initial check in

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diff --git a/src/cdec.cc b/src/cdec.cc
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--- /dev/null
+++ b/src/cdec.cc
@@ -0,0 +1,474 @@
+#include <iostream>
+#include <fstream>
+#include <tr1/unordered_map>
+#include <tr1/unordered_set>
+
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "timing_stats.h"
+#include "translator.h"
+#include "phrasebased_translator.h"
+#include "aligner.h"
+#include "stringlib.h"
+#include "forest_writer.h"
+#include "filelib.h"
+#include "sampler.h"
+#include "sparse_vector.h"
+#include "lexcrf.h"
+#include "weights.h"
+#include "tdict.h"
+#include "ff.h"
+#include "ff_factory.h"
+#include "hg_intersect.h"
+#include "apply_models.h"
+#include "viterbi.h"
+#include "kbest.h"
+#include "inside_outside.h"
+#include "exp_semiring.h"
+#include "sentence_metadata.h"
+
+using namespace std;
+using namespace std::tr1;
+using boost::shared_ptr;
+namespace po = boost::program_options;
+
+// some globals ...
+boost::shared_ptr<RandomNumberGenerator<boost::mt19937> > rng;
+
+namespace Hack { void MaxTrans(const Hypergraph& in, int beam_size); }
+
+void ShowBanner() {
+  cerr << "cdec v1.0 (c) 2009 by Chris Dyer\n";
+}
+
+void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+        ("formalism,f",po::value<string>()->default_value("scfg"),"Translation formalism; values include SCFG, FST, or PB.  Specify LexicalCRF for experimental unsupervised CRF word alignment")
+        ("input,i",po::value<string>()->default_value("-"),"Source file")
+        ("grammar,g",po::value<vector<string> >()->composing(),"Either SCFG grammar file(s) or phrase tables file(s)")
+        ("weights,w",po::value<string>(),"Feature weights file")
+        ("feature_function,F",po::value<vector<string> >()->composing(), "Additional feature function(s) (-L for list)")
+        ("list_feature_functions,L","List available feature functions")
+        ("add_pass_through_rules,P","Add rules to translate OOV words as themselves")
+	("k_best,k",po::value<int>(),"Extract the k best derivations")
+	("unique_k_best,r", "Unique k-best translation list")
+        ("aligner,a", "Run as a word/phrase aligner (src & ref required)")
+        ("cubepruning_pop_limit,K",po::value<int>()->default_value(200), "Max number of pops from the candidate heap at each node")
+        ("goal",po::value<string>()->default_value("S"),"Goal symbol (SCFG & FST)")
+        ("scfg_extra_glue_grammar", po::value<string>(), "Extra glue grammar file (Glue grammars apply when i=0 but have no other span restrictions)")
+        ("scfg_no_hiero_glue_grammar,n", "No Hiero glue grammar (nb. by default the SCFG decoder adds Hiero glue rules)")
+        ("scfg_default_nt,d",po::value<string>()->default_value("X"),"Default non-terminal symbol in SCFG")
+        ("scfg_max_span_limit,S",po::value<int>()->default_value(10),"Maximum non-terminal span limit (except \"glue\" grammar)")
+	("show_tree_structure,T", "Show the Viterbi derivation structure")
+        ("show_expected_length", "Show the expected translation length under the model")
+        ("show_partition,z", "Compute and show the partition (inside score)")
+        ("extract_rules", po::value<string>(), "Extract the rules used in translation (de-duped) to this file")
+        ("graphviz","Show (constrained) translation forest in GraphViz format")
+        ("max_translation_beam,x", po::value<int>(), "Beam approximation to get max translation from the chart")
+        ("max_translation_sample,X", po::value<int>(), "Sample the max translation from the chart")
+        ("pb_max_distortion,D", po::value<int>()->default_value(4), "Phrase-based decoder: maximum distortion")
+        ("gradient,G","Compute d log p(e|f) / d lambda_i and write to STDOUT (src & ref required)")
+        ("feature_expectations","Write feature expectations for all features in chart (**OBJ** will be the partition)")
+        ("vector_format",po::value<string>()->default_value("b64"), "Sparse vector serialization format for feature expectations or gradients, includes (text or b64)")
+        ("combine_size,C",po::value<int>()->default_value(1), "When option -G is used, process this many sentence pairs before writing the gradient (1=emit after every sentence pair)")
+        ("forest_output,O",po::value<string>(),"Directory to write forests to")
+        ("minimal_forests,m","Write minimal forests (excludes Rule information). Such forests can be used for ML/MAP training, but not rescoring, etc.");
+  po::options_description clo("Command line options");
+  clo.add_options()
+        ("config,c", po::value<string>(), "Configuration file")
+        ("help,h", "Print this help message and exit");
+  po::options_description dconfig_options, dcmdline_options;
+  dconfig_options.add(opts);
+  dcmdline_options.add(opts).add(clo);
+
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  if (conf->count("config")) {
+    const string cfg = (*conf)["config"].as<string>();
+    cerr << "Configuration file: " << cfg << endl;
+    ifstream config(cfg.c_str());
+    po::store(po::parse_config_file(config, dconfig_options), *conf);
+  }
+  po::notify(*conf);
+
+  if (conf->count("list_feature_functions")) {
+    cerr << "Available feature functions (specify with -F):\n";
+    global_ff_registry->DisplayList();
+    cerr << endl;
+    exit(1);
+  }
+
+  if (conf->count("help") || conf->count("grammar") == 0) {
+    cerr << dcmdline_options << endl;
+    exit(1);
+  }
+
+  const string formalism = LowercaseString((*conf)["formalism"].as<string>());
+  if (formalism != "scfg" && formalism != "fst" && formalism != "lexcrf" && formalism != "pb") {
+    cerr << "Error: --formalism takes only 'scfg', 'fst', 'pb', or 'lexcrf'\n";
+    cerr << dcmdline_options << endl;
+    exit(1);
+  }
+}
+
+// TODO move out of cdec into some sampling decoder file
+void SampleRecurse(const Hypergraph& hg, const vector<SampleSet>& ss, int n, vector<WordID>* out) {
+  const SampleSet& s = ss[n];
+  int i = rng->SelectSample(s);
+  const Hypergraph::Edge& edge = hg.edges_[hg.nodes_[n].in_edges_[i]];
+  vector<vector<WordID> > ants(edge.tail_nodes_.size());
+  for (int j = 0; j < ants.size(); ++j)
+    SampleRecurse(hg, ss, edge.tail_nodes_[j], &ants[j]);
+
+  vector<const vector<WordID>*> pants(ants.size());
+  for (int j = 0; j < ants.size(); ++j) pants[j] = &ants[j];
+  edge.rule_->ESubstitute(pants, out);
+}
+
+struct SampleSort {
+  bool operator()(const pair<int,string>& a, const pair<int,string>& b) const {
+    return a.first > b.first;
+  }
+};
+
+// TODO move out of cdec into some sampling decoder file
+void MaxTranslationSample(Hypergraph* hg, const int samples, const int k) {
+  unordered_map<string, int, boost::hash<string> > m;
+  hg->PushWeightsToGoal();
+  const int num_nodes = hg->nodes_.size();
+  vector<SampleSet> ss(num_nodes);
+  for (int i = 0; i < num_nodes; ++i) {
+    SampleSet& s = ss[i];
+    const vector<int>& in_edges = hg->nodes_[i].in_edges_;
+    for (int j = 0; j < in_edges.size(); ++j) {
+      s.add(hg->edges_[in_edges[j]].edge_prob_);
+    }
+  }
+  for (int i = 0; i < samples; ++i) {
+    vector<WordID> yield;
+    SampleRecurse(*hg, ss, hg->nodes_.size() - 1, &yield);
+    const string trans = TD::GetString(yield);
+    ++m[trans];
+  }
+  vector<pair<int, string> > dist;
+  for (unordered_map<string, int, boost::hash<string> >::iterator i = m.begin();
+         i != m.end(); ++i) {
+    dist.push_back(make_pair(i->second, i->first));
+  }
+  sort(dist.begin(), dist.end(), SampleSort());
+  if (k) {
+    for (int i = 0; i < k; ++i)
+      cout << dist[i].first << " ||| " << dist[i].second << endl;
+  } else {
+    cout << dist[0].second << endl;
+  }
+}
+
+// TODO decoder output should probably be moved to another file
+void DumpKBest(const int sent_id, const Hypergraph& forest, const int k, const bool unique) {
+  if (unique) {
+    KBest::KBestDerivations<vector<WordID>, ESentenceTraversal, KBest::FilterUnique> kbest(forest, k);
+    for (int i = 0; i < k; ++i) {
+      const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal, KBest::FilterUnique>::Derivation* d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+      cout << sent_id << " ||| " << TD::GetString(d->yield) << " ||| " << d->feature_values << endl;
+    }
+  } else {
+    KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(forest, k);
+    for (int i = 0; i < k; ++i) {
+      const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+      cout << sent_id << " ||| " << TD::GetString(d->yield) << " ||| " << d->feature_values << endl;
+    }
+  }
+}
+
+struct ELengthWeightFunction {
+  double operator()(const Hypergraph::Edge& e) const {
+    return e.rule_->ELength() - e.rule_->Arity();
+  }
+};
+
+
+struct TRPHash {
+  size_t operator()(const TRulePtr& o) const { return reinterpret_cast<size_t>(o.get()); }
+};
+static void ExtractRulesDedupe(const Hypergraph& hg, ostream* os) {
+  static unordered_set<TRulePtr, TRPHash> written;
+  for (int i = 0; i < hg.edges_.size(); ++i) {
+    const TRulePtr& rule = hg.edges_[i].rule_;
+    if (written.insert(rule).second) {
+      (*os) << rule->AsString() << endl;
+    }
+  }
+}
+
+void register_feature_functions();
+
+int main(int argc, char** argv) {
+  global_ff_registry.reset(new FFRegistry);
+  register_feature_functions();
+  ShowBanner();
+  po::variables_map conf;
+  InitCommandLine(argc, argv, &conf);
+  const bool write_gradient = conf.count("gradient");
+  const bool feature_expectations = conf.count("feature_expectations");
+  if (write_gradient && feature_expectations) {
+    cerr << "You can only specify --gradient or --feature_expectations, not both!\n";
+    exit(1);
+  }
+  const bool output_training_vector = (write_gradient || feature_expectations);
+
+  boost::shared_ptr<Translator> translator;
+  const string formalism = LowercaseString(conf["formalism"].as<string>());
+  if (formalism == "scfg")
+    translator.reset(new SCFGTranslator(conf));
+  else if (formalism == "fst")
+    translator.reset(new FSTTranslator(conf));
+  else if (formalism == "pb")
+    translator.reset(new PhraseBasedTranslator(conf));
+  else if (formalism == "lexcrf")
+    translator.reset(new LexicalCRF(conf));
+  else
+    assert(!"error");
+
+  vector<double> wv;
+  Weights w;
+  if (conf.count("weights")) {
+    w.InitFromFile(conf["weights"].as<string>());
+    wv.resize(FD::NumFeats());
+    w.InitVector(&wv);
+  }
+
+  // set up additional scoring features
+  vector<shared_ptr<FeatureFunction> > pffs;
+  vector<const FeatureFunction*> late_ffs;
+  if (conf.count("feature_function") > 0) {
+    const vector<string>& add_ffs = conf["feature_function"].as<vector<string> >();
+    for (int i = 0; i < add_ffs.size(); ++i) {
+      string ff, param;
+      SplitCommandAndParam(add_ffs[i], &ff, &param);
+      if (param.size() > 0) cerr << " (with config parameters '" << param << "')\n";
+      else cerr << " (no config parameters)\n";
+      shared_ptr<FeatureFunction> pff = global_ff_registry->Create(ff, param);
+      if (!pff) { exit(1); }
+      // TODO check that multiple features aren't trying to set the same fid
+      pffs.push_back(pff);
+      late_ffs.push_back(pff.get());
+    }
+  }
+  ModelSet late_models(wv, late_ffs);
+
+  const int sample_max_trans = conf.count("max_translation_sample") ?
+    conf["max_translation_sample"].as<int>() : 0;
+  if (sample_max_trans)
+    rng.reset(new RandomNumberGenerator<boost::mt19937>);
+  const bool aligner_mode = conf.count("aligner");
+  const bool minimal_forests = conf.count("minimal_forests");
+  const bool graphviz = conf.count("graphviz");
+  const bool encode_b64 = conf["vector_format"].as<string>() == "b64";
+  const bool kbest = conf.count("k_best");
+  const bool unique_kbest = conf.count("unique_k_best");
+  shared_ptr<WriteFile> extract_file;
+  if (conf.count("extract_rules"))
+    extract_file.reset(new WriteFile(conf["extract_rules"].as<string>()));
+
+  int combine_size = conf["combine_size"].as<int>();
+  if (combine_size < 1) combine_size = 1;
+  const string input = conf["input"].as<string>();
+  cerr << "Reading input from " << ((input == "-") ? "STDIN" : input.c_str()) << endl;
+  ReadFile in_read(input);
+  istream *in = in_read.stream();
+  assert(*in);
+
+  SparseVector<double> acc_vec;  // accumulate gradient
+  double acc_obj = 0; // accumulate objective
+  int g_count = 0;    // number of gradient pieces computed
+  int sent_id = -1;         // line counter
+
+  while(*in) {
+    Timer::Summarize();
+    ++sent_id;
+    string buf;
+    getline(*in, buf);
+    if (buf.empty()) continue;
+    map<string, string> sgml;
+    ProcessAndStripSGML(&buf, &sgml);
+    if (sgml.find("id") != sgml.end())
+      sent_id = atoi(sgml["id"].c_str());
+
+    cerr << "\nINPUT: ";
+    if (buf.size() < 100)
+      cerr << buf << endl;
+    else {
+     size_t x = buf.rfind(" ", 100);
+     if (x == string::npos) x = 100;
+     cerr << buf.substr(0, x) << " ..." << endl;
+    }
+    cerr << "  id = " << sent_id << endl;
+    string to_translate;
+    Lattice ref;
+    ParseTranslatorInputLattice(buf, &to_translate, &ref);
+    const bool has_ref = ref.size() > 0;
+    SentenceMetadata smeta(sent_id, ref);
+    const bool hadoop_counters = (write_gradient);
+    Hypergraph forest;          // -LM forest
+    Timer t("Translation");
+    if (!translator->Translate(to_translate, &smeta, wv, &forest)) {
+      cerr << "  NO PARSE FOUND.\n";
+      if (hadoop_counters)
+        cerr << "reporter:counter:UserCounters,FParseFailed,1" << endl;
+      cout << endl << flush;
+      continue;
+    }
+    cerr << "  -LM forest (nodes/edges): " << forest.nodes_.size() << '/' << forest.edges_.size() << endl;
+    cerr << "  -LM forest       (paths): " << forest.NumberOfPaths() << endl;
+    if (conf.count("show_expected_length")) {
+      const PRPair<double, double> res =
+        Inside<PRPair<double, double>,
+               PRWeightFunction<double, EdgeProb, double, ELengthWeightFunction> >(forest);
+      cerr << "  Expected length  (words): " << res.r / res.p << "\t" << res << endl;
+    }
+    if (conf.count("show_partition")) {
+      const prob_t z = Inside<prob_t, EdgeProb>(forest);
+      cerr << "  -LM partition     log(Z): " << log(z) << endl;
+    }
+    if (extract_file)
+      ExtractRulesDedupe(forest, extract_file->stream());
+    vector<WordID> trans;
+    const prob_t vs = ViterbiESentence(forest, &trans);
+    cerr << "  -LM Viterbi: " << TD::GetString(trans) << endl;
+    if (conf.count("show_tree_structure"))
+      cerr << "  -LM    tree: " << ViterbiETree(forest) << endl;;
+    cerr << "  -LM Viterbi: " << log(vs) << endl;
+
+    bool has_late_models = !late_models.empty();
+    if (has_late_models) {
+      forest.Reweight(wv);
+      forest.SortInEdgesByEdgeWeights();
+      Hypergraph lm_forest;
+      int cubepruning_pop_limit = conf["cubepruning_pop_limit"].as<int>();
+      ApplyModelSet(forest,
+                    smeta,
+                    late_models,
+                    PruningConfiguration(cubepruning_pop_limit),
+                    &lm_forest);
+      forest.swap(lm_forest);
+      forest.Reweight(wv);
+      trans.clear();
+      ViterbiESentence(forest, &trans);
+      cerr << "  +LM forest (nodes/edges): " << forest.nodes_.size() << '/' << forest.edges_.size() << endl;
+      cerr << "  +LM forest       (paths): " << forest.NumberOfPaths() << endl;
+      cerr << "  +LM Viterbi: " << TD::GetString(trans) << endl;
+    }
+    if (conf.count("forest_output") && !has_ref) {
+      ForestWriter writer(conf["forest_output"].as<string>(), sent_id);
+      assert(writer.Write(forest, minimal_forests));
+    }
+
+    if (sample_max_trans) {
+      MaxTranslationSample(&forest, sample_max_trans, conf.count("k_best") ? conf["k_best"].as<int>() : 0);
+    } else {
+      if (kbest) {
+        DumpKBest(sent_id, forest, conf["k_best"].as<int>(), unique_kbest);
+      } else {
+        if (!graphviz && !has_ref) {
+          cout << TD::GetString(trans) << endl << flush;
+        }
+      }
+    }
+
+    const int max_trans_beam_size = conf.count("max_translation_beam") ?
+      conf["max_translation_beam"].as<int>() : 0;
+    if (max_trans_beam_size) {
+      Hack::MaxTrans(forest, max_trans_beam_size);
+      continue;
+    }
+
+    if (graphviz && !has_ref) forest.PrintGraphviz();
+
+    // the following are only used if write_gradient is true!
+    SparseVector<double> full_exp, ref_exp, gradient;
+    double log_z = 0, log_ref_z = 0;
+    if (write_gradient)
+      log_z = log(
+        InsideOutside<prob_t, EdgeProb, SparseVector<double>, EdgeFeaturesWeightFunction>(forest, &full_exp));
+
+    if (has_ref) {
+      if (HG::Intersect(ref, &forest)) {
+        cerr << "  Constr. forest (nodes/edges): " << forest.nodes_.size() << '/' << forest.edges_.size() << endl;
+        cerr << "  Constr. forest       (paths): " << forest.NumberOfPaths() << endl;
+        forest.Reweight(wv);
+        cerr << "  Constr. VitTree: " << ViterbiFTree(forest) << endl;
+	if (hadoop_counters)
+          cerr << "reporter:counter:UserCounters,SentencePairsParsed,1" << endl;
+        if (conf.count("show_partition")) {
+           const prob_t z = Inside<prob_t, EdgeProb>(forest);
+           cerr << "  Contst. partition  log(Z): " << log(z) << endl;
+        }
+        //DumpKBest(sent_id, forest, 1000);
+        if (conf.count("forest_output")) {
+          ForestWriter writer(conf["forest_output"].as<string>(), sent_id);
+          assert(writer.Write(forest, minimal_forests));
+        }
+        if (aligner_mode && !output_training_vector)
+          AlignerTools::WriteAlignment(to_translate, ref, forest);
+        if (write_gradient) {
+          log_ref_z = log(
+            InsideOutside<prob_t, EdgeProb, SparseVector<double>, EdgeFeaturesWeightFunction>(forest, &ref_exp));
+          if (log_z < log_ref_z) {
+            cerr << "DIFF. ERR! log_z < log_ref_z: " << log_z << " " << log_ref_z << endl;
+            exit(1);
+          }
+          //cerr << "FULL: " << full_exp << endl;
+          //cerr << " REF: " << ref_exp << endl;
+          ref_exp -= full_exp;
+          acc_vec += ref_exp;
+          acc_obj += (log_z - log_ref_z);
+        }
+        if (feature_expectations) {
+          acc_obj += log(
+            InsideOutside<prob_t, EdgeProb, SparseVector<double>, EdgeFeaturesWeightFunction>(forest, &ref_exp));
+          acc_vec += ref_exp;
+        }
+
+        if (output_training_vector) {
+          ++g_count;
+          if (g_count % combine_size == 0) {
+            if (encode_b64) {
+              cout << "0\t";
+              B64::Encode(acc_obj, acc_vec, &cout);
+              cout << endl << flush;
+            } else {
+              cout << "0\t**OBJ**=" << acc_obj << ';' <<  acc_vec << endl << flush;
+            }
+            acc_vec.clear();
+            acc_obj = 0;
+          }
+        }
+        if (conf.count("graphviz")) forest.PrintGraphviz();
+      } else {
+        cerr << "  REFERENCE UNREACHABLE.\n";
+        if (write_gradient) {
+	  if (hadoop_counters)
+            cerr << "reporter:counter:UserCounters,EFParseFailed,1" << endl;
+          cout << endl << flush;
+	}
+      }
+    }
+  }
+  if (output_training_vector && !acc_vec.empty()) {
+    if (encode_b64) {
+      cout << "0\t";
+      B64::Encode(acc_obj, acc_vec, &cout);
+      cout << endl << flush;
+    } else {
+      cout << "0\t**OBJ**=" << acc_obj << ';' << acc_vec << endl << flush;
+    }
+  }
+}
+