From 73f2592edc0c8f510029e4834acd899751c85862 Mon Sep 17 00:00:00 2001
From: Patrick Simianer <p@simianer.de>
Date: Fri, 20 Sep 2013 20:01:03 +0200
Subject: loo

---
 extractor/grammar_extractor.cc |  6 ++++--
 extractor/grammar_extractor.h  |  3 ++-
 extractor/rule_factory.cc      |  5 +++--
 extractor/rule_factory.h       |  3 ++-
 extractor/run_extractor.cc     | 13 +++++++++++--
 extractor/sample_alignment.txt |  3 +++
 extractor/sample_bitext.txt    |  3 +++
 extractor/sampler.cc           | 35 ++++++++++++++++++++++++++++++-----
 extractor/sampler.h            |  5 ++++-
 9 files changed, 62 insertions(+), 14 deletions(-)

(limited to 'extractor')

diff --git a/extractor/grammar_extractor.cc b/extractor/grammar_extractor.cc
index 8050ce7b..1fbdee5b 100644
--- a/extractor/grammar_extractor.cc
+++ b/extractor/grammar_extractor.cc
@@ -3,11 +3,13 @@
 #include <iterator>
 #include <sstream>
 #include <vector>
+#include <unordered_set>
 
 #include "grammar.h"
 #include "rule.h"
 #include "rule_factory.h"
 #include "vocabulary.h"
+#include "data_array.h"
 
 using namespace std;
 
@@ -32,10 +34,10 @@ GrammarExtractor::GrammarExtractor(
     vocabulary(vocabulary),
     rule_factory(rule_factory) {}
 
-Grammar GrammarExtractor::GetGrammar(const string& sentence) {
+Grammar GrammarExtractor::GetGrammar(const string& sentence, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   vector<string> words = TokenizeSentence(sentence);
   vector<int> word_ids = AnnotateWords(words);
-  return rule_factory->GetGrammar(word_ids);
+  return rule_factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
 }
 
 vector<string> GrammarExtractor::TokenizeSentence(const string& sentence) {
diff --git a/extractor/grammar_extractor.h b/extractor/grammar_extractor.h
index b36ceeb9..6c0aafbf 100644
--- a/extractor/grammar_extractor.h
+++ b/extractor/grammar_extractor.h
@@ -4,6 +4,7 @@
 #include <memory>
 #include <string>
 #include <vector>
+#include <unordered_set>
 
 using namespace std;
 
@@ -44,7 +45,7 @@ class GrammarExtractor {
 
   // 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);
+  Grammar GetGrammar(const string& sentence, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  private:
   // Splits the sentence in a vector of words.
diff --git a/extractor/rule_factory.cc b/extractor/rule_factory.cc
index 8c30fb9e..e52019ae 100644
--- a/extractor/rule_factory.cc
+++ b/extractor/rule_factory.cc
@@ -17,6 +17,7 @@
 #include "suffix_array.h"
 #include "time_util.h"
 #include "vocabulary.h"
+#include "data_array.h"
 
 using namespace std;
 using namespace chrono;
@@ -100,7 +101,7 @@ HieroCachingRuleFactory::HieroCachingRuleFactory() {}
 
 HieroCachingRuleFactory::~HieroCachingRuleFactory() {}
 
-Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids) {
+Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   Clock::time_point start_time = Clock::now();
   double total_extract_time = 0;
   double total_intersect_time = 0;
@@ -192,7 +193,7 @@ Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids) {
       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);
+        PhraseLocation sample = sampler->Sample(next_node->matchings, blacklisted_sentence_ids, source_data_array);
         vector<Rule> new_rules =
             rule_extractor->ExtractRules(next_phrase, sample);
         rules.insert(rules.end(), new_rules.begin(), new_rules.end());
diff --git a/extractor/rule_factory.h b/extractor/rule_factory.h
index 52e8712a..c7332720 100644
--- a/extractor/rule_factory.h
+++ b/extractor/rule_factory.h
@@ -3,6 +3,7 @@
 
 #include <memory>
 #include <vector>
+#include <unordered_set>
 
 #include "matchings_trie.h"
 
@@ -71,7 +72,7 @@ class HieroCachingRuleFactory {
 
   // Constructs SCFG rules for a given sentence.
   // (See class description for more details.)
-  virtual Grammar GetGrammar(const vector<int>& word_ids);
+  virtual Grammar GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  protected:
   HieroCachingRuleFactory();
diff --git a/extractor/run_extractor.cc b/extractor/run_extractor.cc
index 8a9ca89d..6eb55073 100644
--- a/extractor/run_extractor.cc
+++ b/extractor/run_extractor.cc
@@ -75,7 +75,9 @@ int main(int argc, char** argv) {
     ("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)");
+        "False if phrases may be loose (better, but slower)")
+    ("leave_one_out", po::value<bool>()->zero_tokens(),
+        "do leave-one-out estimation of grammars (e.g. for extracting grammars for the training set");
 
   po::variables_map vm;
   po::store(po::parse_command_line(argc, argv, desc), vm);
@@ -96,6 +98,11 @@ int main(int argc, char** argv) {
     return 1;
   }
 
+  bool leave_one_out = false;
+  if (vm.count("leave_one_out")) {
+    leave_one_out = true;
+  }
+
   int num_threads = vm["threads"].as<int>();
   cerr << "Grammar extraction will use " << num_threads << " threads." << endl;
 
@@ -223,7 +230,9 @@ int main(int argc, char** argv) {
     }
     suffixes[i] = suffix;
 
-    Grammar grammar = extractor.GetGrammar(sentences[i]);
+    unordered_set<int> blacklisted_sentence_ids;
+    if (leave_one_out) blacklisted_sentence_ids.insert(i);
+    Grammar grammar = extractor.GetGrammar(sentences[i], blacklisted_sentence_ids, source_data_array);
     ofstream output(GetGrammarFilePath(grammar_path, i).c_str());
     output << grammar;
   }
diff --git a/extractor/sample_alignment.txt b/extractor/sample_alignment.txt
index 80b446a4..f0292b01 100644
--- a/extractor/sample_alignment.txt
+++ b/extractor/sample_alignment.txt
@@ -1,2 +1,5 @@
 0-0 1-1 2-2
 1-0 2-1
+0-0
+0-0 1-1
+0-0 1-1
diff --git a/extractor/sample_bitext.txt b/extractor/sample_bitext.txt
index 93d6b39d..2b7c8e40 100644
--- a/extractor/sample_bitext.txt
+++ b/extractor/sample_bitext.txt
@@ -1,2 +1,5 @@
+asdf ||| dontseeme
+qqq asdf ||| zzz fdsa
+asdf qqq ||| fdsa zzz
 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
index d81956b5..2f7738db 100644
--- a/extractor/sampler.cc
+++ b/extractor/sampler.cc
@@ -12,18 +12,43 @@ Sampler::Sampler() {}
 
 Sampler::~Sampler() {}
 
-PhraseLocation Sampler::Sample(const PhraseLocation& location) const {
+PhraseLocation Sampler::Sample(const PhraseLocation& location, unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) 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)));
+    double step = Round(max(1.0, (double) (high - low) / max_samples));
+    int i = location.sa_low;
+    bool found = false;
+    while (sample.size() < max_samples && i <= location.sa_high) {
+      int x = suffix_array->GetSuffix(i);
+      int id = source_data_array->GetSentenceId(x);
+      if (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) != blacklisted_sentence_ids.end()) {
+        int backoff_step = 1;
+        while (true) {
+          int j = i - backoff_step;
+          x = suffix_array->GetSuffix(j);
+          id = source_data_array->GetSentenceId(x);
+          if ((j >= location.sa_low) && (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end())
+              && (find(sample.begin(), sample.end(), x) == sample.end())) { found = true; break; }
+          int k = i + backoff_step;
+          x = suffix_array->GetSuffix(k);
+          id = source_data_array->GetSentenceId(x);
+          if ((k <= location.sa_high) && (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end())
+              && (find(sample.begin(), sample.end(), x) == sample.end())) { found = true; break; }
+          if (j <= location.sa_low && k >= location.sa_high) break;
+          backoff_step++;
+        }
+      } else {
+        found = true;
+      }
+      if (found && (find(sample.begin(), sample.end(), x) == sample.end())) sample.push_back(x);
+      i += step;
+      found = false;
     }
-  } else {
+  } else { // when do we get here?
     // Sample vector of occurrences.
     num_subpatterns = location.num_subpatterns;
     int num_matchings = location.matchings->size() / num_subpatterns;
diff --git a/extractor/sampler.h b/extractor/sampler.h
index be4aa1bb..30e747fd 100644
--- a/extractor/sampler.h
+++ b/extractor/sampler.h
@@ -2,6 +2,9 @@
 #define _SAMPLER_H_
 
 #include <memory>
+#include <unordered_set>
+
+#include "data_array.h"
 
 using namespace std;
 
@@ -20,7 +23,7 @@ class Sampler {
   virtual ~Sampler();
 
   // Samples uniformly at most max_samples phrase occurrences.
-  virtual PhraseLocation Sample(const PhraseLocation& location) const;
+  virtual PhraseLocation Sample(const PhraseLocation& location, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const;
 
  protected:
   Sampler();
-- 
cgit v1.2.3


From eca30edc48af8922e96512f27a98f74d1c8b9721 Mon Sep 17 00:00:00 2001
From: Patrick Simianer <p@simianer.de>
Date: Fri, 20 Sep 2013 20:10:19 +0200
Subject: example file

---
 extractor/sample_source.txt | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 extractor/sample_source.txt

(limited to 'extractor')

diff --git a/extractor/sample_source.txt b/extractor/sample_source.txt
new file mode 100644
index 00000000..9b46dd6a
--- /dev/null
+++ b/extractor/sample_source.txt
@@ -0,0 +1,5 @@
+asdf
+qqq asdf
+asdf qqq
+ana are mere .
+ana bea mult lapte .
-- 
cgit v1.2.3


From 077f83a44c420b42541159271c6482cf068fc972 Mon Sep 17 00:00:00 2001
From: Patrick Simianer <simianer@cl.uni-heidelberg.de>
Date: Tue, 24 Sep 2013 15:50:03 +0200
Subject: loo #2

---
 extractor/sampler.cc | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

(limited to 'extractor')

diff --git a/extractor/sampler.cc b/extractor/sampler.cc
index 2f7738db..cb470962 100644
--- a/extractor/sampler.cc
+++ b/extractor/sampler.cc
@@ -20,35 +20,39 @@ PhraseLocation Sampler::Sample(const PhraseLocation& location, unordered_set<int
     num_subpatterns = 1;
     int low = location.sa_low, high = location.sa_high;
     double step = Round(max(1.0, (double) (high - low) / max_samples));
-    int i = location.sa_low;
-    bool found = false;
-    while (sample.size() < max_samples && i <= location.sa_high) {
+    int i = low, last = i;
+    bool found;
+    while (sample.size() < max_samples && i < high) {
       int x = suffix_array->GetSuffix(i);
       int id = source_data_array->GetSentenceId(x);
       if (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) != blacklisted_sentence_ids.end()) {
+        found = false;
         int backoff_step = 1;
         while (true) {
+          if ((double)backoff_step >= step) break;
           int j = i - backoff_step;
           x = suffix_array->GetSuffix(j);
           id = source_data_array->GetSentenceId(x);
-          if ((j >= location.sa_low) && (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end())
-              && (find(sample.begin(), sample.end(), x) == sample.end())) { found = true; break; }
+          if (j > last && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
+            found = true; last = i; break;
+          }
           int k = i + backoff_step;
           x = suffix_array->GetSuffix(k);
           id = source_data_array->GetSentenceId(x);
-          if ((k <= location.sa_high) && (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end())
-              && (find(sample.begin(), sample.end(), x) == sample.end())) { found = true; break; }
-          if (j <= location.sa_low && k >= location.sa_high) break;
+          if (k < min(i+step, (double)high) && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
+            found = true; last = k; break;
+          }
+          if (j <= last && k >= high) break;
           backoff_step++;
         }
       } else {
         found = true;
+        last = i;
       }
-      if (found && (find(sample.begin(), sample.end(), x) == sample.end())) sample.push_back(x);
+      if (found) sample.push_back(x);
       i += step;
-      found = false;
     }
-  } else { // when do we get here?
+  } else {
     // Sample vector of occurrences.
     num_subpatterns = location.num_subpatterns;
     int num_matchings = location.matchings->size() / num_subpatterns;
-- 
cgit v1.2.3


From 2d3948b98bb9e8c7bad60f1acd99ff0b42b3ae30 Mon Sep 17 00:00:00 2001
From: Chris Dyer <cdyer@Chriss-MacBook-Air.local>
Date: Sun, 10 Nov 2013 00:58:44 -0500
Subject: guard against direct includes of tr1

---
 configure.ac                        |    3 +-
 decoder/Makefile.am                 |    4 -
 decoder/apply_models.cc             |   11 +-
 decoder/cdec_ff.cc                  |   11 -
 decoder/decoder.cc                  |   10 +-
 decoder/dwarf.cc                    | 3209 -----------------------------------
 decoder/dwarf.h                     |  286 ----
 decoder/earley_composer.cc          |   11 +-
 decoder/factored_lexicon_helper.cc  |    1 +
 decoder/factored_lexicon_helper.h   |    3 +-
 decoder/ff_dwarf.cc                 |  894 ----------
 decoder/ff_dwarf.h                  |  100 --
 decoder/ff_lm.cc                    |  101 --
 decoder/ff_lm.h                     |   22 -
 decoder/ff_source_syntax.cc         |    6 +
 decoder/ff_source_syntax2.cc        |    4 +-
 decoder/ff_source_syntax2_p.cc      |   10 +-
 decoder/ff_source_syntax_p.cc       |    9 +-
 decoder/ff_wordalign.cc             |    9 +-
 decoder/ff_wordalign.h              |   13 +-
 decoder/ff_wordset.cc               |   52 +-
 decoder/ff_wordset.h                |   73 +-
 decoder/grammar.cc                  |   11 +-
 decoder/hg_intersect.cc             |    8 +-
 decoder/kbest.h                     |   11 +-
 decoder/maxtrans_blunsom.cc         |   11 +-
 decoder/phrasebased_translator.cc   |   11 +-
 decoder/scfg_translator.cc          |   10 +-
 decoder/sentence_metadata.h         |    4 +-
 extractor/Makefile.am               |   27 +-
 klm/lm/builder/Makefile.am          |    6 +-
 mteval/mbr_kbest.cc                 |    8 +-
 mteval/ns_ter.cc                    |    8 +-
 mteval/scorer.cc                    |   23 +-
 mteval/ter.cc                       |    8 +-
 python/cdec/sa/strmap.cc            |   11 +-
 training/crf/mpi_online_optimize.cc |    8 +-
 training/mira/kbest_cut_mira.cc     |   65 +-
 training/mira/kbest_mira.cc         |   18 +-
 training/mira/mira.py               |   98 +-
 training/pro/mr_pro_map.cc          |    1 -
 training/utils/candidate_set.cc     |   11 +-
 training/utils/online_optimizer.h   |    8 +-
 training/utils/optimize_test.cc     |    6 +-
 utils/hash.h                        |   12 +-
 word-aligner/fast_align.cc          |    8 +-
 word-aligner/ttables.cc             |    1 -
 word-aligner/ttables.h              |   11 +-
 48 files changed, 369 insertions(+), 4877 deletions(-)
 delete mode 100644 decoder/dwarf.cc
 delete mode 100644 decoder/dwarf.h
 delete mode 100644 decoder/ff_dwarf.cc
 delete mode 100644 decoder/ff_dwarf.h

(limited to 'extractor')

diff --git a/configure.ac b/configure.ac
index 37d8cced..c3b749e3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([cdec],[2013-03-08])
+AC_INIT([cdec],[2013-11-10])
 AC_CONFIG_SRCDIR([decoder/cdec.cc])
 AM_INIT_AUTOMAKE
 AC_CONFIG_HEADERS(config.h)
@@ -7,7 +7,6 @@ AC_PROG_LEX
 case $LEX in 
 :) AC_MSG_ERROR([No lex (Flex, lex, etc.) program found]);; 
 esac 
-# CPPFLAGS="$CPPFLAGS -std=c++0x"
 AC_PROG_CC
 AC_PROG_CXX
 AX_CXX_COMPILE_STDCXX_11
diff --git a/decoder/Makefile.am b/decoder/Makefile.am
index 914faaea..39a13ad8 100644
--- a/decoder/Makefile.am
+++ b/decoder/Makefile.am
@@ -41,7 +41,6 @@ libcdec_a_SOURCES = \
   cfg_options.h \
   csplit.h \
   decoder.h \
-  dwarf.h \
   earley_composer.h \
   exp_semiring.h \
   factored_lexicon_helper.h \
@@ -51,7 +50,6 @@ libcdec_a_SOURCES = \
   ff_charset.h \
   ff_context.h \
   ff_csplit.h \
-  ff_dwarf.h \
   ff_external.h \
   ff_factory.h \
   ff_klm.h \
@@ -103,8 +101,6 @@ libcdec_a_SOURCES = \
   maxtrans_blunsom.cc \
   cdec_ff.cc \
   cfg.cc \
-  dwarf.cc \
-  ff_dwarf.cc \
   ff_external.cc \
   rule_lexer.cc \
   fst_translator.cc \
diff --git a/decoder/apply_models.cc b/decoder/apply_models.cc
index 330de9e2..2e093d6a 100644
--- a/decoder/apply_models.cc
+++ b/decoder/apply_models.cc
@@ -8,8 +8,14 @@
 
 #include <vector>
 #include <algorithm>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
+# include <tr1/unordered_map>
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
 
 #include <boost/functional/hash.hpp>
 
@@ -23,7 +29,6 @@
 #define FAST_CP_2 3
 
 using namespace std;
-using namespace std::tr1;
 
 struct Candidate;
 typedef SmallVectorInt JVector;
diff --git a/decoder/cdec_ff.cc b/decoder/cdec_ff.cc
index e7b31f50..09597e87 100644
--- a/decoder/cdec_ff.cc
+++ b/decoder/cdec_ff.cc
@@ -29,12 +29,8 @@
 #include "ff_register.h"
 #include "ff_charset.h"
 #include "ff_wordset.h"
-#include "ff_dwarf.h"
 #include "ff_external.h"
 
-#ifdef HAVE_GLC
-#include <cdec/ff_glc.h>
-#endif
 
 void register_feature_functions() {
   static bool registered = false;
@@ -51,9 +47,6 @@ void register_feature_functions() {
   RegisterFF<BLEUModel>();
 
   //TODO: use for all features the new Register which requires static FF::usage(false,false) give name
-#ifdef HAVE_RANDLM
-  ff_registry.Register("RandLM", new FFFactory<LanguageModelRandLM>);
-#endif
   ff_registry.Register("SpanFeatures", new FFFactory<SpanFeatures>());
   ff_registry.Register("NgramFeatures", new FFFactory<NgramDetector>());
   ff_registry.Register("RuleContextFeatures", new FFFactory<RuleContextFeatures>());
@@ -98,10 +91,6 @@ void register_feature_functions() {
   ff_registry.Register("WordPairFeatures", new FFFactory<WordPairFeatures>);
   ff_registry.Register("SourcePathFeatures", new FFFactory<SourcePathFeatures>);
   ff_registry.Register("WordSet", new FFFactory<WordSet>);
-  ff_registry.Register("Dwarf", new FFFactory<Dwarf>);
   ff_registry.Register("External", new FFFactory<ExternalFeature>);
-#ifdef HAVE_GLC
-  ff_registry.Register("ContextCRF", new FFFactory<Model1Features>);
-#endif
 }
 
diff --git a/decoder/decoder.cc b/decoder/decoder.cc
index 31e6dc46..2c0e07b7 100644
--- a/decoder/decoder.cc
+++ b/decoder/decoder.cc
@@ -1,6 +1,11 @@
 #include "decoder.h"
 
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
 #include <boost/make_shared.hpp>
@@ -61,7 +66,6 @@
 static const double kMINUS_EPSILON = -1e-6;  // don't be too strict
 
 using namespace std;
-using namespace std::tr1;
 namespace po = boost::program_options;
 
 static bool verbose_feature_functions=true;
@@ -90,7 +94,7 @@ struct ELengthWeightFunction {
   }
 };
 inline void ShowBanner() {
-  cerr << "cdec v1.0 (c) 2009-2011 by Chris Dyer\n";
+  cerr << "cdec (c) 2009--2013 by Chris Dyer\n";
 }
 
 inline string str(char const* name,po::variables_map const& conf) {
diff --git a/decoder/dwarf.cc b/decoder/dwarf.cc
deleted file mode 100644
index fb0404a6..00000000
--- a/decoder/dwarf.cc
+++ /dev/null
@@ -1,3209 +0,0 @@
-#include "dwarf.h"
-#include "tdict.h"
-#include "wordid.h"
-#include "lattice.h"
-#include "ff_dwarf.h"
-#include <assert.h>
-#include <algorithm>
-#include <ostream>
-#include <sstream>
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <set>
-#include <boost/functional/hash.hpp>
-#include <tr1/unordered_map>
-#include <boost/tuple/tuple.hpp>
-
-using namespace std;
-using namespace std::tr1;
-using namespace boost::tuples;
-using namespace boost;
-
-Alignment::Alignment() {
-  //unordered_map<std::vector<WordID>,int> XX;
-  _I=0;
-  _J=0;
-  kSOS = TD::Convert("<s>");
-  kEOS = TD::Convert("</s>");
-  kUNK = TD::Convert("**UNKNOWN**");
-  SourceFWAntsIdxs = new int*[MAX_ARITY];
-  SourceFWAntsAbsIdxs = new int*[MAX_ARITY];
-  TargetFWAntsIdxs = new int*[MAX_ARITY];
-  SourceAntsIdxs = new int*[MAX_ARITY];
-  TargetAntsIdxs = new int*[MAX_ARITY];
-  AntsAl = new int*[MAX_ARITY];
-  for (int idx=0; idx<MAX_ARITY; idx++) {
-    SourceAntsIdxs[idx] = new int[40];
-    SourceFWAntsIdxs[idx] = new int[40];
-    SourceFWAntsAbsIdxs[idx] = new int[40];
-    TargetAntsIdxs[idx] = new int[40];
-    TargetFWAntsIdxs[idx] = new int[40];
-    AntsAl[idx] = new int[40];
-  }    
-  for (int j=0; j<MAX_WORDS; j++) 
-    for (int i=0; i<MAX_WORDS; i++) _matrix[j][i]=false; 
-  for (int j=0; j<MAX_WORDS; j++) {
-    _tSpan[j][0]=MINIMUM_INIT;
-    _sSpan[j][1]=MAXIMUM_INIT;
-  }
-  for (int i=0; i<MAX_WORDS; i++) {
-    _sSpan[i][0]=MINIMUM_INIT;
-    _sSpan[i][1]=MAXIMUM_INIT;
-  }
-  alpha_oris=0.1;
-  alpha_orit=0.1;
-  alpha_doms=0.1;
-  alpha_domt=0.1;
-  beta_oris=0.1;
-  beta_orit=0.1;
-  beta_doms=0.1;
-  beta_domt=0.1;
-}
-
-void Alignment::set(int j,int i) {
-// create a link between j and i, update their corresponding span accordingly
-  if (DEBUG) cerr << "set(" << j << "," << i << ")" << endl;
-  assert(0<=j && j<MAX_WORDS);
-  assert(0<=i && i<MAX_WORDS);
-  if (0<=j && j<MAX_WORDS && 0<=i && i<MAX_WORDS) {
-    _matrix[j][i] = true;
-    _tSpan[j][0]=least(i,_tSpan[j][0]);
-    _tSpan[j][1]=most(i,_tSpan[j][1]);
-    _sSpan[i][0]=least(j,_sSpan[i][0]);
-    _sSpan[i][1]=most(j,_sSpan[i][1]);
-  }
-  _J=most(j+1,_J);
-  _I=most(i+1,_I);
-}
-
-void Alignment::reset(int j,int i) { //probably won't be used, since the alignment is not dynamic
-// remove the link between j and i, update their corresponding span accordingly
-  if (DEBUG) cerr << "reset(" << j << "," << i << ")" << endl;
-  assert(0<=j && j<MAX_WORDS);
-  assert(0<=i && i<MAX_WORDS);
-  _matrix[j][i] = false;
-  if (j==_sSpan[i][0] || j==_sSpan[i][1]) {
-    int min=MINIMUM_INIT;
-    int max=MAXIMUM_INIT;
-    for (int idx=_sSpan[i][0]; idx<=_sSpan[i][1]; idx++) {
-      if (_matrix[idx][i]) {
-        min=least(min,idx);
-        max=most(max,idx);
-      }
-    }
-    _sSpan[i][0]=min;
-    _sSpan[i][1]=max;
-  }
-  if (i==_tSpan[j][0] || i==_tSpan[j][1]) {
-    int min=MINIMUM_INIT;
-    int max=MAXIMUM_INIT;
-    for (int idx=_tSpan[j][0]; idx<=_tSpan[j][1]; idx++) {
-      if (_matrix[j][idx]) {
-        min=least(min,idx);
-        max=most(max,idx);
-      }
-    }
-    _tSpan[j][0]=min;
-    _tSpan[j][1]=max;
-  }
-}
-
-int Alignment::targetOf(int j, int start) {
-  assert(j>=0);
-  if (start==-1) start = _tSpan[j][0];
-  if (_tSpan[j][0]==MINIMUM_INIT) return -1;
-  for (int idx=start; idx<=_tSpan[j][1]; idx++) {
-    if (_matrix[j][idx]) return idx;
-  }
-  return -1;
-}
-
-int Alignment::sourceOf(int i, int start) {
-  assert(i>=0);
-  if (start==-1) start = _sSpan[i][0];
-  if (_sSpan[i][0]==MINIMUM_INIT) return -1;
-  for (int idx=start; idx<=_sSpan[i][1]; idx++) {
-    if (_matrix[idx][i]) return idx;
-  }
-  return -1;
-}
-
-void Alignment::clearAls(int prevJ, int prevI) {
-  for (int j=0; j<=prevJ; j++) {
-    for (int i=0; i<prevI; i++) {
-      _matrix[j][i]=false;
-    }
-  }
-  for (int j=0; j<=prevJ; j++) {
-    _tSpan[j][0] = MINIMUM_INIT;
-    _tSpan[j][1] = MAXIMUM_INIT;
-  }
-  for (int i=0; i<=prevI; i++) {
-    _sSpan[i][0] = MINIMUM_INIT;
-    _sSpan[i][1] = MAXIMUM_INIT;
-  }
-  _J=0;
-  _I=0;
-}
-
-int Alignment::DominanceSource(int fw1, int fw2) {
-  // Dominance of fw1 and fw2 
-  // 0 -> neither, 1 -> leftFirst, 2 -> rightFirst, 3 -> dontCare
-  if (DEBUG) cerr << "DominanceSource(" << fw1 << "," << fw2 << ")" << endl;
-  //cerr << TD::Convert(_f[fw1]) << "," << TD::Convert(_f[fw2]) << endl; 
-  //cerr << AsString() << endl;
-  int dom = 0;
-  curr_al.push_back(fw1); curr_al.push_back(fw2);
-  if (doms_hash.find(curr_al)==doms_hash.end()) {
-    int* block = blockSource(fw1,fw2);
-    //cerr << "block = " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    if (block[0]==fw1) { 
-      int tfw10 = _tSpan[fw1][0];
-      int tfw11 = _tSpan[fw1][1];
-      //cerr << "tfw = " << tfw10 << "," << tfw11 << endl;
-      if (tfw11<0) { 
-        dom+=1;
-      } else {
-        if ((block[2]==tfw10 || block[3]==tfw11)) dom+=1;
-      }
-    }
-    if (block[1]==fw2) {
-      int tfw20 = _tSpan[fw2][0];
-      int tfw21 = _tSpan[fw2][1];
-      //cerr << "tfw = " << tfw20 << "," << tfw21 << endl;
-      if (tfw21<0) {
-        dom+=2;
-      } else {
-        if ((block[2]==tfw20 || block[3]==tfw21)) dom+=2;
-      }
-    }
-    delete block;
-    doms_hash.insert(pair<vector<int>,int>(curr_al,dom));
-  } else {
-    dom = doms_hash[curr_al];
-  }
-  if (DEBUG) cerr << "  dom = " << dom << endl;
-  curr_al.pop_back(); curr_al.pop_back();
-  return dom;
-}
-
-vector<int> Alignment::DominanceSource4Sampler(int fw1, int fw2) {
-  if (DEBUG) cerr << "DominanceSource4Sampler(" << fw1 << "," << fw2 << ")" << endl;
-  int dom = 0;
-  int* block = blockSource(fw1,fw2);
-  //cerr << "block = " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-  if (block[0]==fw1) {
-    int tfw10 = _tSpan[fw1][0];
-    int tfw11 = _tSpan[fw1][1];
-    //cerr << "tfw = " << tfw10 << "," << tfw11 << endl;
-    if (tfw11<0) {
-      dom+=1;
-    } else {
-      if ((block[2]==tfw10 || block[3]==tfw11)) dom+=1;
-    }
-  }
-  if (block[1]==fw2) {
-    int tfw20 = _tSpan[fw2][0];
-    int tfw21 = _tSpan[fw2][1];
-    //cerr << "tfw = " << tfw20 << "," << tfw21 << endl;
-    if (tfw21<0) {
-      dom+=2;
-    } else {
-      if ((block[2]==tfw20 || block[3]==tfw21)) dom+=2;
-    }
-  }
-  if (DEBUG) cerr << "doms = " << dom << endl;
-  vector<int> ret;
-  ret.push_back(dom); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-int Alignment::DominanceTarget(int fw1, int fw2) {
-  int dom = 0;
-  curr_al.push_back(fw1); curr_al.push_back(fw2);
-  if (domt_hash.find(curr_al)==domt_hash.end()) {
-    int* block = blockTarget(fw1,fw2);
-    if (block[2]==fw1) {
-      int sfw10 = _sSpan[fw1][0];
-      int sfw11 = _sSpan[fw1][1];
-      if (sfw11<0) {
-        dom+=1;
-      } else {
-        if (block[0]==sfw10 || block[1]==sfw11) dom+=1;
-      }
-    }
-    if (block[3]==fw2) {
-      int sfw20 = _sSpan[fw2][0];
-      int sfw21 = _sSpan[fw2][0];
-      if (sfw21<0) {
-        dom+=2;
-      } else {
-        if (block[0]==sfw20 || block[1]==sfw21) dom+=2;
-      }
-    }
-    delete block;
-    domt_hash.insert(pair<vector<int>,int>(curr_al,dom));
-  } else {
-    dom = domt_hash[curr_al];
-  }
-  curr_al.pop_back(); curr_al.pop_back();
-  return dom;
-}
-
-vector<int> Alignment::DominanceTarget4Sampler(int fw1, int fw2) {
-  int dom = 0;
-  int* block = blockTarget(fw1,fw2);
-  if (block[2]==fw1) {
-    int sfw10 = _sSpan[fw1][0];
-    int sfw11 = _sSpan[fw1][1];
-    if (sfw11<0) {
-      dom+=1;
-    } else {
-      if (block[0]==sfw10 || block[1]==sfw11) dom+=1;
-    }
-  }
-  if (block[3]==fw2) {
-    int sfw20 = _sSpan[fw2][0];
-    int sfw21 = _sSpan[fw2][0];
-    if (sfw21<0) {
-      dom+=2;
-    } else {
-      if (block[0]==sfw20 || block[1]==sfw21) dom+=2;
-    }
-  }
-  vector<int> ret;
-  ret.push_back(dom); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-void Alignment::OrientationSource(int fw, int* oril, int* orir, bool Lcompute, bool Rcompute) {
-  OrientationSource(fw,fw,oril,orir,Lcompute,Rcompute);
-}
-
-vector<int> Alignment::OrientationSourceLeft4Sampler(int fw) {
-  return OrientationSourceLeft4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationSourceLeft4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationSourceLeft4Sampler(" << fw0 << "," << fw1 << ")" << endl;
-  int oril = 0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minTSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_J) {
-    if (minTSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-    fw0 = N1; fw1 = N0;
-  }
-  if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-  if (maxTSpan(N0)<minTSpan(fw0) || maxTSpan(fw0)<minTSpan(N0)) {
-    if (DEBUG) cerr << "N0=" << minTSpan(N0) << "-" << maxTSpan(N0);
-    if (DEBUG) cerr << "fw=" << minTSpan(fw0) << "-" << maxTSpan(fw0) << endl;
-    int *block = blockTarget(minTSpan(N0),maxTSpan(N0));
-    if (block[0]<=fw0 && fw0<=block[1]) oril=5;
-    delete block;
-    if (oril==0) {
-      block = blockTarget(minTSpan(fw0),maxTSpan(fw0));
-      if (block[0]<=N0 && N0<=block[1]) oril=5;
-      delete block;
-    }
-    if (oril==0) {
-      if (maxTSpan(N0)<minTSpan(fw0)) {// if N0 is monotone
-        oril=1;
-        block = blockTarget(maxTSpan(N0),minTSpan(fw0)-1);
-        if (block[0] <= fw0 && fw0 <= block[1]) oril+=2;
-        delete block;
-      } else { //if (maxTSpan(fw0)<minTSpan(N0)) { // if NO is non-monotone
-        oril=2;
-        block = blockTarget(maxTSpan(fw0)+1,minTSpan(N0));
-        if (block[0] <= fw0 && fw0 <= block[1]) oril+=2;
-        delete block;
-      }
-    }
-  } else {
-    oril=5;
-  }
-  if (DEBUG) cerr << "oril = " << oril << endl;
-  int* block = blockSource(N0,fw0);
-  if (DEBUG) {
-    for (int i=0; i<4; i++) cerr << "block[" << i << "]=" << block[i] << endl;
-  }
-  vector<int> ret;
-  ret.push_back(oril); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-vector<int> Alignment::OrientationSourceRight4Sampler(int fw) {
-  return OrientationSourceRight4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationSourceRight4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationSourceLeft4Sampler(" << fw0 << "," << fw1 << ")" << endl;
-  int orir = 0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minTSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_J) {
-    if (minTSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-    fw0 = N1; fw1 = N0;
-  }
-  if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-  if (maxTSpan(N1)<minTSpan(fw1) || maxTSpan(fw1)<minTSpan(N1)) {
-    int* block = blockTarget(minTSpan(N1),maxTSpan(N1));
-    if (block[0]<=fw1 && fw1<=block[2]) orir=5;
-    delete block;
-    if (orir==0) {
-      block = blockTarget(minTSpan(fw1),maxTSpan(fw1));
-      if (block[0]<=N1 && N1 <=block[1]) orir=5;
-      delete block;
-    }
-    if (DEBUG) cerr << "N1=" << minTSpan(N1) << "-" << maxTSpan(N1);
-    if (DEBUG) cerr << "fw1=" << minTSpan(fw1) << "-" << maxTSpan(fw1) << endl;
-    if (orir==0) {
-      if (maxTSpan(fw1)<minTSpan(N1)) { // if N1 is monotone
-        orir = 1;
-        block = blockTarget(maxTSpan(fw1)+1,minTSpan(N1));
-        if (block[0] <= fw1 && fw1 <= block[1]) orir+=2;
-        delete block;
-      } else {// if (maxTSpan(N1)<minTSpan(fw1)) { // if N1 is non-monotone
-        orir = 2;
-        block = blockTarget(maxTSpan(N1),minTSpan(fw1)-1);
-        if (block[0] <= fw1 && fw1 <= block[1]) orir+=2;
-        delete block;
-      }
-    }
-  } else {
-    orir = 5;
-  }
-  if (DEBUG) cerr << "orir = " << orir << endl;
-  int* block = blockSource(fw1,N1);
-  vector<int> ret;
-  ret.push_back(orir); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-void Alignment::OrientationSource(int fw0, int fw1, int* oril, int* orir, bool Lcompute, bool Rcompute) {
-  // Orientation
-  // A bit tricky since fw can be 1) unaligned 2) aligned to many
-  // 1 -> MA, 2 -> RA, 3 -> MG, 4 -> RG, 5 -> Other
-  if (DEBUG) cerr << "OrientationSource(" << fw0 << "," << fw1 << ")" << endl;
-  if (!Lcompute && !Rcompute) return;
-  curr_al.push_back(fw0);
-  curr_al.push_back(fw1);
-  *oril=0;
-  *orir=0;
-  int lr=0;
-  if (oris_hash.find(curr_al)==oris_hash.end()) {
-    // Find first aligned word N0 to the left of fw
-    int N0=fw0-1;
-    while (N0>=0) {
-      if (minTSpan(N0)!=MINIMUM_INIT) break;
-      N0--;
-    }
-    int N1=fw1+1;
-    while (N1<_J) {
-      if (minTSpan(N1)!=MINIMUM_INIT) break;
-      N1++;
-    }
-    if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-      fw0 = N1; fw1 = N0;
-      //cerr << "minTSpan(fw)==MINIMUM_INIT, thus fw0=" << fw0 << ", fw1=" << fw1 << endl;
-    }
-    if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-    if (maxTSpan(N0)<minTSpan(fw0) || maxTSpan(fw0)<minTSpan(N0)) {
-      if (DEBUG) cerr << "N0=" << minTSpan(N0) << "-" << maxTSpan(N0);
-      if (DEBUG) cerr << "fw=" << minTSpan(fw0) << "-" << maxTSpan(fw0) << endl;
-      int *block = blockTarget(minTSpan(N0),maxTSpan(N0));
-      if (block[0]<=fw0 && fw0<=block[1]) *oril=5;
-      delete block;
-      if (*oril==0) {
-        block = blockTarget(minTSpan(fw0),maxTSpan(fw0));
-        if (block[0]<=N0 && N0<=block[1]) *oril=5;
-        delete block;
-      }
-      if (*oril==0) {
-        if (maxTSpan(N0)<minTSpan(fw0)) {// if N0 is monotone
-          *oril=1;
-          block = blockTarget(maxTSpan(N0),minTSpan(fw0)-1);
-          if (block[0] <= fw0 && fw0 <= block[1]) *oril+=2;
-          delete block;
-        } else { //if (maxTSpan(fw0)<minTSpan(N0)) { // if NO is non-monotone
-          *oril=2;
-          block = blockTarget(maxTSpan(fw0)+1,minTSpan(N0));
-          if (block[0] <= fw0 && fw0 <= block[1]) *oril+=2;
-          delete block;
-        }
-      }
-    } else {
-      *oril=5;
-    }
-    if (DEBUG) cerr << "oril =" << *oril << endl;
-    // Right neighbor
-    if (maxTSpan(N1)<minTSpan(fw1) || maxTSpan(fw1)<minTSpan(N1)) {
-      int* block = blockTarget(minTSpan(N1),maxTSpan(N1));
-      if (block[0]<=fw1 && fw1<=block[2]) *orir=5;
-      delete block;
-      if (*orir==0) {
-        block = blockTarget(minTSpan(fw1),maxTSpan(fw1));
-        if (block[0]<=N1 && N1 <=block[1]) *orir=5;
-        delete block;
-      }
-      if (DEBUG) cerr << "N1=" << minTSpan(N1) << "-" << maxTSpan(N1);
-      if (DEBUG) cerr << "fw1=" << minTSpan(fw1) << "-" << maxTSpan(fw1) << endl;
-      if (*orir==0) {
-        if (maxTSpan(fw1)<minTSpan(N1)) { // if N1 is monotone
-          *orir = 1;
-          block = blockTarget(maxTSpan(fw1)+1,minTSpan(N1));
-          if (block[0] <= fw1 && fw1 <= block[1]) *orir+=2;
-          delete block;
-        } else {// if (maxTSpan(N1)<minTSpan(fw1)) { // if N1 is non-monotone
-          *orir = 2;
-          block = blockTarget(maxTSpan(N1),minTSpan(fw1)-1);
-          if (block[0] <= fw1 && fw1 <= block[1]) *orir+=2;
-          delete block;
-        }
-      }
-    } else {
-      *orir = 5;
-    }
-    if (DEBUG) cerr << "orir =" << *orir << endl;
-    lr = link(*oril,*orir);
-    oris_hash.insert(pair<vector<int>,int>(curr_al,lr));  
-  } else {
-    lr = oris_hash[curr_al];  
-  }
-  if (DEBUG) cerr << "Lcompute=" << Lcompute << ", Rcompute=" << Rcompute << endl;
-  if (Lcompute) *oril = source(lr);
-  if (Rcompute) *orir = target(lr);
-  curr_al.pop_back();
-  curr_al.pop_back();
-}
-
-int Alignment::OrientationSource(int* left, int* right) {
-  if (DEBUG) {
-    cerr << "      OrientationSource(";
-    cerr << "left="<<left[0]<<","<<left[1]<<","<<left[2]<<","<<left[3];
-    cerr << " right="<<right[0]<<","<<right[1]<<","<<right[2]<<","<<right[3];
-    cerr << ")" << endl;
-  } 
-  //if ((right[1]<=left[0]) return 5;
-  if (!(left[1]<right[0])) return 5;
-  int ori = 1;
-  if (right[3]<left[2]) ori=2;
-  int gapstart = left[3]+1; int gapend = right[2]-1;
-  if (ori==2) { gapstart = right[3]+1; gapend = left[2]-1; }
-  for (int j=gapstart; j<=gapend; j++) {
-    if (sourceOf(j)!=-1) {
-      ori+=2; break;
-    }
-  }
-  return ori;
-}
-
-void Alignment::OrientationTarget(int fw, int *oril, int *orir, bool Lcompute, bool Rcompute) {
-  OrientationTarget(fw,fw,oril,orir,Lcompute,Rcompute);
-}
-
-vector<int> Alignment::OrientationTargetLeft4Sampler(int fw) {
-  return OrientationTargetLeft4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationTargetLeft4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationTargetLeft4Sampler " << fw0 << "," << fw1 << endl;
-  int oril=0; 
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minSSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_I) {
-    if (minSSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-    fw0=N1; fw1=N0;
-  }
-  if (maxSSpan(N0)<minSSpan(fw0) || maxSSpan(fw0)<minSSpan(N0)) {
-    int *block = blockSource(minSSpan(N0),maxSSpan(N0));
-    if (DEBUG) cerr << "block1[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    if (block[2]<=fw0 && fw0<=block[3])  //source span of fw0 subsumes NO's or the other way around
-      oril=5;
-    delete block;
-    if (oril==0) {
-      block = blockSource(minSSpan(fw0), maxSSpan(fw0));
-      if (DEBUG) cerr << "block2[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-      if (block[2] <= N0 && N0 <= block[3]) oril=5;
-      delete block;
-    }
-    if (oril==0) {
-      if (maxSSpan(N0)<minSSpan(fw0)) {// if N0 is monotone
-        oril=1;
-        block = blockSource(maxSSpan(N0),minSSpan(fw0)-1);
-        if (DEBUG) cerr << "block3[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= fw0 && fw0 <= block[3]) oril+=2;
-        delete block;
-      } else { // (maxSSpan(fw0)<minSSpan(N0)) // if NO is non-monotone
-        oril=2;
-        block = blockSource(maxSSpan(fw0)+1,minSSpan(N0));
-        if (DEBUG) cerr << "block4[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= fw0 && fw0 <= block[3]) oril+=2;
-        delete block;
-      }
-    }
-  } else { //source span of fw0 subsumes NO's or the other way around
-    oril=5;
-  }
-  if (DEBUG) cerr << "oril = " << oril << endl;
-  int* block = blockSource(N0,fw0);
-  vector<int> ret;
-  ret.push_back(oril); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-vector<int> Alignment::OrientationTargetRight4Sampler(int fw) {
-  return OrientationTargetRight4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationTargetRight4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationTargetRight4Sampler " << fw0 << "," << fw1 << endl;
-  int orir=0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minSSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_I) {
-    if (minSSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-    fw0=N1; fw1=N0;
-  }
-  if (maxSSpan(N1)<minSSpan(fw1) || maxSSpan(fw1)<minSSpan(N1)) {
-    int *block = blockSource(minSSpan(N1),maxSSpan(N1));
-    if (block[2]<=fw1 && fw1<=block[3]) orir=5;
-    delete block;
-    if (orir==0) {
-      block = blockSource(minSSpan(fw1),maxSSpan(fw1));
-      if (block[2] <= N1 && N1 <= block[3]) orir=5;
-      delete block;
-    }
-    if (orir==0) {
-      if (maxSSpan(fw1)<minSSpan(N1)) { // if N1 is monotone
-        orir=1;
-        block = blockSource(maxSSpan(fw1)+1,minSSpan(N1));
-        if (block[2] <= fw1 && fw1 <= block[3]) orir+=2;
-        delete block;
-      } else { //if (maxSSpan(N1)<minSSpan(fw1)) { // if N1 is non-monotone
-        orir=2;
-        block = blockSource(maxSSpan(N1),minSSpan(fw1)-1);
-        if (block[2] <= fw1 && fw1 <= block[3]) orir+=2;
-        delete block;
-      }
-    }
-  } else {
-    orir=5;
-  }
-  if (DEBUG) cerr << "orir = " << orir << endl;
-  int* block = blockSource(fw1,N1);
-  vector<int> ret;
-  ret.push_back(orir); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-
-}
-
-void Alignment::OrientationTarget(int fw0, int fw1, int*oril, int*orir, bool Lcompute, bool Rcompute) {
-  if (DEBUG) cerr << "OrientationTarget " << fw0 << "," << fw1 << endl;
-  // Left Neighbor
-  if (!Lcompute && !Rcompute) return;
-  *oril=0;
-  *orir=0;
-  curr_al.push_back(fw0);
-  curr_al.push_back(fw1);
-  int lr = 0;
-  if (orit_hash.find(curr_al)==orit_hash.end()) {
-    // Find first aligned word N0 to the left of fw
-    //int fw0 = fw; int fw1 = fw;
-    int N0=fw0-1;
-    while (N0>=0) {
-      if (minSSpan(N0)!=MINIMUM_INIT) break;
-      N0--;
-    }
-    int N1=fw1+1;
-    while (N1<_I) {
-      if (minSSpan(N1)!=MINIMUM_INIT) break;
-      N1++;
-    }
-    if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-      fw0=N1; fw1=N0;
-    }
-    if (DEBUG) {
-      cerr << "fw0:" << fw0 << ", fw1:" << fw1 << ", N0:" << N0 << ", N1:" << N1 << endl ;
-      cerr << "minSSpan(N0)=" << minSSpan(N0) << " maxSSpan(N0)=" << maxSSpan(N0);
-      cerr << " minSSpan(fw0)="<< minSSpan(fw0) << " maxSSpan(fw0)=" << maxSSpan(fw0) << endl;
-      cerr << "minSSpan(fw1)=" << minSSpan(fw1) << " maxSSpan(fw1)=" << maxSSpan(fw1);
-      cerr << " minSSpan(N1)="<< minSSpan(N1) << " maxSSpan(N1)=" << maxSSpan(N1) << endl;
-    }
-    if (maxSSpan(N0)<minSSpan(fw0) || maxSSpan(fw0)<minSSpan(N0)) {
-      int *block = blockSource(minSSpan(N0),maxSSpan(N0));
-      if (DEBUG) cerr << "block1[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-      if (block[2]<=fw0 && fw0<=block[3])  //source span of fw0 subsumes NO's or the other way around
-        *oril=5;
-      delete block;
-      if (*oril==0) {
-        block = blockSource(minSSpan(fw0), maxSSpan(fw0));
-        if (DEBUG) cerr << "block2[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= N0 && N0 <= block[3]) *oril=5;
-        delete block;
-      }
-      if (*oril==0) {  
-        if (maxSSpan(N0)<minSSpan(fw0)) {// if N0 is monotone
-          *oril=1;
-          block = blockSource(maxSSpan(N0),minSSpan(fw0)-1);
-          if (DEBUG) cerr << "block3[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (block[2] <= fw0 && fw0 <= block[3]) *oril+=2;
-          delete block;
-        } else { // (maxSSpan(fw0)<minSSpan(N0)) // if NO is non-monotone
-          *oril=2;
-          block = blockSource(maxSSpan(fw0)+1,minSSpan(N0));
-          if (DEBUG) cerr << "block4[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (block[2] <= fw0 && fw0 <= block[3]) *oril+=2;
-          delete block;
-        }
-      }
-    } else { //source span of fw0 subsumes NO's or the other way around
-      *oril=5;
-    }
-    if (DEBUG) cerr << "oril = " << *oril << endl;
-    // Right Neighbor
-    if (maxSSpan(N1)<minSSpan(fw1) || maxSSpan(fw1)<minSSpan(N1)) {
-      int *block = blockSource(minSSpan(N1),maxSSpan(N1));
-      if (block[2]<=fw1 && fw1<=block[3]) *orir=5; 
-      delete block;
-      if (*orir==0) {
-        block = blockSource(minSSpan(fw1),maxSSpan(fw1));
-        if (block[2] <= N1 && N1 <= block[3]) *orir=5;
-        delete block;
-      }
-      if (*orir==0) {
-        if (maxSSpan(fw1)<minSSpan(N1)) { // if N1 is monotone
-          *orir=1;
-          block = blockSource(maxSSpan(fw1)+1,minSSpan(N1));
-          if (block[2] <= fw1 && fw1 <= block[3]) *orir+=2;
-          delete block;
-        } else { //if (maxSSpan(N1)<minSSpan(fw1)) { // if N1 is non-monotone
-          *orir=2;
-          block = blockSource(maxSSpan(N1),minSSpan(fw1)-1);
-          if (block[2] <= fw1 && fw1 <= block[3]) *orir+=2;
-          delete block;
-        }
-      }
-    } else {
-      *orir=5;
-    }
-    if (DEBUG) cerr << "orir = " << *orir << endl;
-    lr = link(*oril,*orir);
-    orit_hash.insert(pair<vector<int>,int>(curr_al,lr));
-  } else {
-    lr = orit_hash[curr_al];
-  }
-  if (DEBUG) cerr << "Lcompute=" << Lcompute << ", Rcompute=" << Rcompute << endl;
-  if (DEBUG) cerr << "lr=" << lr << ", l=" << source(lr) << ", r=" << target(lr) << endl;
-  if (Lcompute>0) *oril=source(lr);
-  if (Rcompute>0) *orir=target(lr);
-  curr_al.pop_back();
-  curr_al.pop_back();
-}
-
-int* Alignment::blockSource(int idx1, int idx2) {
-// outputs a minimal block [s1,s2,t1,t2] that contains idx1 and idx2, where idx1 <= idx2
-  if (DEBUG) cerr << "blockSource[" << idx1 << "," << idx2 << "]" << endl;
-  int *curr = new int[4];
-  curr[0]=idx1; curr[1]=idx2; curr[2]=MINIMUM_INIT; curr[3]=MAXIMUM_INIT;
-  for (int j=curr[0]; j<=curr[1]; j++) {
-    curr[2] = least(curr[2],_tSpan[j][0]);
-    curr[3] =  most(curr[3],_tSpan[j][1]);
-  }
-  int next[4];
-  next[0]=curr[0]; next[1]=curr[1];
-  for (int i=curr[2]; i<=curr[3]; i++) {
-    next[0] = least(next[0],_sSpan[i][0]);
-    next[1] =  most(next[1],_sSpan[i][1]);
-  } 
-  next[2] = curr[2]; next[3]= curr[3];
-  int idx=1;
-  do {
-    // update the current
-    for (int j=next[0]; j<curr[0]; j++) {
-      curr[2] = least(curr[2],_tSpan[j][0]);
-      curr[3] =  most(curr[3],_tSpan[j][1]);
-    }
-    for (int j=curr[1]+1; j<=next[1]; j++) {
-      curr[2] = least(curr[2],_tSpan[j][0]);
-      curr[3] =  most(curr[3],_tSpan[j][1]);
-    }
-    curr[0] = next[0]; curr[1] = next[1]; 
-    if (curr[2]==next[2] && curr[3]==next[3]) break;
-    // prepare for the next 
-    for (int i=curr[2]; i<next[2]; i++) {
-      next[0]= least(next[0],_sSpan[i][0]);
-      next[1]=  most(next[1],_sSpan[i][1]);
-    }
-    for (int i=next[3]+1; i<=curr[3]; i++) {
-      next[0] = least(next[0],_sSpan[i][0]);
-      next[1] =  most(next[1],_sSpan[i][1]);
-    }
-    next[2] = curr[2]; next[3]= curr[3];
-    idx++;
-  } while(1);
-  return curr;
-}
-
-int* Alignment::blockTarget(int idx1, int idx2) {
-// outputs a minimal [s1,s2,t1,t2] that contains idx1 and idx2, where idx1<=idx2
-  int *curr = new int[4];
-  curr[0]=MINIMUM_INIT; curr[1]=MAXIMUM_INIT; curr[2]=idx1; curr[3]=idx2;
-        for (int i=curr[2]; i<=curr[3]; i++) {
-                curr[0] = least(curr[0],_sSpan[i][0]);
-                curr[1] =  most(curr[1],_sSpan[i][1]);
-        }
-        int next[4];
-        next[2]=curr[2]; next[3]=curr[3];
-        for (int j=curr[0]; j<=curr[1]; j++) {
-                next[2] = least(next[2],_tSpan[j][0]);
-                next[3] =  most(next[3],_tSpan[j][1]);
-        }
-        next[0] = curr[0]; next[1]= curr[1];
-        int idx=1;
-        do {
-                // update the current
-                for (int i=next[2]; i<curr[2]; i++) {
-                        curr[0] = least(curr[0],_sSpan[i][0]);
-                        curr[1] =  most(curr[1],_sSpan[i][1]);
-                }
-                for (int i=curr[3]+1; i<=next[3]; i++) {
-                        curr[0] = least(curr[0],_sSpan[i][0]);
-                        curr[1] =  most(curr[1],_sSpan[i][1]);
-                }
-                curr[2] = next[2]; curr[3] = next[3];
-                if (curr[0]==next[0] && curr[1]==next[1]) break;
-                // prepare for the next
-                for (int j=curr[0]; j<next[0]; j++) {
-                        next[2]= least(next[2],_tSpan[j][0]);
-                        next[3]=  most(next[3],_tSpan[j][1]);
-                }
-                for (int j=next[1]+1; j<=curr[1]; j++) {
-                        next[2] = least(next[2],_tSpan[j][0]);
-                        next[3] =  most(next[3],_tSpan[j][1]);
-                }
-                next[0] = curr[0]; next[1]= curr[1];
-                idx++;
-        } while(1);
-  return curr;
-}
-
-int Alignment::firstSourceAligned(int start) {
-  for (int j=start; j<_J; j++) 
-    if (_tSpan[j][0]!=MINIMUM_INIT) return j;
-  return -1;
-}
-
-int Alignment::lastSourceAligned(int end) {
-  for (int j=end; j>=0; j--)
-    if (_tSpan[j][0]!=MINIMUM_INIT) return j;
-  return -1;
-}
-
-int Alignment::firstTargetAligned(int start) {
-  for (int i=start; i<_I; i++) 
-    if (_sSpan[i][0]!=MINIMUM_INIT) return i;
-  return -1;
-}
-
-int Alignment::lastTargetAligned(int end) {
-  for (int i=end; i>=0; i--) 
-    if (_sSpan[i][0]!=MINIMUM_INIT) return i;
-  return -1;
-}
-
-void Alignment::BorderingSFWsOnly() {
-// removes the record of all function word alignments, except those at the borders
-// the number of alignments kept may be more than two
-// i.e. where the leftmost / the rightmost alignments are unaligned. 
-// In such cases, this function continues keeping function word alignments until the 
-// first (or last) alignment words. 
-  if (SourceFWIdxs[0]>2) {
-    int firstCut = 1;
-    for (int j=2; j<=SourceFWIdxs[0]; j++) {
-      if (SourceFWIdxs[3*j-2]>fas) break;
-      firstCut=j;
-    }
-    int lastCut  = SourceFWIdxs[0];
-    for (int j=SourceFWIdxs[0]-1; j>=0; j--) {
-      if (SourceFWIdxs[3*j-2]<las) break;
-      lastCut=j;
-    }
-    if (firstCut>=lastCut) return;
-    int delta = 0;
-    for (int j=lastCut; j<=SourceFWIdxs[0]; j++) {
-      delta++;
-      SourceFWIdxs[3*(firstCut+delta)-2]=SourceFWIdxs[3*j-2];
-      SourceFWIdxs[3*(firstCut+delta)-1]=SourceFWIdxs[3*j-1];
-      SourceFWIdxs[3*(firstCut+delta)]  =SourceFWIdxs[3*j];
-    }
-    SourceFWIdxs[0]=firstCut+delta;
-  }
-}
-
-void Alignment::BorderingTFWsOnly() {
-// similar to BorderingSFWsOnly() except this looks at the source side.
-  if (TargetFWIdxs[0]>2) {
-    int firstCut = 1;
-    for (int j=2; j<=TargetFWIdxs[0]; j++) {
-      if (TargetFWIdxs[3*j-2]>fat) break;
-      firstCut=j;
-    }
-    int lastCut  = TargetFWIdxs[0];
-    for (int j=TargetFWIdxs[0]-1; j>=0; j--) {
-      if (TargetFWIdxs[3*j-2]<lat) break;
-      lastCut=j;
-    }
-    if (firstCut>=lastCut) return;
-    int delta = 0;
-    for (int j=lastCut; j<=TargetFWIdxs[0]; j++) {
-      delta++;
-      TargetFWIdxs[3*(firstCut+delta)-2]=TargetFWIdxs[3*j-2];
-      TargetFWIdxs[3*(firstCut+delta)-1]=TargetFWIdxs[3*j-1];
-      TargetFWIdxs[3*(firstCut+delta)]  =TargetFWIdxs[3*j];
-    }
-    TargetFWIdxs[0]=firstCut+delta;
-  }
-}
-
-void Alignment::FillFWIdxsState(int* state, int fas, int las, int fat, int lat) {
-  if (DEBUG) cerr << "FillFWIdxsState ("<< fas <<","<< las<<"," << fat <<"," << lat << ")" << endl;
-  if (fas==las) las+=1;
-  if (fat==lat) lat+=1;
-  for (int idx=0; idx<12; idx++) state[idx]=-1;
-  if (SourceFWIdxs[0]<=2) {
-    if (SourceFWIdxs[0]>=1) {state[0]=SourceFWIdxs[1]; state[1]=SourceFWIdxs[2]; state[2]=SourceFWIdxs[3];}
-    if (SourceFWIdxs[0]==2) {state[3]=SourceFWIdxs[4]; state[4]=SourceFWIdxs[5]; state[5]=SourceFWIdxs[6];}
-  } else {
-    if (SourceFWIdxs[1]>fas) {
-      state[0]=SourceFWIdxs[1]; state[1]=SourceFWIdxs[2]; state[2]=SourceFWIdxs[3];
-    } else {
-      ostringstream issf; ostringstream isse;
-      for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-        if (SourceFWIdxs[3*idx-2]>las) break;
-        if (idx>1) { issf << " "; isse << " ";};
-        issf << TD::Convert(SourceFWIdxs[3*idx-1]);
-        isse << TD::Convert(SourceFWIdxs[3*idx]);
-        state[0]=SourceFWIdxs[3*idx-2];
-        if (state[0]>=fas) break;
-      }
-      if (state[0]>=0) {
-        state[1]=TD::Convert(issf.str())*-1; state[2]=TD::Convert(isse.str()); //multiplying source with -1 as marker
-      }
-    }
-    if (SourceFWIdxs[SourceFWIdxs[0]*3-2]==las) {
-      state[3]=SourceFWIdxs[SourceFWIdxs[0]*3-2];
-      state[4]=SourceFWIdxs[SourceFWIdxs[0]*3-1]; 
-      state[5]=SourceFWIdxs[SourceFWIdxs[0]*3];
-    } else {
-      int lastCut = SourceFWIdxs[0];
-      for (int j=lastCut-1; j>=state[0]+1; j--) {
-        if (SourceFWIdxs[3*j-2]==state[0]) break;
-        if (SourceFWIdxs[3*j-2]<las) break;
-        lastCut=j;
-      }
-      state[3]=SourceFWIdxs[3*lastCut-2];
-      ostringstream issf; ostringstream isse;
-      for (int idx=lastCut; idx<=SourceFWIdxs[0]; idx++) {
-        if (idx>lastCut) { issf << " "; isse << " ";};
-        issf << TD::Convert(SourceFWIdxs[3*idx-1]);
-        isse << TD::Convert(SourceFWIdxs[3*idx]);
-      }
-      if (state[3]>=0) {
-        //multiplying source with -1 as compound marker
-        state[4]=TD::Convert(issf.str())*-1; state[5]=TD::Convert(isse.str()); 
-      }
-    }
-  }
-  if (TargetFWIdxs[0]<=2) {
-    if (TargetFWIdxs[0]>=1) {state[6]=TargetFWIdxs[1]; state[7]=TargetFWIdxs[2]; state[8]=TargetFWIdxs[3];}
-    if (TargetFWIdxs[0]==2) {state[9]=TargetFWIdxs[4]; state[10]=TargetFWIdxs[5]; state[11]=TargetFWIdxs[6];}
-  } else {
-    if (TargetFWIdxs[1]>fat) { //shouldn't come here if SetTargetBorderingFW is invoked
-      state[6]=TargetFWIdxs[1]; state[7]=TargetFWIdxs[2]; state[8]=TargetFWIdxs[3];
-    } else {
-      ostringstream issf; ostringstream isse;
-      for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-        if (TargetFWIdxs[3*idx-2]>fat) break;
-        if (idx>1) { issf << " "; isse << " ";};
-        issf << TD::Convert(TargetFWIdxs[3*idx-1]);
-        isse << TD::Convert(TargetFWIdxs[3*idx]);
-        state[6]=TargetFWIdxs[3*idx-2];
-      }
-      state[7]=TD::Convert(issf.str()); state[8]=TD::Convert(isse.str())*-1; 
-      //multiplying target with -1 as compound marker
-    }
-    if (TargetFWIdxs[TargetFWIdxs[0]*3-2]==lat) {
-      state[9]=TargetFWIdxs[TargetFWIdxs[0]*3-2];
-      state[10]=TargetFWIdxs[TargetFWIdxs[0]*3-1];
-      state[11]=TargetFWIdxs[TargetFWIdxs[0]*3];
-    } else {
-      int lastCut = TargetFWIdxs[0];
-      for (int j=lastCut-1; j>=1; j--) {
-        if (TargetFWIdxs[3*j-2]<=state[9]) break;
-        if (TargetFWIdxs[3*j-2]<lat) break;
-        lastCut=j;
-      }
-      state[9]=TargetFWIdxs[3*lastCut-2];
-      ostringstream issf; ostringstream isse;
-      for (int idx=lastCut; idx<=TargetFWIdxs[0]; idx++) {
-        if (idx>lastCut) issf << " "; isse << " ";;
-        issf << TD::Convert(TargetFWIdxs[3*idx-1]);
-        isse << TD::Convert(TargetFWIdxs[3*idx]);
-      }
-      state[10]=TD::Convert(issf.str()); state[11]=TD::Convert(isse.str())*-1; 
-    }
-  }
-}
-
-void Alignment::simplifyBackward(vector<int *>*blocks, int* block, const vector<int>& danglings) {
-// given a *block*, see whether its target span contains any index inside *danglings*. 
-// if yes, break it; otherwise, keep it. put the result(s) to *blocks*
-  if (DEBUG) cerr << "simplifyBackward[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << "]" << endl;
-  if (DEBUG) for (int i=0; i<danglings.size(); i++) cerr << "danglings[" << i << "] = " << danglings[i] << endl;
-  if (danglings.size()==0) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(0) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return; 
-  }
-  int currIdx = block[2];
-  int i_dangling = 0;
-  while (block[2]>danglings[i_dangling])  {
-    if (i_dangling+1 >= danglings.size()) break;
-    i_dangling++;
-  }
-  while (danglings[i_dangling]==currIdx) {
-    i_dangling++;
-    currIdx++;
-  } 
-  /*if (i_dangling>=danglings.size() && currIdx) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(1) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return;
-  }
-  if (block[3]<danglings[i_dangling]) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(2) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return;
-  }*/
-  if (DEBUG) cerr << "i_dangling = " << i_dangling << endl;
-  int anchorIdx = danglings[i_dangling];
-  if (i_dangling+1>=danglings.size() || anchorIdx>block[3]+1) anchorIdx=block[3]+1;
-  if (DEBUG) cerr << "anchorIdx = " << anchorIdx << ", currIdx = " << currIdx << endl;
-  do {
-    while(currIdx<anchorIdx) {
-      if (DEBUG) cerr << "currIdx = " << currIdx << ", anchorIdx = " << anchorIdx << endl;
-      bool isMoved = false;
-      for (int idx=anchorIdx-1; idx>=currIdx; idx--) {
-        int *nublock = blockTarget(currIdx,idx);
-        if (nublock[2]==currIdx && nublock[3]==idx) {
-          if (nublock[0]!=MINIMUM_INIT) {
-            blocks->push_back(nublock);
-            if (DEBUG) cerr << "pushing(3) " << nublock[0] << "," << nublock[1] << "," << nublock[2] << "," << nublock[3] << endl;
-          } else { 
-            delete nublock; 
-          }
-          isMoved = true;
-          currIdx=idx+1; break;
-        } else {
-          delete nublock;
-        }
-      }
-      if (DEBUG) cerr << "isMoved=" << isMoved << ", currIdx=" << currIdx << endl;
-      if (!isMoved) {
-        int source = sourceOf(currIdx);
-        while (source>=0) {
-          if (source >= block[0]) {
-            int* nublock = new int[4];
-            nublock[0]=source; nublock[1]=source; nublock[2]=currIdx; nublock[3]=currIdx;
-            blocks->push_back(nublock);
-            if (DEBUG) cerr << "pushing(4) " << nublock[0] << "," << nublock[1] << "," << nublock[2] << "," << nublock[3] << endl;
-          } 
-          source = sourceOf(currIdx,source+1);
-        }
-        currIdx++;
-      }
-    }
-    currIdx=anchorIdx+1;
-    anchorIdx=block[3]+1;
-    if (i_dangling+1<danglings.size()) anchorIdx=danglings[++i_dangling];
-  } while(currIdx<=block[3]);
-}
-
-void Alignment::simplify(int* ret) {
-  // the idea is to create blocks of maximal consistent alignment in between a pair of function words
-  // exceptional cases include: one to non-contiguous many (or vice versa) -> treat this as one alignment each
-  // record all function word alignments first, important because it may be unaligned
-  // return true if it's truly simple (no function word alignment involves); false, otherwise
-  if (DEBUG) cerr << "begin simplify" << endl;
-  reset(0,0); reset(_J-1,_I-1); // remove the phrase boundary alignments, NEED TO CHECK AGAIN !!!
-  if (SourceFWIdxs[0]+TargetFWIdxs[0]==0) { // return singleton
-    if (DEBUG) cerr << "no function words" << endl;
-    for (int idx=0; idx<12; idx++) ret[idx]=-1;
-    ret[12]=1; ret[13]=0; ret[14]=0; // 0-0
-    FillFWIdxsState(ret,0,0,0,0);  
-    return;
-  }
-  curr_al.insert(curr_al.begin(),curr_al.size());
-  curr_al.push_back(SourceFWIdxs[0]);
-  for (int i=1; i<=SourceFWIdxs[0]; i++) curr_al.push_back(SourceFWIdxs[3*i-2]);
-  curr_al.push_back(TargetFWIdxs[0]);
-  for (int i=1; i<=TargetFWIdxs[0]; i++) curr_al.push_back(TargetFWIdxs[3*i-2]);
-  vector<int> el;
-  if (simplify_hash.find(curr_al)==simplify_hash.end()) {
-    if (DEBUG) {
-      cerr << "SourceFWIdxs:" << SourceFWIdxs[0] << endl;
-      for (int i=1; i<=SourceFWIdxs[0]; i++)  
-        cerr << SourceFWIdxs[3*i-2] << "," <<  SourceFWIdxs[3*i-1] << "," << SourceFWIdxs[3*i] << endl;  
-      cerr << "TargetFWIdxs:" << TargetFWIdxs[0] << endl;
-      for (int i=1; i<=TargetFWIdxs[0]; i++) { 
-        cerr << TargetFWIdxs[3*i-2] << "," <<  TargetFWIdxs[3*i-1] << "," << TargetFWIdxs[3*i] << endl;  
-      }
-    }
-
-    vector< int* > blocks; // each element contains s1,s2,t1,t2
-    int currIdx = 1; // start from 1 to avoid considering phrase start
-    std::set<int> FWIdxs;
-    std::vector<int> DanglingTargetFWIdxs;
-    for (int i=1; i<= SourceFWIdxs[0]; i++) FWIdxs.insert(SourceFWIdxs[3*i-2]);
-    for (int i=1; i<= TargetFWIdxs[0]; i++) {
-      int source = sourceOf(TargetFWIdxs[3*i-2]);
-      if (source>=0) {
-        do {
-          FWIdxs.insert(source);
-          source = sourceOf(TargetFWIdxs[3*i-2],source+1);
-        } while(source >=0);
-      } else {
-        int *block = new int[4];
-        block[0]=-1; block[1]=-1; block[2]=TargetFWIdxs[3*i-2]; block[3]=TargetFWIdxs[3*i-2];
-        blocks.push_back(block);
-        if (DEBUG) cerr << "pushing[1] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        DanglingTargetFWIdxs.push_back(TargetFWIdxs[3*i-2]);  
-      }
-    }
-    if (DEBUG)
-      for (std::set<int>::const_iterator iter=FWIdxs.begin(); iter!=FWIdxs.end(); iter++) { 
-        cerr << "FWIdxs=" << *iter << endl;
-      }
-    std::set<int>::const_iterator currFWIdx  = FWIdxs.begin();
-    if (currFWIdx == FWIdxs.end()) {
-      int* block = new int[4];
-      block[0]=1; block[1]=_J-2; block[2]=1; block[3]=_I-2; // no need to consider phrase boundaries
-      simplifyBackward(&blocks,block,DanglingTargetFWIdxs);
-    } else {
-      int anchorIdx = *currFWIdx; // also used to denote _J+1
-      do {
-        // add alignments whose source from currIdx to currFWIdx-1
-        while (currIdx<anchorIdx) {
-          bool isMoved = false;
-          //cerr << "anchorIdx = " << anchorIdx << ", currIdx = " << currIdx << endl;
-          for (int idx=anchorIdx-1; idx>=currIdx; idx--) {
-            int* block = blockSource(currIdx,idx);
-            if (block[0]==currIdx&&block[1]==idx) {
-              if (block[2]!=MINIMUM_INIT) { // must be aligned
-                simplifyBackward(&blocks,block,DanglingTargetFWIdxs); 
-              } else {
-                delete block;
-              }
-              currIdx = idx+1; isMoved = true;
-              break;
-            } else {
-              delete block;
-            }
-          }
-          if (!isMoved) {
-            int target = targetOf(currIdx);
-            while (target>=0) {
-              int* block = new int[4];
-              block[0]=currIdx; block[1]=currIdx; block[2]=target; block[3]=target;
-              blocks.push_back(block);
-              if (DEBUG) cerr << "pushing[2] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-              target = targetOf(currIdx,target+1);
-            }
-            currIdx++;
-          }
-        }    
-        // add function word alignments (anchorIdx)
-        if (anchorIdx==getJ()) break;
-        int target = targetOf(anchorIdx);
-        do {
-          int* block = new int[4];
-          block[0]=anchorIdx; block[1]=anchorIdx; block[2]=target; block[3]=target;
-          blocks.push_back(block);
-          if (DEBUG) cerr << "pushing[3] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (target>=0) target = targetOf(anchorIdx,target+1);
-        } while (target>=0);
-        // advance indexes
-        currIdx   = anchorIdx+1;
-        anchorIdx = getJ()-1; // was minus 2
-        if (++currFWIdx!=FWIdxs.end()) anchorIdx = *currFWIdx;
-      } while (currIdx<=getJ()-2);
-    }  
-
-    
-    vector<int> source_block_mapper(getJ(),-1);
-    vector<int> target_block_mapper(getI(),-1);
-    for (int i = 0; i<blocks.size(); i++) {
-      if (DEBUG) cerr << "blocks[" << i << "]=" << blocks[i][0] << "," << blocks[i][1] << "," << blocks[i][2] << "," << blocks[i][3] << endl;
-      if (blocks[i][0]>=0) source_block_mapper[blocks[i][0]]=1;
-      if (blocks[i][2]>=0) target_block_mapper[blocks[i][2]]=1; 
-    }
-    int curr = 1;
-    int prev = -1;
-    for (int idx=0; idx<source_block_mapper.size(); idx++) {
-      if (source_block_mapper[idx]>0) {
-        source_block_mapper[idx]=curr++;
-        prev = curr;
-      } else {
-        source_block_mapper[idx]=prev;
-      }
-    }
-    curr = 1;
-    for (int idx=0; idx<target_block_mapper.size(); idx++) {
-      if (target_block_mapper[idx]>0) {
-        target_block_mapper[idx]=curr++;
-        prev = curr;
-      } else {
-        target_block_mapper[idx]=prev;
-      }
-    }
-    
-    //assert(blocks.size()<=50);
-    if (DEBUG) cerr << "resulting alignment:" << endl;
-    for (int i = 0; i<blocks.size(); i++) {
-      if (blocks[i][2]<0 || blocks[i][0]<0) continue;
-      int source = source_block_mapper[blocks[i][0]]-1;
-      int target = target_block_mapper[blocks[i][2]]-1;
-      el.push_back(link(source,target));
-      if (DEBUG) cerr << source << "-" << target << " ";
-    }
-    el.insert(el.begin(),el.size());
-    if (DEBUG) cerr << endl;
-    el.push_back(SourceFWIdxs[0]);
-    for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-      if (DEBUG) cerr << "SourceFWIdxs[" << (3*idx-2) << "] from " << SourceFWIdxs[3*idx-2] << endl;
-      el.push_back(source_block_mapper[SourceFWIdxs[3*idx-2]]-1);
-    }
-    el.push_back(TargetFWIdxs[0]);
-    for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-      if (DEBUG) cerr << "TargetFWIdxs[" << (3*idx-2) << "] from " << TargetFWIdxs[3*idx-2] << endl;
-      el.push_back(target_block_mapper[TargetFWIdxs[3*idx-2]]-1);
-    }
-    el.push_back(source_block_mapper[fas]-1); 
-    el.push_back(source_block_mapper[las]-1);
-    el.push_back(target_block_mapper[fat]-1);
-    el.push_back(target_block_mapper[lat]-1);
-    if (DEBUG) {
-      cerr << "insert key:el = ";
-      for (int ii=0; ii<el.size(); ii++) 
-        cerr << ii << "." << el[ii] << " ";
-      cerr << " || " << endl;
-    }
-    if (DEBUG) cerr << "trying to insertL " <<  endl;
-    if (DEBUG) {
-      cerr << "size=" << curr_al.size() << " ";
-      for (int ii=0; ii<curr_al.size(); ii++) cerr << "curr_al[" << ii << "]=" << curr_al[ii] << " ";
-      cerr << endl;
-    }
-    simplify_hash.insert(pair<vector<int>, vector<int> > (curr_al,el));
-    if (DEBUG) cerr << "inserted" << endl;
-  } else {
-    el = simplify_hash[curr_al];
-  }
-  if (DEBUG) {
-    cerr << "pull key:el = ";
-    for (int ii=0; ii<el.size(); ii++)
-      cerr << ii << "." << el[ii] << " ";
-    cerr << endl;
-  }
-  ret[12] = el[0];
-  for (int i=1; i<=el[0]; i++) ret[12+i] = el[i];
-  int istart = el[0]+1;
-  assert(el[istart]==SourceFWIdxs[0]);
-  for (int i=1; i<=el[istart]; i++) SourceFWIdxs[3*i-2]=el[istart+i];
-  istart += el[istart]+1;
-  assert(el[istart]==TargetFWIdxs[0]);
-  for (int i=1; i<=el[istart]; i++) TargetFWIdxs[3*i-2]=el[istart+i];
-  istart += el[istart]+1;
-  FillFWIdxsState(ret,el[istart],el[istart+1],el[istart+2],el[istart+3]);
-}
-
-void Alignment::simplify_nofw(int* ret) {
-  for (int i=0; i<12; i++) ret[i]=-1;  
-  ret[12]=1; ret[13]=0; 
-}
-
-void Alignment::sort(int* num) {
-  if (num[0]>1) quickSort(num,1,num[0]);
-}
-
-void Alignment::quickSort(int arr[], int left, int right) {
-  int i = left, j = right;
-  int tmp1,tmp2,tmp3;
-  int mid = (left + right) / 2;
-  int pivot = arr[3*mid-2];
- 
-  /* partition */
-  while (i <= j) {
-    while (arr[3*i-2] < pivot) i++;
-    while (arr[3*j-2] > pivot) j--;
-    if (i <= j) {
-      tmp1 = arr[3*i-2]; tmp2 = arr[3*i-1]; tmp3 = arr[3*i];
-      arr[3*i-2] = arr[3*j-2]; arr[3*i-1] = arr[3*j-1]; arr[3*i] = arr[3*j];
-      arr[3*j-2] = tmp1; arr[3*j-1] = tmp2; arr[3*j] = tmp3;
-      i++;
-      j--;
-    }
-  };
- 
-  /* recursion */
-  if (left < j) quickSort(arr, left, j);
-  if (i < right) quickSort(arr, i, right);
-}
-
-double Alignment::ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2) {
-  string source = TD::Convert(cond1);
-  string sourceidx;
-  if (table.mode == 1) {
-    sourceidx = source; 
-    int slashidx = sourceidx.find_last_of("/");
-    source = sourceidx.substr(0,slashidx);
-    string idx = sourceidx.substr(slashidx+1);
-    if (DEBUG) cerr << "   sourceidx = " << sourceidx << ", idx = " << idx << endl;
-    if (idx == "X") {
-      if (DEBUG) cerr << "        idx == X, returning 0" << endl;
-      return 0;
-    }
-  }
-  string target = TD::Convert(cond2);
-  if (DEBUG) cerr << "sourceidx='" << sourceidx << "', source='" << source << "', target='" << target << "'" << endl;
-  double count = table.ultimate[offset+ori-1];
-  double total = table.ultimate[offset+5];   
-  double alpha = 0.1;
-  double prob = count/total;
-  if (DEBUG) cerr << "level0 " << count << "/" << total << "=" << prob << endl;
-  
-  WordID key_id = (table.mode!=1) ? cond1 : TD::Convert(source); 
-  map<WordID,int*>::const_iterator it = table.model.find(key_id);
-  bool stop = (it==table.model.end());
-  if (!stop) {
-    stop=true;
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      stop = false;
-      if (DEBUG) cerr << "level1 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-  if (stop) return prob;
-
-  string key = source + " " + target;
-  it = table.model.find(TD::Convert(key));
-  stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      stop = false;
-      if (DEBUG) cerr << "level2 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-
-  if (stop || table.mode!=1) return prob;
-  
-  key = sourceidx + " " + target;
-  it = table.model.find(TD::Convert(key));
-  if (it!=table.model.end()) {
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level3 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-
-  return prob;
-}
- 
-void Alignment::ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus,
-  double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientation:" << TD::Convert(cond1) << "," << TD::Convert(cond2) << ", alpha1 = " << alpha1 << ", beta1 = " << beta1 << endl;
-  double ret = ScoreOrientation(table,offset,ori,cond1,cond2);
-  if (isBonus) {
-    if (table.mode == 0) *bonus += log(ret); else *bonus += ret;
-  } else {
-    if (table.mode == 0) *cost += log(ret); else *cost += ret;
-  }
-}
-
-double Alignment::ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,0,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-double Alignment::ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,12,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
- 
-double Alignment::ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,6,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-double Alignment::ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,18,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-void Alignment::ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationLeft(" << isBonus << ")" << endl;
-  ScoreOrientation(table,0,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationLeftBackward" << endl;
-  ScoreOrientation(table,12,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationRight(" << isBonus << ")" << endl;
-  ScoreOrientation(table,6,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2,
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationRightBackward" << endl;
-  ScoreOrientation(table,18,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::computeOrientationSourceBackwardPos(const CountTable& table, double *cost, double *bonus,
-                                                 double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  if (DEBUG) cerr << "computeOrientationSourceBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    if (!(SourceFWRuleAbsIdxs[idx]<=maxdepth1 || maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)) continue;
-    int* fwblock = blockSource(SourceFWRuleIdxs[3*idx-2],SourceFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[2]!=MINIMUM_INIT);
-    if (aligned) {
-      OrientationTarget(fwblock[2],fwblock[3],&oril,&orir);
-    } else {
-      OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if ((aligned && fwblock[2]<=fat)||
-        (!aligned && SourceFWRuleIdxs[3*idx-2]<=fas)) isBonus=true;
-    if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << SourceFWRuleAbsIdxs[idx];
-      ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    isBonus = false;
-    if ((aligned && lat<=fwblock[3])||
-        (!aligned && las<=SourceFWRuleIdxs[3*idx-2])) isBonus=true;
-    if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << SourceFWRuleAbsIdxs[idx];
-      ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    delete fwblock;
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    // antfas -> first aligned source word antecedent-wise
-    // antlas -> last aligned source word antecedent-wise
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    assert(antfat <= antlat);
-    assert(antfas <= antlas);
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      if (!(SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1 || maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)) continue;
-      int* fwblock = blockSource(SourceFWAntsIdxs[i_ant][3*idx-2],SourceFWAntsIdxs[i_ant][3*idx-2]);
-      //bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool aligned = (fwblock[2]!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if (DEBUG) {
-        cerr << " aligned = " << aligned << endl;
-        cerr << "  fwblock = " << fwblock[0] << "," << fwblock[1] << "," << fwblock[2] << "," << fwblock[3] << endl;
-        cerr << "   antfas=" << antfas << ", antlas=" << antlas << ", antfat=" << antfat << ", antlat=" << antlat << endl;
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "laligned" << endl;
-        if (antfat<fwblock[2]) {
-          if (DEBUG) cerr << antfat << "<" << fwblock[2] << endl;
-          Lcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!laligned" << endl;
-        if (antfas<fwblock[0] && fwblock[1] < antlas) Lcompute=false;
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "raligned" << endl;
-        if (fwblock[3]<antlat) {
-          if (DEBUG) cerr << fwblock[3] << "<" << antlat << endl;
-          Rcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!raligned" << endl;
-        if (fwblock[1]<antlas && fwblock[1] < antlas) Rcompute=false;
-      }
-      if (!Lcompute && !Rcompute) continue;
-      if (!aligned) {
-        OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute,Rcompute);
-      } else {
-        OrientationTarget(fwblock[2],fwblock[3],&oril,&orir,Lcompute,Rcompute);
-      }
-      if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-      bool isBonus = false;
-      if (Lcompute) {
-        if ((aligned && fwblock[3]<=fat) ||
-            (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas)) isBonus = true;
-        if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << SourceFWAntsAbsIdxs[i_ant][idx];
-          ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << (-1*(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1));
-          ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && lat<=fwblock[2]) ||
-            (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]))isBonus = true;
-        if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << SourceFWAntsAbsIdxs[i_ant][idx];
-          ScoreOrientationRightBackward(table,orir,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << (-1*(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1));
-          ScoreOrientationRightBackward(table,orir,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      delete fwblock;
-    }
-  }
-}
-
-
-void Alignment::computeOrientationSourceBackward(const CountTable& table, double *cost, double *bonus, 
-                                                 double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationSourceBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    int* fwblock = blockSource(SourceFWRuleIdxs[3*idx-2],SourceFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[2]!=MINIMUM_INIT);
-    if (aligned) {
-      OrientationTarget(fwblock[2],fwblock[3],&oril,&orir);
-    } else {
-      OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if ((aligned && fwblock[2]<=fat)||
-        (!aligned && SourceFWRuleIdxs[3*idx-2]<=fas)) isBonus=true;
-    ScoreOrientationLeftBackward(table,oril,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    isBonus = false;
-    if ((aligned && lat<=fwblock[3])||
-        (!aligned && las<=SourceFWRuleIdxs[3*idx-2])) isBonus=true;
-    ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    delete fwblock;
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    // antfas -> first aligned source word antecedent-wise
-    // antlas -> last aligned source word antecedent-wise
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    assert(antfat <= antlat);
-    assert(antfas <= antlas);
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      int* fwblock = blockSource(SourceFWAntsIdxs[i_ant][3*idx-2],SourceFWAntsIdxs[i_ant][3*idx-2]);
-      //bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool aligned = (fwblock[2]!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if (DEBUG) {
-        cerr << " aligned = " << aligned << endl;
-        cerr << "  fwblock = " << fwblock[0] << "," << fwblock[1] << "," << fwblock[2] << "," << fwblock[3] << endl;
-        cerr << "   antfas=" << antfas << ", antlas=" << antlas << ", antfat=" << antfat << ", antlat=" << antlat << endl; 
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "laligned" << endl;
-        if (antfat<fwblock[2]) { 
-          if (DEBUG) cerr << antfat << "<" << fwblock[2] << endl;
-          Lcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!laligned" << endl;
-        if (antfas<fwblock[0] && fwblock[1] < antlas) Lcompute=false;
-      }
-      if (aligned) { 
-        if (DEBUG) cerr << "raligned" << endl;
-        if (fwblock[3]<antlat) { 
-          if (DEBUG) cerr << fwblock[3] << "<" << antlat << endl;
-          Rcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!raligned" << endl;
-        if (fwblock[1]<antlas && fwblock[1] < antlas) Rcompute=false;
-      }
-      if (!Lcompute && !Rcompute) continue;
-      if (!aligned) {
-        OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute,Rcompute);
-      } else {
-        OrientationTarget(fwblock[2],fwblock[3],&oril,&orir,Lcompute,Rcompute);
-      }
-      if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-      bool isBonus = false;
-      if (Lcompute) {
-        if ((aligned && fwblock[3]<=fat) ||
-            (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas)) isBonus = true;
-        ScoreOrientationLeftBackward(table,oril,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && lat<=fwblock[2]) ||
-            (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]))isBonus = true;
-        ScoreOrientationRightBackward(table,orir,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      delete fwblock;
-    }
-  }
-}
-
-void Alignment::computeOrientationSourcePos(const CountTable& table, double *cost, double *bonus,
-                double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  // This implementation is actually really bad, not reusing codes at all
-  if (DEBUG) cerr << "computeOrientationSourcePos(maxfwidx=" << maxfwidx << ",maxdepth=" << maxdepth1 << "," << maxdepth2 << ")" << endl;
-  if (maxdepth1+maxdepth2==0) return;
-  int oril, orir;
-  ostringstream oss;
-  WordID sourceID;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    //if (!((SourceFWRuleAbsIdxs[idx]<=maxdepth1) || (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2))) continue; 
-    string source = TD::Convert(SourceFWRuleIdxs[3*idx-1]);
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (maxdepth1>0) {
-      oss << source << "/";
-      if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) 
-        oss << SourceFWRuleAbsIdxs[idx];
-      else 
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationLeft(table,oril,sourceID,SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxdepth2>0) {
-      oss << source << "/";
-      if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)
-        oss << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      else 
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationLeft(table,oril,sourceID,SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    } 
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (maxdepth1>0) {
-      oss << source << "/";
-      if (SourceFWRuleAbsIdxs[idx]<=maxdepth1)
-        oss << SourceFWRuleAbsIdxs[idx];
-      else
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationRight(table,orir,sourceID,SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxdepth2>0) {
-      oss << source << "/";
-      if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)
-        oss << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      else
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationRight(table,orir,sourceID,SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      //if (!((SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)||(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2))) continue;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      if (DEBUG) cerr << " SourceFWAntsAbsIdxs[i_ant][3*idx-1]=" << SourceFWAntsAbsIdxs[i_ant][3*idx-1] << endl;
-      string source = TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]); 
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Lcompute=false;
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-        //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        if (maxdepth1>0) {
-          oss << source << "/";
-          if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)
-            oss << SourceFWAntsAbsIdxs[i_ant][idx];
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationLeft(table,oril,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxdepth2>0) {
-          oss << source << "/";
-          if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)
-            oss << ((maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1)*-1);
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationLeft(table,oril,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        if (maxdepth1>0) {
-          oss << source << "/";
-          if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)
-            oss << SourceFWAntsAbsIdxs[i_ant][idx];
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationRight(table,orir,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }	
-       if (maxdepth2>0) {
-          oss << source << "/";
-          if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)
-            oss << ((maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1)*-1);
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationRight(table,orir,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }	
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationSource(const CountTable& table, double *cost, double *bonus, 
-                                         double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-// a bit complex due to imperfect state (TO DO!!!)
-// 1. there are cases where function word alignments come from antecedents, which orientation 
-// (either its left or its right) has been computed earlier.   
-// 2. some orientation will go as bonus
-  if (DEBUG) cerr << "computeOrientationSource" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl; 
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion 
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    ScoreOrientationLeft(table,oril,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris); 
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    ScoreOrientationRight(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas)) 
-          Lcompute=false; 
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas)) 
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-        //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris); 
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        ScoreOrientationRight(table,orir,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationSourceGen(const CountTable& table, double *cost, double *bonus,
-                                         double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, const map<WordID,WordID>& tags) {
-  if (DEBUG) cerr << "computeOrientationSourceGen" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion 
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    ScoreOrientationLeft(table,oril,generalize(SourceFWRuleIdxs[3*idx-1],tags),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    ScoreOrientationRight(table,orir,generalize(SourceFWRuleIdxs[3*idx-1],tags),SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Lcompute=false;
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-       //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,generalize(SourceFWAntsIdxs[i_ant][3*idx-1],tags),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        ScoreOrientationRight(table,orir,generalize(SourceFWAntsIdxs[i_ant][3*idx-1],tags),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-    }
-  }
-}
-void Alignment::computeOrientationTarget(const CountTable& table, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationTarget" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering TargetFWRuleIdxs[" << idx << "]: " << TargetFWRuleIdxs[3*idx-2] << endl;
-    OrientationTarget(TargetFWRuleIdxs[3*idx-2],&oril,&orir);
-    // the second and the third parameters of ScoreOrientationLeft must be e and f (not f and then e) 
-    bool isBonus = false;
-    if (TargetFWRuleIdxs[3*idx-2]<=fat) isBonus = true;
-    if (!isBonus)
-      if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    ScoreOrientationLeft(table,oril,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit); 
-    isBonus = false;
-    if (lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    if (!isBonus)
-      if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && TargetFWRuleIdxs[3*idx-2]<=fat) isBonus=true;
-    ScoreOrientationRight(table,orir,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << "considering TargetFWAntsIdxs[" << i_ant << "][" << idx << "]: " << TargetFWAntsIdxs[i_ant][3*idx-2] << endl; 
-      int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-      int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-      int aligned = (minSSpan( TargetFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if ((aligned && antfat<TargetFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfat < TargetFWAntsIdxs[i_ant][3*idx-2] && TargetFWAntsIdxs[i_ant][3*idx-2] < antlat)) 
-          Lcompute=false;
-      if ((aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<antlat) ||
-          (!aligned && antfat < TargetFWAntsIdxs[i_ant][3*idx-2] && TargetFWAntsIdxs[i_ant][3*idx-2] < antlat)) 
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      bool isBonus = false;
-      OrientationTarget(TargetFWAntsIdxs[i_ant][3*idx-2],&oril,&orir, Lcompute, Rcompute);
-      if (Lcompute) {
-        if (TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        //if (!isBonus) 
-        //  if (!aligned && lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit); 
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        if (!isBonus)
-          //if (!aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        ScoreOrientationRight(table,orir,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationTargetBackward(const CountTable& table, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationTargetBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering TargetFWRuleIdxs[" << idx << "]: " << TargetFWRuleIdxs[3*idx-2] << endl;
-    int* fwblock = blockSource(TargetFWRuleIdxs[3*idx-2],TargetFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[0] == MINIMUM_INIT);
-    if (aligned) {
-      OrientationSource(fwblock[0],fwblock[1],&oril,&orir);
-    } else {
-      OrientationTarget(TargetFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    delete fwblock;
-    // the second and the third parameters of ScoreOrientationLeft must be e and f (not f and then e)
-    bool isBonus = false;
-    if (TargetFWRuleIdxs[3*idx-2]<=fat) isBonus = true;
-    //if (!isBonus)  // unnecessary
-      //if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    ScoreOrientationLeftBackward(table,oril,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-    isBonus = false;
-    if (lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    //if (!isBonus) // unnecessary
-      //if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && TargetFWRuleIdxs[3*idx-2]<=fat) isBonus=true;
-    ScoreOrientationRightBackward(table,orir,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << "considering TargetFWAntsIdxs[" << i_ant << "][" << idx << "]: " << TargetFWAntsIdxs[i_ant][3*idx-2] << endl;
-      int* fwblock = blockTarget(TargetFWAntsIdxs[i_ant][3*idx-2],TargetFWAntsIdxs[i_ant][3*idx-2]);
-      bool aligned = (fwblock[0]!=MINIMUM_INIT);
-      //bool aligned = (minSSpan( TargetFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if ((aligned && antfas<fwblock[0]) ||
-          (!aligned && antfat < fwblock[2]))
-          Lcompute=false;
-      if ((aligned && fwblock[0]<antlas) ||
-          (!aligned && fwblock[3] < antlat))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      bool isBonus = false;
-      if (aligned) {
-        OrientationSource(fwblock[0],fwblock[1],&oril,&orir,Lcompute,Rcompute);
-      } else { 
-        OrientationTarget(TargetFWAntsIdxs[i_ant][3*idx-2],&oril,&orir, Lcompute, Rcompute);
-      }
-      if (Lcompute) {
-        if ((aligned && fwblock[1]<=fas) ||
-            (!aligned && fwblock[3]<=fat))
-            isBonus=true;
-        //if (!isBonus)
-        //  if (!aligned && lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeftBackward(table,oril,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && las<=fwblock[0]) ||
-            (!aligned && lat<=fwblock[2]))
-            isBonus=true;
-        if (!isBonus)
-          //if (!aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        ScoreOrientationRightBackward(table,orir,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-      delete fwblock;
-    }
-  }
-}
-
-bool Alignment::MemberOf(int* FWIdxs, int pos1, int pos2) {
-  for (int idx=2; idx<=FWIdxs[0]; idx++) { 
-    if (FWIdxs[3*(idx-1)-2]==pos1 && FWIdxs[3*idx-2]==pos2) return true;
-  }
-  return false;
-}
-
-void Alignment::computeDominanceSource(const CountTable& table, WordID lfw, WordID rfw, 
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  // no bonus yet
-  if (DEBUG) cerr << "computeDominanceSource" << endl;
-  if (DEBUG) cerr << " initial cost=" << *cost << ", initial bonus=" << *bonus << endl;
-  for (int idx=2; idx<=SourceFWIdxs[0]; idx++) {
-    if (DEBUG) { 
-      cerr << "PrevSourceFWIdxs :" << SourceFWIdxs[3*(idx-1)-2] << "," << SourceFWIdxs[3*(idx-1)-1] 
-           << "," << SourceFWIdxs[3*(idx-1)] << endl;
-      cerr << "CurrSourceFWIdxs :" << SourceFWIdxs[3*(idx)-2] << "," << SourceFWIdxs[3*(idx)-1] 
-           << "," << SourceFWIdxs[3*(idx)] << endl;
-    }
-    bool compute = true;
-    for (int i_ant=0; i_ant<_Arity && compute; i_ant++) {
-      if (MemberOf(SourceFWAntsIdxs[i_ant],SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*(idx)-2])) {
-        //cerr << "Skipping, they have been calculated in the  " << (i_ant+1) << "-th branch" << endl;
-        compute=false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceSource(SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*idx-2]);
-      if (DEBUG) cerr << "dom = " << dom << endl;
-      ScoreDominance(table,dom,SourceFWIdxs[3*(idx-1)-1],SourceFWIdxs[3*idx-1],SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-      if (DEBUG) cerr << "cost now is " << *cost << endl;
-    }
-  }
-  if (SourceFWIdxs[0]>0) {
-    if (lfw>=0) {
-      int dom = DominanceSource(0,SourceFWIdxs[1]);
-      if (DEBUG) cerr << " --> lfw = " << lfw << "-" << TD::Convert(lfw) << endl;
-      if (DEBUG) cerr << " --> rfw = " << rfw << "-" << TD::Convert(rfw) << endl;
-      ScoreDominance(table,dom,lfw,SourceFWIdxs[2],lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-    }
-    if (rfw>=0) {
-      int dom = DominanceSource(SourceFWIdxs[3*SourceFWIdxs[0]-2],_J-1);
-      ScoreDominance(table,dom,SourceFWIdxs[3*SourceFWIdxs[0]-1],rfw,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-    }
-  }
-}
-
-void Alignment::computeDominanceSourcePos(const CountTable& table, WordID lfw, WordID rfw,
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  if (DEBUG) cerr << "computeDominanceSourcePos" << endl;
-  if (DEBUG) cerr << " initial cost=" << *cost << ", initial bonus=" << *bonus << endl;
-  ostringstream oss;
-  for (int idx=2; idx<=SourceFWIdxs[0]; idx++) {
-    if (DEBUG) {
-      cerr << "PrevSourceFWIdxs :" << SourceFWIdxs[3*(idx-1)-2] << "," << SourceFWIdxs[3*(idx-1)-1]
-           << "," << SourceFWIdxs[3*(idx-1)] << endl;
-      cerr << "CurrSourceFWIdxs :" << SourceFWIdxs[3*(idx)-2] << "," << SourceFWIdxs[3*(idx)-1]
-           << "," << SourceFWIdxs[3*(idx)] << endl;
-    }
-    //if (!((SourceFWAbsIdxs[3*(idx-1)-2]<=maxdepth1 && SourceFWAbsIdxs[3*idx-2]<=maxdepth1) ||
-    //      (maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1<=maxdepth2 && maxfwidx-SourceFWAbsIdxs[3*idx-2]+1<=maxdepth2))) continue;
-    bool compute = true;
-    for (int i_ant=0; i_ant<_Arity && compute; i_ant++) {
-      if (MemberOf(SourceFWAntsIdxs[i_ant],SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*(idx)-2])) {
-        //cerr << "Skipping, they have been calculated in the  " << (i_ant+1) << "-th branch" << endl;
-        compute=false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceSource(SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*idx-2]);
-      if (DEBUG) cerr << "dom = " << dom << endl;
-      if (maxdepth1+maxdepth2>0) {
-        string source1 = TD::Convert(SourceFWIdxs[3*(idx-1)-1]);
-        string source2 = TD::Convert(SourceFWIdxs[3*(idx)-1]);
-        if (maxdepth1>0) {
-          oss << source1 << "/";
-          if (SourceFWAbsIdxs[3*(idx-1)-2]<=maxdepth1) 
-            oss << SourceFWAbsIdxs[3*(idx-1)-2];
-          else 
-            oss << "X";
-          WordID source1id = TD::Convert(oss.str());
-          oss.str("");
-          oss << source2 << "/";
-          if (SourceFWAbsIdxs[3*idx-2]<=maxdepth1)
-            oss << SourceFWAbsIdxs[3*idx-2];
-          else
-            oss << "X";
-          WordID source2id = TD::Convert(oss.str());
-          oss.str("");    
-          ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-        }  
-        if (maxdepth2>0) {
-          oss << source1 << "/";
-          if (maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1<=maxdepth2) 
-            oss << ((maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1)*-1);
-          else
-            oss << "X";
-          WordID source1id = TD::Convert(oss.str());
-          oss.str("");
-          oss << source2 << "/";
-          if (maxfwidx-SourceFWAbsIdxs[3*idx-2]+1<=maxdepth2) 
-            oss << ((maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1)*-1);
-          else
-            oss << "X";
-          WordID source2id = TD::Convert(oss.str());
-          oss.str("");
-          ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-        }
-      }
-    }
-  }
-  if (SourceFWIdxs[0]>0) {
-    if (lfw>=0) {
-      int dom = DominanceSource(0,SourceFWIdxs[1]);
-      string source1 = TD::Convert(lfw);
-      string source2 = TD::Convert(SourceFWIdxs[2]);
-      if (maxdepth1>0) {
-        oss << source1 << "/";
-        if (SourceFWAbsIdxs[1]-1<=maxdepth1) 
-          oss << (SourceFWAbsIdxs[1]-1);
-        else
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (SourceFWAbsIdxs[1]<=maxdepth1)
-          oss << SourceFWAbsIdxs[1];
-        else
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-      if (maxdepth2>0) { 
-        oss << source1 << "/";
-        if (maxfwidx-(SourceFWAbsIdxs[1]-1)+1<=maxdepth2) 
-          oss << ((maxfwidx-(SourceFWAbsIdxs[1]-1)+1)*-1);
-        else 
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (maxfwidx-SourceFWAbsIdxs[1]+1<=maxdepth2) 
-          oss << ((maxfwidx-SourceFWAbsIdxs[1]+1)*-1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-    }
-    if (rfw>=0) {
-      int dom = DominanceSource(SourceFWIdxs[3*SourceFWIdxs[0]-2],_J-1);
-      string source1 = TD::Convert(SourceFWIdxs[3*SourceFWIdxs[0]-1]);
-      string source2 = TD::Convert(rfw);
-      if (maxdepth1>0) {
-        oss << source1 << "/";
-        if (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]<=maxdepth1)
-          oss << SourceFWAbsIdxs[3*SourceFWIdxs[0]-2];
-        else
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1<=maxdepth1)
-          oss << (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-      if (maxdepth2>0) {
-        oss << source1 << "/";
-        if (maxfwidx-SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1<=maxdepth2) 
-          oss << ((maxfwidx-SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)*-1);
-        else 
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (maxfwidx-(SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)+1<=maxdepth2) 
-          oss << ((maxfwidx-(SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)+1)*-1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-    }
-  }
-}
-
-
-void Alignment::computeDominanceTarget(const CountTable& table, WordID lfw, WordID rfw,
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-   if (DEBUG) cerr << "computeDominanceTarget" << endl;
-  for (int idx=2; idx<=TargetFWIdxs[0]; idx++) {
-    if (DEBUG) cerr << "PrevTargetFWIdxs :" << TargetFWIdxs[3*(idx-1)-2] << "," << TargetFWIdxs[3*(idx-1)-1] << "," <<TargetFWIdxs[3*(idx-1)] << endl;
-    if (DEBUG) cerr << "CurrTargetFWIdxs :" << TargetFWIdxs[3*(idx)-2] << "," << TargetFWIdxs[3*(idx)-1] << "," <<TargetFWIdxs[3*(idx)] << endl;
-    bool compute = true;
-    for (int i_ant=0; i_ant <_Arity && compute; i_ant++) {
-      if (MemberOf(TargetFWAntsIdxs[i_ant],TargetFWIdxs[3*(idx-1)-2],TargetFWIdxs[3*idx-2])) {
-        if (DEBUG) cerr << "Skipping, they have been calculated in the " << (i_ant+1) << "-th branch" << endl;
-        compute = false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceTarget(TargetFWIdxs[3*(idx-1)-2],TargetFWIdxs[3*idx-2]);
-      //cerr << (3*(idx-1)) << "," << (3*idx) << "," << (3*(idx-1)-1) << "," << (3*idx-1) << endl;
-      if (DEBUG) cerr << "dom target = " << dom << endl;
-      ScoreDominance(table,dom,TargetFWIdxs[3*(idx-1)],TargetFWIdxs[3*idx],TargetFWIdxs[3*(idx-1)-1],TargetFWIdxs[3*idx-1],
-              cost,bo1,bo2,false,alpha_domt,beta_domt);
-    }
-  }
-  if (TargetFWIdxs[0]>0) {
-    if (DEBUG) cerr << "backoff dominance " << endl;
-    if (lfw>=0) {
-      int dom = DominanceTarget(0,TargetFWIdxs[1]);
-      if (DEBUG) cerr << "dom target (with left) = " << dom << endl;
-      ScoreDominance(table,dom,lfw,lfw,TargetFWIdxs[2],TargetFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_domt,beta_domt);
-    }
-    if (rfw>=0) {
-      int dom = DominanceTarget(TargetFWIdxs[3*TargetFWIdxs[0]-2],_I-1);
-      if (DEBUG) cerr << "dom target (with right) = " << dom << endl;
-      ScoreDominance(table,dom,TargetFWIdxs[3*TargetFWIdxs[0]-1],TargetFWIdxs[3*TargetFWIdxs[0]],
-                     rfw,rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_domt,beta_domt);
-    }
-  }
-
-  //cerr << "END of computeDominanceTarget" << endl;
-}
-
-double Alignment::ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2) {
-  if (DEBUG) {
-     cerr << "ScoreDominance(source1=" << TD::Convert(source1) << ",source2=" << TD::Convert(source2)
-          << ",target1=" << TD::Convert(target1) << ",target2=" << TD::Convert(target2) << ", dom=" << dom << endl;
-  }
-  string _source1 = TD::Convert(source1);
-  string _source2 = TD::Convert(source2);
-  string _source1idx; string _source2idx;
-  if (table.mode==1) {
-    _source1idx = _source1; _source2idx = _source2;
-    _source1 = _source1idx.substr(0,_source1idx.find_last_of("/"));
-    _source2 = _source2idx.substr(0,_source2idx.find_last_of("/"));
-  }
-  string _target1 = TD::Convert(target1);
-  string _target2 = TD::Convert(target2);
-
-  double count = table.ultimate[dom];
-  double total = table.ultimate[4];
-  double prob = count/total;
-  if (DEBUG) cerr << "level0 " << count << "/" << total << "=" << prob << endl;
-  double alpha = 0.1;
-  
-  string key = _source1 + " " + _source2;
-  WordID key_id = TD::Convert(key);
-  map<WordID,int*>::const_iterator it = table.model.find(key_id); 
-  bool stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level1 " << count << "/" << total << "=" << prob << endl;
-      stop = false;
-    }
-  } 
-  if (stop) return prob;
- 
-  key = _source1 + " " + _source2 + " " + _target1 + " " + _target2; 
-  key_id = TD::Convert(key);  
-  it = table.model.find(key_id);
-  stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level2 " << count << "/" << total << "=" << prob << endl;
-      stop = false;
-    }
-  } 
- 
-  if (table.mode!=1 || stop) return prob;
-  key = _source1 + " " + _source2 + " " + _target1 + " " + _target2;
-  key_id = TD::Convert(key);
-  it = table.model.find(key_id);
-  if (it!=table.model.end()) {
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      if (DEBUG) cerr << "level3 " << count << "/" << total << "=" << prob << endl;
-      prob = count/total;
-    }
-  }
-
-  return prob;
-}
-
-void Alignment::ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2, double *cost, double *bo1, double *bo2, bool isBonus, double alpha2, double beta2) {
-  if (DEBUG) 
-    cerr << "ScoreDominance(source1=" << TD::Convert(source1) << ",source2=" << TD::Convert(source2) 
-         << ",target1=" << TD::Convert(target1) << ",target2=" << TD::Convert(target2) << ",isBonus=" << isBonus << ", alpha2 = " << alpha2 << ", beta2 = " << beta2 << endl;
-  if (DEBUG) cerr << "    BEFORE=" << *cost << endl;
-  *cost += ScoreDominance(table,dom,source1,source2,target1,target2);
-  if (DEBUG) cerr << "    AFTER=" << *cost << endl;
-}
-
-WordID Alignment::F2EProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter) {
-  if (DEBUG) {
-    cerr << "F2EProjectionFromExternal=" << idx << endl;
-    for (int i=0; i< als.size(); i++) cerr << "als[" << i << "]=" << als[i] << " ";
-    cerr << endl;
-  }
-  vector<int> alignedTo;
-  for (int i=0; i<als.size(); i++) {
-    if (DEBUG) cerr << als[i] << " ";
-    if (als[i].s_==idx) 
-      alignedTo.push_back(als[i].t_);
-  }
-  if (DEBUG) {
-    cerr << endl;
-    cerr << "alignedTo = ";
-    for (int i=0; i<alignedTo.size(); i++) cerr << alignedTo[i] << " ";
-    cerr << endl;
-  }
-  if (alignedTo.size()==0) {
-    if (DEBUG) cerr << "returns [NULL] : " << TD::Convert("NULL") << endl;
-    return TD::Convert("NULL");
-  } else if (alignedTo.size()==1) {
-    if (DEBUG) cerr << "returns [" << TD::Convert(_e[alignedTo[0]]) << "] : " << _e[alignedTo[0]] << endl;
-    return _e[alignedTo[0]]; // if not aligned to many, why bother continuing
-  } else {
-    ostringstream projection;
-    for (int i=0; i<alignedTo.size(); i++) {
-      if (i>0) projection << delimiter;
-      projection << TD::Convert(_e[alignedTo[i]]);
-    }
-    if (DEBUG) {
-      cerr << "projection = " << projection.str() << endl;
-      cerr << "returns = " << TD::Convert(projection.str()) << endl;
-    }
-    return TD::Convert(projection.str());
-  }
-}
-
-WordID Alignment::E2FProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter) {
-  vector<int> alignedTo;
-  for (int i=0; i<als.size(); i++)
-    if (als[i].t_==idx) alignedTo.push_back(als[i].s_);
-  if (alignedTo.size()==0) {
-    return TD::Convert("NULL");
-  } else if (alignedTo.size()==1) {
-    return _f[alignedTo[0]]; // if not aligned to many, why bother continuing
-  } else {
-    ostringstream projection;
-    for (int i=0; i<alignedTo.size(); i++) {
-      if (i>0) projection << delimiter;
-      projection << TD::Convert(_f[alignedTo[i]]);
-    }
-    return TD::Convert(projection.str());
-  }
-}
-
-
-WordID Alignment::F2EProjection(int idx, const string& delimiter) {
-  if (DEBUG) cerr << "F2EProjection(" << idx << ")" << endl;
-  int e = targetOf(idx);
-  if (e<0) {
-    if (DEBUG) cerr << "projection = NULL" << endl;
-    return TD::Convert("NULL");
-  } else {
-    if (targetOf(idx,e+1)<0) {
-      if (DEBUG) cerr << "e-1=" << (e-1) << ", size=" << _e.size() << endl;
-      return getE(e-1); // if not aligned to many, why bother continuing
-    }
-    ostringstream projection;
-    bool firstTime = true;
-    do {
-      if (!firstTime) projection << delimiter; 
-      projection << TD::Convert(_e[e-1]); // transform space
-      firstTime = false;
-      e = targetOf(idx,e+1);
-      //if (DEBUG) cerr << "projection = " << projection.str() << endl;
-    } while(e>=0);
-    return TD::Convert(projection.str());
-  }
-}
-
-WordID Alignment::E2FProjection(int idx, const string& delimiter) {
-  //cerr << "E2FProjection(" << idx << ")" << endl;
-  //cerr << "i" << endl;
-  int f = sourceOf(idx);
-  //cerr << "j, f=" << f << endl;
-  if (f<0) {
-    //cerr << "projection = NULL" << endl;
-    return TD::Convert("NULL");
-  } else {
-    if (sourceOf(idx,f+1)<0) return getF(f-1);
-    bool firstTime = true;
-    ostringstream projection(ostringstream::out);
-    do {
-      if (!firstTime) projection << delimiter;
-      projection << TD::Convert(_f[f-1]); //transform space
-      firstTime = false;
-      f = sourceOf(idx,f+1);
-      //cerr << "projection = " << projection.str() << endl;
-    } while(f>=0);
-    return TD::Convert(projection.str());
-  }
-}
-void Alignment::computeBorderDominanceSource(const CountTable& table, double *cost, double *bonus, double *state_mono, 
-        double *state_nonmono, TRule &rule, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw) {
-  // HACK: GOAL is assumed to always be "S"
-  if (DEBUG) cerr << "computeBorderDominanceSource" << endl;
-  std::vector<WordID> f = rule.f();
-  std::vector<WordID> e = rule.e();
-  int nt_index[f.size()];
-  int nt_count=0;
-  for (int i=0; i<f.size(); i++) nt_index[i] = (f[i]<0)? ++nt_count : 0;
-  if (DEBUG) {
-    cerr << "f = ";
-    for (int i=0; i<f.size(); i++) cerr << i << "." << "[" << f[i] << "] ";
-    cerr << endl;
-    cerr << "e = ";
-    for (int i=0; i<e.size(); i++) cerr << i << "." << "[" << e[i] << "] ";
-    cerr << endl;
-  }
-  bool flag[f.size()]; 
-  for (int idx=0; idx<f.size(); idx++) flag[idx]=false;
-  //collect alignments
-  vector<int> als;
-  for (std::vector<AlignmentPoint>::const_iterator i = rule.als().begin(); i != rule.als().end(); ++i) {
-    int s = i->s_; int t = i->t_;
-    als.push_back(link(t,s));
-  }
-  if (DEBUG) cerr << "rule.Arity=" << rule.Arity() << endl;
-  if (rule.Arity()>0) {
-    int ntc=0;
-    for (int s=0; s<f.size(); s++) {
-      if (f[s]<=0) {
-        if (DEBUG) cerr << "f[s]=" << f[s] << "+" << s << " - ";
-        for (int t=0; t<e.size(); t++) {
-          if (e[t]==ntc) {
-            if (DEBUG) cerr << "e[t]=" << e[t] << "+" << t <<endl;
-            als.push_back(link(t,s));
-            ntc--;  break;
-          }
-        }
-      } 
-    }
-  }
-  if (DEBUG) {
-    cerr << "unsorted alignments (nonterminals and terminals)" << endl;
-    for (int i=0; i<als.size(); i++)
-      cerr << source(als[i]) << "-" << target(als[i]) << " ";
-    cerr << endl;
-  }
-  // sort alignments according to target
-  std::sort(als.begin(),als.end());
-  if (DEBUG) {
-    cerr << "sorted alignments (nonterminals and terminals)" << endl;
-    for (int i=0; i<als.size(); i++) 
-      cerr << source(als[i]) << "-" << target(als[i]) << " ";
-    cerr << endl;
-  }
-  // 0 -> neither, 1 -> leftFirst, 2 -> rightFirst, 3 -> dontCare
-  // ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2)
-  int prevs = 0;
-  for (int i=0; i<als.size(); i++) {
-    int currs = target(als[i]); //int currt = source(als[i]);
-    if (DEBUG) cerr << "prevs=" << prevs << ", currs=" << currs << endl << endl;
-    if (currs<prevs) {
-      if (DEBUG) cerr << "currs<prevs" << endl;
-      for (int s = currs; s <= prevs; s++) {
-        if (sfw.find(f[s])!=sfw.end()) {
-          WordID target = F2EProjectionFromExternal(s,rule.a_,"_SEP_");
-          if (DEBUG) cerr<<"  f[s]="<<TD::Convert(f[s])<<" is a function word, target="<<TD::Convert(target)<<endl;
-          //*cost += ScoreDominance(table,1,kSOS,f[s],kSOS,target) + ScoreDominance(table,2,f[s],kEOS,target,kEOS);
-          *cost += ScoreDominance(table,1,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,2,f[s],kEOS,kUNK,kUNK);
-          if (DEBUG) cerr << "  resulting cost="<< *cost << endl;
-        } else if (f[s]<=0) {
-          if (DEBUG) cerr << "  f[s]= is a nonterminal" << endl;
-          const int* ants = reinterpret_cast<const int *>(ant_contexts[nt_index[s]-1]);
-          *cost += Dwarf::IntegerToDouble(ants[51]); // 50->mono, 51->non-mono 
-          if (DEBUG) cerr << "  adding "<< Dwarf::IntegerToDouble(ants[51]) << " into cost, resulting = " << *cost << endl;
-        } 
-        flag[s] = true;
-      }
-    }
-    prevs = currs;
-  } 
-  if (DEBUG) cerr << "bonus and state matter" << endl;
-  for (int s=0; s<rule.f().size(); s++) {
-    if (!flag[s]) {
-      if (sfw.find(f[s])!=sfw.end()) {
-        WordID target = F2EProjectionFromExternal(s,rule.a_,"_SEP_");
-        if (DEBUG) cerr<<"  f[s]="<<TD::Convert(f[s])<<" is a function word, target="<<TD::Convert(target)<<endl;
-        //double indbonus = ScoreDominance(table,3,kSOS,f[s],kSOS,target) + ScoreDominance(table,3,f[s],kEOS,target,kEOS);
-        double indbonus = ScoreDominance(table,3,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,3,f[s],kEOS,kUNK,kUNK);
-        *bonus += indbonus;
-        *state_mono += indbonus;
-        //*state_nonmono += ScoreDominance(table,1,kSOS,f[s],kSOS,target) + ScoreDominance(table,2,f[s],kEOS,target,kEOS);
-        *state_nonmono += ScoreDominance(table,1,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,2,f[s],kEOS,kUNK,kUNK);
-        if (DEBUG) cerr<<"  new bonus="<<*bonus<<", new state="<<*state_mono<<","<<*state_nonmono<<endl;
-      } else if (f[s]<=0) {
-        if (DEBUG) cerr << "  f[s]="<< f[s] <<" is a nonterminal" << endl;
-        const int* ants = reinterpret_cast<const int *>(ant_contexts[nt_index[s]-1]);
-        double indbonus = Dwarf::IntegerToDouble(ants[50]);
-        *bonus += indbonus;
-        *state_mono += indbonus;
-        *state_nonmono += Dwarf::IntegerToDouble(ants[51]);
-        if (DEBUG) cerr << "  propagating state=" << *state_mono <<","<< *state_nonmono<< endl;
-      }
-    }
-  }
-  if (DEBUG) cerr << "LHS:" << rule.GetLHS() << ":" << TD::Convert(rule.GetLHS()*-1) <<endl;
-  if (rule.GetLHS()*-1==TD::Convert("S")) {
-    *state_mono = 0;
-    *state_nonmono = 0;
-    for (int i=0; i<rule.Arity(); i++) { 
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i]);
-      *cost += Dwarf::IntegerToDouble(ants[50]);
-    }
-    *bonus = 0;
-  }
-  if (DEBUG) cerr << "-->>>> cost="<<*cost<<", bonus="<<*bonus<<", state_mono="<<*state_mono<<", state_nonmono="<<*state_nonmono<<endl;
-}
-
-bool Alignment::prepare(TRule& rule, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw, const map<WordID,int>& tfw,const Lattice& sourcelattice, int spanstart, int spanend) {  
-  if (DEBUG) cerr << "===Rule===" << rule.AsString() << endl;
-  _f = rule.f();
-  _e = rule.e();
-  _Arity = rule.Arity();
-  if (DEBUG) {
-    cerr << "F: ";
-    for (int idx=0; idx<_f.size(); idx++) cerr << _f[idx] << " ";
-    cerr << endl;
-    cerr << "F': ";
-    for (int idx=0; idx<_f.size(); idx++) 
-      if (_f[idx]>=0) {
-        cerr << TD::Convert(_f[idx]) << " "; 
-      } else {
-        cerr << TD::Convert(_f[idx]*-1);
-      }
-    cerr << endl;
-    cerr << "E: ";
-    for (int idx=0; idx<_e.size(); idx++) 
-      cerr << _e[idx] << " ";
-    cerr << endl;
-    cerr << "E': ";
-    for (int idx=0; idx<_e.size(); idx++) 
-      if (_e[idx]>0) {
-        cerr << TD::Convert(_e[idx]) << " "; 
-      } else {
-        cerr << "[NT]" << " ";
-      }
-    cerr << endl;
-  }
-
-  SourceFWRuleIdxs[0]=0;
-  SourceFWRuleAbsIdxs[0]=0;
-  for (int idx=1; idx<=_f.size(); idx++) { // in transformed space
-    if (sfw.find(_f[idx-1])!=sfw.end()) {
-      SourceFWRuleIdxs[0]++;
-      SourceFWRuleAbsIdxs[++SourceFWRuleAbsIdxs[0]]=GetFWGlobalIdx(idx,sourcelattice,_f,spanstart,spanend,ant_contexts,sfw);
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]-2]=idx;
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]-1]=_f[idx-1];
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]]  =F2EProjectionFromExternal(idx-1,rule.a_,"_SEP_");
-    }
-  }
-  TargetFWRuleIdxs[0]=0;
-  for (int idx=1; idx<=_e.size(); idx++) { // in transformed space
-    if (tfw.find(_e[idx-1])!=tfw.end()) {
-      TargetFWRuleIdxs[0]++;
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]-2]=idx;
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]-1]=E2FProjectionFromExternal(idx-1,rule.a_,"_SEP_");
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]]  =_e[idx-1];
-    }
-  }
-
-  if (DEBUG) {
-    cerr << "SourceFWRuleIdxs[" << SourceFWRuleIdxs[0] << "]:";
-    for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-      cerr << " idx:" << SourceFWRuleIdxs[3*idx-2];
-      cerr << " absidx:" << SourceFWRuleAbsIdxs[idx];
-      cerr << " F:" << SourceFWRuleIdxs[3*idx-1];
-      cerr << " E:" << SourceFWRuleIdxs[3*idx];
-      cerr << "; ";
-    }
-    cerr << endl;
-    cerr << "TargetFWRuleIdxs[" << TargetFWRuleIdxs[0] << "]:";
-    for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-      cerr << " idx:" << TargetFWRuleIdxs[3*idx-2];
-      cerr << " F:" << TargetFWRuleIdxs[3*idx-1];
-      cerr << " E:" << TargetFWRuleIdxs[3*idx];
-    }
-    cerr << endl;
-  }
-  if (SourceFWRuleIdxs[0]+TargetFWRuleIdxs[0]==0) {
-    bool nofw = true;
-    for (int i_ant=0; i_ant<_Arity && nofw; i_ant++) { 
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant]);
-      if (ants[0]>=0||ants[3]>=0||ants[6]>=0||ants[9]>=0) nofw=false;
-    } 
-    if (nofw) return true;
-  }
-  //cerr << "clearing als first" << endl;
-  clearAls(_J,_I);
-
-  if (DEBUG) cerr << "A["<< rule.a_.size() << "]: " ;
-  RuleAl[0]=0;
-  // add phrase start boundary
-  RuleAl[0]++; RuleAl[RuleAl[0]*2-1]=0; RuleAl[RuleAl[0]*2]=0;
-  if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  for (int idx=0; idx<rule.a_.size(); idx++) {
-    RuleAl[0]++;
-    RuleAl[RuleAl[0]*2-1]=rule.a_[idx].s_+1;
-    RuleAl[RuleAl[0]*2]  =rule.a_[idx].t_+1;
-    if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  }
-  // add phrase end boundary
-  RuleAl[0]++; RuleAl[RuleAl[0]*2-1]=_f.size()+1; RuleAl[RuleAl[0]*2]=_e.size()+1;
-  if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  if (DEBUG) cerr << endl;
-
-  SourceRuleIdxs[0] = _f.size()+2; // +2 (phrase boundaries)
-  TargetRuleIdxs[0] = _e.size()+2; 
-  int ntidx=-1;
-  for (int idx=0; idx<_f.size()+2; idx++) { // idx in transformed space
-    SourceRuleIdxs[idx+1]=idx;
-    if (0<idx && idx<=_f.size()) if (_f[idx-1]<0) SourceRuleIdxs[idx+1]=ntidx--;
-  }
-  for (int idx=0; idx<_e.size()+2; idx++) {
-    TargetRuleIdxs[idx+1]=idx;
-    if (0<idx && idx<=_e.size()) {
-      //cerr << "_e[" <<(idx-1)<< "]=" << _e[idx-1] << endl;
-      if (_e[idx-1]<=0) TargetRuleIdxs[idx+1]=_e[idx-1]-1;
-    }
-  }
-  if (DEBUG) {
-    cerr << "SourceRuleIdxs:";
-    for (int idx=0; idx<SourceRuleIdxs[0]+1; idx++) 
-      cerr << " " << SourceRuleIdxs[idx];
-    cerr << endl;
-    cerr << "TargetRuleIdxs:";
-    for (int idx=0; idx<TargetRuleIdxs[0]+1; idx++) 
-      cerr << " " << TargetRuleIdxs[idx];
-    cerr << endl;
-  }
-
-  // sloppy, the integrity of anstates is assumed
-  // total = 50 bytes
-  // first 3 ints for leftmost source function words (1 for index, 4 for source WordID and 4 for target WordI
-  // second 3 for rightmost source function words
-  // third 3 for leftmost target function words
-  // fourth 3 for rightmost target function words
-  // the next 1 int for the number of alignments
-  // the remaining 37 ints for alignments (source then target)
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant]);
-    int span = ants[Dwarf::STATE_SIZE-1];
-    if (DEBUG) {
-      cerr << "antcontexts[" << i_ant << "] ";
-      for (int idx=0; idx<Dwarf::STATE_SIZE; idx++) cerr << idx << "." << ants[idx] << " ";
-      cerr << endl;
-      cerr << "i,j = " << source(ants[Dwarf::STATE_SIZE-1]) << "," << target(ants[Dwarf::STATE_SIZE-1]) << endl;
-    }
-    SourceFWAntsIdxs[i_ant][0]=0;
-    SourceFWAntsAbsIdxs[i_ant][0]=0;
-    if (ants[0]>=0) {
-      // Given a span, give the index of the first function word
-      int firstfwidx = GetFirstFWIdx(source(span),target(span),sourcelattice,sfw);
-      if (DEBUG) cerr << "  firstfwidx = " << firstfwidx << endl;
-      int fwcount = 0;
-      if (ants[1]>=0) { // one function word
-        SourceFWAntsIdxs[i_ant][0]++; SourceFWAntsIdxs[i_ant][1]=ants[0];
-        SourceFWAntsIdxs[i_ant][2]=ants[1]; SourceFWAntsIdxs[i_ant][3]=ants[2]; 
-        fwcount++;
-      } else { // if ants[1] < 0 then compound fws
-        //cerr << "ants[1]<0" << endl;
-        istringstream ossf(TD::Convert(ants[1]*-1)); string ffw;
-        istringstream osse(TD::Convert(ants[2])); string efw; //projection would be mostly NULL
-        int delta=ants[0];
-        while (osse >> efw && ossf >> ffw) {
-          SourceFWAntsIdxs[i_ant][0]++; 
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[0]-(delta--);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);  
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-          fwcount++;
-        }
-      }
-      if (DEBUG) cerr << " fwcount=" << fwcount << endl;
-      SourceFWAntsAbsIdxs[i_ant][0]=fwcount;
-      for (int i=1; i<=fwcount; i++) SourceFWAntsAbsIdxs[i_ant][i]=firstfwidx++;
-    }
-    if (ants[3]>=0) {
-      int lastfwidx = GetLastFWIdx(source(span),target(span),sourcelattice,sfw);
-      if (DEBUG) cerr << "  lastfwidx = " << lastfwidx << endl;
-      int fwcount=0;
-      if (ants[4]>=0) {
-        fwcount++;
-        SourceFWAntsIdxs[i_ant][0]++; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[3]; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=ants[4]; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =ants[5];
-      } else { // if ants[4] < 0 then compound fws
-        //cerr << "ants[4]<0" << endl;
-        istringstream ossf(TD::Convert(ants[4]*-1)); string ffw;
-        istringstream osse(TD::Convert(ants[5]));    string efw;
-        int delta=0;
-        while (osse >> efw && ossf >> ffw) {
-          fwcount++;
-          SourceFWAntsIdxs[i_ant][0]++;
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[3]+(delta++);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-      if (DEBUG) cerr << " fwcount=" << fwcount << endl;
-      for (int i=1; i<=fwcount; i++) SourceFWAntsAbsIdxs[i_ant][SourceFWAntsAbsIdxs[i_ant][0]+i]=lastfwidx-fwcount+i;
-      SourceFWAntsAbsIdxs[i_ant][0]+=fwcount;
-    }
-    TargetFWAntsIdxs[i_ant][0]=0;
-    if (ants[6]>=0) {
-      if (ants[8]>=0) { // check the e part 
-        TargetFWAntsIdxs[i_ant][0]++; 
-        TargetFWAntsIdxs[i_ant][1]=ants[6];
-        TargetFWAntsIdxs[i_ant][2]=ants[7]; 
-        TargetFWAntsIdxs[i_ant][3]=ants[8];
-      } else { // if ants[8] < 0 then compound fws
-        //cerr << "ants[8]<0" << endl;
-        //cerr << "ants[7]=" << TD::Convert(ants[7]) << endl;
-        //cerr << "ants[8]=" << TD::Convert(ants[8]*-1) << endl;
-        istringstream ossf(TD::Convert(ants[7]));    string ffw;
-        istringstream osse(TD::Convert(ants[8]*-1)); string efw;
-        int delta=ants[6];
-        while (osse >> efw && ossf >> ffw) {
-          //cerr << "efw="<< efw << ",ffw=" << ffw << endl;
-          TargetFWAntsIdxs[i_ant][0]++;
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[6]-(delta--);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-    }
-    if (ants[9]>=0) {
-      if (ants[11]>=0) {
-        TargetFWAntsIdxs[i_ant][0]++; 
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[9];
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=ants[10];
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =ants[11];
-      } else {
-        //cerr << "ants[11]<0" << endl;
-        //cerr << "ants[10]=" << TD::Convert(ants[10]) << endl;
-        //cerr << "ants[11]=" << TD::Convert(ants[11]*-1) << endl;
-        istringstream ossf(TD::Convert(ants[10]));    string ffw;
-        istringstream osse(TD::Convert(ants[11]*-1)); string efw;
-        int delta = 0;
-        while (osse >> efw && ossf >> ffw) {
-          //cerr << "efw="<< efw << ",ffw=" << ffw << endl;
-          TargetFWAntsIdxs[i_ant][0]++;
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[9]+(delta++);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-    }
-    AntsAl[i_ant][0]=ants[12];//number of alignments
-    for (int idx=1; idx<=AntsAl[i_ant][0]; idx++) {
-      AntsAl[i_ant][idx*2-1] = source(ants[12+idx]);
-      AntsAl[i_ant][idx*2]   = target(ants[12+idx]);
-    }
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    int length = AntsAl[i_ant][0];
-    int maxs = -1000;
-    int maxt = -1000;
-    for (int idx=0; idx<length; idx++) {
-      if (maxs<AntsAl[i_ant][2*idx+1]) maxs = AntsAl[i_ant][2*idx+1];
-      if (maxt<AntsAl[i_ant][2*idx+2]) maxt = AntsAl[i_ant][2*idx+2];
-    }
-    if (DEBUG) cerr << "SourceFWAntsIdxs[" <<i_ant<<"][0]=" << SourceFWAntsIdxs[i_ant][0] << endl;
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << "SourceFWAntsIdxs["<<i_ant<<"]["<<(3*idx-2)<<"]="<<SourceFWAntsIdxs[i_ant][3*idx-2];
-        cerr << ","<<SourceFWAntsIdxs[i_ant][3*idx-1]<<","<<SourceFWAntsIdxs[i_ant][3*idx]<<endl;
-        cerr << "SourceFWAntsAbsIdxs["<<i_ant<<"]["<<idx<<"]="<<SourceFWAntsAbsIdxs[i_ant][idx] << endl;
-      }
-      if (maxs<SourceFWAntsIdxs[i_ant][3*idx-2]) maxs=SourceFWAntsIdxs[i_ant][3*idx-2];
-    }
-    if (DEBUG) cerr << "TargetFWAntsIdxs[" <<i_ant<<"][0]=" << TargetFWAntsIdxs[i_ant][0] << endl;
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << "TargetFWAntsIdxs["<<i_ant<<"]["<<(3*idx-2)<<"]="<<TargetFWAntsIdxs[i_ant][3*idx-2];
-        cerr << ","<<TargetFWAntsIdxs[i_ant][3*idx-1]<<","<<TargetFWAntsIdxs[i_ant][3*idx]<<endl;
-      }
-      if (maxt<TargetFWAntsIdxs[i_ant][3*idx-2]) maxt=TargetFWAntsIdxs[i_ant][3*idx-2];
-    }
-    SourceAntsIdxs[i_ant][0] = maxs+1;
-    if (DEBUG) cerr << "SourceAntsIdxs[" << i_ant << "][0]=" <<SourceAntsIdxs[i_ant][0] << endl;
-    for (int idx=0; idx<SourceAntsIdxs[i_ant][0]; idx++) SourceAntsIdxs[i_ant][idx+1]=idx;
-    TargetAntsIdxs[i_ant][0] = maxt+1;
-    if (DEBUG) cerr << "TargetAntsIdxs[" << i_ant << "][0]=" <<TargetAntsIdxs[i_ant][0] << endl;
-    for (int idx=0; idx<TargetAntsIdxs[i_ant][0]; idx++) TargetAntsIdxs[i_ant][idx+1]=idx;
-  }
-  int TotalSource = SourceRuleIdxs[0] - _Arity;
-  for (int idx=0; idx<_Arity; idx++) TotalSource += SourceAntsIdxs[idx][0];
-  int TotalTarget = TargetRuleIdxs[0] - _Arity;
-  for (int idx=0; idx<_Arity; idx++) TotalTarget += TargetAntsIdxs[idx][0];
-  if (DEBUG) cerr << "TotalSource = "<< TotalSource << ", TotalTarget = "<< TotalTarget << endl;
-  int curr = 0;
-  for (int idx=1; idx<=SourceRuleIdxs[0]; idx++) {
-    if (SourceRuleIdxs[idx]>=0) {
-      SourceRuleIdxs[idx]=curr++;
-    } else {
-      int i_ant = SourceRuleIdxs[idx]*-1-1;
-      if (DEBUG) cerr << "SourceAntsIdxs[" << i_ant << "]" << endl;
-      for (int idx2=1; idx2<=SourceAntsIdxs[i_ant][0]; idx2++) {
-        SourceAntsIdxs[i_ant][idx2]=curr++;
-        if (DEBUG) cerr << SourceAntsIdxs[i_ant][idx2] << " ";
-      }
-      if (DEBUG) cerr << endl;
-    }
-  }
-  if (DEBUG) {
-    cerr << "SourceRuleIdxs" << endl;
-    for (int idx=1; idx<=SourceRuleIdxs[0]; idx++) cerr << SourceRuleIdxs[idx] << " ";
-    cerr << endl;
-  }
-  curr = 0;
-  for (int idx=1; idx<=TargetRuleIdxs[0]; idx++) {
-    if (TargetRuleIdxs[idx]>=0) {
-      TargetRuleIdxs[idx]=curr++;
-    } else {
-      int i_ant = TargetRuleIdxs[idx]*-1-1;
-      if (DEBUG) cerr << "TargetRuleIdxs[" << i_ant << "]" << endl;
-      for (int idx2=1; idx2<=TargetAntsIdxs[i_ant][0]; idx2++) {
-        TargetAntsIdxs[i_ant][idx2]=curr++;
-        if (DEBUG) cerr << TargetAntsIdxs[i_ant][idx2] << " ";
-      }
-      if (DEBUG) cerr << endl;
-    }
-  }
-  if (DEBUG) {
-    cerr << "TargetRuleIdxs" << endl;
-    for (int idx=1; idx<=TargetRuleIdxs[0]; idx++) cerr << TargetRuleIdxs[idx] << " ";
-    cerr << endl;
-  }
-  for (int idx=1; idx<=RuleAl[0]; idx++) {
-    if (DEBUG) {
-      cerr << RuleAl[idx*2-1] << " - " << RuleAl[idx*2] << " to ";
-      cerr << SourceRuleIdxs[RuleAl[idx*2-1]+1] << " - " << TargetRuleIdxs[RuleAl[idx*2]+1] << endl;
-    }
-    set(SourceRuleIdxs[RuleAl[idx*2-1]+1],TargetRuleIdxs[RuleAl[idx*2]+1]);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=AntsAl[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << AntsAl[i_ant][2*idx-1] << " - " << AntsAl[i_ant][2*idx] << " to ";
-        cerr << SourceAntsIdxs[i_ant][AntsAl[i_ant][2*idx-1]+1] << " - ";
-        cerr << TargetAntsIdxs[i_ant][AntsAl[i_ant][2*idx]+1] << endl;
-      }
-      set(SourceAntsIdxs[i_ant][AntsAl[i_ant][2*idx-1]+1],TargetAntsIdxs[i_ant][AntsAl[i_ant][2*idx]+1]);
-    }
-  }
-  SourceFWIdxs[0]=0;
-  SourceFWAbsIdxs[0]=0;
-  if (DEBUG) cerr << "SourceFWRuleIdxs:" << endl;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << SourceFWRuleIdxs[3*idx-2] << " to " << SourceRuleIdxs[SourceFWRuleIdxs[3*idx-2]+1] << endl;
-    SourceFWRuleIdxs[3*idx-2] = SourceRuleIdxs[SourceFWRuleIdxs[3*idx-2]+1];
-    SourceFWAbsIdxs[0]++;
-    SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]=SourceFWRuleAbsIdxs[idx];
-    SourceFWIdxs[0]++;
-    SourceFWIdxs[3*SourceFWIdxs[0]-2]=SourceFWRuleIdxs[3*idx-2];
-    SourceFWIdxs[3*SourceFWIdxs[0]-1]=SourceFWRuleIdxs[3*idx-1];
-    SourceFWIdxs[3*SourceFWIdxs[0]]  =SourceFWRuleIdxs[3*idx];
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    if (DEBUG) cerr << "SourceFWAntsIdxs[" << i_ant << "]" << endl;
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) 
-        cerr << SourceFWAntsIdxs[i_ant][3*idx-2] << " to " << SourceAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][3*idx-2]+1] << endl;
-      SourceFWAntsIdxs[i_ant][3*idx-2] = SourceAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][3*idx-2]+1];
-      SourceFWAbsIdxs[0]++;
-      SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]=SourceFWAntsAbsIdxs[i_ant][idx];
-      SourceFWIdxs[0]++;
-      SourceFWIdxs[3*SourceFWIdxs[0]-2]=SourceFWAntsIdxs[i_ant][3*idx-2];
-      SourceFWIdxs[3*SourceFWIdxs[0]-1]=SourceFWAntsIdxs[i_ant][3*idx-1];
-      SourceFWIdxs[3*SourceFWIdxs[0]]  =SourceFWAntsIdxs[i_ant][3*idx];
-    }
-  }
-  sort(SourceFWIdxs);
-  sort(SourceFWAbsIdxs);
-  if (DEBUG) {
-    cerr << "SourceFWIdxs : ";
-    for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-      cerr << "idx:" << SourceFWIdxs[3*idx-2] << ",";
-      cerr << "F:" << SourceFWIdxs[3*idx-1] << ",";
-      cerr << "E:" << SourceFWIdxs[3*idx] << " ";
-    }
-    cerr << endl;
-  }
-  TargetFWIdxs[0]=0;
-  if (DEBUG) cerr << "TargetFWRuleIdxs:" << endl;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << TargetFWRuleIdxs[3*idx-2] << " to " << TargetRuleIdxs[TargetFWRuleIdxs[3*idx-2]+1] << endl;
-    TargetFWRuleIdxs[3*idx-2] = TargetRuleIdxs[TargetFWRuleIdxs[3*idx-2]+1];
-    TargetFWIdxs[0]++;    
-    TargetFWIdxs[3*TargetFWIdxs[0]-2]=TargetFWRuleIdxs[3*idx-2];
-    TargetFWIdxs[3*TargetFWIdxs[0]-1]=TargetFWRuleIdxs[3*idx-1];
-    TargetFWIdxs[3*TargetFWIdxs[0]]  =TargetFWRuleIdxs[3*idx];
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    if (DEBUG) cerr << "TargetFWAntsIdxs[" << i_ant << "]" << endl;
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << TargetFWAntsIdxs[i_ant][3*idx-2] << " to " << TargetAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][3*idx-2]+1] << endl;
-      TargetFWAntsIdxs[i_ant][3*idx-2] = TargetAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][3*idx-2]+1];
-      TargetFWIdxs[0]++;
-      TargetFWIdxs[3*TargetFWIdxs[0]-2]=TargetFWAntsIdxs[i_ant][3*idx-2];
-      TargetFWIdxs[3*TargetFWIdxs[0]-1]=TargetFWAntsIdxs[i_ant][3*idx-1];
-      TargetFWIdxs[3*TargetFWIdxs[0]]  =TargetFWAntsIdxs[i_ant][3*idx];
-    }
-  }
-  sort(TargetFWIdxs);
-  if (DEBUG) {
-    cerr << "TargetFWIdxs : ";
-    for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-      cerr << "idx:" << TargetFWIdxs[3*idx-2]<< ",";
-      cerr << "E:" << TargetFWIdxs[3*idx-1]<< ",";
-      cerr << "F:" << TargetFWIdxs[3*idx]<< " ";
-    }
-    cerr << endl;
-    cerr << AsString() << endl;
-  }
-  fas = firstSourceAligned(1); las = lastSourceAligned(_J-2);
-  fat = firstTargetAligned(1); lat = lastTargetAligned(_I-2); 
-  if (DEBUG) cerr << "fas=" << fas << ", las=" << las << ", fat=" << fat << ", lat=" << lat << endl;
-  assert(fas<=las);
-  assert(fat<=lat);
-  SetCurrAlVector();
-  if (DEBUG) cerr << "end prepare" << endl;
-  return false;
-}      
-
-string Alignment::AsStringSimple() {
-  ostringstream stream;
-  for (int j=0; j<getJ(); j++) {
-    int t = targetOf(j,minTSpan(j));
-    while (t>=0) {
-      stream << " " << j << "-" << t;
-      t = targetOf(j,t+1);
-    }
-  }
-  return stream.str();
-};
-
-
-string Alignment::AsString() {
-  ostringstream stream;
-  stream << "J:" << getJ() << " I:" << getI();
-  for (int j=0; j<getJ(); j++) {
-    int t = targetOf(j,minTSpan(j));
-    while (t>=0) {
-      stream << " " << j << "-" << t;
-      t = targetOf(j,t+1);
-    }
-  }
-  stream << " TargetSpan:";
-  for (int j=0; j<getJ(); j++)
-    if (minTSpan(j)!=MINIMUM_INIT)
-      stream << " " << j << "[" << minTSpan(j) << "," << maxTSpan(j) << "]";
-    else
-      stream << " " << j << "[-,-]";
-  stream << " SourceSpan:";
-  for (int i=0; i<getI(); i++)
-    if (minSSpan(i)!=MINIMUM_INIT)
-      stream << " " << i << "[" << minSSpan(i) << "," << maxSSpan(i) << "]";
-    else
-      stream << " " << i << "[-,-]";
-  return stream.str();
-};
-
-void Alignment::SetCurrAlVector() {
-  curr_al.clear();
-  for (int j=0; j<_J; j++) {
-    int i = targetOf(j);
-    while (i>=0) {
-      curr_al.push_back(link(j,i));
-      i = targetOf(j,i+1);
-    }
-  }
-}
-
-void CountTable::print() const {
-  cerr << "+++ Model +++" << endl;
-  for (map<WordID,int*>::const_iterator iter=model.begin(); iter!=model.end(); iter++) {
-    cerr << TD::Convert(iter->first) << " ";
-    for (int i=0; i<numColumn; i++) cerr << iter->second[i] << " ";
-    cerr << endl;
-  }
-  cerr << "+++ Ultimate +++" << endl;
-  for (int i=0; i<numColumn; i++) cerr << ultimate[i] << " ";
-  cerr << endl;
-}
-
-void Alignment::ToArrayInt(vector<int>* ret) {
-  ret->clear();
-  for (int i=0; i<_J; i++) {
-    int t = targetOf(i);
-    while (t>=0) {
-      ret->push_back(link(i,t));
-      t = targetOf(i,t+1);
-    }
-  }
-}
-
-int Alignment::GetFWGlobalIdx(int idx, const Lattice& sourcelattice, vector<WordID>& sources, int spanstart, int spanend, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw) {
-  // get the index of the function word in the lattice
-  if (DEBUG) cerr << "   GetFWGlobalIdx(" << idx << "," << spanstart << "," << spanend << ")" << endl;
-  int curr = spanstart; int i_ant = 0;
-  for (int i=1; i<sources.size() && i<idx; i++) { // sources contain <s> and </s> 
-    if (sources[i]<0) {
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant++]);
-      int antstate = ants[Dwarf::STATE_SIZE-1];
-      if (DEBUG) cerr << "    found NT[" << target(antstate) << "," << source(antstate) << "]" << endl;
-      curr += target(antstate)-source(antstate);
-    } else {
-      curr++;
-    }
-  }
-  if (DEBUG) cerr << "    curr = " << curr << endl;
-  //compute the fw index
-  int ret = 1;
-  for (int i=0; i<curr; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) ret++;
-  }
-  if (DEBUG) cerr << "    ret = " << ret << endl;
-  return ret;
-}
-
-int Alignment::GetFirstFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw) {
-  if (DEBUG) cerr << "   GetFirstFWIdx(" << spanstart << "," << spanend << ")" << endl;  
-  int curr=0;
-  for (int i=0; i<spanend; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) {
-      curr++;
-      if (i>=spanstart) return curr;
-    } 
-  }
-//  assert(0);
-  return curr;
-}
-
-int Alignment::GetLastFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw) {
-  if (DEBUG) cerr << "   GetLastFWIdx(" << spanstart << "," << spanend << ")" << endl;
-  int curr=0;
-  for (int i=0; i<spanend; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) {
-      curr++;
-    } 
-  }
-  return curr;
-}
-
-WordID Alignment::generalize(WordID original, const map<WordID,WordID>& tags, bool pos) {
-  if (!pos) {
-    map<WordID,WordID>::const_iterator it = tags.find(original);
-    if (it!=tags.end()) {
-      return it->second;
-    }
-  } else {
-    string key,idx;
-    Dwarf::stripIndex(TD::Convert(original),&key,&idx);
-    map<WordID,WordID>::const_iterator it = tags.find(TD::Convert(key)); 
-    if (it!=tags.end()) {
-      ostringstream oss;
-      oss << TD::Convert(it->second) << "/" << idx;
-      return TD::Convert(oss.str());   
-    }
-  }
-  return original;
-}
-
-int* Alignment::SOS() {
-  int* neighbor = new int[4];
-  neighbor[0]=0; neighbor[1]=0;
-  neighbor[2]=0; neighbor[3]=0;
-  return neighbor;
-}
-
-int* Alignment::EOS() {
-  int* neighbor = new int[4];
-  neighbor[0]=getJ()-1; neighbor[1]=neighbor[0];
-  neighbor[2]=getI()-1; neighbor[3]=neighbor[2];
-  return neighbor;
-}
-
-int* Alignment::neighborLeft(int startidx, int endidx, bool* getit) {
-  if (DEBUG) cerr << "   neighborLeft("<<startidx<<","<<endidx<<")"<<endl;
-  int lborder = startidx;
-  int* ret;
-  while(lborder<=endidx) {
-    ret = blockSource(lborder,endidx);
-    if (ret[0]==lborder && ret[1]==endidx && ret[2]!=MINIMUM_INIT) {
-      *getit = true;
-      return ret;
-    } else {
-      delete[] ret;
-      lborder++;
-    }
-  }
-  ret = new int[4];
-  ret[0]=-1; ret[1]=-1; ret[2]=-1; ret[3]=-1;
-  *getit = false;
-  return ret;
-}
-
-int* Alignment:: neighborRight(int startidx, int endidx, bool* getit) {
-  if (DEBUG) cerr << "   neighborRight("<<startidx<<","<<endidx<<")"<<endl;
-  int rborder = endidx;
-  int* ret;
-  while(startidx<=rborder) {
-    ret = blockSource(startidx,rborder);
-    if (ret[0]==startidx && ret[1]==rborder && ret[2]!=MINIMUM_INIT) {
-      *getit = true;
-      return ret;
-    } else {
-      delete[] ret;
-      rborder--;
-    }
-  }
-  ret = new int[4];
-  ret[0]=-1; ret[1]=-1; ret[2]=-1; ret[3]=-1;
-  *getit = false;
-  return ret;
-}
diff --git a/decoder/dwarf.h b/decoder/dwarf.h
deleted file mode 100644
index 49d2a3b7..00000000
--- a/decoder/dwarf.h
+++ /dev/null
@@ -1,286 +0,0 @@
-#ifndef DWARF_H
-#define DWARF_H
-
-#include <cstdlib>
-#include <vector>
-#include <map>
-#include <string>
-#include <ostream>
-#include "wordid.h"
-#include "lattice.h"
-#include "trule.h"
-#include "tdict.h"
-#include <boost/functional/hash.hpp>
-#include <tr1/unordered_map>
-#include <boost/tuple/tuple.hpp>
-
-using namespace std;
-using namespace std::tr1;
-using namespace boost::tuples;
-using namespace boost;
-
-const static bool DEBUG = false;
-
-class CountTable {
-public:
-        int* ultimate;
-        map<WordID,int*> model;
-        int mode;
-        int numColumn;
-        void print() const;
-        void setup(int _numcolumn, int _mode) {
-          mode = _mode; numColumn = _numcolumn;
-        }
-};
-
-class Alignment {
-/* Alignment represents an alignment object in a 2D format to support function word-based models calculation 
-
-   A note about model's parameter estimation:
-   ==========================================
-   The model is estimated as a two-level Dirichlet process. 
-   For orientation model, the first tier estimation is:
-   P(o|f,e) where *o* is the orientation value to estimate, *f* is the source function word aligned to *e* 
-   its second tier is: P(o|f), while its third tier is P(o)
-   For dominance model, the first tier estimation is:
-   P(d|f1,f2,e1,e2) where *d* is a dominance value to estimate, *f1,f2* are the neighboring function words on the source
-   aligned to *e1,e2* on the target side
-   its second tier is: P(d|f1,f2) while its third tier is P(d)
-    
-   Taking orientation model as a case in point, a two level estimation proceeds as follow:
-   P(o|f,e) = c(o,f,e) + alpha { c(o,f) + beta [ c (o) / c(.) ] }
-                                 ------------------------------
-                                 c(f)   + beta
-              -------------------------------------------------
-              c(f,e)   + alpha
-   where c() is a count function, alpha and beta are the concentration parameter 
-         of the first and second Dirichlet process respectively 
-   To encourage or penalize the use of second and third tier statistics, bo1 and bo2 binary features are introduced 
-*/
-public:
-  const static int MAX_WORDS = 200;  
-  const static int MINIMUM_INIT = 1000;
-  const static int MAXIMUM_INIT = -1000;
-  const static int MAX_ARITY = 2;
-  WordID kSOS;
-  WordID kEOS;
-  WordID kUNK;
-  double alpha_oris; // 1st concentration parameter for orientation model 
-  double beta_oris;  // 2nd concentration parameter for orientation model
-  double alpha_orit; // 1st concentration parameter for orientation model 
-  double beta_orit;  // 2nd concentration parameter for orientation model
-  double alpha_doms; // idem as above but for dominance model
-  double beta_doms;
-  double alpha_domt; // idem as above but for dominance model
-  double beta_domt;
-  
-  // ACCESS to alignment
-  void set(int j,int i);   // j is the source index, while i is the target index
-  void reset(int j,int i); // idem as above
-  inline bool at(int j, int i) { return _matrix[j][i]; };
-  inline int getJ() {return _J;}; // max source of the current alignment
-  inline int getI() {return _I;}; // max target of the current alignment
-  inline void setI(int I) { _I = I; };
-  inline void setJ(int J) { _J = J; };
-  inline void setF(vector<WordID> f) { _f=f;};
-  inline void setE(vector<WordID> e) { _e=e;};
-  inline WordID getF(int id) { if (id<0) return TD::Convert("<s>"); if (id>=_f.size()) return TD::Convert("</s>"); return _f[id];};
-  inline WordID getE(int id) { if (id<0) return TD::Convert("<s>"); if (id>=_e.size()) return TD::Convert("</s>"); return _e[id];};
-  void clearAls(int prevJ=200, int prevI=200);
-  int sourceOf(int i, int start = -1);
-  int targetOf(int j, int start = -1);
-  inline int minSSpan(int i) { return _sSpan[i][0];}
-  inline int maxSSpan(int i) { return _sSpan[i][1];}
-  inline int minTSpan(int j) { return _tSpan[j][0];}
-  inline int maxTSpan(int j) { return _tSpan[j][1];}
-  static inline int link(int s, int t) { return (s << 16) | t; }
-  static inline int source(int st) {return st >> 16; }
-  static inline int target(int st) {return st & 0xffff; }
-  inline void setAlphaOris(double val) { alpha_oris=val; }
-  inline void setAlphaOrit(double val) { alpha_orit=val; }
-  inline void setAlphaDoms(double val) { alpha_doms=val; }
-  inline void setAlphaDomt(double val) { alpha_domt=val; }
-  inline void setBetaOris(double val) { beta_oris=val; }
-  inline void setBetaOrit(double val) { beta_orit=val; }
-  inline void setBetaDoms(double val) { beta_doms=val; }
-  inline void setBetaDomt(double val) { beta_domt=val; }
-  inline void setFreqCutoff(int val) { cout << _freq_cutoff << " to " << val << endl;  _freq_cutoff=val; }
-  string AsString();
-  string AsStringSimple();
-  int* SOS();
-  int* EOS();
-
-  // Model related function  
-  Alignment();
-  // Given the current *rule* and its antecedents, construct an alignment space and mark the function word alignments 
-  // according *sfw* and *tfw*
-  bool prepare(TRule& rule, const std::vector<const void*>& ant_contexts, 
-               const map<WordID,int>& sfw, const map<WordID,int>& tfw, const Lattice& sourcelattice, int spanstart, int spanend);
-
-  // Compute orientation model score which parameters are stored in *table* and pass the values accordingly
-  // will call Orientation(Source|Target) and ScoreOrientation(Source|Target)
-  void computeOrientationSource(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus);
-  void computeOrientationSourcePos(const CountTable& table, double *cost, double *bonus,
-                double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2);
-  void computeOrientationSourceGen(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus, const map<WordID,WordID>& tags);
-  void computeOrientationSourceBackward(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus);
-  void computeOrientationSourceBackwardPos(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2);
-  void computeOrientationTarget(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus);
-  void computeOrientationTargetBackward(const CountTable& table, double *cost, double *bonus, double *bo1, 
-                                double *bo1_bonus, double *bo2, double *bo2_bonus);
-  // Get the orientation value of a function word at a particular index *fw*
-  // assign the value to either *oril* or *orir* accoring to *Lcompute* and *Rcompute*
-  void OrientationSource(int fw, int*oril, int* orir, bool Lcompute=true, bool Rcompute=true);
-  void OrientationSource(int fw0, int fw1, int*oril, int* orir, bool Lcompute=true, bool Rcompute=true);
-  int  OrientationSource(int* left, int* right);
-  void OrientationTarget(int fw, int*oril, int* orir, bool Lcompute=true, bool Rcompute=true);
-  void OrientationTarget(int fw0, int fw1, int*oril, int* orir, bool Lcompute=true, bool Rcompute=true);
-
-  vector<int> OrientationSourceLeft4Sampler(int fw0, int fw1);
-  vector<int> OrientationSourceLeft4Sampler(int fw);
-  vector<int> OrientationSourceRight4Sampler(int fw0, int fw1);
-  vector<int> OrientationSourceRight4Sampler(int fw);
-  vector<int> OrientationTargetLeft4Sampler(int fw0, int fw1);
-  vector<int> OrientationTargetLeft4Sampler(int fw);
-  vector<int> OrientationTargetRight4Sampler(int fw0, int fw1);
-  vector<int> OrientationTargetRight4Sampler(int fw);
-
-  // Given an orientation value *ori*, estimate the score accoding to *cond1*, *cond2* 
-  // and assign the value accordingly according to *isBonus* and whether the first or the second tier estimation
-  // is used or not
-  void ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-                             bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, 
-                             double *bo2, double *bo2_bonus, double alpha1, double beta1);
-  void ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond, 
-                            bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, 
-                            double *bo2, double *bo2_bonus, double alpha1, double beta1);
-  double ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2); 
-  double ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond); 
-  void ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-                             bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, 
-                             double *bo2, double *bo2_bonus, double alpha1, double beta1);
-  void ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond, 
-                            bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, 
-                            double *bo2, double *bo2_bonus, double alpha1, double beta1);
-  double ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2); 
-  double ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond); 
-  void ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2, 
-                            bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, 
-                            double *bo2, double *bo2_bonus, double alpha1, double beta1);
-  double ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2); 
-
-  // idem as above except these are for dominance model
-  void computeDominanceSource(const CountTable& table, WordID lfw, WordID rfw, double *cost, double *bonus, 
-                              double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus);
-  void computeDominanceSourcePos(const CountTable& table, WordID lfw, WordID rfw, double *cost, double *bonus, 
-                              double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2);
-  void computeDominanceTarget(const CountTable& table, WordID lfw, WordID rfw, double *cost, double *bonus, 
-                              double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus);
-  void computeBorderDominanceSource(const CountTable& table, double *cost, double *bonus, 
-        double *state_mono, double *state_nonmono,
-        TRule &rule, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw);
-  int DominanceSource(int fw1, int fw2);
-  int DominanceTarget(int fw1, int fw2);
-  vector<int> DominanceSource4Sampler(int fw1, int fw2);
-  vector<int> DominanceTarget4Sampler(int fw1, int fw2);
-  void ScoreDominance(const CountTable& table, int dom, WordID s1, WordID s2, WordID t1, WordID t2, 
-                      double *cost, double *bo1, double *bo2, bool isBonus, double alpha2, double beta2);
-  double ScoreDominance(const CountTable& table, int dom, WordID s1, WordID s2, WordID t1, WordID t2); 
-
-  // Remove all function word alignments except those at the borders
-  // May result in more than two function word alignments at each side, because this function 
-  // will continue keeping function word alignments until the first aligned word at each side
-  void BorderingSFWsOnly();
-  void BorderingTFWsOnly();
-  void simplify(int *ret); // preparing the next state
-  void simplify_nofw(int *ret); // preparing the next state when no function word appears
-  // set the first part of the next state, which concerns with function word
-  // fas, las, fat, lat is the (f)irst or (l)ast function word alignments either on the (s)ource or (t)arget
-  // these parameters to anticipate cases where there are more than two function word alignments
-  void FillFWIdxsState(int *state, int fas, int las, int fat, int lat);
-
-  // Helper function to obtain the aligned words on the other side 
-  // WARNING!!! Only to be used if the als are in sync with either source or target sentences
-  WordID F2EProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter=" ");
-  WordID E2FProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter=" ");
-  // WARNING!!! Only to be used in dwarf_main.cc 
-  // These two function words assume that the alignment contains phrase boundary 
-  // but the source and target sentences do not
-  WordID F2EProjection(int idx, const string& delimiter=" ");
-  WordID E2FProjection(int idx, const string& delimiter=" ");
-  void SetCurrAlVector();
-  int* blockSource(int fw1, int fw2);
-  int* blockTarget(int fw1, int fw2);
-  void ToArrayInt(vector<int>* arr);
-  int* neighborLeft(int startidx, int endidx, bool* found);
-  int* neighborRight(int startidx, int endidx, bool* found);
-private:
-  // Hash to avoid redundancy
-  unordered_map<vector<int>, int, boost::hash<vector<int> > > oris_hash;
-  unordered_map<vector<int>, int, boost::hash<vector<int> > > orit_hash;
-  unordered_map<vector<int>, int, boost::hash<vector<int> > > doms_hash;
-  unordered_map<vector<int>, int, boost::hash<vector<int> > > domt_hash;
-  unordered_map<vector<int>, vector<int>, boost::hash<vector<int> > > simplify_hash;
-  unordered_map<vector<int>, vector<int>, boost::hash<vector<int> > > prepare_hash;
- 
-  int _J; // effective source length;
-  int _I; // effective target length;
-  bool _matrix[MAX_WORDS][MAX_WORDS]; // true if aligned 
-  short _sSpan[MAX_WORDS][2]; //the source span of a target index; 0->min, 1->max
-  short _tSpan[MAX_WORDS][2]; //the target span of a source index; 0->min, 2->max
-  int _freq_cutoff;
-  int SourceFWRuleIdxs[40]; //the indexes of function words in the rule; 
-          // The following applies to all *FW*Idxs
-          // *FW*Idxs[0] = size
-          // *FW*Idxs[idx*3-2] = index in the alignment, where idx starts from 1 to size
-          // *FW*Idxs[idx*3-1] = source WordID
-          // *FW*Idxs[idx*3]   = target WordID
-  int SourceFWRuleAbsIdxs[40];
-  int TargetFWRuleIdxs[40]; //the indexes of function words in the rule; zeroth element is the count
-  int ** SourceFWAntsIdxs;  //the indexes of function words in antecedents
-  int ** SourceFWAntsAbsIdxs;
-  int ** TargetFWAntsIdxs;  //the indexes of function words in antecedents
-  int SourceRuleIdxs[40]; //the indexes of SOURCE tokens (zeroth element is the number of source tokens)
-        //>0 means terminal, -i means the i-th Xs
-  int TargetRuleIdxs[40]; //the indexes of TARGET tokens (zeroth element is the number of target tokens)
-  int ** SourceAntsIdxs;  //the array of indexes of a particular antecedent's SOURCE tokens
-  int ** TargetAntsIdxs;  //the array of indexes of a particular antecedent's TARGET tokens
-  int SourceFWIdxs[40];
-  int SourceFWAbsIdxs[40];
-  int TargetFWIdxs[40];
-  // *sort* and *quickSort* are used to sort *FW*Idxs
-  void sort(int* num);
-  void quickSort(int arr[], int top, int bottom);
-
-  // *block(Source|Target)* finds the minimum block that containts two indexes (fw1 and fw2)
-  inline int least(int i1, int i2) { return (i1<i2)?i1:i2; }
-  inline int most(int i1, int i2) { return (i1>i2)?i1:i2; }
-  void simplifyBackward(vector<int *>*blocks, int* block, const vector<int>& danglings);
-  // used in simplify to check whether an atomic block according to source function words is also atomic according
-  // to target function words as well, otherwise break it 
-  // the resulting blocks are added into *blocks*
-  int _Arity;
-  std::vector<WordID> _f; // the source sentence of the **current** rule (may not consistent with the current alignment)
-  std::vector<WordID> _e; // the target sentence of the **current** rule
-  int RuleAl[40];
-  int **AntsAl;
-  int firstSourceAligned(int start);
-  int firstTargetAligned(int start);
-  int lastSourceAligned(int end);
-  int lastTargetAligned(int end);
-  int fas, las, fat, lat; // first aligned source, last aligned source, first aligned target, last aligned target
-  bool MemberOf(int* FWIdxs, int pos1, int pos2); // whether FWIdxs contains pos1 and pos2 consecutively
-  // Convert the alignment to vector form, will be used for hashing purposes
-  vector<int> curr_al;
-  int GetFWGlobalIdx(int idx, const Lattice& sourcelattice, vector<WordID>& sources, int spanstart, int spanend, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw);
-  int GetFirstFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw);
-  int GetLastFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw);
-  WordID generalize(WordID original, const map<WordID,WordID>& tags, bool pos=false);
-};
-
-#endif
diff --git a/decoder/earley_composer.cc b/decoder/earley_composer.cc
index efce70a6..32c387d3 100644
--- a/decoder/earley_composer.cc
+++ b/decoder/earley_composer.cc
@@ -4,8 +4,14 @@
 #include <fstream>
 #include <map>
 #include <queue>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
+# include <tr1/unordered_map>
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_multiset; using std::tr1::unordered_set; }
+#endif
 
 #include <boost/shared_ptr.hpp>
 #include <boost/program_options.hpp>
@@ -19,7 +25,6 @@
 #include "hg_remove_eps.h"
 
 using namespace std;
-using namespace std::tr1;
 
 // Define the following macro if you want to see lots of debugging output
 // when you run the chart parser
diff --git a/decoder/factored_lexicon_helper.cc b/decoder/factored_lexicon_helper.cc
index 7203b325..e7899215 100644
--- a/decoder/factored_lexicon_helper.cc
+++ b/decoder/factored_lexicon_helper.cc
@@ -2,6 +2,7 @@
 
 #include "filelib.h"
 #include "stringlib.h"
+#include "sentence_metadata.h"
 
 using namespace std;
 
diff --git a/decoder/factored_lexicon_helper.h b/decoder/factored_lexicon_helper.h
index 81c75275..7fedc517 100644
--- a/decoder/factored_lexicon_helper.h
+++ b/decoder/factored_lexicon_helper.h
@@ -6,7 +6,8 @@
 #include <string>
 #include <map>
 #include "tdict.h"
-#include "sentence_metadata.h"
+
+struct SentenceMetadata;
 
 // when computing features, it can be advantageous to:
 //   1) back off to less specific forms (e.g., less highly inflected forms, POS tags, etc)
diff --git a/decoder/ff_dwarf.cc b/decoder/ff_dwarf.cc
deleted file mode 100644
index fe7a472e..00000000
--- a/decoder/ff_dwarf.cc
+++ /dev/null
@@ -1,894 +0,0 @@
-#include <vector>
-#include <sstream>
-#include <fstream>
-#include <string>
-#include <iostream>
-#include <map>
-#include "hg.h"
-#include "ff_dwarf.h"
-#include "dwarf.h"
-#include "wordid.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "sentence_metadata.h"
-#include "stringlib.h"
-
-using namespace std;
-
-Dwarf::Dwarf(const std::string& param) { 
-/* Param is a space separated string which contains any or all of the following:
-   oris|orit|doms|domt=filename 
-   e.g. oris=/fs/clip-galep3eval/hendra/z2e/oris128.gz
-*/
-  sSOS="<s>";
-  sEOS="</s>";
-  kSOS=TD::Convert(sSOS);
-  kEOS=TD::Convert(sEOS);
-  kGOAL=TD::Convert("S")*-1;
-  _sent_id = (int *)malloc(sizeof(int));
-  *_sent_id = -1;
-  if (DEBUG) cerr << "here = " << *_sent_id << endl;
-  _fwcount = (int *)malloc(sizeof(int));
-  *_fwcount = -1;
-  cerr << "initializing dwarf" << endl;
-  flag_oris=false; flag_orit=false; flag_doms=false; flag_domt=false; flag_tfw_count=false;
-  flag_bdoms=false; flag_porislr=false, flag_porisrl=false, flag_goris=false; flag_pgorislr=false, flag_pgorisrl=false;
-  flag_pdomslr=false; flag_pdomsrl=false; flag_pgdomslr=false; flag_pgdomsrl=false; flag_gdoms=false;
-  flag_oris_backward=false; flag_orit_backward=false; 
-  explicit_soseos=false;
-  SetStateSize(STATE_SIZE*sizeof(int));   
-  als = new Alignment();  
-  als->clearAls(Alignment::MAX_WORDS,Alignment::MAX_WORDS);
-  istringstream iss(param); string w;
-  while(iss >> w) {
-    int equal = w.find_first_of("=");
-    if (equal!=string::npos) {
-      string model = w.substr(0,equal);
-      vector<string> params; 
-      Tokenize(w.substr(equal+1),',',&params);
-      string fn = params[0];
-      if (model == "minfreq") {
-        cerr << "model minfreq " << fn << endl;
-        als->setFreqCutoff(atoi(fn.c_str()));
-      } else if (model == "oris") {
-        flag_oris = readOrientation(&toris,fn,&sfw); 
-        if (flag_oris) {
-          oris_ = FD::Convert("OrientationSource");
-          //oris_bo1_ = FD::Convert("OrientationSource_BO1");
-          //oris_bo2_ = FD::Convert("OrientationSource_BO2");
-        }
-        if (params.size()>1) als->setAlphaOris(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaOris(atof(params[2].c_str()));
-      } else if (model == "porislr") {
-        flag_porislr = readOrientation(&tporislr,fn,&sfw,true);
-        poris_nlr = 0;
-        if (flag_porislr) {
-          porislr_ = FD::Convert("OrientationSourcePositionfulLeftRight");
-        }
-        if (params.size()>1) poris_nlr = atoi(params[1].c_str());
-        if (DEBUG) cerr << "  maximum poris depth=" << poris_nlr  << endl;
-      } else if (model == "porisrl") {
-        flag_porisrl = readOrientation(&tporisrl,fn,&sfw,true);
-        poris_nrl = 0;
-        if (flag_porisrl) {
-          porisrl_ = FD::Convert("OrientationSourcePositionfulRightLeft");
-        }
-        if (params.size()>1) poris_nrl = atoi(params[1].c_str());
-        if (DEBUG) cerr << "  maximum poris depth=" << poris_nrl  << endl;
-      } else if (model=="goris") {
-        flag_goris = readOrientation(&tgoris,fn,&sfw);
-        if (flag_goris) {
-          goris_ = FD::Convert("OrientationSourceGeneralized");
-        }
-        if (params.size()>1) {
-          readTags(params[1],&tags);
-          generalizeOrientation(&tgoris,tags);          
-        }
-      } else if (model=="pgorislr") {
-        flag_pgorislr = readOrientation(&tpgorislr,fn,&sfw,true);
-        pgoris_nlr = 0;
-        if (flag_pgorislr) {
-          pgorislr_ = FD::Convert("OrientationSourceGeneralizedPositionfulLeftRight");
-        }
-        if (DEBUG) {
-          cerr << "BEFORE GENERALIZATION" << endl;
-          tpgorislr.print();
-        }
-        if (params.size()>1) pgoris_nlr = atoi(params[1].c_str());
-        if (params.size()>2) {
-          readTags(params[2],&tags);
-          generalizeOrientation(&tpgorislr,tags,true);
-        }
-        if (DEBUG) {
-          cerr << "AFTER GENERALIZATION" << endl;
-          tpgorislr.print();
-        }
-      } else if (model=="pgorisrl") {
-        flag_pgorisrl = readOrientation(&tpgorisrl,fn,&sfw,true);
-        pgoris_nrl = 0;
-        if (flag_pgorisrl) {
-          pgorisrl_ = FD::Convert("OrientationSourceGeneralizedPositionfulLeftRight");
-        } 
-        if (params.size()>1) pgoris_nrl = atoi(params[1].c_str());
-        if (params.size()>2) {
-          readTags(params[2],&tags);
-          generalizeOrientation(&tpgorisrl,tags,true);
-        }
-      } else if (model == "oris_backward") {
-        flag_oris_backward = true;
-        if (!flag_oris) readOrientation(&toris,fn,&sfw);
-        oris_backward_ = FD::Convert("OrientationSourceBackward");
-        if (params.size()>1) als->setAlphaOris(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaOris(atof(params[2].c_str()));
-      } else if (model == "orit") {
-        flag_orit = readOrientation(&torit,fn,&tfw); 
-        if (flag_orit) {
-          orit_ = FD::Convert("OrientationTarget");
-          //orit_bo1_ = FD::Convert("OrientationTarget_BO1");
-          //orit_bo2_ = FD::Convert("OrientationTarget_BO2");
-        }
-        if (params.size()>1) als->setAlphaOrit(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaOrit(atof(params[2].c_str()));
-      } else if (model == "orit_backward") {
-        flag_orit_backward = true;
-        if (!flag_orit) readOrientation(&torit,fn,&tfw);
-        orit_backward_ = FD::Convert("OrientationTargetBackward");
-        if (params.size()>1) als->setAlphaOrit(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaOrit(atof(params[2].c_str()));
-      } else if (model == "doms") {
-        flag_doms = readDominance(&tdoms,fn,&sfw); 
-        if (flag_doms) {
-          doms_ = FD::Convert("DominanceSource");
-          //doms_bo1_ = FD::Convert("DominanceSource_BO1");
-          //doms_bo2_ = FD::Convert("DominanceSource_BO2");
-        }
-        if (params.size()>1) als->setAlphaDoms(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaDoms(atof(params[2].c_str()));
-      } else if (model == "pdomsrl") {
-        flag_pdomsrl = readDominance(&tpdomsrl,fn,&sfw,true);
-        if (flag_pdomsrl) {
-          pdomsrl_ = FD::Convert("DominanceSourcePositionfulRightLeft");
-        }
-        if (params.size()>1) pdoms_nrl = atoi(params[1].c_str());
-      } else if (model == "pdomslr") {
-        flag_pdomslr = readDominance(&tpdomslr,fn,&sfw,true);
-        tpdomslr.print();
-        if (flag_pdomslr) {
-          pdomslr_ = FD::Convert("DominanceSourcePositionfulLeftRight");
-        }
-        if (params.size()>1) pdoms_nlr = atoi(params[1].c_str());
-      } else if (model == "pgdomsrl") {
-        flag_pgdomsrl = readDominance(&tpgdomsrl,fn,&sfw,true);
-        if (flag_pgdomsrl) {
-          pgdomsrl_ = FD::Convert("DominanceSourceGeneralizedPositionfulRightLeft");
-        }
-        if (params.size()>1) pgdoms_nrl = atoi(params[1].c_str());
-        if (params.size()>2) {
-          readTags(params[2],&tags);
-          generalizeDominance(&tpgdomsrl,tags,true);
-        }
-      } else if (model == "pgdomslr") {
-        flag_pgdomslr = readDominance(&tpgdomslr,fn,&sfw,true);
-        if (flag_pgdomslr) {
-          pgdomslr_ = FD::Convert("DominanceSourceGeneralizedPositionfulLeftRight");
-        }
-        if (params.size()>1) pgdoms_nlr = atoi(params[1].c_str());
-        if (params.size()>2) {
-          readTags(params[2],&tags);
-          if (DEBUG) {
-            for (map<WordID,WordID>::const_iterator it=tags.begin(); it!=tags.end(); it++) {
-              cerr << "tags = " << TD::Convert(it->first) << ", " << TD::Convert(it->second) << endl;
-            }
-          } 
-          generalizeDominance(&tpgdomslr,tags,true);
-        }
-        if (DEBUG) tpgdomslr.print();
-      } else if (model == "bdoms") {
-        flag_bdoms = readDominance(&tbdoms,fn,&sfw);
-        if (flag_bdoms) {
-          bdoms_ = FD::Convert("BorderDominanceSource");
-        }
-      } else if (model == "domt") {
-        flag_domt = readDominance(&tdomt,fn,&tfw); 
-        if (flag_domt) {
-          domt_ = FD::Convert("DominanceTarget");
-          //domt_bo1_ = FD::Convert("DominanceTarget_BO1");
-          //domt_bo2_ = FD::Convert("DominanceTarget_BO2");
-        }
-        if (params.size()>1) als->setAlphaDomt(atof(params[1].c_str()));
-        if (params.size()>2) als->setBetaDomt(atof(params[2].c_str()));
-      } else if (model== "tfw_count") {
-        flag_tfw_count = readList(fn,&tfw);
-        tfw_count_ = FD::Convert("TargetFunctionWordsCount");        
-      } else {
-        cerr << "DWARF doesn't understand this model: " << model << endl;
-      }
-    } else {
-      if (w=="tfw_count") {
-        flag_tfw_count = true;
-        tfw_count_ = FD::Convert("TargetFunctionWordsCount");
-      } else if (w=="oris_backward") {
-        flag_oris_backward = true;
-        oris_backward_ = FD::Convert("OrientationSourceBackward"); 
-      } else if (w=="orit_backward") {
-        flag_orit_backward = true;
-        orit_backward_ = FD::Convert("OrientationTargetBackward");
-      } else if (w=="explicit_soseos") {
-        explicit_soseos=true;
-      } else {
-        cerr << "DWARF doesn't need this param: " << param << endl; 
-      }
-    }  
-  }
-  for (map<WordID,int>::const_iterator it=sfw.begin(); it!=sfw.end() && DEBUG; it++) {
-    cerr << "   FW:" << TD::Convert(it->first) << endl;
-  }
-}
-
-void Dwarf::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     SparseVector<double>* features,
-                                     SparseVector<double>* estimated_features,
-                                     void* context) const {
-  if (DEBUG) cerr << "TraversalFeaturesImpl" << endl;
-  double cost, bonus, bo1, bo2, bo1_bonus, bo2_bonus;
-  double bdoms_state_mono= 0; double bdoms_state_nonmono = 0;
-  TRule r = *edge.rule_;
-  if (DEBUG) cerr << " sent_id=" << *_sent_id << ", " << smeta.GetSentenceID() << endl;
-  if (DEBUG) cerr << "rule = " << r.AsString() << endl; 
-  if (DEBUG) cerr << "rule[i,j] = " << edge.i_ << "," << edge.j_ << endl;
-  if (*_sent_id != smeta.GetSentenceID()) { //new sentence
-    *_sent_id = smeta.GetSentenceID();
-    const Lattice l = smeta.GetSourceLattice();
-    *_fwcount=0;
-    for (int i=0; i<smeta.GetSourceLength(); i++) {
-      if (sfw.find(l[i][0].label)!=sfw.end()) {
-        *_fwcount+=1;
-      }
-    }
-    if (DEBUG) cerr << "new sentence[" << *_sent_id << "]="<<*_fwcount<<endl;
-  }
-  bool nofw = als->prepare(*edge.rule_, ant_contexts, sfw, tfw,smeta.GetSourceLattice(),edge.i_,edge.j_); 
-  bool isFinal = (edge.i_==0 && edge.j_==smeta.GetSourceLength() && r.GetLHS()==kGOAL);
-  // prepare *nofw* outputs whether the resulting alignment, contains function words or not
-  // if not, the models do not have to be calcualted and *simplify* is very simple
-  if (DEBUG) cerr << "nofw = " << nofw << endl;
-  if (flag_tfw_count) {
-    double count = 0;
-    for (int i=0; i<r.e_.size(); i++) {
-      if (tfw.find(r.e_[i])!=tfw.end()) count++;
-    }
-    features->set_value(tfw_count_,count);  
-  }
-  if (flag_oris) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeOrientationSource(toris,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus); 
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(oris_,cost); 
-    //features->set_value(oris_bo1_,bo1); 
-    //features->set_value(oris_bo2_,bo2);
-    estimated_features->set_value(oris_,bonus); 
-    //estimated_features->set_value(oris_bo1_,bo1_bonus); 
-    //estimated_features->set_value(oris_bo2_,bo2_bonus);
-  }
-  if (flag_porislr) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) 
-      als->computeOrientationSourcePos(tporislr,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,poris_nlr,0);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(porislr_,cost);
-    estimated_features->set_value(porislr_,bonus);
-  }
-  if (flag_porisrl) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw)
-      als->computeOrientationSourcePos(tporisrl,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,0,poris_nrl);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(porisrl_,cost);
-    estimated_features->set_value(porisrl_,bonus);
-  }
-  if (flag_pgorislr) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw)
-      als->computeOrientationSourcePos(tpgorislr,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,pgoris_nlr,0);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pgorislr_,cost);
-    estimated_features->set_value(pgorislr_,bonus);
-  }
-  if (flag_pgorisrl) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw)
-      als->computeOrientationSourcePos(tpgorisrl,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,0,pgoris_nrl);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pgorisrl_,cost);
-    estimated_features->set_value(pgorisrl_,bonus);
-  }
-  if (flag_goris) {
-    cost=0; bonus=0;
-    if (!nofw) als->computeOrientationSource(tgoris,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(goris_,cost);
-    estimated_features->set_value(goris_,bonus);
-  }
-  if (flag_oris_backward) {
-    cost=0; bonus=0;
-    if (!nofw) 
-      als->computeOrientationSourceBackward(toris,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(oris_backward_,cost);
-    estimated_features->set_value(oris_backward_,bonus);
-  }
-  WordID _lfw = kSOS;
-  WordID _rfw = kEOS; 
-  if (flag_doms || flag_pdomslr || flag_pdomsrl || flag_pgdomslr || flag_pgdomsrl) {
-    if (DEBUG) cerr << "   seeking lfw and rfw" << endl;
-    int start = edge.i_;
-    int end   = edge.j_;
-    if (DEBUG) cerr << "   start=" << start << ", end=" << end << endl;
-    const Lattice l = smeta.GetSourceLattice();
-    for (int idx=start-1; idx>=0; idx--) {
-      if (DEBUG) cerr << "  checking idx=" << idx << ", label=" << l[idx][0].label << "-" << TD::Convert(l[idx][0].label) << endl;
-      if (sfw.find(l[idx][0].label) !=sfw.end()) {
-        if (DEBUG) cerr << "+";
-        _lfw=l[idx][0].label; break;
-      }
-    }
-    for (int idx=end; idx<l.size(); idx++) { // end or end+1
-      if (DEBUG) cerr << "  checking idx=" << idx << ", label=" << l[idx][0].label << "-" << TD::Convert(l[idx][0].label) << endl;
-      if (sfw.find(l[idx][0].label)!=sfw.end()) {
-        if (DEBUG) cerr << ".";
-        _rfw=l[idx][0].label; break;
-      }
-    }
-    if (isFinal&&!explicit_soseos) {
-      _lfw=kSOS; _rfw=kEOS;
-    }
-  }
-  if (flag_doms) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeDominanceSource(tdoms,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus); 
-    if (DEBUG) cerr << "   COST=" << cost << ", BONUS=" << bonus << endl;
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      if (DEBUG) cerr << "    final and !explicit_soseos, thus cost = " << cost <<  endl;
-      bonus = 0;
-    }
-    features->set_value(doms_,cost); 
-    estimated_features->set_value(doms_,bonus);
-  }
-  if (flag_pdomslr) {
-   if (DEBUG) cerr << " flag_pdomslr true, nofw=" << nofw << endl;
-   if (DEBUG) cerr << "   lfw=" << _lfw << ", rfw=" << _rfw << endl;
-   if (DEBUG) cerr << "   kSOS=" << kSOS << ", kEOS=" << kEOS << endl;
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeDominanceSourcePos(tpdomslr,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,pdoms_nlr,0);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pdomslr_,cost);
-    estimated_features->set_value(pdomslr_,bonus);  
-  }
-  if (flag_pdomsrl) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeDominanceSourcePos(tpdomsrl,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,0,pdoms_nrl);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pdomsrl_,cost);
-    estimated_features->set_value(pdomsrl_,bonus); 
-  }
-  if (flag_pgdomslr) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeDominanceSourcePos(tpgdomslr,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,pgdoms_nlr,0);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pgdomslr_,cost);
-    estimated_features->set_value(pgdomslr_,bonus);  
-  }
-  if (flag_pgdomsrl) {    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeDominanceSourcePos(tpgdomsrl,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus,*_fwcount,0,pgdoms_nrl);
-    if (isFinal&&!explicit_soseos) {
-      cost += bonus;
-      bonus = 0;
-    }
-    features->set_value(pgdomsrl_,cost);
-    estimated_features->set_value(pgdomsrl_,bonus); 
-  }
-
-
-  if (flag_bdoms) {
-    cost=0; bonus=0; bdoms_state_mono=0; bdoms_state_nonmono=0; 
-    if (!nofw)
-      als->computeBorderDominanceSource(tbdoms,&cost,&bonus,
-        &bdoms_state_mono, &bdoms_state_nonmono,*edge.rule_, ant_contexts, sfw);
-    features->set_value(bdoms_,cost);
-    estimated_features->set_value(bdoms_,bonus); 
-  }
-  if (flag_orit) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    if (!nofw) als->computeOrientationTarget(torit,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus); 
-    if (DEBUG) cerr << "cost=" << cost << ", bonus=" << bonus << ", bo1=" << bo1 << ", bo1_bonus=" << bo1_bonus << ", bo2=" << bo2 << ", bo2_bonus=" << bo2_bonus << endl;
-    features->set_value(orit_,cost); 
-    //features->set_value(orit_bo1_,bo1); 
-    //features->set_value(orit_bo2_,bo2);
-    estimated_features->set_value(orit_,bonus);
-    //estimated_features->set_value(orit_bo1_,bo1_bonus);
-    //estimated_features->set_value(orit_bo2_,bo2_bonus);
-  }
-  if (flag_orit_backward) {
-    cost=0; bonus=0;
-    if (!nofw) als->computeOrientationTargetBackward(torit,&cost,&bonus,&bo1,&bo1_bonus,&bo2,&bo2_bonus);
-    features->set_value(orit_backward_,cost);
-    estimated_features->set_value(orit_backward_,bonus);
-  }
-  if (flag_domt) {
-    cost=0; bonus=0; bo1=0; bo2=0; bo1_bonus=0; bo2_bonus=0;
-    WordID _lfw=-1; int start = edge.i_;
-    WordID _rfw=-1; int end   = edge.j_;
-    if (smeta.HasReference()) {
-      const Lattice l = smeta.GetReference();
-      for (int idx=start-1; idx>=0; idx--) {
-        if (l.size()>0)
-          if (tfw.find(l[idx][0].label) !=tfw.end()) {
-            _lfw=l[idx][0].label; break;
-          }
-      }
-      for (int idx=end; idx<l.size(); idx++) { // end or end+1
-        if (l[idx].size()>0)
-          if (tfw.find(l[idx][0].label)!=tfw.end()) {
-            _rfw=l[idx][0].label; break;
-          }
-      }
-    }
-    //neighboringFWs(smeta.GetReference(),edge.i_,edge.j_,tfw,&_lfw,&_rfw);
-    if (!nofw) als->computeDominanceTarget(tdomt,_lfw,_rfw,&cost,&bonus,
-                                           &bo1,&bo1_bonus,&bo2,&bo2_bonus);
-    features->set_value(domt_,cost); 
-    //features->set_value(domt_bo1_,bo1); 
-    //features->set_value(domt_bo2_,bo2);
-    estimated_features->set_value(domt_,bonus);
-    //estimated_features->set_value(domt_bo1_,bo1_bonus);
-    //estimated_features->set_value(domt_bo2_,bo2_bonus);
-  }
-  int* vcontext = reinterpret_cast<int *>(context);
-  if (!nofw) {
-    als->BorderingSFWsOnly();
-    als->BorderingTFWsOnly();
-    als->simplify(vcontext);  
-  } else {
-    als->simplify_nofw(vcontext);
-  }
-  vcontext[50] = DoubleToInteger(bdoms_state_mono);
-  vcontext[51] = DoubleToInteger(bdoms_state_nonmono);
-  vcontext[STATE_SIZE-1] = Alignment::link(edge.i_,edge.j_); 
-  if (DEBUG) {
-    cerr << "state@traverse = ";
-    for (int idx=0; idx<STATE_SIZE; idx++) cerr << idx << "." << vcontext[idx] << " ";
-    cerr << endl;
-    cerr << "bdoms_state_mono=" << bdoms_state_mono << ", state[50]=" << IntegerToDouble(vcontext[50]) << endl;
-    cerr << "bdoms_state_nonmono=" << bdoms_state_nonmono << ", state[51]=" << IntegerToDouble(vcontext[51]) << endl;
-  }
-}
-
-int Dwarf::DoubleToInteger(double val) {
-  float x = (float)val;
-  float* px = &x;
-  int* pix = reinterpret_cast<int *>(px);
-  return *pix; 
-}
-
-double Dwarf::IntegerToDouble(int val) {
-  int *py = &val;
-  float* pd = reinterpret_cast<float *>(py);
-  return (double)*pd;
-}
-
-void Dwarf::neighboringFWs(const Lattice& l, const int& i, const int& j, const map<WordID,int>& fw_hash, int* lfw, int* rfw) {
-  *lfw=0; *rfw=0;
-  int idx=i-l[i][0].dist2next;
-  while (idx>=0) {
-    if (l[idx].size()>0) { 
-      if (fw_hash.find(l[idx][0].label)!=fw_hash.end()) {
-        lfw++;  
-      }
-    }
-    idx-=l[idx][0].dist2next;
-  }
-  idx=j+l[j][0].dist2next;
-  while (idx<l.size()) {
-    if (l[idx].size()>0) { 
-      if (fw_hash.find(l[idx][0].label)!=fw_hash.end()) {
-        rfw++;
-      }
-    }
-    idx+=l[idx][0].dist2next;
-  }
-}
-
-bool Dwarf::readOrientation(CountTable* table, const std::string& filename, std::map<WordID,int> *fw, bool pos) {
-  // the input format is
-  // source target 0 1 2 3 4 0 1 2 3 4
-  // 0 -> MA, 1 -> RA, 2 -> MG, 3 -> RG, 4 -> NO_NEIGHBOR
-  // first 01234 corresponds to the left neighbor, the second 01234 corresponds to the right neighbor
-  // append 2 more at the end as precomputed total
-  
-  // TONS of hack here. CountTable should be wrapped as a class  
-  // TODO: check whether the file exists or not, return false if not
-  if (DEBUG) cerr << "  readOrientation(" << filename << ", pos=" << pos << ")" << endl;
-  ReadFile rf(filename);  
-  istream& in = *rf.stream();
-  table->setup(24,pos);
-  table->ultimate = new int[24];
-  for (int i=0; i<24; i++) table->ultimate[i]=0;
-  ostringstream oss;
-  while (in) {
-    string line;
-    getline(in,line);
-    if (line=="") break;
-    istringstream tokenizer(line);
-    string sourceidx, source, target, word;
-    tokenizer >> source >> target; 
-    if (pos) {
-      sourceidx = source;
-      source = sourceidx.substr(0,sourceidx.find_last_of("/"));
-    }
-    if (fw->find(TD::Convert(source))==fw->end()) fw->insert(pair<WordID,int>(TD::Convert(source),1));
-
-
-    int* element = new int[24];
-    element[5] = 0;
-    for (int i=0; i<5; i++) {
-      element[i] = 0;
-      if (tokenizer >> word) element[i] = atoi(word.c_str());
-      element[5] += element[i];
-    }
-    element[11] = 0;
-    for (int i=6; i<11; i++) {
-      element[i] = 0;
-      if (tokenizer >> word) element[i] = atoi(word.c_str());
-      element[11] += element[i];
-    }
-    element[17] = 0;
-    for (int i=12; i<17; i++) {
-      element[i] = 0;
-      if (tokenizer >> word) element[i] = atoi(word.c_str());
-      element[17] += element[i];
-    }
-    element[23] = 0;
-    for (int i=18; i<23; i++) {
-      element[i] = 0;
-      if (tokenizer >> word) element[i] = atoi(word.c_str());
-      element[23] += element[i];
-    }
-    for (int i=0; i<24; i++) table->ultimate[i] += element[i];
-    oss << source << " " << target;
-    WordID key_id = TD::Convert(oss.str());
-    oss.str("");
-    if (table->model.find(key_id)!=table->model.end()) {  
-      for (int i=0; i<24; i++) table->model[key_id][i]+=element[i];
-    } else {
-      int* el2 = new int[24];
-      for (int i=0; i<24; i++) el2[i] = element[i];
-      table->model.insert(pair<WordID,int*>(key_id,el2));
-    }
-    
-    oss << source;
-    key_id = TD::Convert(oss.str());
-    oss.str("");
-    if (table->model.find(key_id)!=table->model.end()) {    
-      for (int i=0; i<24; i++) table->model[key_id][i]+=element[i];
-    } else {
-      int* el2 = new int[24];
-      for (int i=0; i<24; i++) el2[i] = element[i];
-      table->model.insert(pair<WordID,int*>(key_id,el2));
-    }
-
-    if (pos) {
-      oss << sourceidx << " " << target;
-      key_id = TD::Convert(oss.str());
-      oss.str(""); 
-      if (table->model.find(key_id)!=table->model.end()) {
-        for (int i=0; i<24; i++) table->model[key_id][i]+=element[i];
-      } else {
-        int* el2 = new int[24];
-        for (int i=0; i<24; i++) el2[i] = element[i];
-        table->model.insert(pair<WordID,int*>(key_id,el2));
-      }
-    }
-    delete[] element;
-  }  
-  return true;    
-}
-
-bool Dwarf::readList(const std::string& filename, std::map<WordID,int>* fw) {
-  ReadFile rf(filename);
-  istream& in = *rf.stream();
-  while (in) {
-    string word;
-    getline(in,word);
-    if (fw->find(TD::Convert(word))==fw->end()) fw->insert(pair<WordID,int>(TD::Convert(word),1)); 
-  }
-  return true;
-}
-
-bool Dwarf::readDominance(CountTable* table, const std::string& filename, std::map<WordID,int>* fw, bool pos) {
-  // the input format is 
-  // source1 source2 target1 target2 0 1 2 3
-  // 0 -> dontcase 1->leftfirst 2->rightfirst 3->neither 
-  if (DEBUG) cerr << "readDominance(" << filename << ",pos="<< pos << ")" << endl;
-  ReadFile rf(filename);
-  istream& in = *rf.stream();
-  table->ultimate = new int[5];
-  table->setup(5,pos);
-  for (int i=0; i<5; i++) table->ultimate[i]=0;
-  while (in) {
-    string line, word;
-    getline(in,line);
-    if (line=="") break;
-    string source1idx, source2idx, target1, target2, source1, source2;
-    ostringstream oss; 
-    WordID key_id;
-    istringstream tokenizer(line);
-    tokenizer >> source1 >> source2 >> target1 >> target2; 
-    if (pos) {
-      source1idx = source1;
-      source2idx = source2;
-      source1 = source1idx.substr(0,source1idx.find_last_of("/"));
-      source2 = source2idx.substr(0,source2idx.find_last_of("/"));
-    }
-    if (fw->find(TD::Convert(source1))==fw->end()) fw->insert(pair<WordID,int>(TD::Convert(source1),1));
-    if (fw->find(TD::Convert(source2))==fw->end()) fw->insert(pair<WordID,int>(TD::Convert(source2),1));
-
-    int* element = new int[5];
-    element[4]=0;
-    for (int i=0; i<4; i++) {
-      element[i]  = 0;
-      if (tokenizer >> word) element[i] = atoi(word.c_str());
-      element[4]+=element[i];
-    }
-    for (int i=0; i<5; i++) table->ultimate[i] += element[i];
-
-    oss << source1 << " " << source2 << " " << target1 << " " << target2;
-    key_id = TD::Convert(oss.str());
-    oss.str("");
-    if (table->model.find(key_id)!=table->model.end()) { 
-      for (int i=0; i<5; i++) table->model[key_id][i]+=element[i];
-    } else {
-      int* el2 = new int[5]; 
-      for (int i=0; i<5; i++) el2[i]=element[i];
-      table->model.insert(pair<WordID,int*>(key_id,el2));
-    }
-
-    oss << source1 << " " << source2;
-    key_id = TD::Convert(oss.str());
-    oss.str("");
-    if (table->model.find(key_id)!=table->model.end()) {  
-      for (int i=0; i<5; i++) table->model[key_id][i]+=element[i];
-    } else {
-      int* el2 = new int[5]; 
-      for (int i=0; i<5; i++) el2[i]=element[i];
-      table->model.insert(pair<WordID,int*>(key_id,el2));
-    }
-
-    if (pos) {
-      oss << source1idx << " " << source2idx << " " << target1 << " " << target2;
-      key_id = TD::Convert(oss.str());
-      oss.str("");
-      if (table->model.find(key_id)!=table->model.end()) {  
-        for (int i=0; i<5; i++) table->model[key_id][i]+=element[i];
-      } else {
-        int* el2 = new int[5]; 
-        for (int i=0; i<5; i++) el2[i]=element[i];
-        table->model.insert(pair<WordID,int*>(key_id,el2));
-      }
-    }
-    delete element;
-  }
-
-  return true;    
-}
-
-bool Dwarf::readTags(const std::string& filename, std::map<WordID,WordID>* tags) {
-  ReadFile rf(filename);
-  istream& in = *rf.stream();
-  while(in) {
-    string line, word, tag;
-    getline(in,line);
-    if (line=="") break;
-    istringstream tokenizer(line);
-    tokenizer >> tag >> word;
-    tags->insert(pair<WordID,WordID>(TD::Convert(word),TD::Convert(tag)));
-  }
-  return true;
-}
-
-bool Dwarf::generalizeOrientation(CountTable* table, const std::map<WordID,WordID>& tags, bool pos) {
-  map<string,int*> generalized;
-  for (map<WordID,int*>::iterator it=table->model.begin(); it!=table->model.end(); it++) {
-    string source, target;
-    istringstream tokenizer(TD::Convert(it->first));
-    tokenizer >> source >> target;
-    string idx = "";
-    if (pos) {
-      int found = source.find_last_of("/");
-      if (found!=string::npos && found>0) { 
-        idx = source.substr(found+1);
-        source = source.substr(0,found);
-      }
-    }
-    map<WordID,WordID>::const_iterator tags_iter = tags.find(TD::Convert(source));
-    if (tags_iter!=tags.end()) {
-      ostringstream genkey;
-      genkey << TD::Convert(tags_iter->second);
-      if (idx!="") genkey << "/" << idx;
-      if (target!="") genkey << " " << target;
-      int* model;
-      if (generalized.find(genkey.str())!=generalized.end()) {
-        model = generalized[genkey.str()];
-        for (int i=0; i<24; i++) model[i] += it->second[i];
-      } else {
-        int* el = new int[24];
-        for (int i=0; i<24; i++) el[i] = it->second[i];
-        generalized.insert(pair<string,int*>(genkey.str(),el));
-      }
-    }
-  }
-  for (map<WordID,int*>::iterator it=table->model.begin(); it!=table->model.end(); it++) {
-    string source, target;
-    istringstream tokenizer(TD::Convert(it->first));
-    tokenizer >> source >> target;
-    string idx = "";
-    if (pos) {
-      int found = source.find_last_of("/");
-      if (found!=string::npos && found>0) {
-        idx = source.substr(found+1);
-        source = source.substr(0,found);
-      }
-    }
-    map<WordID,WordID>::const_iterator tags_iter = tags.find(TD::Convert(source));
-    if (tags_iter!=tags.end()) {
-      ostringstream genkey;
-      genkey << TD::Convert(tags_iter->second);
-      if (idx!="") genkey << "/" << idx;
-      if (target!="") genkey << " " << target;
-      if (generalized.find(genkey.str())!=generalized.end()) {
-        delete it->second;
-        it->second = generalized[genkey.str()];
-      }
-    }
-  }
-  return false; // no idea if this is right
-}
- 
-
-
-bool Dwarf::generalizeDominance(CountTable* table, const std::map<WordID,WordID>& tags, bool pos) {
-  map<string,int*> generalized;
-  ostringstream oss;
-  for (map<WordID,int*>::iterator it=table->model.begin(); it!=table->model.end(); it++) {
-    string source1, source2, target1, target2;
-    string idx1 = ""; string idx2 = "";
-    istringstream tokenizer(TD::Convert(it->first));
-    tokenizer >> source1 >> source2 >> target1 >> target2;
-    if (DEBUG) cerr << "source1=|" << source1 << "|, source2=|" << source2 << "|, target1=|" << target1 << "|, target2=|" << target2 << "|" << endl;
-    if (pos) {
-      int found1 = source1.find_last_of("/");
-      int found2 = source2.find_last_of("/");
-      if (found1!=string::npos && found2!=string::npos && found1>0 && found2>0) {
-        idx1 = source1.substr(found1+1);
-        source1 = source1.substr(0,found1);
-        idx2 = source2.substr(found2+1);
-        source2 = source2.substr(0,found2);
-      }
-    }
-    if (DEBUG) 
-      cerr << "[U]source1='" << source1 << "', idx1='"<< idx1 << "', source2='" << source2 << "', idx2='"<< idx2 << "', target1='" << target1 << "', target2='" << target2 << "'" << endl;
-    map<WordID,WordID>::const_iterator tags_iter1 = tags.find(TD::Convert(source1));
-    map<WordID,WordID>::const_iterator tags_iter2 = tags.find(TD::Convert(source2));
-    if (tags_iter1!=tags.end()) 
-      source1 = TD::Convert(tags_iter1->second);
-    oss << source1;
-    if (idx1!="") oss << "/" << idx1;
-    if (tags_iter2!=tags.end())
-      source2 = TD::Convert(tags_iter2->second);
-    oss << " " << source2;
-    if (idx2!="") oss << "/" << idx2;
-    if (target1!="" && target2!="") oss << " " << target1 << " " << target2;
-    
-    if (DEBUG) cerr << "generalized key = '" << oss.str() << "'" << endl; 
-    if (generalized.find(oss.str())!=generalized.end()) {
-      int* model = generalized[oss.str()];
-      for (int i=0; i<5; i++) model[i] += it->second[i];
-    } else {
-      int* model = new int[5];
-      for (int i=0; i<5; i++) model[i] = it->second[i];
-      generalized.insert(pair<string,int*>(oss.str(),model));
-    }    
-    oss.str("");
-  }
-  
-  if (DEBUG) {
-    for (map<string,int*>::const_iterator it=generalized.begin(); it!=generalized.end(); it++) {
-      cerr << "GENERALIZED = " << it->first << ", ";
-      for (int i=0; i<5; i++) cerr << it->second[i] << " ";
-      cerr << endl;
-    }
-  }
-
-  for (map<WordID,int*>::iterator it=table->model.begin(); it!=table->model.end(); it++) {
-    string source1, source2, target1, target2;
-    string idx1 = ""; string idx2 = "";
-    istringstream tokenizer(TD::Convert(it->first));
-    tokenizer >> source1 >> source2 >> target1 >> target2;
-    if (pos) {
-      int found1 = source1.find_last_of("/");
-      int found2 = source2.find_last_of("/");
-      if (found1!=string::npos && found2!=string::npos && found1>0 && found2>0) {
-        idx1 = source1.substr(found1+1);
-        source1 = source1.substr(0,found1);
-        idx2 = source2.substr(found2+1);
-        source2 = source2.substr(0,found2);
-      }
-    }
-    map<WordID,WordID>::const_iterator tags_iter1 = tags.find(TD::Convert(source1));
-    map<WordID,WordID>::const_iterator tags_iter2 = tags.find(TD::Convert(source2));
-    if (tags_iter1!=tags.end())
-      source1 = TD::Convert(tags_iter1->second);
-    oss << source1;
-    if (idx1!="") oss << "/" << idx1;
-    if (tags_iter2!=tags.end())
-      source2 = TD::Convert(tags_iter2->second);
-    oss << " " << source2;
-    if (idx2!="") oss << "/" << idx2;
-    if (target1!="" && target2!="") oss << " " << target1 << " " << target2;
-    
-    if (generalized.find(oss.str())!=generalized.end()) {
-      if (DEBUG) cerr << " generalizing "<< TD::Convert(it->first) << " into " << oss.str() << endl; 
-      if (DEBUG) {
-        cerr << "  model from ";
-        for (int i=0; i<5; i++) cerr << it->second[i] << " "; 
-        cerr << endl;
-      }
-      delete it->second;
-      it->second = generalized[oss.str()];
-      if (DEBUG) {
-        cerr << "  into ";
-        for (int i=0; i<5; i++) cerr << it->second[i] << " "; 
-        cerr << endl;
-      }
-    }    
-    oss.str("");
-  }
-
-}
diff --git a/decoder/ff_dwarf.h b/decoder/ff_dwarf.h
deleted file mode 100644
index 3d6a7da6..00000000
--- a/decoder/ff_dwarf.h
+++ /dev/null
@@ -1,100 +0,0 @@
-#include <vector>
-#include <map>
-#include <string>
-#include "ff.h"
-#include "dwarf.h"
-#include "lattice.h"
-
-using namespace std;
-
-class Dwarf : public FeatureFunction {
- public:
-  Dwarf(const std::string& param);
-  /* State-related param
-     STATE_SIZE: the number of ints 
-     MAXIMUM_ALIGNMENTS: the maximum number of alignments in the states, 
-                         each alignment point is encoded in one int 
-                         (the first two bytes for source, and the remaining one for target)
-  */
-  static const int STATE_SIZE=53; 
-  static const int IMPOSSIBLY_LARGE_POS = 9999999;
-  static const int MAXIMUM_ALIGNMENTS=37;
-  /* Read from file the Orientation(Source|Target model parameter. */ 
-  static bool readOrientation(CountTable* table, const std::string& filename, std::map<WordID,int> *fw, bool pos=false);
-  /* Read from file the Dominance(Source|Target) model parameter. */ 
-  static bool readDominance(CountTable* table, const std::string& filename, std::map<WordID,int> *fw, bool pos=false);
-  static bool readList(const std::string& filename, std::map<WordID,int>* fw);     
-  static double IntegerToDouble(int val);
-  static int DoubleToInteger(double val);
-  bool readTags(const std::string& filename, std::map<WordID,WordID>* tags);
-  bool generalizeOrientation(CountTable* table, const std::map<WordID,WordID>& tags, bool pos=false);  
-  bool generalizeDominance(CountTable* table, const std::map<WordID,WordID>& tags, bool pos=false);  
-  static void stripIndex(const string& source, string* pkey, string* pidx) {
-    if (DEBUG) cerr << "    stripIndex(" << source << ")" << endl;
-    int found = source.find_last_of("/");
-    string idx = source.substr(found+1);
-    string key = source.substr(0,found);
-    if (DEBUG) cerr << "      found=" << found << "," << key << "," << idx << endl;
-    pkey = &key;
-    pidx = &idx;
-  }
-
-
- protected:
-  /* The high-level workflow is as follow:
-     1. call *als->prepare*, which constructs the full alignment of the edge while taking into account the antecedents
-        also in this call, function words are identified. Most of the work in this call is to make sure the indexes 
-        of the alignments (including the function words) are consistent with the newly created alignment
-     2. call *als->computeOrientationSource*, *als->computeOrientationTarget*, 
-        *als->computeDominanceSource*, or *als->computeDominanceTarget*
-        and pass the resulting score to either *features* or to *estimated_features*
-     3. call *als->BorderingSFWsOnly()* and *als->BorderingTFWsOnly()*, which removes records of all function word
-        alignments except those at the borders. Note that fw alignments kept may be more than two on each side
-        for examples if there are a number of unaligned fw alignments before the leftmost alignment or the rightmost one
-     4. call *als->simplify()*, which assigns the state of this edge (*context*). It simplifies the alignment space to 
-        its most compact representation, enough to compute the unscored models. This is done by observing the surviving
-        function word alignments set by 3.
-  */ 
-  void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const HG::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     SparseVector<double>* features,
-                                     SparseVector<double>* estimated_features,
-                                     void* context) const;
- private:
-  Alignment* als;
-  /* Feature IDs set by calling FD::Convert(model's string) */
-  int oris_, oris_bo1_, oris_bo2_, orit_, orit_bo1_, orit_bo2_;
-  int oris_backward_, orit_backward_, porislr_, porisrl_, goris_, pgorislr_, pgorisrl_;
-  int pdomslr_, pdomsrl_, pgdomslr_, pgdomsrl_;
-  int doms_, doms_bo1_, doms_bo2_, domt_, domt_bo1_, domt_bo2_;
-  int tfw_count_;
-  int bdoms_; 
-  int poris_count;
-  int pgoris_count;
-  int poris_nlr, poris_nrl; // maximum depth (1->from the beginning of the sentence, 2-> from the end of the sentence)
-  int pgoris_nlr, pgoris_nrl;
-  int pdoms_nlr, pdoms_nrl;
-  int pgdoms_nlr, pgdoms_nrl;
-  int* _sent_id;
-  int* _fwcount;
-  WordID kSOS;
-  WordID kEOS;
-  string sSOS;
-  string sEOS;
-  WordID kGOAL;
-  /* model's flag, if set true will invoke the model scoring */
-  bool flag_oris, flag_orit, flag_doms, flag_domt, flag_tfw_count, flag_oris_backward, flag_orit_backward, flag_bdoms;
-  bool flag_porislr, flag_porisrl, flag_goris, flag_pgorislr, flag_pgorisrl;
-  bool explicit_soseos;
-  bool flag_pdomslr, flag_pdomsrl, flag_pgdomslr, flag_pgdomsrl, flag_gdoms;
-  /* a collection of Source function words (sfw) and Target function words (tfw) */
-  std::map<WordID,int> sfw;
-  std::map<WordID,int> tfw;
-  std::map<WordID,WordID> tags;
-  /* a collection of model's parameter */
-  CountTable toris, torit, tdoms, tbdoms, tdomt, tporislr, tporisrl, tgoris, tpgorislr, tpgorisrl;
-  CountTable tpdomslr, tpdomsrl, tpgdomslr, tpgdomsrl;
-  void neighboringFWs(const Lattice& l, const int& i, const int& j, const map<WordID,int>& fw_hash, int* lfw, int* rfw);
-};
-
diff --git a/decoder/ff_lm.cc b/decoder/ff_lm.cc
index 6ec7b4f3..bc51076f 100644
--- a/decoder/ff_lm.cc
+++ b/decoder/ff_lm.cc
@@ -61,11 +61,6 @@ char const* usage_verbose="-n determines the name of the feature (and its weight
 #include "hg.h"
 #include "stringlib.h"
 
-#ifdef HAVE_RANDLM
-// http://randlm.sourceforge.net/
-#include "RandLM.h"
-#endif
-
 using namespace std;
 
 string LanguageModel::usage(bool param,bool verbose) {
@@ -542,99 +537,3 @@ void LanguageModel::FinalTraversalFeatures(const void* ant_state,
   features->set_value(fid_, imp().FinalTraversalCost(ant_state));
 }
 
-#ifdef HAVE_RANDLM
-struct RandLMImpl : public LanguageModelImpl {
-  RandLMImpl(int order, randlm::RandLM* rlm) :
-      LanguageModelImpl(order),
-      rlm_(rlm),
-      oov_(rlm->getWordID(rlm->getOOV())),
-      rb_(1000, oov_) {
-    map<int, randlm::WordID> map_cdec2randlm;
-    int max_wordid = 0;
-    for(map<randlm::Word, randlm::WordID>::const_iterator it = rlm->vocabStart();
-        it != rlm->vocabEnd(); ++it) {
-      const int cur = TD::Convert(it->first);
-      map_cdec2randlm[TD::Convert(it->first)] = it->second;
-      if (cur > max_wordid) max_wordid = cur;
-    }
-    cdec2randlm_.resize(max_wordid + 1, oov_);
-    for (map<int, randlm::WordID>::iterator it = map_cdec2randlm.begin();
-         it != map_cdec2randlm.end(); ++it)
-      cdec2randlm_[it->first] = it->second;
-    map_cdec2randlm.clear();
-  }
-
-  inline randlm::WordID Convert2RandLM(int w) {
-    return (w < cdec2randlm_.size() ? cdec2randlm_[w] : oov_);
-  }
-
-  virtual double WordProb(int word, int* context) {
-    int i = order_;
-    int c = 1;
-    rb_[i] = Convert2RandLM(word);
-    while (i > 1 && *context > 0) {
-      --i;
-      rb_[i] = Convert2RandLM(*context);
-      ++context;
-      ++c;
-    }
-    const void* finalState = 0;
-    int found;
-    //cerr << "I = " << i << endl;
-    return rlm_->getProb(&rb_[i], c, &found, &finalState);
-  }
- private:
-  boost::shared_ptr<randlm::RandLM> rlm_;
-  randlm::WordID oov_;
-  vector<randlm::WordID> cdec2randlm_;
-  vector<randlm::WordID> rb_;
-};
-
-LanguageModelRandLM::LanguageModelRandLM(const string& param) :
-    fid_(FD::Convert("RandLM")) {
-  vector<string> argv;
-  int argc = SplitOnWhitespace(param, &argv);
-  int order = 3;
-  // TODO add support for -n FeatureName
-  string filename;
-  if (argc < 1) { cerr << "RandLM requires a filename, minimally!\n"; abort(); }
-  else if (argc == 1) { filename = argv[0]; }
-  else if (argc == 2 || argc > 3) { cerr << "Don't understand 'RandLM " << param << "'\n"; }
-  else if (argc == 3) {
-    if (argv[0] == "-o") {
-      order = atoi(argv[1].c_str());
-      filename = argv[2];
-    } else if (argv[1] == "-o") {
-      order = atoi(argv[2].c_str());
-      filename = argv[0];
-    }
-  }
-//  set_order(order);
-  int cache_MB = 200; // increase cache size
-  randlm::RandLM* rlm = randlm::RandLM::initRandLM(filename, order, cache_MB);
-  assert(rlm != NULL);
-  pimpl_ = new RandLMImpl(order, rlm);
-}
-
-LanguageModelRandLM::~LanguageModelRandLM() {
-  delete pimpl_;
-}
-
-void LanguageModelRandLM::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                          const Hypergraph::Edge& edge,
-                                          const vector<const void*>& ant_states,
-                                          SparseVector<double>* features,
-                                          SparseVector<double>* estimated_features,
-                                          void* state) const {
-  (void) smeta;
-  features->set_value(fid_, imp().LookupWords(*edge.rule_, ant_states, state));
-  estimated_features->set_value(fid_, imp().EstimateProb(state));
-}
-
-void LanguageModelRandLM::FinalTraversalFeatures(const void* ant_state,
-                                           SparseVector<double>* features) const {
-  features->set_value(fid_, imp().FinalTraversalCost(ant_state));
-}
-
-#endif
-
diff --git a/decoder/ff_lm.h b/decoder/ff_lm.h
index 94e18f00..85e79704 100644
--- a/decoder/ff_lm.h
+++ b/decoder/ff_lm.h
@@ -69,26 +69,4 @@ class LanguageModel : public FeatureFunction {
   /* mutable */ LanguageModelInterface* pimpl_;
 };
 
-#ifdef HAVE_RANDLM
-class LanguageModelRandLM : public FeatureFunction {
- public:
-  // param = "filename.lm [-o n]"
-  LanguageModelRandLM(const std::string& param);
-  ~LanguageModelRandLM();
-  virtual void FinalTraversalFeatures(const void* context,
-                                      SparseVector<double>* features) const;
-  std::string DebugStateToString(const void* state) const;
- protected:
-  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const HG::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     SparseVector<double>* features,
-                                     SparseVector<double>* estimated_features,
-                                     void* out_context) const;
- private:
-  const int fid_;
-  mutable LanguageModelImpl* pimpl_;
-};
-#endif
-
 #endif
diff --git a/decoder/ff_source_syntax.cc b/decoder/ff_source_syntax.cc
index a1997695..95709076 100644
--- a/decoder/ff_source_syntax.cc
+++ b/decoder/ff_source_syntax.cc
@@ -2,6 +2,12 @@
 
 #include <sstream>
 #include <stack>
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_set; }
+#endif
 
 #include "hg.h"
 #include "sentence_metadata.h"
diff --git a/decoder/ff_source_syntax2.cc b/decoder/ff_source_syntax2.cc
index 08ece917..622c6908 100644
--- a/decoder/ff_source_syntax2.cc
+++ b/decoder/ff_source_syntax2.cc
@@ -3,7 +3,6 @@
 #include <sstream>
 #include <stack>
 #include <string>
-#include <tr1/unordered_set>
 
 #include "sentence_metadata.h"
 #include "array2d.h"
@@ -126,8 +125,7 @@ struct SourceSyntaxFeatures2Impl {
 
   Array2D<WordID> src_tree;  // src_tree(i,j) NT = type
   mutable Array2D<map<const TRule*, int> > fids_ef;    // fires for fully lexicalized
-  tr1::unordered_set<int> feature_filter;
-
+  unordered_set<int> feature_filter;
 };
 
 SourceSyntaxFeatures2::SourceSyntaxFeatures2(const string& param) :
diff --git a/decoder/ff_source_syntax2_p.cc b/decoder/ff_source_syntax2_p.cc
index dfa791ea..130144fa 100644
--- a/decoder/ff_source_syntax2_p.cc
+++ b/decoder/ff_source_syntax2_p.cc
@@ -3,7 +3,12 @@
 #include <sstream>
 #include <stack>
 #include <string>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_set; }
+#endif
 
 #include "sentence_metadata.h"
 #include "array2d.h"
@@ -133,8 +138,7 @@ struct PSourceSyntaxFeatures2Impl {
 
   Array2D<WordID> src_tree;  // src_tree(i,j) NT = type
   mutable Array2D<map<const TRule*, int> > fids_ef;    // fires for fully lexicalized
-  tr1::unordered_set<int> feature_filter;
-
+  unordered_set<int> feature_filter;
 };
 
 PSourceSyntaxFeatures2::PSourceSyntaxFeatures2(const string& param) :
diff --git a/decoder/ff_source_syntax_p.cc b/decoder/ff_source_syntax_p.cc
index cd081544..1d3dc497 100644
--- a/decoder/ff_source_syntax_p.cc
+++ b/decoder/ff_source_syntax_p.cc
@@ -2,7 +2,12 @@
 
 #include <sstream>
 #include <stack>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
 
 #include "sentence_metadata.h"
 #include "array2d.h"
@@ -139,7 +144,7 @@ struct PSourceSyntaxFeaturesImpl {
   Array2D<WordID> src_tree;  // src_tree(i,j) NT = type
   // mutable Array2D<int> fids_cat;   // this tends to overfit baddly
   mutable Array2D<map<const TRule*, int> > fids_ef;    // fires for fully lexicalized
-  tr1::unordered_set<int> feature_filter;
+  unordered_set<int> feature_filter;
 };
 
 PSourceSyntaxFeatures::PSourceSyntaxFeatures(const string& param) :
diff --git a/decoder/ff_wordalign.cc b/decoder/ff_wordalign.cc
index 1491819d..8ed053c2 100644
--- a/decoder/ff_wordalign.cc
+++ b/decoder/ff_wordalign.cc
@@ -7,7 +7,12 @@
 #include <string>
 #include <cmath>
 #include <bitset>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 #include <boost/tuple/tuple.hpp>
 #include "boost/tuple/tuple_comparison.hpp"
@@ -249,7 +254,7 @@ void NewJump::FireFeature(const SentenceMetadata& smeta,
   if (fp1_)   get<6>(key) = GetSourceWord(id, cur_src_index + 1);
   if (fprev_) get<7>(key) = GetSourceWord(id, prev_src_index);
 
-  static std::tr1::unordered_map<NewJumpFeatureKey, int, KeyHash> fids;
+  static std::unordered_map<NewJumpFeatureKey, int, KeyHash> fids;
   int& fid = fids[key];
   if (!fid) {
     ostringstream os;
diff --git a/decoder/ff_wordalign.h b/decoder/ff_wordalign.h
index ba3d0b9b..50f0dafa 100644
--- a/decoder/ff_wordalign.h
+++ b/decoder/ff_wordalign.h
@@ -5,8 +5,16 @@
 #include "array2d.h"
 #include "factored_lexicon_helper.h"
 
+#include <boost/functional/hash.hpp>
+#include <cassert>
 #include <boost/scoped_ptr.hpp>
 #include <boost/multi_array.hpp>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 class RelativeSentencePosition : public FeatureFunction {
  public:
@@ -124,9 +132,6 @@ class LexicalTranslationTrigger : public FeatureFunction {
   std::vector<std::vector<WordID> > triggers_;
 };
 
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include <cassert>
 class BlunsomSynchronousParseHack : public FeatureFunction {
  public:
   BlunsomSynchronousParseHack(const std::string& param);
@@ -196,7 +201,7 @@ class BlunsomSynchronousParseHack : public FeatureFunction {
 
   const int fid_;
   mutable int cur_sent_;
-  typedef std::tr1::unordered_map<std::vector<WordID>, int, boost::hash<std::vector<WordID> > > Vec2Int;
+  typedef std::unordered_map<std::vector<WordID>, int, boost::hash<std::vector<WordID> > > Vec2Int;
   mutable Vec2Int cur_map_;
   const std::vector<WordID> mutable * cur_ref_;
   mutable std::vector<std::vector<WordID> > refs_;
diff --git a/decoder/ff_wordset.cc b/decoder/ff_wordset.cc
index 70cea7de..9be6f2e0 100644
--- a/decoder/ff_wordset.cc
+++ b/decoder/ff_wordset.cc
@@ -2,21 +2,67 @@
 
 #include "hg.h"
 #include "fdict.h"
+#include "filelib.h"
+#include <boost/algorithm/string.hpp>
 #include <sstream>
 #include <iostream>
 
 using namespace std;
 
+void WordSet::parseArgs(const string& args, string* featName, string* vocabFile, bool* oovMode) {
+  vector<string> toks(10);
+  boost::split(toks, args, boost::is_any_of(" "));
+
+  *oovMode = false;
+
+  // skip initial feature name
+  for(vector<string>::const_iterator it = toks.begin(); it != toks.end(); ++it) {
+    if(*it == "-v") {
+      *vocabFile = *++it; // copy
+
+    } else if(*it == "-N") {
+      *featName = *++it;
+    } else if(*it == "--oov") {
+       *oovMode = true;
+    } else {
+       cerr << "Unrecognized argument: " << *it << endl;
+       exit(1);
+    }
+  }
+
+  if(*featName == "") {
+    cerr << "featName (-N) not specified for WordSet" << endl;
+    exit(1);
+  }
+  if(*vocabFile == "") {
+    cerr << "vocabFile (-v) not specified for WordSet" << endl;
+    exit(1);
+  }
+}
+
+void WordSet::loadVocab(const string& vocabFile, unordered_set<WordID>* vocab) {
+  ReadFile rf(vocabFile);
+  if (!rf) {
+    cerr << "Unable to open file: " << vocabFile; 
+    abort();
+  }
+  string line;
+  while (getline(*rf.stream(), line)) {
+    boost::trim(line);
+    if(line.empty()) continue;
+    WordID vocabId = TD::Convert(line);
+    vocab->insert(vocabId);
+  }
+}
+
 void WordSet::TraversalFeaturesImpl(const SentenceMetadata& /*smeta*/ ,
 				    const Hypergraph::Edge& edge,
 				    const vector<const void*>& /* ant_contexts */,
 				    SparseVector<double>* features,
 				    SparseVector<double>* /* estimated_features */,
 				    void* /* context */) const {
-
   double addScore = 0.0;
-  for(std::vector<WordID>::const_iterator it = edge.rule_->e_.begin(); it != edge.rule_->e_.end(); ++it) {
-    
+  for(vector<WordID>::const_iterator it = edge.rule_->e_.begin(); it != edge.rule_->e_.end(); ++it) {
     bool inVocab = (vocab_.find(*it) != vocab_.end());
     if(oovMode_ && !inVocab) {
       addScore += 1.0;
diff --git a/decoder/ff_wordset.h b/decoder/ff_wordset.h
index 639e1514..affee2f4 100644
--- a/decoder/ff_wordset.h
+++ b/decoder/ff_wordset.h
@@ -4,14 +4,18 @@
 #include "ff.h"
 #include "tdict.h"
 
-#include <tr1/unordered_set>
-#include <boost/algorithm/string.hpp>
-
 #include <vector>
 #include <string>
 #include <iostream>
 #include <fstream>
 
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_set; }
+#endif
+
 class WordSet : public FeatureFunction {
  public:
 // we depend on the order of the initializer list
@@ -42,69 +46,12 @@ class WordSet : public FeatureFunction {
                                      void* context) const;
  private:
 
-  static void loadVocab(const std::string& vocabFile, std::tr1::unordered_set<WordID>* vocab) {
-
-      std::ifstream file;
-      std::string line;
-
-      file.open(vocabFile.c_str(), std::fstream::in);
-      if (file.is_open()) {
-	unsigned lineNum = 0;
-	while (!file.eof()) {
-	  ++lineNum;
-	  getline(file, line);
-	  boost::trim(line);
-	  if(line.empty()) {
-	    continue;
-	  }
-	  
-	  WordID vocabId = TD::Convert(line);
-	  vocab->insert(vocabId);
-	}
-	file.close();
-      } else {
-	std::cerr << "Unable to open file: " << vocabFile; 
-	exit(1);
-      }
-  }
-
-  static void parseArgs(const std::string& args, std::string* featName, std::string* vocabFile, bool* oovMode) {
-
-    std::vector<std::string> toks(10);
-    boost::split(toks, args, boost::is_any_of(" "));
-
-    *oovMode = false;
-
-    // skip initial feature name
-    for(std::vector<std::string>::const_iterator it = toks.begin(); it != toks.end(); ++it) {
-      if(*it == "-v") {
-	*vocabFile = *++it; // copy
-
-      } else if(*it == "-N") {
-	*featName = *++it;
-
-      } else if(*it == "--oov") {
-	*oovMode = true;
-
-      } else {
-	std::cerr << "Unrecognized argument: " << *it << std::endl;
-	exit(1);
-      }
-    }
-
-    if(*featName == "") {
-      std::cerr << "featName (-N) not specified for WordSet" << std::endl;
-      exit(1);
-    }
-    if(*vocabFile == "") {
-      std::cerr << "vocabFile (-v) not specified for WordSet" << std::endl;
-      exit(1);
-    }
-  }
+  static void parseArgs(const std::string& args, std::string* featName, std::string* vocabFile, bool* oovMode);
+  static void loadVocab(const std::string& vocabFile, std::unordered_set<WordID>* vocab);
 
   int fid_;
   bool oovMode_;
-  std::tr1::unordered_set<WordID> vocab_;
+  std::unordered_set<WordID> vocab_;
 };
 
 #endif
diff --git a/decoder/grammar.cc b/decoder/grammar.cc
index ee43f537..f2530d35 100644
--- a/decoder/grammar.cc
+++ b/decoder/grammar.cc
@@ -3,15 +3,20 @@
 #include <algorithm>
 #include <utility>
 #include <map>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
+# include <tr1/unordered_map>
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
 
 #include "rule_lexer.h"
 #include "filelib.h"
 #include "tdict.h"
 
 using namespace std;
-using namespace std::tr1;
 
 const vector<TRulePtr> Grammar::NO_RULES;
 
diff --git a/decoder/hg_intersect.cc b/decoder/hg_intersect.cc
index ad5b701a..c5f1cc91 100644
--- a/decoder/hg_intersect.cc
+++ b/decoder/hg_intersect.cc
@@ -1,7 +1,12 @@
 #include "hg_intersect.h"
 
 #include <vector>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 #include "fast_lexical_cast.hpp"
 #include <boost/functional/hash.hpp>
 
@@ -13,7 +18,6 @@
 #include "bottom_up_parser.h"
 
 using boost::lexical_cast;
-using namespace std::tr1;
 using namespace std;
 
 struct RuleFilter {
diff --git a/decoder/kbest.h b/decoder/kbest.h
index 44c23151..cd386aef 100644
--- a/decoder/kbest.h
+++ b/decoder/kbest.h
@@ -3,7 +3,12 @@
 
 #include <vector>
 #include <utility>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_set; }
+#endif
 
 #include <boost/shared_ptr.hpp>
 #include <boost/type_traits.hpp>
@@ -22,7 +27,7 @@ namespace KBest {
 
   // optional, filter unique yield strings
   struct FilterUnique {
-    std::tr1::unordered_set<std::vector<WordID>, boost::hash<std::vector<WordID> > > unique;
+    std::unordered_set<std::vector<WordID>, boost::hash<std::vector<WordID> > > unique;
 
     bool operator()(const std::vector<WordID>& yield) {
       return !unique.insert(yield).second;
@@ -111,7 +116,7 @@ namespace KBest {
     };
     typedef std::vector<Derivation*> CandidateHeap;
     typedef std::vector<Derivation*> DerivationList;
-    typedef std::tr1::unordered_set<
+    typedef std::unordered_set<
        const Derivation*, DerivationUniquenessHash, DerivationUniquenessEquals> UniqueDerivationSet;
 
     struct NodeDerivationState {
diff --git a/decoder/maxtrans_blunsom.cc b/decoder/maxtrans_blunsom.cc
index 774e4170..8d1d471c 100644
--- a/decoder/maxtrans_blunsom.cc
+++ b/decoder/maxtrans_blunsom.cc
@@ -2,8 +2,14 @@
 
 #include <vector>
 #include <algorithm>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
+# include <tr1/unordered_map>
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
 
 #include <boost/tuple/tuple.hpp>
 #include <boost/functional/hash.hpp>
@@ -14,7 +20,6 @@
 
 using boost::tuple;
 using namespace std;
-using namespace std::tr1;
 
 namespace Hack {
 
diff --git a/decoder/phrasebased_translator.cc b/decoder/phrasebased_translator.cc
index d65e44d1..321fb286 100644
--- a/decoder/phrasebased_translator.cc
+++ b/decoder/phrasebased_translator.cc
@@ -2,8 +2,14 @@
 
 #include <queue>
 #include <iostream>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
+# include <tr1/unordered_map>
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
 
 #include <boost/tuple/tuple.hpp>
 #include <boost/functional/hash.hpp>
@@ -17,7 +23,6 @@
 #include "array2d.h"
 
 using namespace std;
-using namespace std::tr1;
 using namespace boost::tuples;
 
 struct Coverage : public vector<bool> {
diff --git a/decoder/scfg_translator.cc b/decoder/scfg_translator.cc
index 6f0b003b..a506c591 100644
--- a/decoder/scfg_translator.cc
+++ b/decoder/scfg_translator.cc
@@ -1,13 +1,9 @@
-//TODO: bottom-up pruning, with actual final models' (appropriately weighted) heuristics and local scores.
-
-//TODO: grammar heuristic (min cost of reachable rule set) for binarizations (active edges) if we wish to prune those also
-
-#include "hash.h"
-#include "translator.h"
 #include <algorithm>
 #include <vector>
 #include <boost/foreach.hpp>
 #include <boost/functional/hash.hpp>
+#include "hash.h"
+#include "translator.h"
 #include "hg.h"
 #include "grammar.h"
 #include "bottom_up_parser.h"
@@ -16,13 +12,11 @@
 #include "tdict.h"
 #include "viterbi.h"
 #include "verbose.h"
-#include <tr1/unordered_map>
 
 #define foreach         BOOST_FOREACH
 #define reverse_foreach BOOST_REVERSE_FOREACH
 
 using namespace std;
-using namespace std::tr1;
 static bool printGrammarsUsed = false;
 
 struct GlueGrammar : public TextGrammar {
diff --git a/decoder/sentence_metadata.h b/decoder/sentence_metadata.h
index eab9f15d..52586331 100644
--- a/decoder/sentence_metadata.h
+++ b/decoder/sentence_metadata.h
@@ -5,7 +5,9 @@
 #include <map>
 #include <cassert>
 #include "lattice.h"
-#include "scorer.h"
+
+struct DocScorer;  // deprecated, will be removed
+struct Score;     // deprecated, will be removed
 
 struct SentenceMetadata {
   friend class DecoderImpl;
diff --git a/extractor/Makefile.am b/extractor/Makefile.am
index e94a9b91..65a3d436 100644
--- a/extractor/Makefile.am
+++ b/extractor/Makefile.am
@@ -1,7 +1,8 @@
-if HAVE_CXX11
 
 bin_PROGRAMS = compile run_extractor
 
+if HAVE_CXX11
+
 EXTRA_PROGRAMS = alignment_test \
     data_array_test \
     fast_intersector_test \
@@ -113,7 +114,29 @@ libcompile_a_SOURCES = \
   precomputation.cc \
   suffix_array.cc \
   time_util.cc \
-  translation_table.cc
+  translation_table.cc \
+  alignment.h \
+  data_array.h \
+  fast_intersector.h \
+  grammar.h \
+  grammar_extractor.h \
+  matchings_finder.h \
+  matchings_trie.h \
+  phrase.h \
+  phrase_builder.h \
+  phrase_location.h \
+  precomputation.h \
+  rule.h \
+  rule_extractor.h \
+  rule_extractor_helper.h \
+  rule_factory.h \
+  sampler.h \
+  scorer.h \
+  suffix_array.h \
+  target_phrase_extractor.h \
+  time_util.h \
+  translation_table.h \
+  vocabulary.h
 
 libextractor_a_SOURCES = \
   alignment.cc \
diff --git a/klm/lm/builder/Makefile.am b/klm/lm/builder/Makefile.am
index 317e03ce..38259c51 100644
--- a/klm/lm/builder/Makefile.am
+++ b/klm/lm/builder/Makefile.am
@@ -1,6 +1,6 @@
-bin_PROGRAMS = builder
+bin_PROGRAMS = lmplz
 
-builder_SOURCES = \
+lmplz_SOURCES = \
   lmplz_main.cc \
   adjust_counts.cc \
   adjust_counts.hh \
@@ -22,7 +22,7 @@ builder_SOURCES = \
   print.hh \
   sort.hh
 
-builder_LDADD = ../libklm.a ../../util/double-conversion/libklm_util_double.a ../../util/stream/libklm_util_stream.a ../../util/libklm_util.a $(BOOST_THREAD_LIBS)
+lmplz_LDADD = ../libklm.a ../../util/double-conversion/libklm_util_double.a ../../util/stream/libklm_util_stream.a ../../util/libklm_util.a $(BOOST_THREAD_LIBS)
 
 AM_CPPFLAGS = -W -Wall -I$(top_srcdir)/klm
 
diff --git a/mteval/mbr_kbest.cc b/mteval/mbr_kbest.cc
index 2519bc01..787c03bd 100644
--- a/mteval/mbr_kbest.cc
+++ b/mteval/mbr_kbest.cc
@@ -1,9 +1,14 @@
 #include <iostream>
 #include <vector>
-#include <tr1/unordered_map>
 
 #include <boost/program_options.hpp>
 #include <boost/functional/hash.hpp>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 #include "prob.h"
 #include "tdict.h"
@@ -12,7 +17,6 @@
 #include "stringlib.h"
 
 using namespace std;
-using namespace std::tr1;
 
 namespace po = boost::program_options;
 
diff --git a/mteval/ns_ter.cc b/mteval/ns_ter.cc
index 0e1008db..f0d84098 100644
--- a/mteval/ns_ter.cc
+++ b/mteval/ns_ter.cc
@@ -4,7 +4,12 @@
 #include <cassert>
 #include <iostream>
 #include <limits>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 #include <set>
 #include <boost/functional/hash.hpp>
 #include "tdict.h"
@@ -20,7 +25,6 @@ static const unsigned kREF_WORDCOUNT = 4;
 static const unsigned kDUMMY_LAST_ENTRY = 5;
 
 using namespace std;
-using namespace std::tr1;
 
 bool TERMetric::IsErrorMetric() const {
   return true;
diff --git a/mteval/scorer.cc b/mteval/scorer.cc
index de84e076..9eb9a76e 100644
--- a/mteval/scorer.cc
+++ b/mteval/scorer.cc
@@ -594,26 +594,29 @@ void DocScorer::Init(
       const ScoreType type,
       const vector<string>& ref_files,
       const string& src_file, bool verbose) {
+  cerr << "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
+          "!!! This code is using the deprecated DocScorer interface, please fix !!!\n"
+          "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
   scorers_.clear();
-  // TODO stop using valarray, start using ReadFile
+  static const WordID kDIV = TD::Convert("|||");
   cerr << "Loading references (" << ref_files.size() << " files)\n";
   ReadFile srcrf;
   if (type == AER && src_file.size() > 0) {
     cerr << "  (source=" << src_file << ")\n";
     srcrf.Init(src_file);
   }
+  std::vector<WordID> tmp;
   std::vector<ReadFile> ifs(ref_files.begin(),ref_files.end());
   for (int i=0; i < ref_files.size(); ++i) ifs[i].Init(ref_files[i]);
   char buf[64000];
   bool expect_eof = false;
   int line=0;
   while (ifs[0].get()) {
-    vector<vector<WordID> > refs(ref_files.size());
+    vector<vector<WordID> > refs;
     for (int i=0; i < ref_files.size(); ++i) {
       istream &in=ifs[i].get();
       if (in.eof()) break;
       in.getline(buf, 64000);
-      refs[i].clear();
       if (strlen(buf) == 0) {
         if (in.eof()) {
           if (!expect_eof) {
@@ -622,9 +625,17 @@ void DocScorer::Init(
           }
           break;
         }
-      } else {
-        TD::ConvertSentence(buf, &refs[i]);
-        assert(!refs[i].empty());
+      } else { // process reference
+        tmp.clear();
+        TD::ConvertSentence(buf, &tmp);
+        unsigned last = 0;
+        for (unsigned j = 0; j < tmp.size(); ++j) {
+          if (tmp[j] == kDIV) {
+            refs.push_back(vector<WordID>(tmp.begin() + last, tmp.begin() + j));
+            last = j + 1;
+          }
+        }
+        refs.push_back(vector<WordID>(tmp.begin() + last, tmp.end()));
       }
       assert(!expect_eof);
     }
diff --git a/mteval/ter.cc b/mteval/ter.cc
index cacc5b00..9da54306 100644
--- a/mteval/ter.cc
+++ b/mteval/ter.cc
@@ -5,7 +5,12 @@
 #include <iostream>
 #include <limits>
 #include <sstream>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 #include <set>
 #include <valarray>
 #include <boost/functional/hash.hpp>
@@ -16,7 +21,6 @@ const bool ter_use_average_ref_len = true;
 const int ter_short_circuit_long_sentences = -1;
 
 using namespace std;
-using namespace std::tr1;
 
 struct COSTS {
   static const float substitution;
diff --git a/python/cdec/sa/strmap.cc b/python/cdec/sa/strmap.cc
index 5040477e..d7c4f2a3 100644
--- a/python/cdec/sa/strmap.cc
+++ b/python/cdec/sa/strmap.cc
@@ -2,11 +2,16 @@
 
 #include <vector>
 #include <string>
-#include <tr1/unordered_map>
-#include <stdint.h>
+#include <cstdint>
+
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 using namespace std;
-using namespace std::tr1;
 
 #undef HAVE_64_BITS
 
diff --git a/training/crf/mpi_online_optimize.cc b/training/crf/mpi_online_optimize.cc
index 9e1ae34c..6b5b7d64 100644
--- a/training/crf/mpi_online_optimize.cc
+++ b/training/crf/mpi_online_optimize.cc
@@ -4,11 +4,11 @@
 #include <vector>
 #include <cassert>
 #include <cmath>
-#include <tr1/memory>
 #include <ctime>
 
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
+#include <boost/shared_ptr.hpp>
 
 #include "stringlib.h"
 #include "verbose.h"
@@ -219,7 +219,7 @@ int main(int argc, char** argv) {
 #endif
   if (size > 1) SetSilent(true);  // turn off verbose decoder output
   register_feature_functions();
-  std::tr1::shared_ptr<MT19937> rng;
+  boost::shared_ptr<MT19937> rng;
 
   po::variables_map conf;
   if (!InitCommandLine(argc, argv, &conf))
@@ -264,8 +264,8 @@ int main(int argc, char** argv) {
   ReadTrainingCorpus(conf["training_data"].as<string>(), rank, size, &corpus, &ids);
   assert(corpus.size() > 0);
 
-  std::tr1::shared_ptr<OnlineOptimizer> o;
-  std::tr1::shared_ptr<LearningRateSchedule> lr;
+  boost::shared_ptr<OnlineOptimizer> o;
+  boost::shared_ptr<LearningRateSchedule> lr;
 
   const unsigned size_per_proc = conf["minibatch_size_per_proc"].as<unsigned>();
   if (size_per_proc > corpus.size()) {
diff --git a/training/mira/kbest_cut_mira.cc b/training/mira/kbest_cut_mira.cc
index 59fa860a..3b1108e0 100644
--- a/training/mira/kbest_cut_mira.cc
+++ b/training/mira/kbest_cut_mira.cc
@@ -30,7 +30,6 @@
 #include "sparse_vector.h"
 
 using namespace std;
-using boost::shared_ptr;
 namespace po = boost::program_options;
 
 bool invert_score;
@@ -149,7 +148,7 @@ struct HypothesisInfo {
   double alpha;
   double oracle_loss;
   SparseVector<double> oracle_feat_diff;
-  shared_ptr<HypothesisInfo> oracleN;
+  boost::shared_ptr<HypothesisInfo> oracleN;
 };
 
 bool ApproxEqual(double a, double b) {
@@ -157,7 +156,7 @@ bool ApproxEqual(double a, double b) {
   return (fabs(a-b)/fabs(b)) < EPSILON;
 }
 
-typedef shared_ptr<HypothesisInfo> HI;
+typedef boost::shared_ptr<HypothesisInfo> HI;
 bool HypothesisCompareB(const HI& h1, const HI& h2 ) 
 {
   return h1->mt_metric > h2->mt_metric;
@@ -185,11 +184,11 @@ bool HypothesisCompareG(const HI& h1, const HI& h2 )
 };
 
 
-void CuttingPlane(vector<shared_ptr<HypothesisInfo> >* cur_c, bool* again, vector<shared_ptr<HypothesisInfo> >& all_hyp, vector<weight_t> dense_weights)
+void CuttingPlane(vector<boost::shared_ptr<HypothesisInfo> >* cur_c, bool* again, vector<boost::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;
+  boost::shared_ptr<HypothesisInfo> max_fear, max_fear_in_set;
+  vector<boost::shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
 
   if(no_reweight)
     {
@@ -235,9 +234,9 @@ void CuttingPlane(vector<shared_ptr<HypothesisInfo> >* cur_c, bool* again, vecto
 }
 
 
-double ComputeDelta(vector<shared_ptr<HypothesisInfo> >* cur_p, double max_step_size,vector<weight_t> dense_weights )
+double ComputeDelta(vector<boost::shared_ptr<HypothesisInfo> >* cur_p, double max_step_size,vector<weight_t> dense_weights )
 {
-  vector<shared_ptr<HypothesisInfo> >& cur_pair = *cur_p;
+  vector<boost::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));
@@ -261,12 +260,12 @@ double ComputeDelta(vector<shared_ptr<HypothesisInfo> >* cur_p, double max_step_
 }
 
 
-vector<shared_ptr<HypothesisInfo> > SelectPair(vector<shared_ptr<HypothesisInfo> >* cur_c)
+vector<boost::shared_ptr<HypothesisInfo> > SelectPair(vector<boost::shared_ptr<HypothesisInfo> >* cur_c)
 {
   bool DEBUG_SELECT= false;
-  vector<shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
+  vector<boost::shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
   
-  vector<shared_ptr<HypothesisInfo> > pair;
+  vector<boost::shared_ptr<HypothesisInfo> > pair;
 
   if (no_select || optimizer == 2){ //skip heuristic search and return oracle and fear for pa-mira
 
@@ -278,7 +277,7 @@ vector<shared_ptr<HypothesisInfo> > SelectPair(vector<shared_ptr<HypothesisInfo>
   
   for(int u=0;u != cur_constraint.size();u++)	
     {
-      shared_ptr<HypothesisInfo> max_fear;
+      boost::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
@@ -323,8 +322,8 @@ vector<shared_ptr<HypothesisInfo> > SelectPair(vector<shared_ptr<HypothesisInfo>
 }
 
 struct GoodBadOracle {
-  vector<shared_ptr<HypothesisInfo> > good;
-  vector<shared_ptr<HypothesisInfo> > bad;
+  vector<boost::shared_ptr<HypothesisInfo> > good;
+  vector<boost::shared_ptr<HypothesisInfo> > bad;
 };
 
 struct BasicObserver: public DecoderObserver {
@@ -367,8 +366,8 @@ struct TrainingObserver : public DecoderObserver {
   const DocScorer& ds;
   vector<ScoreP>& corpus_bleu_sent_stats;
   vector<GoodBadOracle>& oracles;
-  vector<shared_ptr<HypothesisInfo> > cur_best;
-  shared_ptr<HypothesisInfo> cur_oracle;
+  vector<boost::shared_ptr<HypothesisInfo> > cur_best;
+  boost::shared_ptr<HypothesisInfo> cur_oracle;
   const int kbest_size;
   Hypergraph forest;
   int cur_sent;
@@ -386,7 +385,7 @@ struct TrainingObserver : public DecoderObserver {
     return *cur_best[0];
   }
 
-  const vector<shared_ptr<HypothesisInfo> > GetCurrentBest() const {
+  const vector<boost::shared_ptr<HypothesisInfo> > GetCurrentBest() const {
     return cur_best;
   }
   
@@ -411,8 +410,8 @@ struct TrainingObserver : public DecoderObserver {
     
   }
 
-  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score, const vector<WordID>& hyp) {
-    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+  boost::shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score, const vector<WordID>& hyp) {
+    boost::shared_ptr<HypothesisInfo> h(new HypothesisInfo);
     h->features = feats;
     h->mt_metric = score;
     h->hyp = hyp;
@@ -424,14 +423,14 @@ struct TrainingObserver : public DecoderObserver {
 
 	if (stream) sent_id = 0;
     bool PRINT_LIST= false;
-    vector<shared_ptr<HypothesisInfo> >& cur_good = oracles[sent_id].good;
-    vector<shared_ptr<HypothesisInfo> >& cur_bad = oracles[sent_id].bad;
+    vector<boost::shared_ptr<HypothesisInfo> >& cur_good = oracles[sent_id].good;
+    vector<boost::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;
+    vector<boost::shared_ptr<HypothesisInfo> > all_hyp;
 
     typedef KBest::KBestDerivations<vector<WordID>, ESentenceTraversal,Filter> K;
     K kbest(forest,kbest_size);
@@ -527,7 +526,7 @@ struct TrainingObserver : public DecoderObserver {
     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];
+    boost::shared_ptr<HypothesisInfo>& oracleN = cur_good[0];
 
     if(fear_select == 1){   //compute fear hyps with model - bleu
       if (PRINT_LIST) cerr << "FEAR " << endl;
@@ -663,13 +662,13 @@ int main(int argc, char** argv) {
     invert_score = false;
   }
 
-  shared_ptr<DocScorer> ds;
+  boost::shared_ptr<DocScorer> ds;
   //normal: load references, stream: start stream scorer
   if (stream) {
-	  ds = shared_ptr<DocScorer>(new DocStreamScorer(type, vector<string>(0), ""));
+	  ds = boost::shared_ptr<DocScorer>(new DocStreamScorer(type, vector<string>(0), ""));
 	  cerr << "Scoring doc stream with " << metric_name << endl;
   } else {
-      ds = shared_ptr<DocScorer>(new DocScorer(type, conf["reference"].as<vector<string> >(), ""));
+      ds = boost::shared_ptr<DocScorer>(new DocScorer(type, conf["reference"].as<vector<string> >(), ""));
       cerr << "Loaded " << ds->size() << " references for scoring with " << metric_name << endl;
   }
   vector<ScoreP> corpus_bleu_sent_stats;
@@ -774,9 +773,9 @@ int main(int argc, char** argv) {
       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();
+      vector<boost::shared_ptr<HypothesisInfo> >& cur_good_v = oracles[cur_sent].good;
+      vector<boost::shared_ptr<HypothesisInfo> >& cur_bad_v = oracles[cur_sent].bad;
+      vector<boost::shared_ptr<HypothesisInfo> > cur_best_v = observer.GetCurrentBest();
 
       tot_loss += cur_hyp.mt_metric;
       
@@ -824,13 +823,13 @@ int main(int argc, char** argv) {
 	}
       else if(optimizer == 5) //full mira with n-best list of constraints from hope, fear, model best
 	{
-	  vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	  vector<boost::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;
+	  vector<boost::shared_ptr<HypothesisInfo> > cur_pair;
 	  //SMO 
 	  for(int u=0;u!=cur_constraint.size();u++)	
 	    cur_constraint[u]->alpha =0;	      
@@ -879,7 +878,7 @@ int main(int argc, char** argv) {
       else if(optimizer == 2 || optimizer == 3) //PA and Cutting Plane MIRA update
 	  {
 	    bool DEBUG_SMO= true;
-	    vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	    vector<boost::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;
@@ -919,7 +918,7 @@ int main(int argc, char** argv) {
 		    while (iter < smo_iter)
 		      {			
 			//select pair to optimize from constraint set
-			vector<shared_ptr<HypothesisInfo> > cur_pair = SelectPair(&cur_constraint);
+			vector<boost::shared_ptr<HypothesisInfo> > cur_pair = SelectPair(&cur_constraint);
 			
 			if(cur_pair.empty()){
 			  iter=MAX_SMO; 
diff --git a/training/mira/kbest_mira.cc b/training/mira/kbest_mira.cc
index d59b4224..2868de0c 100644
--- a/training/mira/kbest_mira.cc
+++ b/training/mira/kbest_mira.cc
@@ -3,10 +3,10 @@
 #include <vector>
 #include <cassert>
 #include <cmath>
-#include <tr1/memory>
 
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
+#include <boost/shared_ptr.hpp>
 
 #include "stringlib.h"
 #include "hg_sampler.h"
@@ -30,7 +30,7 @@ using namespace std;
 namespace po = boost::program_options;
 
 bool invert_score;
-std::tr1::shared_ptr<MT19937> rng;
+boost::shared_ptr<MT19937> rng;
 
 void RandomPermutation(int len, vector<int>* p_ids) {
   vector<int>& ids = *p_ids;
@@ -88,8 +88,8 @@ struct HypothesisInfo {
 };
 
 struct GoodBadOracle {
-  std::tr1::shared_ptr<HypothesisInfo> good;
-  std::tr1::shared_ptr<HypothesisInfo> bad;
+  boost::shared_ptr<HypothesisInfo> good;
+  boost::shared_ptr<HypothesisInfo> bad;
 };
 
 struct TrainingObserver : public DecoderObserver {
@@ -97,7 +97,7 @@ struct TrainingObserver : public DecoderObserver {
   const DocumentScorer& ds;
   const EvaluationMetric& metric;
   vector<GoodBadOracle>& oracles;
-  std::tr1::shared_ptr<HypothesisInfo> cur_best;
+  boost::shared_ptr<HypothesisInfo> cur_best;
   const int kbest_size;
   const bool sample_forest;
 
@@ -109,16 +109,16 @@ struct TrainingObserver : public DecoderObserver {
     UpdateOracles(smeta.GetSentenceID(), *hg);
   }
 
-  std::tr1::shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score) {
-    std::tr1::shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+  boost::shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score) {
+    boost::shared_ptr<HypothesisInfo> h(new HypothesisInfo);
     h->features = feats;
     h->mt_metric = score;
     return h;
   }
 
   void UpdateOracles(int sent_id, const Hypergraph& forest) {
-    std::tr1::shared_ptr<HypothesisInfo>& cur_good = oracles[sent_id].good;
-    std::tr1::shared_ptr<HypothesisInfo>& cur_bad = oracles[sent_id].bad;
+    boost::shared_ptr<HypothesisInfo>& cur_good = oracles[sent_id].good;
+    boost::shared_ptr<HypothesisInfo>& cur_bad = oracles[sent_id].bad;
     cur_bad.reset();  // TODO get rid of??
 
     if (sample_forest) {
diff --git a/training/mira/mira.py b/training/mira/mira.py
index 29c51e1d..7b2d06a3 100755
--- a/training/mira/mira.py
+++ b/training/mira/mira.py
@@ -4,8 +4,17 @@ import subprocess, shlex, glob
 import argparse
 import logging
 import random, time
-import cdec.score
 import gzip, itertools
+try:
+  import cdec.score
+except ImportError:
+  sys.stderr.write('Could not import pycdec, see cdec/python/README.md for details\n')
+  sys.exit(1)
+have_mpl = True
+try: 
+  import matplotlib.pyplot as plt
+except ImportError:
+  have_mpl = False
 
 #mira run script
 #requires pycdec to be built, since it is used for scoring hypothesis
@@ -16,17 +25,17 @@ import gzip, itertools
 #scoring function using pycdec scoring
 def fast_score(hyps, refs, metric):
   scorer = cdec.score.Scorer(metric)
-  logging.info('loaded {0} references for scoring with {1}\n'.format(
+  logging.info('loaded {0} references for scoring with {1}'.format(
                 len(refs), metric))
   if metric=='BLEU':
     logging.warning('BLEU is ambiguous, assuming IBM_BLEU\n')
     metric = 'IBM_BLEU'
   elif metric=='COMBI':
     logging.warning('COMBI metric is no longer supported, switching to '
-                    'COMB:TER=-0.5;BLEU=0.5\n')
+                    'COMB:TER=-0.5;BLEU=0.5')
     metric = 'COMB:TER=-0.5;BLEU=0.5'
   stats = sum(scorer(r).evaluate(h) for h,r in itertools.izip(hyps,refs))
-  logging.info(stats.detail+'\n')
+  logging.info('Score={} ({})'.format(stats.score, stats.detail))
   return stats.score
 
 #create new parallel input file in output directory in sgml format
@@ -71,6 +80,8 @@ def main():
   #set logging to write all info messages to stderr
   logging.basicConfig(level=logging.INFO)
   script_dir = os.path.dirname(os.path.abspath(sys.argv[0]))
+  if not have_mpl:
+    logging.warning('Failed to import matplotlib, graphs will not be generated.')
 
   parser= argparse.ArgumentParser(
             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -181,10 +192,11 @@ def main():
   dev_size = enseg(args.devset, newdev, args.grammar_prefix)
   args.devset = newdev
   
-  write_config(args)
+  log_config(args)
   args.weights, hope_best_fear = optimize(args, script_dir, dev_size)
   
-  graph_file = graph(args.output_dir, hope_best_fear, args.metric)
+  graph_file = ''
+  if have_mpl: graph_file = graph(args.output_dir, hope_best_fear, args.metric)
 
   dev_results, dev_bleu = evaluate(args.devset, args.weights, args.config, 
                          script_dir, args.output_dir)
@@ -205,17 +217,12 @@ def main():
 
   if graph_file:
     logging.info('A graph of the best/hope/fear scores over the iterations '
-                 'has been saved to {}\n'.format(graph_file))
+                 'has been saved to {}'.format(graph_file))
 
   print 'final weights:\n{}\n'.format(args.weights)
 
 #graph of hope/best/fear metric values across all iterations
 def graph(output_dir, hope_best_fear, metric):
-  try: 
-    import matplotlib.pyplot as plt
-  except ImportError:
-    logging.error('Error importing matplotlib. Graphing disabled.\n')
-    return ''
   max_y = float(max(hope_best_fear['best']))*1.5
   plt.plot(hope_best_fear['best'], label='best')
   plt.plot(hope_best_fear['hope'], label='hope')
@@ -308,6 +315,7 @@ def optimize(args, script_dir, dev_size):
   decoder = script_dir+'/kbest_cut_mira'
   (source, refs) = split_devset(args.devset, args.output_dir)
   port = random.randint(15000,50000)
+  logging.info('using port {}'.format(port))
   num_features = 0
   last_p_score = 0
   best_score_iter = -1
@@ -316,8 +324,8 @@ def optimize(args, script_dir, dev_size):
   hope_best_fear = {'hope':[],'best':[],'fear':[]}
   #main optimization loop
   while i<args.max_iterations:
-    logging.info('\n\nITERATION {}\n========\n'.format(i))
-    logging.info('using port {}\n'.format(port))
+    logging.info('======= STARTING ITERATION {} ======='.format(i))
+    logging.info('Starting at {}'.format(time.asctime()))
 
     #iteration specific files
     runfile = args.output_dir+'/run.raw.'+str(i)
@@ -327,10 +335,8 @@ def optimize(args, script_dir, dev_size):
     weightdir = args.output_dir+'/weights.pass'+str(i)
     os.mkdir(logdir)
     os.mkdir(weightdir)
-    
-    logging.info('RUNNING DECODER AT {}'.format(time.asctime()))
     weightsfile = args.output_dir+'/weights.'+str(i)
-    logging.info('ITER {}\n'.format(i))
+    logging.info('  log directory={}'.format(logdir))
     curr_pass = '0{}'.format(i)
     decoder_cmd = ('{0} -c {1} -w {2} -r{3} -m {4} -s {5} -b {6} -k {7} -o {8}'
                    ' -p {9} -O {10} -D {11} -h {12} -f {13} -C {14}').format(
@@ -350,7 +356,7 @@ def optimize(args, script_dir, dev_size):
                     parallelize, logdir, args.jobs)
     
     cmd = parallel_cmd + ' ' + decoder_cmd
-    logging.info('COMMAND: \n{}\n'.format(cmd))
+    logging.info('OPTIMIZATION COMMAND: {}'.format(cmd))
    
     dlog = open(decoderlog,'w')
     runf = open(runfile,'w')
@@ -365,27 +371,26 @@ def optimize(args, script_dir, dev_size):
       p1.stdout.close()
       
       if exit_code:
-        logging.error('Failed with exit code {}\n'.format(exit_code))
+        logging.error('Failed with exit code {}'.format(exit_code))
         sys.exit(exit_code)
 
       try:
         f = open(runfile)
       except IOError, msg:
-        logging.error('Unable to open {}\n'.format(runfile))
+        logging.error('Unable to open {}'.format(runfile))
         sys.exit()
       
       num_topbest = sum(1 for line in f)
       f.close()
       if num_topbest == dev_size: break
-      logging.warning('Incorrect number of top best. '
-                      'Waiting for distributed filesystem and retrying.')
+      logging.warning('Incorrect number of top best. Sleeping for 10 seconds and retrying...')
       time.sleep(10)
       retries += 1
     
     if dev_size != num_topbest:
       logging.error("Dev set contains "+dev_size+" sentences, but we don't "
                     "have topbest for all of these. Decoder failure? "
-                    " Check "+decoderlog+'\n')
+                    " Check "+decoderlog)
       sys.exit()
     dlog.close()
     runf.close()
@@ -427,7 +432,7 @@ def optimize(args, script_dir, dev_size):
     hope_best_fear['hope'].append(dec_score)
     hope_best_fear['best'].append(dec_score_h)
     hope_best_fear['fear'].append(dec_score_f)
-    logging.info('DECODER SCORE: {0} HOPE: {1} FEAR: {2}\n'.format(
+    logging.info('DECODER SCORE: {0} HOPE: {1} FEAR: {2}'.format(
                   dec_score, dec_score_h, dec_score_f))
     if dec_score > best_score:
       best_score_iter = i
@@ -436,12 +441,13 @@ def optimize(args, script_dir, dev_size):
     new_weights_file = '{}/weights.{}'.format(args.output_dir, i+1)
     last_weights_file = '{}/weights.{}'.format(args.output_dir, i)
     i += 1
-    weight_files = weightdir+'/weights.mira-pass*.*[0-9].gz'
+    weight_files = args.output_dir+'/weights.pass*/weights.mira-pass*[0-9].gz'
     average_weights(new_weights_file, weight_files)
 
-  logging.info('\nBEST ITER: {} :: {}\n\n'.format(
+  logging.info('BEST ITERATION: {} (SCORE={})'.format(
                best_score_iter, best_score))
   weights_final = args.output_dir+'/weights.final'
+  logging.info('WEIGHTS FILE: {}'.format(weights_final))
   shutil.copy(last_weights_file, weights_final)
   average_final_weights(args.output_dir)
   
@@ -481,15 +487,15 @@ def gzip_file(filename):
 
 #average the weights for a given pass
 def average_weights(new_weights, weight_files):
-  logging.info('AVERAGE {} {}\n'.format(new_weights, weight_files))
+  logging.info('AVERAGE {} {}'.format(new_weights, weight_files))
   feature_weights = {}
   total_mult = 0.0
   for path in glob.glob(weight_files):
     score = gzip.open(path)
     mult = 0
-    logging.info('FILE {}\n'.format(path))
+    logging.info('  FILE {}'.format(path))
     msg, ran, mult = score.readline().strip().split(' ||| ')
-    logging.info('Processing {} {}'.format(ran, mult))
+    logging.info('  Processing {} {}'.format(ran, mult))
     for line in score:
       f,w = line.split(' ',1)
       if f in feature_weights:
@@ -500,34 +506,30 @@ def average_weights(new_weights, weight_files):
     score.close()
   
   #write new weights to outfile
+  logging.info('Writing averaged weights to {}'.format(new_weights))
   out = open(new_weights, 'w')
   for f in iter(feature_weights):
     avg = feature_weights[f]/total_mult
-    logging.info('{} {} {} ||| Printing {} {}\n'.format(f,feature_weights[f], 
-                 total_mult, f, avg))
     out.write('{} {}\n'.format(f,avg))
 
-def write_config(args):
-  config = ('\n'
-            'DECODER: '
-            '/usr0/home/eschling/cdec/training/mira/kbest_cut_mira\n'
-            'INI FILE: '+args.config+'\n'
-            'WORKING DIRECTORY: '+args.output_dir+'\n'
-            'DEVSET: '+args.devset+'\n'
-            'EVAL METRIC: '+args.metric+'\n'
-            'MAX ITERATIONS: '+str(args.max_iterations)+'\n'
-            'DECODE NODES: '+str(args.jobs)+'\n'
-            'INITIAL WEIGHTS: '+args.weights+'\n')
+def log_config(args):
+  logging.info('WORKING DIRECTORY={}'.format(args.output_dir))
+  logging.info('INI FILE={}'.format(args.config))
+  logging.info('DEVSET={}'.format(args.devset))
+  logging.info('EVAL METRIC={}'.format(args.metric))
+  logging.info('MAX ITERATIONS={}'.format(args.max_iterations))
+  logging.info('PARALLEL JOBS={}'.format(args.jobs))
+  logging.info('INITIAL WEIGHTS={}'.format(args.weights))
   if args.grammar_prefix:
-    config += 'GRAMMAR PREFIX: '+str(args.grammar_prefix)+'\n'
+    logging.info('GRAMMAR PREFIX={}'.format(args.grammar_prefix))
   if args.test:
-    config += 'TEST SET: '+args.test+'\n'
+    logging.info('TEST SET={}'.format(args.test))
+  else:
+    logging.info('TEST SET=none specified')
   if args.test_config:
-    config += 'TEST CONFIG: '+args.test_config+'\n'
+    logging.info('TEST CONFIG={}'.format(args.test_config))
   if args.email:
-    config += 'EMAIL: '+args.email+'\n'
-           
-  logging.info(config)
+    logging.info('EMAIL={}'.format(args.email))
 
 if __name__=='__main__':
   main()
diff --git a/training/pro/mr_pro_map.cc b/training/pro/mr_pro_map.cc
index eef40b8a..a5e6e48f 100644
--- a/training/pro/mr_pro_map.cc
+++ b/training/pro/mr_pro_map.cc
@@ -2,7 +2,6 @@
 #include <iostream>
 #include <fstream>
 #include <vector>
-#include <tr1/unordered_map>
 
 #include <boost/functional/hash.hpp>
 #include <boost/shared_ptr.hpp>
diff --git a/training/utils/candidate_set.cc b/training/utils/candidate_set.cc
index 087efec3..1dec9609 100644
--- a/training/utils/candidate_set.cc
+++ b/training/utils/candidate_set.cc
@@ -1,6 +1,11 @@
 #include "candidate_set.h"
 
-#include <tr1/unordered_set>
+#ifdef HAVE_CXX11
+# include <unordered_set>
+#else
+# include <tr1/unordered_set>
+namespace std { using std::tr1::unordered_set; }
+#endif
 
 #include <boost/functional/hash.hpp>
 
@@ -139,12 +144,12 @@ void CandidateSet::ReadFromFile(const string& file) {
 
 void CandidateSet::Dedup() {
   if(!SILENT) cerr << "Dedup in=" << cs.size();
-  tr1::unordered_set<Candidate, CandidateHasher, CandidateCompare> u;
+  unordered_set<Candidate, CandidateHasher, CandidateCompare> u;
   while(cs.size() > 0) {
     u.insert(cs.back());
     cs.pop_back();
   }
-  tr1::unordered_set<Candidate, CandidateHasher, CandidateCompare>::iterator it = u.begin();
+  unordered_set<Candidate, CandidateHasher, CandidateCompare>::iterator it = u.begin();
   while (it != u.end()) {
     cs.push_back(*it);
     it = u.erase(it);
diff --git a/training/utils/online_optimizer.h b/training/utils/online_optimizer.h
index 28d89344..19223e9d 100644
--- a/training/utils/online_optimizer.h
+++ b/training/utils/online_optimizer.h
@@ -1,10 +1,10 @@
 #ifndef _ONL_OPTIMIZE_H_
 #define _ONL_OPTIMIZE_H_
 
-#include <tr1/memory>
 #include <set>
 #include <string>
 #include <cmath>
+#include <boost/shared_ptr.hpp>
 #include "sparse_vector.h"
 
 struct LearningRateSchedule {
@@ -56,7 +56,7 @@ struct ExponentialDecayLearningRate : public LearningRateSchedule {
 class OnlineOptimizer {
  public:
   virtual ~OnlineOptimizer();
-  OnlineOptimizer(const std::tr1::shared_ptr<LearningRateSchedule>& s,
+  OnlineOptimizer(const boost::shared_ptr<LearningRateSchedule>& s,
                   size_t batch_size,
                   const std::vector<int>& frozen_feats = std::vector<int>())
       : N_(batch_size),schedule_(s),k_() {
@@ -77,13 +77,13 @@ class OnlineOptimizer {
   std::set<int> frozen_;  // frozen (non-optimizing) features
 
  private:
-  std::tr1::shared_ptr<LearningRateSchedule> schedule_;
+  boost::shared_ptr<LearningRateSchedule> schedule_;
   int k_;  // iteration count
 };
 
 class CumulativeL1OnlineOptimizer : public OnlineOptimizer {
  public:
-  CumulativeL1OnlineOptimizer(const std::tr1::shared_ptr<LearningRateSchedule>& s,
+  CumulativeL1OnlineOptimizer(const boost::shared_ptr<LearningRateSchedule>& s,
                               size_t training_instances, double C,
                               const std::vector<int>& frozen) :
     OnlineOptimizer(s, training_instances, frozen), C_(C), u_() {}
diff --git a/training/utils/optimize_test.cc b/training/utils/optimize_test.cc
index bff2ca03..72fcef6d 100644
--- a/training/utils/optimize_test.cc
+++ b/training/utils/optimize_test.cc
@@ -2,6 +2,7 @@
 #include <iostream>
 #include <sstream>
 #include <boost/program_options/variables_map.hpp>
+#include <boost/shared_ptr.hpp>
 #include "optimize.h"
 #include "online_optimizer.h"
 #include "sparse_vector.h"
@@ -96,14 +97,11 @@ void TestOptimizerVariants(int num_vars) {
   cerr << oa.Name() << " SUCCESS\n";
 }
 
-using namespace std::tr1;
-
 void TestOnline() {
   size_t N = 20;
   double C = 1.0;
   double eta0 = 0.2;
-  std::tr1::shared_ptr<LearningRateSchedule> r(new ExponentialDecayLearningRate(N, eta0, 0.85));
-  //shared_ptr<LearningRateSchedule> r(new StandardLearningRate(N, eta0));
+  boost::shared_ptr<LearningRateSchedule> r(new ExponentialDecayLearningRate(N, eta0, 0.85));
   CumulativeL1OnlineOptimizer opt(r, N, C, std::vector<int>());
   assert(r->eta(10) < r->eta(1));
 }
diff --git a/utils/hash.h b/utils/hash.h
index 189ed1ae..e56fca06 100644
--- a/utils/hash.h
+++ b/utils/hash.h
@@ -20,11 +20,17 @@
 # define HASH_MAP_RESERVED(h,empty,deleted) do { (h).set_empty_key(empty); (h).set_deleted_key(deleted); } while(0)
 # define HASH_MAP_EMPTY(h,empty) do { (h).set_empty_key(empty); } while(0)
 #else
+#ifdef HAVE_CXX11
+# include <unordered_map>
+# include <unordered_set>
+#else
 # include <tr1/unordered_map>
 # include <tr1/unordered_set>
-# define SPARSE_HASH_MAP std::tr1::unordered_map
-# define HASH_MAP std::tr1::unordered_map
-# define HASH_SET std::tr1::unordered_set
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
+# define SPARSE_HASH_MAP std::unordered_map
+# define HASH_MAP std::unordered_map
+# define HASH_SET std::unordered_set
 # define HASH_MAP_DELETED(h,deleted)
 # define HASH_MAP_RESERVED(h,empty,deleted)
 # define HASH_MAP_EMPTY(h,empty)
diff --git a/word-aligner/fast_align.cc b/word-aligner/fast_align.cc
index fddcba9c..589ca62d 100644
--- a/word-aligner/fast_align.cc
+++ b/word-aligner/fast_align.cc
@@ -1,7 +1,12 @@
 #include <iostream>
 #include <cmath>
 #include <utility>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 #include <boost/functional/hash.hpp>
 #include <boost/program_options.hpp>
@@ -17,7 +22,6 @@
 
 namespace po = boost::program_options;
 using namespace std;
-using namespace std::tr1;
 
 bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   po::options_description opts("Configuration options");
diff --git a/word-aligner/ttables.cc b/word-aligner/ttables.cc
index c177aa30..a56bbcef 100644
--- a/word-aligner/ttables.cc
+++ b/word-aligner/ttables.cc
@@ -5,7 +5,6 @@
 #include "dict.h"
 
 using namespace std;
-using namespace std::tr1;
 
 void TTable::DeserializeProbsFromText(std::istream* in) {
   int c = 0;
diff --git a/word-aligner/ttables.h b/word-aligner/ttables.h
index 507f591a..1785e064 100644
--- a/word-aligner/ttables.h
+++ b/word-aligner/ttables.h
@@ -2,7 +2,12 @@
 #define _TTABLES_H_
 
 #include <iostream>
-#include <tr1/unordered_map>
+#ifdef HAVE_CXX11
+# include <unordered_map>
+#else
+# include <tr1/unordered_map>
+namespace std { using std::tr1::unordered_map; }
+#endif
 
 #include "sparse_vector.h"
 #include "m.h"
@@ -12,8 +17,8 @@
 class TTable {
  public:
   TTable() {}
-  typedef std::tr1::unordered_map<WordID, double> Word2Double;
-  typedef std::tr1::unordered_map<WordID, Word2Double> Word2Word2Double;
+  typedef std::unordered_map<WordID, double> Word2Double;
+  typedef std::unordered_map<WordID, Word2Double> Word2Word2Double;
   inline double prob(const int& e, const int& f) const {
     const Word2Word2Double::const_iterator cit = ttable.find(e);
     if (cit != ttable.end()) {
-- 
cgit v1.2.3


From 2d2d5eced93d58bc77894d8c328195cd9950b96d Mon Sep 17 00:00:00 2001
From: Patrick Simianer <p@simianer.de>
Date: Wed, 13 Nov 2013 18:00:10 +0100
Subject: unit tests for extractor loo sampling

---
 extractor/grammar_extractor_test.cc |   7 ++-
 extractor/mocks/mock_rule_factory.h |   2 +-
 extractor/rule_factory_test.cc      |   8 ++-
 extractor/sampler.cc                |  18 +++----
 extractor/sampler_test.cc           |  24 +++++----
 extractor/sampler_test_blacklist.cc | 102 ++++++++++++++++++++++++++++++++++++
 6 files changed, 138 insertions(+), 23 deletions(-)
 create mode 100644 extractor/sampler_test_blacklist.cc

(limited to 'extractor')

diff --git a/extractor/grammar_extractor_test.cc b/extractor/grammar_extractor_test.cc
index 823bb8b4..f32a9599 100644
--- a/extractor/grammar_extractor_test.cc
+++ b/extractor/grammar_extractor_test.cc
@@ -39,12 +39,15 @@ TEST(GrammarExtractorTest, TestAnnotatingWords) {
   vector<Rule> rules;
   vector<string> feature_names;
   Grammar grammar(rules, feature_names);
-  EXPECT_CALL(*factory, GetGrammar(word_ids))
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  EXPECT_CALL(*factory, GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array))
       .WillOnce(Return(grammar));
 
   GrammarExtractor extractor(vocabulary, factory);
   string sentence = "Anna has many many apples .";
-  extractor.GetGrammar(sentence);
+
+  extractor.GetGrammar(sentence, blacklisted_sentence_ids, source_data_array);
 }
 
 } // namespace
diff --git a/extractor/mocks/mock_rule_factory.h b/extractor/mocks/mock_rule_factory.h
index 7389b396..86a084b5 100644
--- a/extractor/mocks/mock_rule_factory.h
+++ b/extractor/mocks/mock_rule_factory.h
@@ -7,7 +7,7 @@ namespace extractor {
 
 class MockHieroCachingRuleFactory : public HieroCachingRuleFactory {
  public:
-  MOCK_METHOD1(GetGrammar, Grammar(const vector<int>& word_ids));
+  MOCK_METHOD3(GetGrammar, Grammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array));
 };
 
 } // namespace extractor
diff --git a/extractor/rule_factory_test.cc b/extractor/rule_factory_test.cc
index 08af3dcd..f26cc567 100644
--- a/extractor/rule_factory_test.cc
+++ b/extractor/rule_factory_test.cc
@@ -76,7 +76,9 @@ TEST_F(RuleFactoryTest, TestGetGrammarDifferentWords) {
       .WillRepeatedly(Return(PhraseLocation(0, 1)));
 
   vector<int> word_ids = {2, 3, 4};
-  Grammar grammar = factory->GetGrammar(word_ids);
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  Grammar grammar = factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
   EXPECT_EQ(feature_names, grammar.GetFeatureNames());
   EXPECT_EQ(7, grammar.GetRules().size());
 }
@@ -94,7 +96,9 @@ TEST_F(RuleFactoryTest, TestGetGrammarRepeatingWords) {
       .WillRepeatedly(Return(PhraseLocation(0, 1)));
 
   vector<int> word_ids = {2, 3, 4, 2, 3};
-  Grammar grammar = factory->GetGrammar(word_ids);
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  Grammar grammar = factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
   EXPECT_EQ(feature_names, grammar.GetFeatureNames());
   EXPECT_EQ(28, grammar.GetRules().size());
 }
diff --git a/extractor/sampler.cc b/extractor/sampler.cc
index cb470962..d332dd90 100644
--- a/extractor/sampler.cc
+++ b/extractor/sampler.cc
@@ -19,25 +19,25 @@ PhraseLocation Sampler::Sample(const PhraseLocation& location, unordered_set<int
     // Sample suffix array range.
     num_subpatterns = 1;
     int low = location.sa_low, high = location.sa_high;
-    double step = Round(max(1.0, (double) (high - low) / max_samples));
-    int i = low, last = i;
+    double step = max(1.0, (double) (high - low) / max_samples);
+    double i = low, last = i;
     bool found;
     while (sample.size() < max_samples && i < high) {
-      int x = suffix_array->GetSuffix(i);
+      int x = suffix_array->GetSuffix(Round(i));
       int id = source_data_array->GetSentenceId(x);
       if (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) != blacklisted_sentence_ids.end()) {
         found = false;
-        int backoff_step = 1;
+        double backoff_step = 1;
         while (true) {
           if ((double)backoff_step >= step) break;
-          int j = i - backoff_step;
-          x = suffix_array->GetSuffix(j);
+          double j = i - backoff_step;
+          x = suffix_array->GetSuffix(Round(j));
           id = source_data_array->GetSentenceId(x);
-          if (j > last && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
+          if (x >= 0 && j > last && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
             found = true; last = i; break;
           }
-          int k = i + backoff_step;
-          x = suffix_array->GetSuffix(k);
+          double k = i + backoff_step;
+          x = suffix_array->GetSuffix(Round(k));
           id = source_data_array->GetSentenceId(x);
           if (k < min(i+step, (double)high) && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
             found = true; last = k; break;
diff --git a/extractor/sampler_test.cc b/extractor/sampler_test.cc
index e9abebfa..965567ba 100644
--- a/extractor/sampler_test.cc
+++ b/extractor/sampler_test.cc
@@ -3,6 +3,7 @@
 #include <memory>
 
 #include "mocks/mock_suffix_array.h"
+#include "mocks/mock_data_array.h"
 #include "phrase_location.h"
 #include "sampler.h"
 
@@ -15,6 +16,8 @@ namespace {
 class SamplerTest : public Test {
  protected:
   virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*source_data_array, GetSentenceId(_)).WillRepeatedly(Return(9999));
     suffix_array = make_shared<MockSuffixArray>();
     for (int i = 0; i < 10; ++i) {
       EXPECT_CALL(*suffix_array, GetSuffix(i)).WillRepeatedly(Return(i));
@@ -23,51 +26,54 @@ class SamplerTest : public Test {
 
   shared_ptr<MockSuffixArray> suffix_array;
   shared_ptr<Sampler> sampler;
+  shared_ptr<MockDataArray> source_data_array;
 };
 
 TEST_F(SamplerTest, TestSuffixArrayRange) {
   PhraseLocation location(0, 10);
+  unordered_set<int> blacklist;
 
   sampler = make_shared<Sampler>(suffix_array, 1);
   vector<int> expected_locations = {0};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 2);
   expected_locations = {0, 5};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 3);
   expected_locations = {0, 3, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 4);
   expected_locations = {0, 3, 5, 8};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   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));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 }
 
 TEST_F(SamplerTest, TestSubstringsSample) {
   vector<int> locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+  unordered_set<int> blacklist;
   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));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 2);
   expected_locations = {0, 1, 6, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 3);
   expected_locations = {0, 1, 4, 5, 6, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   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));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 }
 
 } // namespace
diff --git a/extractor/sampler_test_blacklist.cc b/extractor/sampler_test_blacklist.cc
new file mode 100644
index 00000000..3305b990
--- /dev/null
+++ b/extractor/sampler_test_blacklist.cc
@@ -0,0 +1,102 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "mocks/mock_suffix_array.h"
+#include "mocks/mock_data_array.h"
+#include "phrase_location.h"
+#include "sampler.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class SamplerTestBlacklist : public Test {
+ protected:
+  virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    for (int i = 0; i < 10; ++i) {
+      EXPECT_CALL(*source_data_array, GetSentenceId(i)).WillRepeatedly(Return(i));
+    }
+    for (int i = -10; i < 0; ++i) {
+      EXPECT_CALL(*source_data_array, GetSentenceId(i)).WillRepeatedly(Return(0));
+    }
+    suffix_array = make_shared<MockSuffixArray>();
+    for (int i = -10; i < 10; ++i) {
+      EXPECT_CALL(*suffix_array, GetSuffix(i)).WillRepeatedly(Return(i));
+    }
+  }
+
+  shared_ptr<MockSuffixArray> suffix_array;
+  shared_ptr<Sampler> sampler;
+  shared_ptr<MockDataArray> source_data_array;
+};
+
+TEST_F(SamplerTestBlacklist, TestSuffixArrayRange) {
+  PhraseLocation location(0, 10);
+  unordered_set<int> blacklist;
+  vector<int> expected_locations;
+   
+  blacklist.insert(0);
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  expected_locations = {1};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+  
+  for (int i = 0; i < 9; i++) {
+    blacklist.insert(i);
+  }
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  expected_locations = {9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(5);
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {1, 4};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(1);
+  blacklist.insert(2);
+  blacklist.insert(3);
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {4, 5};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(3);
+  blacklist.insert(7);
+  sampler = make_shared<Sampler>(suffix_array, 3);
+  expected_locations = {1, 2, 6};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(3);
+  blacklist.insert(5);
+  blacklist.insert(8);
+  sampler = make_shared<Sampler>(suffix_array, 4);
+  expected_locations = {1, 2, 4, 7};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+  
+  blacklist.insert(0);
+  sampler = make_shared<Sampler>(suffix_array, 100);
+  expected_locations = {1, 2, 3, 4, 5, 6, 7, 8, 9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+ 
+  blacklist.insert(9);
+  sampler = make_shared<Sampler>(suffix_array, 100);
+  expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+}
+
+} // namespace
+} // namespace extractor
-- 
cgit v1.2.3


From ff4c76719cfea5ab067b92f1030881b186033f3c Mon Sep 17 00:00:00 2001
From: Patrick Simianer <p@simianer.de>
Date: Wed, 13 Nov 2013 18:17:54 +0100
Subject: remove crap

---
 extractor/sample_alignment.txt | 3 ---
 extractor/sample_bitext.txt    | 3 ---
 extractor/sample_source.txt    | 3 ---
 3 files changed, 9 deletions(-)

(limited to 'extractor')

diff --git a/extractor/sample_alignment.txt b/extractor/sample_alignment.txt
index f0292b01..80b446a4 100644
--- a/extractor/sample_alignment.txt
+++ b/extractor/sample_alignment.txt
@@ -1,5 +1,2 @@
 0-0 1-1 2-2
 1-0 2-1
-0-0
-0-0 1-1
-0-0 1-1
diff --git a/extractor/sample_bitext.txt b/extractor/sample_bitext.txt
index 2b7c8e40..93d6b39d 100644
--- a/extractor/sample_bitext.txt
+++ b/extractor/sample_bitext.txt
@@ -1,5 +1,2 @@
-asdf ||| dontseeme
-qqq asdf ||| zzz fdsa
-asdf qqq ||| fdsa zzz
 ana are mere . ||| anna has apples .
 ana bea mult lapte . ||| anna drinks a lot of milk .
diff --git a/extractor/sample_source.txt b/extractor/sample_source.txt
index 9b46dd6a..971baf6d 100644
--- a/extractor/sample_source.txt
+++ b/extractor/sample_source.txt
@@ -1,5 +1,2 @@
-asdf
-qqq asdf
-asdf qqq
 ana are mere .
 ana bea mult lapte .
-- 
cgit v1.2.3


From d32361ce37f794ae92f852ae2c7c3e6ef440ff07 Mon Sep 17 00:00:00 2001
From: Patrick Simianer <p@simianer.de>
Date: Wed, 13 Nov 2013 20:27:52 +0100
Subject: fix

---
 extractor/grammar_extractor.cc | 2 +-
 extractor/grammar_extractor.h  | 2 +-
 extractor/rule_factory.cc      | 2 +-
 extractor/rule_factory.h       | 2 +-
 extractor/sampler.cc           | 2 +-
 extractor/sampler.h            | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

(limited to 'extractor')

diff --git a/extractor/grammar_extractor.cc b/extractor/grammar_extractor.cc
index 1fbdee5b..487abcaf 100644
--- a/extractor/grammar_extractor.cc
+++ b/extractor/grammar_extractor.cc
@@ -34,7 +34,7 @@ GrammarExtractor::GrammarExtractor(
     vocabulary(vocabulary),
     rule_factory(rule_factory) {}
 
-Grammar GrammarExtractor::GetGrammar(const string& sentence, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
+Grammar GrammarExtractor::GetGrammar(const string& sentence, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   vector<string> words = TokenizeSentence(sentence);
   vector<int> word_ids = AnnotateWords(words);
   return rule_factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
diff --git a/extractor/grammar_extractor.h b/extractor/grammar_extractor.h
index 6c0aafbf..ae407b47 100644
--- a/extractor/grammar_extractor.h
+++ b/extractor/grammar_extractor.h
@@ -45,7 +45,7 @@ class GrammarExtractor {
 
   // 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, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
+  Grammar GetGrammar(const string& sentence, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  private:
   // Splits the sentence in a vector of words.
diff --git a/extractor/rule_factory.cc b/extractor/rule_factory.cc
index e52019ae..6ae2d792 100644
--- a/extractor/rule_factory.cc
+++ b/extractor/rule_factory.cc
@@ -101,7 +101,7 @@ HieroCachingRuleFactory::HieroCachingRuleFactory() {}
 
 HieroCachingRuleFactory::~HieroCachingRuleFactory() {}
 
-Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
+Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   Clock::time_point start_time = Clock::now();
   double total_extract_time = 0;
   double total_intersect_time = 0;
diff --git a/extractor/rule_factory.h b/extractor/rule_factory.h
index c7332720..df63a9d8 100644
--- a/extractor/rule_factory.h
+++ b/extractor/rule_factory.h
@@ -72,7 +72,7 @@ class HieroCachingRuleFactory {
 
   // Constructs SCFG rules for a given sentence.
   // (See class description for more details.)
-  virtual Grammar GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
+  virtual Grammar GetGrammar(const vector<int>& word_ids, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  protected:
   HieroCachingRuleFactory();
diff --git a/extractor/sampler.cc b/extractor/sampler.cc
index d332dd90..963afa7a 100644
--- a/extractor/sampler.cc
+++ b/extractor/sampler.cc
@@ -12,7 +12,7 @@ Sampler::Sampler() {}
 
 Sampler::~Sampler() {}
 
-PhraseLocation Sampler::Sample(const PhraseLocation& location, unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const {
+PhraseLocation Sampler::Sample(const PhraseLocation& location, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const {
   vector<int> sample;
   int num_subpatterns;
   if (location.matchings == NULL) {
diff --git a/extractor/sampler.h b/extractor/sampler.h
index 30e747fd..de450c48 100644
--- a/extractor/sampler.h
+++ b/extractor/sampler.h
@@ -23,7 +23,7 @@ class Sampler {
   virtual ~Sampler();
 
   // Samples uniformly at most max_samples phrase occurrences.
-  virtual PhraseLocation Sample(const PhraseLocation& location, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const;
+  virtual PhraseLocation Sample(const PhraseLocation& location, const unordered_set<int>& blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const;
 
  protected:
   Sampler();
-- 
cgit v1.2.3