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Posted to commits@joshua.apache.org by mj...@apache.org on 2016/06/01 02:51:50 UTC

[55/94] [abbrv] incubator-joshua git commit: Rebased with JOSHUA-252 and resolved merge conflicts

Rebased with JOSHUA-252 and resolved merge conflicts


Project: http://git-wip-us.apache.org/repos/asf/incubator-joshua/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-joshua/commit/9d6f84d3
Tree: http://git-wip-us.apache.org/repos/asf/incubator-joshua/tree/9d6f84d3
Diff: http://git-wip-us.apache.org/repos/asf/incubator-joshua/diff/9d6f84d3

Branch: refs/heads/master
Commit: 9d6f84d35754a099123c256b9932a89a2bd316aa
Parents: 1586853 02f3ef1
Author: Thamme Gowda <tg...@gmail.com>
Authored: Wed May 25 22:34:57 2016 -0700
Committer: Thamme Gowda <tg...@gmail.com>
Committed: Wed May 25 22:34:57 2016 -0700

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 .gitmodules                                     |    7 -
 Dockerfile                                      |   39 -
 bin/bleu                                        |   15 +
 bin/extract-1best                               |   15 +
 bin/joshua-decoder                              |   16 +
 bin/meteor                                      |   15 +
 docker/Dockerfile                               |   39 +
 docker/ar-en-phrase/Dockerfile                  |   11 +
 docker/zh-en-hiero/Dockerfile                   |   11 +
 examples/README.md                              |   39 +-
 examples/README.sp_to_en                        |   32 -
 examples/docker/ar-en-phrase/Dockerfile         |   11 -
 examples/docker/zh-en-hiero/Dockerfile          |   11 -
 ext/berkeleylm                                  |    1 -
 ext/giza-pp/GIZA++-v2/ATables.cpp               |  119 -
 ext/giza-pp/GIZA++-v2/ATables.h                 |  172 -
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 ext/giza-pp/GIZA++-v2/MoveSwapMatrix.cpp        |  231 -
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 ext/giza-pp/GIZA++-v2/collCounts.cpp            |  293 -
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 ext/giza-pp/GIZA++-v2/file_spec.h               |   59 -
 ext/giza-pp/GIZA++-v2/getSentence.cpp           |  340 --
 ext/giza-pp/GIZA++-v2/getSentence.h             |  123 -
 ext/giza-pp/GIZA++-v2/hmm.cpp                   |  405 --
 ext/giza-pp/GIZA++-v2/hmm.h                     |   82 -
 ext/giza-pp/GIZA++-v2/logprob.cpp               |  154 -
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 ext/giza-pp/GIZA++-v2/main.cpp                  |  719 ---
 ext/giza-pp/GIZA++-v2/model1.cpp                |  283 -
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 ext/giza-pp/GIZA++-v2/model3.h                  |  132 -
 ext/giza-pp/GIZA++-v2/model345-peg.cpp          |  191 -
 ext/giza-pp/GIZA++-v2/model3_viterbi.cpp        |  656 --
 .../GIZA++-v2/model3_viterbi_with_tricks.cpp    |  690 ---
 ext/giza-pp/GIZA++-v2/myassert.cpp              |   20 -
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 ext/giza-pp/GIZA++-v2/mystl.h                   |  321 -
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 ext/giza-pp/GIZA++-v2/small_snt2cooc.cpp        |   91 -
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 ext/giza-pp/mkcls-v2/KategProblem.cpp           | 1001 ---
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 ext/giza-pp/mkcls-v2/LICENSE                    |  282 -
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 ext/symal/giza2bal.pl                           |  112 -
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 jni/kenlm_wrap.cc                               |   17 +
 scripts/training/pipeline.pl                    |   15 +
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 .../apache/joshua/corpus/ContiguousPhrase.java  |   60 +-
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 test/pipeline/test-ghkm.sh                      |   43 -
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 test/prune-equivalent-translations.py           |   47 -
 test/run-all-tests.sh                           |   55 -
 test/scripts/.gitignore                         |    1 -
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 test/scripts/normalization/.gitignore           |    2 -
 test/scripts/normalization/data/train.en        |   21 -
 test/scripts/normalization/data/train.en.norm   |   21 -
 test/scripts/normalization/test.sh              |   29 -
 test/scripts/run_bundler_test.py                |  378 --
 test/scripts/support/moses_grammar/input        |   10 -
 .../support/moses_grammar/output.expected       |   10 -
 test/scripts/support/moses_grammar/test.sh      |   30 -
 test/server/http/expected                       |   15 -
 test/server/http/test.sh                        |   36 -
 test/server/tcp-text/expected                   |    9 -
 test/server/tcp-text/test.sh                    |   45 -
 test/testng.xml                                 |   13 -
 test/thrax/.gitignore                           |    5 -
 test/thrax/extraction/input/thrax.conf          |   71 -
 test/thrax/extraction/input/train.a             |  100 -
 test/thrax/extraction/input/train.en            |  100 -
 test/thrax/extraction/input/train.ps            |  100 -
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 test/thrax/filtering/test-fast.sh               |   34 -
 test/thrax/filtering/test-loose.sh              |   34 -
 1006 files changed, 44235 insertions(+), 69597 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/scripts/training/pipeline.pl
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/corpus/Vocabulary.java
----------------------------------------------------------------------
diff --cc src/main/java/org/apache/joshua/corpus/Vocabulary.java
index 42ce482,582efc6..2bcc447
--- a/src/main/java/org/apache/joshua/corpus/Vocabulary.java
+++ b/src/main/java/org/apache/joshua/corpus/Vocabulary.java
@@@ -45,9 -46,8 +48,9 @@@ import org.slf4j.LoggerFactory
   * @author Juri Ganitkevitch
   */
  
- public class Vocabulary {
+ public class Vocabulary implements Externalizable {
  
 +  private static final Logger LOG = LoggerFactory.getLogger(Vocabulary.class);
    private final static ArrayList<NGramLanguageModel> LMs = new ArrayList<>();
  
    private static List<String> idToString;

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ArgsParser.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/Decoder.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/DecoderThread.java
----------------------------------------------------------------------
diff --cc src/main/java/org/apache/joshua/decoder/DecoderThread.java
index 486df4b,0f80335..d6f5233
--- a/src/main/java/org/apache/joshua/decoder/DecoderThread.java
+++ b/src/main/java/org/apache/joshua/decoder/DecoderThread.java
@@@ -104,10 -103,10 +105,10 @@@ public class DecoderThread extends Thre
  
      // skip blank sentences
      if (sentence.isEmpty()) {
 -      Decoder.LOG(1, String.format("Translation %d: Translation took 0 seconds", sentence.id()));
 +      LOG.info("Translation {}: Translation took 0 seconds", sentence.id());
        return new Translation(sentence, null, featureFunctions, joshuaConfiguration);
      }
-     
+ 
      long startTime = System.currentTimeMillis();
  
      int numGrammars = allGrammars.size();
@@@ -137,12 -136,12 +138,12 @@@
              joshuaConfiguration.goal_symbol, joshuaConfiguration);
  
          hypergraph = (joshuaConfiguration.use_dot_chart) 
-           ? chart.expand() 
-           : chart.expandSansDotChart();
+             ? chart.expand() 
+                 : chart.expandSansDotChart();
        }
-       
+ 
      } catch (java.lang.OutOfMemoryError e) {
 -      Decoder.LOG(1, String.format("Input %d: out of memory", sentence.id()));
 +      LOG.error("Input {}: out of memory", sentence.id());
        hypergraph = null;
      }
  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/JoshuaConfiguration.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/JoshuaDecoder.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/NbestMinRiskReranker.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/Translation.java
----------------------------------------------------------------------
diff --cc src/main/java/org/apache/joshua/decoder/Translation.java
index 9ae1aaa,0ee1f08..ab37814
--- a/src/main/java/org/apache/joshua/decoder/Translation.java
+++ b/src/main/java/org/apache/joshua/decoder/Translation.java
@@@ -84,14 -81,15 +84,14 @@@ public class Translation 
            // We must put this weight as zero, otherwise we get an error when we try to retrieve it
            // without checking
            Decoder.weights.increment("BLEU", 0);
-           
+ 
            if (joshuaConfiguration.topN == 0) {
-             
+ 
              /* construct Viterbi output */
              final String best = getViterbiString(hypergraph);
-             
+ 
 -            Decoder.LOG(1, String.format("Translation %d: %.3f %s", source.id(), hypergraph.goalNode.getScore(),
 -                best));
 +            LOG.info("Translation {}: {} {}", source.id(), hypergraph.goalNode.getScore(), best);
-             
+ 
              /*
               * Setting topN to 0 turns off k-best extraction, in which case we need to parse through
               * the output-string, with the understanding that we can only substitute variables for the
@@@ -131,26 -129,26 +131,26 @@@
            }
  
            float seconds = (float) (System.currentTimeMillis() - startTime) / 1000.0f;
 -          Decoder.LOG(1, String.format("Input %d: %d-best extraction took %.3f seconds", id(),
 -              joshuaConfiguration.topN, seconds));
 +          LOG.info("Input {}: {}-best extraction took {} seconds", id(),
 +              joshuaConfiguration.topN, seconds);
  
-       } else {
-         
-         // Failed translations and blank lines get empty formatted outputs
-         // @formatter:off
-         String outputString = joshuaConfiguration.outputFormat
-             .replace("%s", source.source())
-             .replace("%e", "")
-             .replace("%S", "")
-             .replace("%t", "()")
-             .replace("%i", Integer.toString(source.id()))
-             .replace("%f", "")
-             .replace("%c", "0.000");
-         // @formatter:on
- 
-         out.write(outputString);
-         out.newLine();
-       }
+         } else {
+ 
+           // Failed translations and blank lines get empty formatted outputs
+           // @formatter:off
+           String outputString = joshuaConfiguration.outputFormat
+               .replace("%s", source.source())
+               .replace("%e", "")
+               .replace("%S", "")
+               .replace("%t", "()")
+               .replace("%i", Integer.toString(source.id()))
+               .replace("%f", "")
+               .replace("%c", "0.000");
+           // @formatter:on
+ 
+           out.write(outputString);
+           out.newLine();
+         }
  
          out.flush();
        } catch (IOException e) {

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/chart_parser/Chart.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/chart_parser/ComputeNodeResult.java
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diff --cc src/main/java/org/apache/joshua/decoder/chart_parser/ComputeNodeResult.java
index 105565d,73c3cd0..e691da6
--- a/src/main/java/org/apache/joshua/decoder/chart_parser/ComputeNodeResult.java
+++ b/src/main/java/org/apache/joshua/decoder/chart_parser/ComputeNodeResult.java
@@@ -70,9 -73,11 +77,8 @@@ public class ComputeNodeResult 
      // The total Viterbi cost of this edge. This is the Viterbi cost of the tail nodes, plus
      // whatever costs we incur applying this rule to create a new hyperedge.
      float viterbiCost = 0.0f;
-     
 -
 -    if (Decoder.VERBOSE >= 4) {
 -      System.err.println("ComputeNodeResult():");
 -      System.err.println("-> RULE " + rule);
 -    }
 +    LOG.debug("ComputeNodeResult():");
 +    LOG.info("-> RULE {}", rule);
  
      /*
       * Here we sum the accumulated cost of each of the tail nodes. The total cost of the new
@@@ -106,19 -113,22 +112,18 @@@
        DPState newState = feature.compute(rule, tailNodes, i, j, sourcePath, sentence, acc);
        transitionCost += acc.getScore();
  
 -      if (Decoder.VERBOSE >= 4)
 -        System.err.println(String.format("-> FEATURE %s = %.3f * %.3f = %.3f", 
 -            feature.getName(), acc.getScore() / Decoder.weights.getSparse(feature.getName()),
 -            Decoder.weights.getSparse(feature.getName()), acc.getScore()));
++
 +      LOG.debug("FEATURE {} = {} * {} = {}", feature.getName(),
 +          acc.getScore() / Decoder.weights.getSparse(feature.getName()),
 +          Decoder.weights.getSparse(feature.getName()), acc.getScore());
  
        if (feature.isStateful()) {
          futureCostEstimate += feature.estimateFutureCost(rule, newState, sentence);
          allDPStates.add(((StatefulFF)feature).getStateIndex(), newState);
        }
      }
-   
 -
      viterbiCost += transitionCost;
 -
 -    if (Decoder.VERBOSE >= 4)
 -      System.err.println(String.format("-> COST = %.3f", transitionCost));
 -
 +    LOG.debug("-> COST = {}", transitionCost);
-     
      // Set the final results.
      this.pruningCostEstimate = viterbiCost + futureCostEstimate;
      this.viterbiCost = viterbiCost;

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/chart_parser/ManualConstraintsHandler.java
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diff --cc src/main/java/org/apache/joshua/decoder/chart_parser/ManualConstraintsHandler.java
index 99cbf7f,06a14ee..3b7c644
--- a/src/main/java/org/apache/joshua/decoder/chart_parser/ManualConstraintsHandler.java
+++ b/src/main/java/org/apache/joshua/decoder/chart_parser/ManualConstraintsHandler.java
@@@ -27,11 -29,9 +27,11 @@@ import org.apache.joshua.decoder.ff.tm.
  import org.apache.joshua.decoder.ff.tm.Rule;
  import org.apache.joshua.decoder.segment_file.ConstraintRule;
  import org.apache.joshua.decoder.segment_file.ConstraintSpan;
 +import org.slf4j.Logger;
 +import org.slf4j.LoggerFactory;
  
  /**
-  * @author Zhifei Li, <zh...@gmail.com>
+  * @author Zhifei Li, zhifei.work@gmail.com
   */
  
  public class ManualConstraintsHandler {

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/StatefulFF.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/fragmentlm/FragmentLMFF.java
----------------------------------------------------------------------
diff --cc src/main/java/org/apache/joshua/decoder/ff/fragmentlm/FragmentLMFF.java
index 232b2b9,f969396..b191c2f
--- a/src/main/java/org/apache/joshua/decoder/ff/fragmentlm/FragmentLMFF.java
+++ b/src/main/java/org/apache/joshua/decoder/ff/fragmentlm/FragmentLMFF.java
@@@ -36,37 -36,35 +36,37 @@@ import org.apache.joshua.decoder.ff.tm.
  import org.apache.joshua.decoder.hypergraph.HGNode;
  import org.apache.joshua.decoder.hypergraph.HyperEdge;
  import org.apache.joshua.decoder.segment_file.Sentence;
 +import org.slf4j.Logger;
 +import org.slf4j.LoggerFactory;
  
  /**
-  * Feature function that reads in a list of language model fragments and matches them against the
+  * <p>Feature function that reads in a list of language model fragments and matches them against the
   * hypergraph. This allows for language model fragment "glue" features, which fire when LM fragments
   * (supplied as input) are assembled. These LM fragments are presumably useful in ensuring
-  * grammaticality and can be independent of the translation model fragments.
+  * grammaticality and can be independent of the translation model fragments.</p>
   * 
-  * Usage: in the Joshua Configuration file, put
+  * <p>Usage: in the Joshua Configuration file, put</p>
   * 
-  * feature-function = FragmentLM -lm LM_FRAGMENTS_FILE -map RULE_FRAGMENTS_MAP_FILE
+  * <code>feature-function = FragmentLM -lm LM_FRAGMENTS_FILE -map RULE_FRAGMENTS_MAP_FILE</code>
   * 
-  * LM_FRAGMENTS_FILE is a pointer to a file containing a list of fragments that it should look for.
-  * The format of the file is one fragment per line in PTB format, e.g.:
+  * <p>LM_FRAGMENTS_FILE is a pointer to a file containing a list of fragments that it should look for.
+  * The format of the file is one fragment per line in PTB format, e.g.:</p>
   * 
-  * (S NP (VP (VBD said) SBAR) (. .))
+  * <code>(S NP (VP (VBD said) SBAR) (. .))</code>
   * 
-  * RULE_FRAGMENTS_MAP_FILE points to a file that maps fragments to the flattened SCFG rule format
+  * <p>RULE_FRAGMENTS_MAP_FILE points to a file that maps fragments to the flattened SCFG rule format
   * that Joshua uses. This mapping is necessary because Joshua's rules have been flattened, meaning
   * that their internal structure has been removed, yet this structure is needed for matching LM
-  * fragments. The format of the file is
+  * fragments. The format of the file is</p>
   * 
-  * FRAGMENT ||| RULE-TARGET-SIDE
+  * <code>FRAGMENT ||| RULE-TARGET-SIDE</code>
   * 
-  * for example,
+  * <p>for example,</p>
   * 
-  * (S (NP (DT the) (NN man)) VP .) ||| the man [VP,1] [.,2] (SBAR (IN that) (S (NP (PRP he)) (VP
-  * (VBD was) (VB done)))) ||| that he was done (VP (VBD said) SBAR) ||| said SBAR
+  * <code>(S (NP (DT the) (NN man)) VP .) ||| the man [VP,1] [.,2] (SBAR (IN that) (S (NP (PRP he)) (VP
+  * (VBD was) (VB done)))) ||| that he was done (VP (VBD said) SBAR) ||| said SBAR</code>
   * 
-  * @author Matt Post <po...@cs.jhu.edu>
+  * @author Matt Post post@cs.jhu.edu
   */
  public class FragmentLMFF extends StatefulFF {
  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/fragmentlm/Tree.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/lm/DefaultNGramLanguageModel.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/lm/KenLM.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/lm/LanguageModelFF.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/lm/bloomfilter_lm/BloomFilterLanguageModel.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/lm/buildin_lm/TrieLM.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/AbstractGrammar.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/GrammarReader.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/MonolingualRule.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/Rule.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/SentenceFilteredGrammar.java
----------------------------------------------------------------------
diff --cc src/main/java/org/apache/joshua/decoder/ff/tm/SentenceFilteredGrammar.java
index 42652ce,ce04e15..2362cfd
--- a/src/main/java/org/apache/joshua/decoder/ff/tm/SentenceFilteredGrammar.java
+++ b/src/main/java/org/apache/joshua/decoder/ff/tm/SentenceFilteredGrammar.java
@@@ -34,12 -32,9 +34,12 @@@ import org.slf4j.LoggerFactory
   * trie, a subset of the original trie, that only contains trie paths that are reachable from
   * traversals of the current sentence.
   * 
-  * @author Matt Post <po...@cs.jhu.edu>
+  * @author Matt Post post@cs.jhu.edu
   */
  public class SentenceFilteredGrammar extends MemoryBasedBatchGrammar {
 +
 +  private static final Logger LOG = LoggerFactory.getLogger(SentenceFilteredGrammar.class);
 +
    private AbstractGrammar baseGrammar;
    private SentenceFilteredTrie filteredTrie;
    private int[] tokens;

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/hash_based/MemoryBasedBatchGrammar.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/ff/tm/packed/PackedGrammar.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/hypergraph/HyperGraph.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/phrase/Future.java
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diff --cc src/main/java/org/apache/joshua/decoder/phrase/Future.java
index 3cceb76,aa24390..0ece4a3
--- a/src/main/java/org/apache/joshua/decoder/phrase/Future.java
+++ b/src/main/java/org/apache/joshua/decoder/phrase/Future.java
@@@ -18,10 -18,8 +18,9 @@@
   */
  package org.apache.joshua.decoder.phrase;
  
--import org.apache.joshua.decoder.Decoder;
  import org.apache.joshua.util.ChartSpan;
 +import org.slf4j.Logger;
 +import org.slf4j.LoggerFactory;
  
  public class Future {
  
@@@ -74,18 -71,16 +74,18 @@@
          }
        }
      }
-     
+ 
 -    if (Decoder.VERBOSE >= 3) {
 -      for (int i = 1; i < chart.SentenceLength(); i++)
 -        for (int j = i + 1; j < chart.SentenceLength(); j++)
 -          System.err.println(String.format("future cost from %d to %d is %.3f", i-1, j-2, getEntry(i, j)));
 +    if (LOG.isDebugEnabled()) {
 +      for (int i = 1; i < chart.SentenceLength(); i++) {
 +        for (int j = i + 1; j < chart.SentenceLength(); j++) {
 +          LOG.debug("future cost from {} to {} is {}", i - 1, j - 2, getEntry(i, j));
 +        }
 +      }
      }
    }
-   
+ 
    public float Full() {
- //    System.err.println("Future::Full(): " + Entry(1, sentlen));
+     //    System.err.println("Future::Full(): " + Entry(1, sentlen));
      return getEntry(1, sentlen);
    }
  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/phrase/PhraseChart.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/phrase/Stack.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/phrase/Stacks.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/segment_file/Sentence.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/decoder/segment_file/Token.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/lattice/Lattice.java
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diff --cc src/main/java/org/apache/joshua/lattice/Lattice.java
index 7679cfd,d89c948..2332159
--- a/src/main/java/org/apache/joshua/lattice/Lattice.java
+++ b/src/main/java/org/apache/joshua/lattice/Lattice.java
@@@ -37,12 -37,11 +37,11 @@@ import org.slf4j.LoggerFactory
  
  /**
   * A lattice representation of a directed graph.
 - * 
 + *
   * @author Lane Schwartz
-  * @author Matt Post <po...@cs.jhu.edu>
+  * @author Matt Post post@cs.jhu.edu
   * @since 2008-07-08
 - * 
 + *
-  * @param Label Type of label associated with an arc.
   */
  public class Lattice<Value> implements Iterable<Node<Value>> {
  
@@@ -71,8 -70,9 +70,9 @@@
     * <p>
     * The list of nodes must already be in topological order. If the list is not in topological
     * order, the behavior of the lattice is not defined.
 -   * 
 +   *
     * @param nodes A list of nodes which must be in topological order.
+    * @param config a populated {@link org.apache.joshua.decoder.JoshuaConfiguration}
     */
    public Lattice(List<Node<Value>> nodes, JoshuaConfiguration config) {
      this.nodes = nodes;
@@@ -90,8 -90,9 +90,9 @@@
  
    /**
     * Instantiates a lattice from a linear chain of values, i.e., a sentence.
 -   * 
 +   *
     * @param linearChain a sequence of Value objects
+    * @param config a populated {@link org.apache.joshua.decoder.JoshuaConfiguration}
     */
    public Lattice(Value[] linearChain, JoshuaConfiguration config) {
      this.latticeHasAmbiguity = false;
@@@ -125,10 -126,9 +126,9 @@@
    /**
     * Computes the shortest distance between two nodes, which is used (perhaps among other places) in
     * computing which rules can apply over which spans of the input
 -   * 
 +   *
-    * @param tail
-    * @param head
-    * @return the distance, a positive number, or -1 if there is no path between the nodes
+    * @param arc an {@link org.apache.joshua.lattice.Arc} of values
+    * @return the shortest distance between two nodes
     */
    public int distance(Arc<Value> arc) {
      return this.getShortestPath(arc.getTail().getNumber(), arc.getHead().getNumber());
@@@ -140,8 -140,9 +140,9 @@@
  
    /**
     * Convenience method to get a lattice from a linear sequence of {@link Token} objects.
 -   * 
 +   *
-    * @param linearChain
+    * @param source input string from which to create a {@link org.apache.joshua.lattice.Lattice}
+    * @param config a populated {@link org.apache.joshua.decoder.JoshuaConfiguration}
     * @return Lattice representation of the linear chain.
     */
    public static Lattice<Token> createTokenLatticeFromString(String source, JoshuaConfiguration config) {
@@@ -243,8 -244,9 +244,9 @@@
  
    /**
     * Constructs a lattice from a given string representation.
 -   * 
 +   *
     * @param data String representation of a lattice.
+    * @param config a populated {@link org.apache.joshua.decoder.JoshuaConfiguration}
     * @return A lattice that corresponds to the given string.
     */
    public static Lattice<String> createStringLatticeFromString(String data, JoshuaConfiguration config) {
@@@ -443,10 -445,10 +445,10 @@@
    /**
     * Replaced the arc from node i to j with the supplied lattice. This is used to do OOV
     * segmentation of words in a lattice.
 -   * 
 +   *
-    * @param i
-    * @param j
-    * @param lattice
+    * @param i start node of arc
+    * @param j end node of arc
+    * @param newNodes new nodes used within the replacement operation
     */
    public void insert(int i, int j, List<Node<Value>> newNodes) {
  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/metrics/BLEU.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/server/ServerThread.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/server/TcpServer.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/subsample/Subsampler.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/tools/GrammarPacker.java
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diff --cc src/main/java/org/apache/joshua/tools/GrammarPacker.java
index 93cb610,517b744..8bdeb3b
--- a/src/main/java/org/apache/joshua/tools/GrammarPacker.java
+++ b/src/main/java/org/apache/joshua/tools/GrammarPacker.java
@@@ -148,10 -147,10 +148,10 @@@ public class GrammarPacker 
    /**
     * Executes the packing.
     * 
-    * @throws IOException
+    * @throws IOException if there is an error reading the grammar
     */
    public void pack() throws IOException {
 -    logger.info("Beginning exploration pass.");
 +    LOG.info("Beginning exploration pass.");
      LineReader grammar_reader = null;
      LineReader alignment_reader = null;
  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/tools/LabelPhrases.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/tools/TestSetFilter.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/util/CompareGrammars.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/util/ExtractTopCand.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/util/FormatUtils.java
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http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/9d6f84d3/src/main/java/org/apache/joshua/util/io/BinaryOut.java
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