareB);
+      
+    }
+    else if(fear_select == 2) //select fear based on cost
+      {
+	sort(all_hyp.begin(),all_hyp.end(),HypothesisCompareG);
+      }
+    else //max model score, also known as prediction-based
+      {
+	sort(all_hyp.begin(),all_hyp.end(),FearComparePred);
+      }
+    cur_bad.insert(cur_bad.begin(), all_hyp.begin(), all_hyp.begin()+temp_update_size); 
+
+    if(PRINT_LIST){ cerr<< "BAD"<<endl; for(int u=0;u!=cur_bad.size();u++) cerr << cur_bad[u]->mt_metric << " H:" << cur_bad[u]->hope << " F:" << cur_bad[u]->fear << endl;}
+    
+    cerr << "GOOD (BEST): " << cur_good[0]->mt_metric << endl;
+    cerr << " CUR: " << cur_best[0]->mt_metric << endl;
+    cerr << " BAD (WORST): " << cur_bad[0]->mt_metric << endl;
+  }
+};
+
+void ReadTrainingCorpus(const string& fname, vector<string>* c) {
+
+
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  string line;
+  while(in) {
+    getline(in, line);
+    if (!in) break;
+    c->push_back(line);
+  }
+}
+
+void ReadPastTranslationForScore(const int cur_pass, vector<ScoreP>* c, DocScorer& ds, const string& od)
+{
+  cerr << "Reading BLEU gain file ";
+  string fname;
+  if(cur_pass == 0)
+    {
+      fname = od + "/run.raw.init";
+    }
+  else
+    {
+      int last_pass = cur_pass - 1; 
+      fname = od + "/run.raw."  +  boost::lexical_cast<std::string>(last_pass) + ".B";
+    }
+  cerr << fname << "\n";
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  ScoreP acc;
+  string line;
+  int lc = 0;
+  while(in) {
+    getline(in, line);
+    if (line.empty() && !in) break;
+    vector<WordID> sent;
+    TD::ConvertSentence(line, &sent);
+    ScoreP sentscore = ds[lc]->ScoreCandidate(sent);
+    c->push_back(sentscore);
+    if (!acc) { acc = sentscore->GetZero(); }
+    acc->PlusEquals(*sentscore);
+    ++lc;
+ 
+  }
+  
+  assert(lc > 0);
+  float score = acc->ComputeScore();
+  string details;
+  acc->ScoreDetails(&details);
+  cerr << "Previous run: " << details << score << endl;
+
+}
+
+
+int main(int argc, char** argv) {
+  register_feature_functions();
+  SetSilent(true);  // turn off verbose decoder output
+
+  po::variables_map conf;
+  if (!InitCommandLine(argc, argv, &conf)) return 1;
+
+  if (conf.count("random_seed"))
+    rng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
+  else
+    rng.reset(new MT19937);
+  
+  vector<string> corpus;
+
+  const string metric_name = conf["mt_metric"].as<string>();
+  optimizer = conf["optimizer"].as<int>();
+  fear_select = conf["fear"].as<int>();
+  hope_select = conf["hope"].as<int>();
+  mt_metric_scale = conf["mt_metric_scale"].as<double>();
+  approx_score = conf.count("approx_score");
+  no_reweight = conf.count("no_reweight");
+  no_select = conf.count("no_select");
+  update_list_size = conf["update_k_best"].as<int>();
+  unique_kbest = conf.count("unique_k_best");
+  pseudo_doc = conf.count("pseudo_doc");
+  sent_approx = conf.count("sent_approx");
+  cerr << "Using pseudo-doc:" << pseudo_doc << " Sent:" << sent_approx << endl;
+  if(pseudo_doc)
+    mt_metric_scale=1;
+
+  const string weights_dir = conf["weights_output"].as<string>();
+  const string output_dir = conf["output_dir"].as<string>();
+  ScoreType type = ScoreTypeFromString(metric_name);
+
+  //establish metric used for tuning
+  if (type == TER) {
+    invert_score = true;
+  } else {
+    invert_score = false;
+  }
+
+  //load references
+  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  vector<ScoreP> corpus_bleu_sent_stats;
+  
+  //check training pass,if >0, then use previous iterations corpus bleu stats
+  cur_pass = conf["pass"].as<int>();
+  if(cur_pass > 0)
+    {
+      ReadPastTranslationForScore(cur_pass, &corpus_bleu_sent_stats, ds, output_dir);
+    }
+  
+  cerr << "Using optimizer:" << optimizer << endl;
+    
+  ReadFile ini_rf(conf["decoder_config"].as<string>());
+  Decoder decoder(ini_rf.stream());
+
+  vector<weight_t>& dense_weights = decoder.CurrentWeightVector();
+  
+  SparseVector<weight_t> lambdas;
+  Weights::InitFromFile(conf["input_weights"].as<string>(), &dense_weights);
+  Weights::InitSparseVector(dense_weights, &lambdas);
+
+  const string input = decoder.GetConf()["input"].as<string>();
+  if (!SILENT) cerr << "Reading input from " << ((input == "-") ? "STDIN" : input.c_str()) << endl;
+  ReadFile in_read(input);
+  istream *in = in_read.stream();
+  assert(*in);  
+  string buf;
+  
+  const double max_step_size = conf["max_step_size"].as<double>();
+
+  vector<GoodBadOracle> oracles(ds.size());
+
+  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, &oracles, &corpus_bleu_sent_stats);
+
+  int cur_sent = 0;
+  int lcount = 0;
+  double objective=0;
+  double tot_loss = 0;
+  int dots = 0;
+  SparseVector<double> tot;
+  SparseVector<double> final_tot;
+
+  SparseVector<double> old_lambdas = lambdas;
+  tot.clear();
+  tot += lambdas;
+  cerr << "PASS " << cur_pass << " " << endl << lambdas << endl; 
+  ScoreP acc, acc_h, acc_f;
+  
+  while(*in) {
+      getline(*in, buf);
+      if (buf.empty()) continue;
+      //TODO: allow batch updating
+      lambdas.init_vector(&dense_weights);
+      dense_w_local = dense_weights;
+      decoder.SetId(cur_sent);
+      decoder.Decode(buf, &observer);  // decode the sentence, calling Notify to get the hope,fear, and model best hyps. 
+      
+      cur_sent = observer.GetCurrentSent();
+      cerr << "SENT: " << cur_sent << endl;
+      const HypothesisInfo& cur_hyp = observer.GetCurrentBestHypothesis();
+      const HypothesisInfo& cur_good = *oracles[cur_sent].good[0];
+      const HypothesisInfo& cur_bad = *oracles[cur_sent].bad[0];
+
+      vector<shared_ptr<HypothesisInfo> >& cur_good_v = oracles[cur_sent].good;
+      vector<shared_ptr<HypothesisInfo> >& cur_bad_v = oracles[cur_sent].bad;
+      vector<shared_ptr<HypothesisInfo> > cur_best_v = observer.GetCurrentBest();
+
+      tot_loss += cur_hyp.mt_metric;
+      
+      //score hyps to be able to compute corpus level bleu after we finish this iteration through the corpus
+      ScoreP sentscore = ds[cur_sent]->ScoreCandidate(cur_hyp.hyp);
+      if (!acc) { acc = sentscore->GetZero(); }
+      acc->PlusEquals(*sentscore);
+
+      ScoreP hope_sentscore = ds[cur_sent]->ScoreCandidate(cur_good.hyp);
+      if (!acc_h) { acc_h = hope_sentscore->GetZero(); }
+      acc_h->PlusEquals(*hope_sentscore);
+
+      ScoreP fear_sentscore = ds[cur_sent]->ScoreCandidate(cur_bad.hyp);
+      if (!acc_f) { acc_f = fear_sentscore->GetZero(); }
+      acc_f->PlusEquals(*fear_sentscore);
+      
+      if(optimizer == 4) { //passive-aggresive update (single dual coordinate step)
+      
+	  double margin = cur_bad.features.dot(dense_weights) - cur_good.features.dot(dense_weights);
+	  double mt_loss = (cur_good.mt_metric - cur_bad.mt_metric);
+	  const double loss = margin +  mt_loss;
+	  cerr << "LOSS: " << loss << " Margin:" << margin << " BLEUL:" << mt_loss << " " << cur_bad.features.dot(dense_weights) << " " << cur_good.features.dot(dense_weights) <<endl;
+	  if (loss > 0.0 || !checkloss) {
+	    SparseVector<double> diff = cur_good.features;
+	    diff -= cur_bad.features;	    
+
+	    double diffsqnorm = diff.l2norm_sq();
+	    double delta;
+	    if (diffsqnorm > 0)
+	      delta = loss / (diffsqnorm);
+	    else
+	      delta = 0;
+	    
+	    if (delta > max_step_size) delta = max_step_size;
+	    lambdas += (cur_good.features * delta);
+	    lambdas -= (cur_bad.features * delta);
+	    
+	  }
+      }
+      else if(optimizer == 1) //sgd - nonadapted step size
+	{
+	   
+	  lambdas += (cur_good.features) * max_step_size;
+	  lambdas -= (cur_bad.features) * max_step_size;
+	}
+      else if(optimizer == 5) //full mira with n-best list of constraints from hope, fear, model best
+	{
+	  vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	  cur_constraint.insert(cur_constraint.begin(), cur_bad_v.begin(), cur_bad_v.end());
+	  cur_constraint.insert(cur_constraint.begin(), cur_best_v.begin(), cur_best_v.end());
+	  cur_constraint.insert(cur_constraint.begin(), cur_good_v.begin(), cur_good_v.end());
+
+	  bool optimize_again;
+	  vector<shared_ptr<HypothesisInfo> > cur_pair;
+	  //SMO 
+	  for(int u=0;u!=cur_constraint.size();u++)	
+	    cur_constraint[u]->alpha =0;	      
+	  
+	  cur_constraint[0]->alpha =1; //set oracle to alpha=1
+
+	  cerr <<"Optimizing with " << cur_constraint.size() << " constraints" << endl;
+	  int smo_iter = MAX_SMO, smo_iter2 = MAX_SMO;
+	  int iter, iter2 =0;
+	  bool DEBUG_SMO = false;
+	  while (iter2 < smo_iter2)
+	    {
+	      iter =0;
+	      while (iter < smo_iter)
+		{
+		  optimize_again = true;
+		  for (int i = 0; i< cur_constraint.size(); i++)
+		    for (int j = i+1; j< cur_constraint.size(); j++)
+		      {
+			if(DEBUG_SMO) cerr << "start " << i << " " << j <<  endl;
+			cur_pair.clear();
+			cur_pair.push_back(cur_constraint[j]);
+			cur_pair.push_back(cur_constraint[i]);
+			double delta = ComputeDelta(&cur_pair,max_step_size, dense_weights);
+			
+			if (delta == 0) optimize_again = false;
+			cur_constraint[j]->alpha += delta;
+			cur_constraint[i]->alpha -= delta;
+			double step_size = delta * max_step_size;
+			
+			lambdas += (cur_constraint[i]->features) * step_size;
+			lambdas -= (cur_constraint[j]->features) * step_size;
+			if(DEBUG_SMO) cerr << "SMO opt " << iter << " " << i << " " << j << " " <<  delta << " " << cur_pair[0]->alpha << " " << cur_pair[1]->alpha <<  endl;		
+		      }
+		  iter++;
+		  
+		  if(!optimize_again)
+		    { 
+		      iter = MAX_SMO;
+		      cerr << "Optimization stopped, delta =0" << endl;
+		    }		  
+		}
+	      iter2++;
+	    }	  
+	}
+      else if(optimizer == 2 || optimizer == 3) //PA and Cutting Plane MIRA update
+	  {
+	    bool DEBUG_SMO= true;
+	    vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	    cur_constraint.push_back(cur_good_v[0]); //add oracle to constraint set
+	    bool optimize_again = true;
+	    int cut_plane_calls = 0;
+	    while (optimize_again)
+	      { 
+		if(DEBUG_SMO) cerr<< "optimize again: " << optimize_again << endl;
+		if(optimizer == 2){ //PA
+		  cur_constraint.push_back(cur_bad_v[0]);
+
+		  //check if we have a violation
+		  if(!(cur_constraint[1]->fear > cur_constraint[0]->fear + SMO_EPSILON))
+		    {
+		      optimize_again = false;
+		      cerr << "Constraint not violated" << endl;
+		    }
+		}
+		else
+		  { //cutting plane to add constraints
+		    if(DEBUG_SMO) cerr<< "Cutting Plane " << cut_plane_calls << " with " << lambdas << endl;
+		    optimize_again = false;
+		    cut_plane_calls++;
+		    CuttingPlane(&cur_constraint, &optimize_again, oracles[cur_sent].bad, dense_weights);
+		    if (cut_plane_calls >= MAX_SMO) optimize_again = false;
+		  }
+
+		if(optimize_again)
+		  {
+		    //SMO 
+		    for(int u=0;u!=cur_constraint.size();u++)	
+		      { 
+			cur_constraint[u]->alpha =0;
+		      }
+		    cur_constraint[0]->alpha = 1;
+		    cerr <<" Optimizing with " << cur_constraint.size() << " constraints" << endl;
+		    int smo_iter = MAX_SMO;
+		    int iter =0;
+		    while (iter < smo_iter)
+		      {			
+			//select pair to optimize from constraint set
+			vector<shared_ptr<HypothesisInfo> > cur_pair = SelectPair(&cur_constraint);
+			
+			if(cur_pair.empty()){
+			  iter=MAX_SMO; 
+			  cerr << "Undefined pair " << endl; 
+			  continue;
+			} //pair is undefined so we are done with this smo 
+
+			double delta = ComputeDelta(&cur_pair,max_step_size, dense_weights);
+
+			cur_pair[0]->alpha += delta;
+			cur_pair[1]->alpha -= delta;
+			double step_size = delta * max_step_size;
+			cerr << "step " << step_size << endl;
+
+			lambdas += (cur_pair[1]->features) * step_size;
+			lambdas -= (cur_pair[0]->features) * step_size;
+			cerr << " Lambdas " << lambdas << endl;
+			//reload weights based on update
+
+			dense_weights.clear();
+			lambdas.init_vector(&dense_weights);
+			dense_w_local = dense_weights;
+			iter++;
+					
+			if(DEBUG_SMO) cerr << "SMO opt " << iter << " " << delta << " " << cur_pair[0]->alpha << " " << cur_pair[1]->alpha <<  endl;		
+			if(no_select) //don't use selection heuristic to determine when to stop SMO, rather just when delta =0 
+			  if (delta == 0) iter = MAX_SMO;
+			
+			//only perform one dual coordinate ascent step
+			if(optimizer == 2) 
+			  {
+			    optimize_again = false;
+			    iter = MAX_SMO;
+			  }					
+		      }
+		    if(optimizer == 3)
+		      {
+			if(!no_reweight) //reweight the forest and select a new k-best
+			  {
+			    if(DEBUG_SMO) cerr<< "Decoding with new weights -- now orac are " << oracles[cur_sent].good.size() << endl;
+			    Hypergraph hg = observer.GetCurrentForest();
+			    hg.Reweight(dense_weights);
+			    if(unique_kbest)
+                              observer.UpdateOracles<KBest::FilterUnique>(cur_sent, hg);
+                            else
+                              observer.UpdateOracles<KBest::NoFilter<std::vector<WordID> > >(cur_sent, hg);			    
+			  }
+		      }
+		  }
+		
+	      }
+	   
+	    //print objective after this sentence
+	    double lambda_change = (lambdas - old_lambdas).l2norm_sq();
+	    double max_fear = cur_constraint[cur_constraint.size()-1]->fear;
+	    double temp_objective = 0.5 * lambda_change;// + max_step_size * max_fear;
+
+	    for(int u=0;u!=cur_constraint.size();u++)	
+	      { 
+		cerr << cur_constraint[u]->alpha << " " << cur_constraint[u]->hope << " " << cur_constraint[u]->fear << endl;
+		temp_objective += cur_constraint[u]->alpha * cur_constraint[u]->fear;
+	      }
+	    objective += temp_objective;
+	    
+	    cerr << "SENT OBJ: " << temp_objective << " NEW OBJ: " << objective << endl;
+	  }
+      
+    
+      if ((cur_sent * 40 / ds.size()) > dots) { ++dots; cerr << '.'; }
+      tot += lambdas;
+      ++lcount;
+      cur_sent++;
+      
+      cout << TD::GetString(cur_good_v[0]->hyp) << " ||| " << TD::GetString(cur_best_v[0]->hyp) << " ||| " << TD::GetString(cur_bad_v[0]->hyp) << endl;
+
+    }
+
+    cerr << "FINAL OBJECTIVE: "<< objective << endl;
+    final_tot += tot;
+    cerr << "Translated " << lcount << " sentences " << endl;
+    cerr << " [AVG METRIC LAST PASS=" << (tot_loss / lcount) << "]\n";
+    tot_loss = 0;
+    
+    int node_id = rng->next() * 100000;
+    cerr << " Writing weights to " << node_id << endl;
+    Weights::ShowLargestFeatures(dense_weights);
+    dots = 0;
+    ostringstream os;
+    os << weights_dir << "/weights.mira-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "." << node_id << ".gz";
+    string msg = "# MIRA tuned weights ||| " + boost::lexical_cast<std::string>(node_id) + " ||| " + boost::lexical_cast<std::string>(lcount);
+    lambdas.init_vector(&dense_weights);
+    Weights::WriteToFile(os.str(), dense_weights, true, &msg);
+
+    SparseVector<double> x = tot;
+    x /= lcount+1;
+    ostringstream sa;
+    string msga = "# MIRA tuned weights AVERAGED ||| " + boost::lexical_cast<std::string>(node_id) + " ||| " + boost::lexical_cast<std::string>(lcount);
+    sa << weights_dir << "/weights.mira-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "." << node_id << "-avg.gz";
+    x.init_vector(&dense_weights);
+    Weights::WriteToFile(sa.str(), dense_weights, true, &msga);
+    
+    cerr << "Optimization complete.\n";
+    return 0;
+}
+
diff --git a/training/mira/kbest_mira.cc b/training/mira/kbest_mira.cc
index 8b7993dd..d59b4224 100644
--- a/training/mira/kbest_mira.cc
+++ b/training/mira/kbest_mira.cc
@@ -8,9 +8,11 @@
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
 
+#include "stringlib.h"
 #include "hg_sampler.h"
 #include "sentence_metadata.h"
-#include "scorer.h"
+#include "ns.h"
+#include "ns_docscorer.h"
 #include "verbose.h"
 #include "viterbi.h"
 #include "hg.h"
@@ -91,8 +93,9 @@ struct GoodBadOracle {
 };
 
 struct TrainingObserver : public DecoderObserver {
-  TrainingObserver(const int k, const DocScorer& d, bool sf, vector<GoodBadOracle>* o) : ds(d), oracles(*o), kbest_size(k), sample_forest(sf) {}
-  const DocScorer& ds;
+  TrainingObserver(const int k, const DocumentScorer& d, const EvaluationMetric& m, bool sf, vector<GoodBadOracle>* o) : ds(d), metric(m), oracles(*o), kbest_size(k), sample_forest(sf) {}
+  const DocumentScorer& ds;
+  const EvaluationMetric& metric;
   vector<GoodBadOracle>& oracles;
   std::tr1::shared_ptr<HypothesisInfo> cur_best;
   const int kbest_size;
@@ -121,13 +124,16 @@ struct TrainingObserver : public DecoderObserver {
     if (sample_forest) {
       vector<WordID> cur_prediction;
       ViterbiESentence(forest, &cur_prediction);
-      float sentscore = ds[sent_id]->ScoreCandidate(cur_prediction)->ComputeScore();
+      SufficientStats sstats;
+      ds[sent_id]->Evaluate(cur_prediction, &sstats);
+      float sentscore = metric.ComputeScore(sstats);
       cur_best = MakeHypothesisInfo(ViterbiFeatures(forest), sentscore);
 
       vector<HypergraphSampler::Hypothesis> samples;
       HypergraphSampler::sample_hypotheses(forest, kbest_size, &*rng, &samples);
       for (unsigned i = 0; i < samples.size(); ++i) {
-        sentscore = ds[sent_id]->ScoreCandidate(samples[i].words)->ComputeScore();
+        ds[sent_id]->Evaluate(samples[i].words, &sstats);
+        float sentscore = metric.ComputeScore(sstats);
         if (invert_score) sentscore *= -1.0;
         if (!cur_good || sentscore > cur_good->mt_metric)
           cur_good = MakeHypothesisInfo(samples[i].fmap, sentscore);
@@ -136,11 +142,13 @@ struct TrainingObserver : public DecoderObserver {
       }
     } else {
       KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(forest, kbest_size);
+      SufficientStats sstats;
       for (int i = 0; i < kbest_size; ++i) {
         const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
           kbest.LazyKthBest(forest.nodes_.size() - 1, i);
         if (!d) break;
-        float sentscore = ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore();
+        ds[sent_id]->Evaluate(d->yield, &sstats);
+        float sentscore = metric.ComputeScore(sstats);
         if (invert_score) sentscore *= -1.0;
         // cerr << TD::GetString(d->yield) << " ||| " << d->score << " ||| " << sentscore << endl;
         if (i == 0)
@@ -192,15 +200,20 @@ int main(int argc, char** argv) {
   }
   vector<string> corpus;
   ReadTrainingCorpus(conf["source"].as<string>(), &corpus);
-  const string metric_name = conf["mt_metric"].as<string>();
-  ScoreType type = ScoreTypeFromString(metric_name);
-  if (type == TER) {
-    invert_score = true;
-  } else {
-    invert_score = false;
+
+  string metric_name = UppercaseString(conf["mt_metric"].as<string>());
+  if (metric_name == "COMBI") {
+    cerr << "WARNING: 'combi' metric is no longer supported, switching to 'COMB:TER=-0.5;IBM_BLEU=0.5'\n";
+    metric_name = "COMB:TER=-0.5;IBM_BLEU=0.5";
+  } else if (metric_name == "BLEU") {
+    cerr << "WARNING: 'BLEU' is ambiguous, assuming 'IBM_BLEU'\n";
+    metric_name = "IBM_BLEU";
   }
-  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  EvaluationMetric* metric = EvaluationMetric::Instance(metric_name);
+  DocumentScorer ds(metric, conf["reference"].as<vector<string> >());
   cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  invert_score = metric->IsErrorMetric();
+
   if (ds.size() != corpus.size()) {
     cerr << "Mismatched number of references (" << ds.size() << ") and sources (" << corpus.size() << ")\n";
     return 1;
@@ -221,7 +234,7 @@ int main(int argc, char** argv) {
   assert(corpus.size() > 0);
   vector<GoodBadOracle> oracles(corpus.size());
 
-  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, sample_forest, &oracles);
+  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, *metric, sample_forest, &oracles);
   int cur_sent = 0;
   int lcount = 0;
   int normalizer = 0;
diff --git a/training/mira/run_mira.pl b/training/mira/run_mira.pl
new file mode 100755
index 00000000..d71590ba
--- /dev/null
+++ b/training/mira/run_mira.pl
@@ -0,0 +1,630 @@
+#!/usr/bin/env perl
+use strict;
+my @ORIG_ARGV=@ARGV;
+use Cwd qw(getcwd);
+my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0));
+push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../../environment"; }
+
+# Skip local config (used for distributing jobs) if we're running in local-only mode
+use LocalConfig;
+use Getopt::Long;
+use IPC::Open2;
+use POSIX ":sys_wait_h";
+my $QSUB_CMD = qsub_args(mert_memory());
+my $default_jobs = env_default_jobs();
+
+my $srcFile;
+my $refFiles;
+my $bin_dir = $SCRIPT_DIR;
+die "Bin directory $bin_dir missing/inaccessible" unless -d $bin_dir;
+my $FAST_SCORE="$bin_dir/../../mteval/fast_score";
+die "Can't execute $FAST_SCORE" unless -x $FAST_SCORE;
+
+my $iteration = 0.0;
+my $max_iterations = 10;
+my $metric = "ibm_bleu";
+my $iniFile;
+my $weights;
+my $initialWeights;
+my $jobs = $default_jobs;   # number of decode nodes
+my $pmem = "1g";
+my $dir;
+
+my $SCORER = $FAST_SCORE;
+
+my $UTILS_DIR="$SCRIPT_DIR/../utils";
+require "$UTILS_DIR/libcall.pl";
+
+my $parallelize = "$UTILS_DIR/parallelize.pl";
+my $libcall = "$UTILS_DIR/libcall.pl";
+my $sentserver = "$UTILS_DIR/sentserver";
+my $sentclient = "$UTILS_DIR/sentclient";
+
+my $run_local = 0;
+my $pass_suffix = '';
+
+my $cdec ="$bin_dir/kbest_cut_mira"; 
+
+die "Can't find decoder in $cdec" unless -x $cdec;
+my $decoder = $cdec;
+my $decoderOpt;
+my $update_size;
+my $approx_score;
+my $kbest_size=250;
+my $metric_scale=1;
+my $optimizer=2;
+my $disable_clean = 0;
+my $use_make=0;  
+my $density_prune;
+my $cpbin=1;
+my $help = 0;
+my $epsilon = 0.0001;
+my $step_size = 0.01;
+my $gpref;
+my $unique_kbest;
+my $freeze;
+my $hopes=1;
+my $fears=1;
+my $sent_approx=0;
+my $pseudo_doc=0;
+
+my $range = 35000;
+my $minimum = 15000;
+my $portn = int(rand($range)) + $minimum;
+
+
+# Process command-line options
+Getopt::Long::Configure("no_auto_abbrev");
+if (GetOptions(
+        "decoder=s" => \$decoderOpt,
+        "jobs=i" => \$jobs,
+        "density-prune=f" => \$density_prune,
+        "dont-clean" => \$disable_clean,
+        "pass-suffix=s" => \$pass_suffix,
+        "epsilon=s" => \$epsilon,
+        "help" => \$help,
+        "local" => \$run_local,
+        "use-make=i" => \$use_make,
+        "max-iterations=i" => \$max_iterations,
+        "pmem=s" => \$pmem,
+        "cpbin!" => \$cpbin,
+        "ref-files=s" => \$refFiles,
+        "metric=s" => \$metric,
+        "source-file=s" => \$srcFile,
+        "weights=s" => \$initialWeights,
+	"optimizer=i" => \$optimizer,
+	"metric-scale=i" => \$metric_scale,
+	"kbest-size=i" => \$kbest_size,
+	"update-size=i" => \$update_size,
+	"step-size=f" => \$step_size,
+	"hope-select=i" => \$hopes,
+	"fear-select=i" => \$fears,
+	"sent-approx" => \$sent_approx,
+        "pseudo-doc" => \$pseudo_doc,
+	"unique-kbest" => \$unique_kbest,
+        "grammar-prefix=s" => \$gpref,
+	"freeze" => \$freeze,
+        "workdir=s" => \$dir,
+	) == 0 || @ARGV!=1 || $help) {
+        print_help();
+        exit;
+}
+
+($iniFile) = @ARGV;
+
+
+sub write_config;
+sub enseg;
+sub print_help;
+
+my $nodelist;
+my $host =check_output("hostname"); chomp $host;
+my $bleu;
+my $interval_count = 0;
+my $logfile;
+my $projected_score;
+
+
+#my $refs_comma_sep = get_comma_sep_refs($refFiles);
+my $refs_comma_sep = get_comma_sep_refs('r',$refFiles);
+
+#my $refs_comma_sep_4cdec = get_comma_sep_refs_4cdec($refFiles);
+
+unless ($dir){
+        $dir = "mira";
+}
+unless ($dir =~ /^\//){  # convert relative path to absolute path
+        my $basedir = check_output("pwd");
+        chomp $basedir;
+        $dir = "$basedir/$dir";
+}
+
+if ($decoderOpt){ $decoder = $decoderOpt; }
+
+# Initializations and helper functions
+srand;
+
+my @childpids = ();
+my @cleanupcmds = ();
+
+sub cleanup {
+        print STDERR "Cleanup...\n";
+        for my $pid (@childpids){ unchecked_call("kill $pid"); }
+        for my $cmd (@cleanupcmds){ unchecked_call("$cmd"); }
+        exit 1;
+};
+
+# Always call cleanup, no matter how we exit
+*CORE::GLOBAL::exit =
+    sub{ cleanup(); };
+$SIG{INT} = "cleanup";
+$SIG{TERM} = "cleanup";
+$SIG{HUP} = "cleanup";
+
+
+my $decoderBase = check_output("basename $decoder"); chomp $decoderBase;
+my $newIniFile = "$dir/$decoderBase.ini";
+my $inputFileName = "$dir/input";
+my $user = $ENV{"USER"};
+
+
+# process ini file
+-e $iniFile || die "Error: could not open $iniFile for reading\n";
+open(INI, $iniFile);
+
+use File::Basename qw(basename);
+#pass bindir, refs to vars holding bin
+sub modbin {
+    local $_;
+    my $bindir=shift;
+    check_call("mkdir -p $bindir");
+    -d $bindir || die "couldn't make bindir $bindir";
+    for (@_) {
+        my $src=$$_;
+        $$_="$bindir/".basename($src);
+        check_call("cp -p $src $$_");
+    }
+}
+sub dirsize {
+    opendir ISEMPTY,$_[0];
+    return scalar(readdir(ISEMPTY))-1;
+}
+
+
+
+
+if (-e $dir && dirsize($dir)>1 && -e "$dir/weights" ){ # allow preexisting logfile, binaries, but not dist-vest.pl outputs
+    die "ERROR: working dir $dir already exists\n\n";
+} else {
+    -e $dir || mkdir $dir;
+    mkdir "$dir/scripts";
+    my $cmdfile="$dir/rerun-mira.sh";
+    open CMD,'>',$cmdfile;
+    print CMD "cd ",&getcwd,"\n";
+    my $cline=&cmdline."\n";
+    print CMD $cline;
+    close CMD;
+    print STDERR $cline;
+    chmod(0755,$cmdfile);
+    unless (-e $initialWeights) {
+        print STDERR "Please specify an initial weights file with --initial-weights\n";
+        print_help();
+        exit;
+    }
+    check_call("cp $initialWeights $dir/weights.0");
+    die "Can't find weights.0" unless (-e "$dir/weights.0");
+}
+write_config(*STDERR);
+
+# Generate initial files and values
+check_call("cp $iniFile $newIniFile");
+$iniFile = $newIniFile;
+
+my $newsrc = "$dir/dev.input";
+enseg($srcFile, $newsrc, $gpref);
+
+$srcFile = $newsrc;
+my $devSize = 0;
+open F, "<$srcFile" or die "Can't read $srcFile: $!";
+while(<F>) { $devSize++; }
+close F;
+
+my $lastPScore = 0;
+my $lastWeightsFile;
+my $bestScoreIter=-1;
+my $bestScore=-1;
+unless ($update_size){$update_size = $kbest_size;}
+# main optimization loop
+#while (1){
+for (my $opt_iter=0; $opt_iter<$max_iterations; $opt_iter++) {
+
+	print STDERR "\n\nITERATION $opt_iter\n==========\n";
+	print STDERR "Using port $portn\n";
+
+	# iteration-specific files
+	my $runFile="$dir/run.raw.$opt_iter";
+	my $onebestFile="$dir/1best.$opt_iter";
+	my $logdir="$dir/logs.$opt_iter";
+	my $decoderLog="$logdir/decoder.sentserver.log.$opt_iter";
+	my $scorerLog="$logdir/scorer.log.$opt_iter";
+	my $weightdir="$dir/weights.pass$opt_iter/";
+	check_call("mkdir -p $logdir");
+	check_call("mkdir -p $weightdir");
+
+	#decode
+	print STDERR "RUNNING DECODER AT ";
+	print STDERR unchecked_output("date");
+#	my $im1 = $opt_iter - 1;
+	my $weightsFile="$dir/weights.$opt_iter";
+	print "ITER $iteration " ;
+	my $cur_pass = "-p 0$opt_iter";
+	my $decoder_cmd = "$decoder -c $iniFile -w $weightsFile $refs_comma_sep -m $metric -s $metric_scale -b $update_size -k $kbest_size -o $optimizer $cur_pass -O $weightdir -D $dir  -h $hopes -f $fears -C $step_size";
+	if($unique_kbest){
+		$decoder_cmd .= " -u";
+	}
+	if($sent_approx){
+		$decoder_cmd .= " -a";
+	}
+	if($pseudo_doc){
+                $decoder_cmd .= " -e";
+        }
+	if ($density_prune) {
+		$decoder_cmd .= " --density_prune $density_prune";
+	}
+	my $pcmd;
+	if ($run_local) {
+		$pcmd = "cat $srcFile |";
+	} elsif ($use_make) {
+	    # TODO: Throw error when jobs is speong with use_make
+		$pcmd = "cat $srcFile | $parallelize --use-fork -p $pmem -e $logdir -j $use_make --";
+	} 
+	else {
+	    $pcmd = "cat $srcFile | $parallelize -p $pmem -e $logdir -j $jobs --baseport $portn --";
+	}
+	my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $runFile";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_bash_call($cmd);
+
+	my $retries = 0;
+        my $num_topbest;
+        while($retries < 6) {
+            $num_topbest = check_output("wc -l < $runFile");
+            print STDERR "NUMBER OF TOP-BEST HYPs: $num_topbest\n";
+            if($devSize == $num_topbest) {
+                last;
+            } else {
+                print STDERR "Incorrect number of topbest. Waiting for distributed filesystem and retrying...\n";
+                sleep(10);
+            }
+            $retries++;
+        }
+	 die "Dev set contains $devSize sentences, but we don't have topbest for all these! Decoder failure? Check $decoderLog\n" if ($devSize != $num_topbest);
+
+
+	#score the output from this iteration
+	open RUN, "<$runFile" or die "Can't read $runFile: $!";
+	open H, ">$runFile.H" or die;
+	open F, ">$runFile.F" or die;
+	open B, ">$runFile.B" or die;
+	while(<RUN>) {
+	    chomp();
+	    (my $hope,my $best,my $fear) = split(/ \|\|\| /);
+	    print H "$hope \n"; 	    
+	    print B "$best \n";
+ 	    print F "$fear \n";
+	}
+	close RUN;
+	close F; close B; close H;
+	
+	my $dec_score = check_output("cat $runFile.B | $SCORER $refs_comma_sep -m $metric");
+	my $dec_score_h = check_output("cat $runFile.H | $SCORER $refs_comma_sep -m $metric");
+	my $dec_score_f = check_output("cat $runFile.F | $SCORER $refs_comma_sep -m $metric");
+	chomp $dec_score; chomp $dec_score_h; chomp $dec_score_f;
+	print STDERR "DECODER SCORE: $dec_score HOPE: $dec_score_h FEAR: $dec_score_f\n";
+	if ($dec_score> $bestScore){
+		$bestScoreIter=$opt_iter; 
+		$bestScore=$dec_score;
+	}
+	# save space
+	check_call("gzip -f $runFile");
+	check_call("gzip -f $decoderLog");
+		my $iter_filler="";
+	if($opt_iter < 10)
+	{$iter_filler="0";}
+
+	my $nextIter = $opt_iter + 1;
+	my $newWeightsFile = "$dir/weights.$nextIter";
+	$lastWeightsFile = "$dir/weights.$opt_iter";
+
+	average_weights("$weightdir/weights.mira-pass*.*[0-9].gz", $newWeightsFile, $logdir);
+	system("gzip -f $logdir/kbes*");
+	print STDERR "\n==========\n";
+	$iteration++;
+}
+print STDERR "\nBEST ITER: $bestScoreIter :: $bestScore\n\n\n";
+
+print STDOUT "$lastWeightsFile\n";
+
+sub get_lines {
+  my $fn = shift @_;
+  open FL, "<$fn" or die "Couldn't read $fn: $!";
+  my $lc = 0;
+  while(<FL>) { $lc++; }
+  return $lc;
+}
+
+sub get_comma_sep_refs {
+  my ($r,$p) = @_;
+  my $o = check_output("echo $p");
+  chomp $o;
+  my @files = split /\s+/, $o;
+  return "-$r " . join(" -$r ", @files);
+}
+
+
+sub read_weights_file {
+  my ($file) = @_;
+  open F, "<$file" or die "Couldn't read $file: $!";
+  my @r = ();
+  my $pm = -1;
+  while(<F>) {
+    next if /^#/;
+    next if /^\s*$/;
+    chomp;
+    if (/^(.+)\s+(.+)$/) {
+      my $m = $1;
+      my $w = $2;
+      die "Weights out of order: $m <= $pm" unless $m > $pm;
+      push @r, $w;
+    } else {
+      warn "Unexpected feature name in weight file: $_";
+    }
+  }
+  close F;
+  return join ' ', @r;
+}
+
+sub write_config {
+	my $fh = shift;
+	my $cleanup = "yes";
+	if ($disable_clean) {$cleanup = "no";}
+
+	print $fh "\n";
+	print $fh "DECODER:          $decoder\n";
+	print $fh "INI FILE:         $iniFile\n";
+	print $fh "WORKING DIR:      $dir\n";
+	print $fh "SOURCE (DEV):     $srcFile\n";
+	print $fh "REFS (DEV):       $refFiles\n";
+	print $fh "EVAL METRIC:      $metric\n";
+	print $fh "START ITERATION:  $iteration\n";
+	print $fh "MAX ITERATIONS:   $max_iterations\n";
+	print $fh "DECODE NODES:     $jobs\n";
+	print $fh "HEAD NODE:        $host\n";
+	print $fh "PMEM (DECODING):  $pmem\n";
+	print $fh "CLEANUP:          $cleanup\n";
+	print $fh "INITIAL WEIGHTS:  $initialWeights\n";
+        print $fh "GRAMMAR PREFIX:   $gpref\n";
+}
+
+sub update_weights_file {
+  my ($neww, $rfn, $rpts) = @_;
+  my @feats = @$rfn;
+  my @pts = @$rpts;
+  my $num_feats = scalar @feats;
+  my $num_pts = scalar @pts;
+  die "$num_feats (num_feats) != $num_pts (num_pts)" unless $num_feats == $num_pts;
+  open G, ">$neww" or die;
+  for (my $i = 0; $i < $num_feats; $i++) {
+    my $f = $feats[$i];
+    my $lambda = $pts[$i];
+    print G "$f $lambda\n";
+  }
+  close G;
+}
+
+sub enseg {
+    my $src = shift;
+    my $newsrc = shift;
+    my $grammarpref = shift;
+
+    open(SRC, $src);
+    open(NEWSRC, ">$newsrc");
+    my $i=0;
+    while (my $line=<SRC>){
+	chomp $line;
+	if ($line =~ /^\s*<seg/i) {
+	    if($line =~ /id="[0-9]+"/) {
+		print NEWSRC "$line\n";
+	    } else {
+		die "When using segments with pre-generated <seg> tags, you must include a zero-based id attribute";
+	    }
+	}
+	elsif (defined $grammarpref) {
+	    print NEWSRC "<seg id=\"$i\" grammar=\"$grammarpref.$i.gz\">$line</seg>\n";}
+	else {
+	    print NEWSRC "<seg id=\"$i\">$line</seg>\n";
+	}
+	$i++;
+    }
+    close SRC;
+    close NEWSRC;
+}
+
+sub print_help {
+ my $executable = check_output("basename $0"); chomp $executable;
+        print << "Help";
+
+Usage: $executable [options] <ini file>
+        Runs a complete MIRA optimization using the ini file specified.
+	Example invocation:
+	run_mira.pl \
+        --pmem 3g \
+        --max-iterations 20 \
+        --optimizer 2 \
+        --unique-kbest \
+        --jobs 15 \
+        --kbest-size 500 \
+        --hope-select 1 \
+        --fear-select 1  \
+        --ref-files "ref.0.soseos ref.1.soseos" \
+        --source-file src.soseos \
+        --weights weights.init \
+        --workdir workdir \
+        --grammar-prefix grammars/grammar \
+        --step-size 0.01 \
+        --metric-scale 10000 \
+
+Required:
+
+        --ref-files <files>
+                Dev set ref files.  This option takes only a single string argument.
+                To use multiple files (including file globbing), this argument should
+                be quoted.
+        --source-file <file>
+                Dev set source file.
+        --weights <file>
+                Initial weights file
+
+General options:
+
+        --help
+                Print this message and exit.
+
+       --max-iterations <M>
+                Maximum number of iterations to run.  If not specified, defaults
+                to $max_iterations.
+
+        --metric <method>
+                Metric to optimize.
+                Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
+
+        --workdir <dir>
+                Directory for intermediate and output files.  If not specified, the
+                name is derived from the ini filename.  Assuming that the ini
+                filename begins with the decoder name and ends with ini, the default
+                name of the working directory is inferred from the middle part of
+                the filename.  E.g. an ini file named decoder.foo.ini would have
+                a default working directory name foo.
+	--optimizer <I>
+		Learning method to use for weight update. Choice are 1) SGD, 2) PA MIRA with Selection from Cutting Plane, 3) Cutting Plane MIRA, 4) PA MIRA,5) nbest MIRA with hope, fear, and model constraints
+	--metric-scale <I>
+		Scale MT loss by this amount when computing hope/fear candidates
+	--kbest-size <I>
+		Size of k-best list to extract from forest
+	--update-size <I>
+		Size of k-best list to use for update (applies to optimizer 5)
+	--step-size <F>
+		Controls aggresiveness of update (C) 
+	--hope-select<I>
+		How to select hope candidate. Choices are 1) model score - cost, 2) min cost
+	--fear-select <I>
+		How to select fear candodate. Choices are 1) model score + cost, 2) max cost, 3) max score
+	--sent-approx
+		Use smoothed sentence-level MT metric
+	--pseudo-doc
+		Use pseudo document to approximate MT metric
+	--unique-kbest
+		Extract unique k-best from forest
+	--grammar-prefix <path>
+		Path to sentence-specific grammar files
+
+Job control options:
+
+        --jobs <I>
+                Number of decoder processes to run in parallel. [default=$default_jobs]
+
+        --pmem <N>
+                Amount of physical memory requested for parallel decoding jobs
+                (used with qsub requests only)
+
+	--local 
+		Run single learner
+	--use-make <I>
+		Run parallel learners on a single machine through fork.
+
+
+Help
+}
+
+
+sub cmdline {
+    return join ' ',($0,@ORIG_ARGV);
+}
+
+#buggy: last arg gets quoted sometimes?
+my $is_shell_special=qr{[ \t\n\\><|&;"'`~*?{}$!()]};
+my $shell_escape_in_quote=qr{[\\"\$`!]};
+
+sub escape_shell {
+    my ($arg)=@_;
+    return undef unless defined $arg;
+    if ($arg =~ /$is_shell_special/) {
+        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
+        return "\"$arg\"";
+    }
+    return $arg;
+}
+
+sub escaped_shell_args {
+    return map {local $_=$_;chomp;escape_shell($_)} @_;
+}
+
+sub escaped_shell_args_str {
+    return join ' ',&escaped_shell_args(@_);
+}
+
+sub escaped_cmdline {
+    return "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
+}
+
+sub average_weights {
+
+    my $path = shift;
+    my $out = shift;
+    my $logpath = shift;
+    print "AVERAGE $path $out\n";
+    my %feature_weights= ();
+    my $total =0;
+    my $total_mult =0;
+    sleep(10);
+    foreach my $file (glob "$path")
+    {
+	$file =~ /\/([^\/]+).gz$/;
+	my $fname = $1;
+	my $cmd = "gzip -d $file";
+	$file =~ s/\.gz//;
+	check_bash_call($cmd);
+	my $mult = 0;
+	print "FILE $file \n";
+	open SCORE, "< $file" or next;
+	$total++;
+	while( <SCORE> ) {
+	    my $line = $_;
+	    if ($line !~ m/^\#/)
+	    {
+		my @s = split(" ",$line);
+		$feature_weights{$s[0]}+= $mult * $s[1];
+	    }
+	    else
+	    {
+		(my $msg,my $ran,$mult) = split(/ \|\|\| /);
+		print "Processing $ran $mult\n";
+	    }
+	}
+	$total_mult += $mult;
+	
+	close SCORE;
+	$cmd = "gzip $file"; check_bash_call($cmd);
+    }
+    
+#print out new averaged weights
+    open OUT, "> $out" or next;
+    for my $f ( keys %feature_weights ) {
+	print "$f $feature_weights{$f} $total_mult\n";
+	my $ave = $feature_weights{$f} / $total_mult;
+	
+	print "Printing $f $ave ||| ";
+	print OUT "$f $ave\n";
+    }
+    
+}
diff --git a/utils/filelib.h b/utils/filelib.h
index bb6e7415..b9ea3940 100644
--- a/utils/filelib.h
+++ b/utils/filelib.h
@@ -27,7 +27,7 @@ struct BaseFile {
   }
   bool is_null() const { return !ps_; }
   operator bool() const {
-    return ps_;
+    return ps_.get();
   }
   S* stream() { return ps_.get(); }
   S* operator->() { return ps_.get(); } // compat with old ReadFile * -> new Readfile. remove?