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Posted to commits@joshua.apache.org by mj...@apache.org on 2016/06/01 02:51:43 UTC

[48/94] [abbrv] [partial] incubator-joshua git commit: Pulled JOSHUA-252 changes and Resolved Merge Conflicts

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/dependencies
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diff --git a/ext/giza-pp/GIZA++-v2/dependencies b/ext/giza-pp/GIZA++-v2/dependencies
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@@ -1,635 +0,0 @@
-#Automatically generated dependecy list
-optimized/alignment.o: alignment.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h
-optimized/AlignTables.o: AlignTables.cpp AlignTables.h defs.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h transpair_model1.h NTables.h vocab.h \
-  ATables.h Array4.h TTables.h Globals.h alignment.h
-optimized/ATables.o: ATables.cpp ATables.h defs.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h Array4.h Globals.h Parameter.h Pointer.h
-optimized/collCounts.o: collCounts.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  collCounts.h MoveSwapMatrix.h D4Tables.h WordClasses.h \
-  transpair_model4.h D5Tables.h transpair_model5.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h Parameter.h Pointer.h
-optimized/Dictionary.o: Dictionary.cpp Dictionary.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h
-optimized/ForwardBackward.o: ForwardBackward.cpp ForwardBackward.h myassert.h \
-  Array.h Vector.h mystl.h mymath.h Array2.h Globals.h defs.h HMMTables.h \
-  FlexArray.h
-optimized/getSentence.o: getSentence.cpp getSentence.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h vocab.h Globals.h Parameter.h Pointer.h
-optimized/hmm.o: hmm.cpp hmm.h Vector.h mystl.h myassert.h mymath.h Array2.h \
-  TTables.h defs.h vocab.h Globals.h ATables.h Array4.h getSentence.h \
-  model2.h model1.h Perplexity.h Dictionary.h WordClasses.h HMMTables.h \
-  FlexArray.h Array.h ForwardBackward.h utility.h Parameter.h Pointer.h \
-  HMMTables.cpp
-optimized/HMMTables.o: HMMTables.cpp HMMTables.h FlexArray.h Array.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h Globals.h defs.h Parameter.h \
-  Pointer.h
-optimized/logprob.o: logprob.cpp logprob.h
-optimized/main.o: main.cpp getSentence.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h defs.h vocab.h Globals.h TTables.h model1.h Perplexity.h \
-  Dictionary.h model2.h ATables.h Array4.h model3.h MoveSwapMatrix.h \
-  alignment.h transpair_model3.h NTables.h transpair_model2.h \
-  transpair_model1.h transpair_modelhmm.h ForwardBackward.h Array.h hmm.h \
-  WordClasses.h HMMTables.h FlexArray.h D4Tables.h AlignTables.h \
-  file_spec.h utility.h Parameter.h Pointer.h D5Tables.h \
-  transpair_model4.h transpair_model5.h
-optimized/model1.o: model1.cpp model1.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h vocab.h defs.h TTables.h Globals.h getSentence.h Perplexity.h \
-  Dictionary.h utility.h Parameter.h Pointer.h
-optimized/model2.o: model2.cpp model2.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h TTables.h defs.h vocab.h Globals.h ATables.h Array4.h \
-  getSentence.h model1.h Perplexity.h Dictionary.h utility.h Parameter.h \
-  Pointer.h
-optimized/model2to3.o: model2to3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h utility.h
-optimized/model345-peg.o: model345-peg.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h collCounts.h transpair_model4.h
-optimized/model3.o: model3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h collCounts.h transpair_model4.h utility.h D5Tables.h \
-  transpair_model5.h Parameter.h Pointer.h
-optimized/model3_viterbi.o: model3_viterbi.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h utility.h
-optimized/model3_viterbi_with_tricks.o: model3_viterbi_with_tricks.cpp mystl.h \
-  myassert.h mymath.h Array2.h model3.h Vector.h MoveSwapMatrix.h \
-  alignment.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  getSentence.h model2.h model1.h Perplexity.h Dictionary.h \
-  transpair_modelhmm.h ForwardBackward.h Array.h hmm.h WordClasses.h \
-  HMMTables.h FlexArray.h D4Tables.h AlignTables.h collCounts.h \
-  transpair_model4.h utility.h D5Tables.h transpair_model5.h Parameter.h \
-  Pointer.h collCounts.cpp
-optimized/MoveSwapMatrix.o: MoveSwapMatrix.cpp MoveSwapMatrix.h alignment.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h transpair_model4.h D4Tables.h \
-  WordClasses.h transpair_model5.h D5Tables.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h
-optimized/myassert.o: myassert.cpp mystl.h myassert.h mymath.h Array2.h
-optimized/NTables.o: NTables.cpp NTables.h Array2.h mystl.h myassert.h mymath.h \
-  Vector.h defs.h vocab.h Parameter.h Pointer.h Globals.h
-optimized/Parameter.o: Parameter.cpp Parameter.h mystl.h myassert.h mymath.h \
-  Array2.h Pointer.h Globals.h defs.h Vector.h
-optimized/parse.o: parse.cpp defs.h utility.h Perplexity.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h TTables.h vocab.h getSentence.h \
-  D4Tables.h WordClasses.h D5Tables.h ATables.h Array4.h Parameter.h \
-  Pointer.h
-optimized/Perplexity.o: Perplexity.cpp Perplexity.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h Globals.h
-optimized/plain2snt.o: plain2snt.cpp
-optimized/reports.o: reports.cpp defs.h vocab.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h Perplexity.h Globals.h getSentence.h TTables.h Parameter.h \
-  Pointer.h
-optimized/snt2cooc.o: snt2cooc.cpp
-optimized/snt2plain.o: snt2plain.cpp
-optimized/transpair_model3.o: transpair_model3.cpp transpair_model3.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h transpair_model2.h \
-  transpair_model1.h
-optimized/transpair_model4.o: transpair_model4.cpp transpair_model4.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D4Tables.h WordClasses.h \
-  transpair_model3.h transpair_model2.h transpair_model1.h Parameter.h \
-  Pointer.h
-optimized/transpair_model5.o: transpair_model5.cpp transpair_model5.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D5Tables.h D4Tables.h \
-  WordClasses.h transpair_model4.h transpair_model3.h transpair_model2.h \
-  transpair_model1.h Parameter.h Pointer.h
-optimized/TTables.o: TTables.cpp TTables.h defs.h vocab.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h Parameter.h Pointer.h
-optimized/utility.o: utility.cpp mymath.h
-optimized/vocab.o: vocab.cpp vocab.h defs.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h
-#Automatically generated dependecy list
-debug/alignment.o: alignment.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h
-debug/AlignTables.o: AlignTables.cpp AlignTables.h defs.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h transpair_model1.h NTables.h vocab.h \
-  ATables.h Array4.h TTables.h Globals.h alignment.h
-debug/ATables.o: ATables.cpp ATables.h defs.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h Array4.h Globals.h Parameter.h Pointer.h
-debug/collCounts.o: collCounts.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  collCounts.h MoveSwapMatrix.h D4Tables.h WordClasses.h \
-  transpair_model4.h D5Tables.h transpair_model5.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h Parameter.h Pointer.h
-debug/Dictionary.o: Dictionary.cpp Dictionary.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h
-debug/ForwardBackward.o: ForwardBackward.cpp ForwardBackward.h myassert.h \
-  Array.h Vector.h mystl.h mymath.h Array2.h Globals.h defs.h HMMTables.h \
-  FlexArray.h
-debug/getSentence.o: getSentence.cpp getSentence.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h vocab.h Globals.h Parameter.h Pointer.h
-debug/hmm.o: hmm.cpp hmm.h Vector.h mystl.h myassert.h mymath.h Array2.h \
-  TTables.h defs.h vocab.h Globals.h ATables.h Array4.h getSentence.h \
-  model2.h model1.h Perplexity.h Dictionary.h WordClasses.h HMMTables.h \
-  FlexArray.h Array.h ForwardBackward.h utility.h Parameter.h Pointer.h \
-  HMMTables.cpp
-debug/HMMTables.o: HMMTables.cpp HMMTables.h FlexArray.h Array.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h Globals.h defs.h Parameter.h \
-  Pointer.h
-debug/logprob.o: logprob.cpp logprob.h
-debug/main.o: main.cpp getSentence.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h defs.h vocab.h Globals.h TTables.h model1.h Perplexity.h \
-  Dictionary.h model2.h ATables.h Array4.h model3.h MoveSwapMatrix.h \
-  alignment.h transpair_model3.h NTables.h transpair_model2.h \
-  transpair_model1.h transpair_modelhmm.h ForwardBackward.h Array.h hmm.h \
-  WordClasses.h HMMTables.h FlexArray.h D4Tables.h AlignTables.h \
-  file_spec.h utility.h Parameter.h Pointer.h D5Tables.h \
-  transpair_model4.h transpair_model5.h
-debug/model1.o: model1.cpp model1.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h vocab.h defs.h TTables.h Globals.h getSentence.h Perplexity.h \
-  Dictionary.h utility.h Parameter.h Pointer.h
-debug/model2.o: model2.cpp model2.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h TTables.h defs.h vocab.h Globals.h ATables.h Array4.h \
-  getSentence.h model1.h Perplexity.h Dictionary.h utility.h Parameter.h \
-  Pointer.h
-debug/model2to3.o: model2to3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h utility.h
-debug/model345-peg.o: model345-peg.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h collCounts.h transpair_model4.h
-debug/model3.o: model3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h collCounts.h transpair_model4.h utility.h D5Tables.h \
-  transpair_model5.h Parameter.h Pointer.h
-debug/model3_viterbi.o: model3_viterbi.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h utility.h
-debug/model3_viterbi_with_tricks.o: model3_viterbi_with_tricks.cpp mystl.h \
-  myassert.h mymath.h Array2.h model3.h Vector.h MoveSwapMatrix.h \
-  alignment.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  getSentence.h model2.h model1.h Perplexity.h Dictionary.h \
-  transpair_modelhmm.h ForwardBackward.h Array.h hmm.h WordClasses.h \
-  HMMTables.h FlexArray.h D4Tables.h AlignTables.h collCounts.h \
-  transpair_model4.h utility.h D5Tables.h transpair_model5.h Parameter.h \
-  Pointer.h collCounts.cpp
-debug/MoveSwapMatrix.o: MoveSwapMatrix.cpp MoveSwapMatrix.h alignment.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h transpair_model4.h D4Tables.h \
-  WordClasses.h transpair_model5.h D5Tables.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h
-debug/myassert.o: myassert.cpp mystl.h myassert.h mymath.h Array2.h
-debug/NTables.o: NTables.cpp NTables.h Array2.h mystl.h myassert.h mymath.h \
-  Vector.h defs.h vocab.h Parameter.h Pointer.h Globals.h
-debug/Parameter.o: Parameter.cpp Parameter.h mystl.h myassert.h mymath.h \
-  Array2.h Pointer.h Globals.h defs.h Vector.h
-debug/parse.o: parse.cpp defs.h utility.h Perplexity.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h TTables.h vocab.h getSentence.h \
-  D4Tables.h WordClasses.h D5Tables.h ATables.h Array4.h Parameter.h \
-  Pointer.h
-debug/Perplexity.o: Perplexity.cpp Perplexity.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h Globals.h
-debug/plain2snt.o: plain2snt.cpp
-debug/reports.o: reports.cpp defs.h vocab.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h Perplexity.h Globals.h getSentence.h TTables.h Parameter.h \
-  Pointer.h
-debug/snt2cooc.o: snt2cooc.cpp
-debug/snt2plain.o: snt2plain.cpp
-debug/transpair_model3.o: transpair_model3.cpp transpair_model3.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h transpair_model2.h \
-  transpair_model1.h
-debug/transpair_model4.o: transpair_model4.cpp transpair_model4.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D4Tables.h WordClasses.h \
-  transpair_model3.h transpair_model2.h transpair_model1.h Parameter.h \
-  Pointer.h
-debug/transpair_model5.o: transpair_model5.cpp transpair_model5.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D5Tables.h D4Tables.h \
-  WordClasses.h transpair_model4.h transpair_model3.h transpair_model2.h \
-  transpair_model1.h Parameter.h Pointer.h
-debug/TTables.o: TTables.cpp TTables.h defs.h vocab.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h Parameter.h Pointer.h
-debug/utility.o: utility.cpp mymath.h
-debug/vocab.o: vocab.cpp vocab.h defs.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h
-#Automatically generated dependecy list
-vdebug/alignment.o: alignment.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h
-vdebug/AlignTables.o: AlignTables.cpp AlignTables.h defs.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h transpair_model1.h NTables.h vocab.h \
-  ATables.h Array4.h TTables.h Globals.h alignment.h
-vdebug/ATables.o: ATables.cpp ATables.h defs.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h Array4.h Globals.h Parameter.h Pointer.h
-vdebug/collCounts.o: collCounts.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  collCounts.h MoveSwapMatrix.h D4Tables.h WordClasses.h \
-  transpair_model4.h D5Tables.h transpair_model5.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h Parameter.h Pointer.h
-vdebug/Dictionary.o: Dictionary.cpp Dictionary.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h
-vdebug/ForwardBackward.o: ForwardBackward.cpp ForwardBackward.h myassert.h \
-  Array.h Vector.h mystl.h mymath.h Array2.h Globals.h defs.h HMMTables.h \
-  FlexArray.h
-vdebug/getSentence.o: getSentence.cpp getSentence.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h vocab.h Globals.h Parameter.h Pointer.h
-vdebug/hmm.o: hmm.cpp hmm.h Vector.h mystl.h myassert.h mymath.h Array2.h \
-  TTables.h defs.h vocab.h Globals.h ATables.h Array4.h getSentence.h \
-  model2.h model1.h Perplexity.h Dictionary.h WordClasses.h HMMTables.h \
-  FlexArray.h Array.h ForwardBackward.h utility.h Parameter.h Pointer.h \
-  HMMTables.cpp
-vdebug/HMMTables.o: HMMTables.cpp HMMTables.h FlexArray.h Array.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h Globals.h defs.h Parameter.h \
-  Pointer.h
-vdebug/logprob.o: logprob.cpp logprob.h
-vdebug/main.o: main.cpp getSentence.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h defs.h vocab.h Globals.h TTables.h model1.h Perplexity.h \
-  Dictionary.h model2.h ATables.h Array4.h model3.h MoveSwapMatrix.h \
-  alignment.h transpair_model3.h NTables.h transpair_model2.h \
-  transpair_model1.h transpair_modelhmm.h ForwardBackward.h Array.h hmm.h \
-  WordClasses.h HMMTables.h FlexArray.h D4Tables.h AlignTables.h \
-  file_spec.h utility.h Parameter.h Pointer.h D5Tables.h \
-  transpair_model4.h transpair_model5.h
-vdebug/model1.o: model1.cpp model1.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h vocab.h defs.h TTables.h Globals.h getSentence.h Perplexity.h \
-  Dictionary.h utility.h Parameter.h Pointer.h
-vdebug/model2.o: model2.cpp model2.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h TTables.h defs.h vocab.h Globals.h ATables.h Array4.h \
-  getSentence.h model1.h Perplexity.h Dictionary.h utility.h Parameter.h \
-  Pointer.h
-vdebug/model2to3.o: model2to3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h utility.h
-vdebug/model345-peg.o: model345-peg.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h collCounts.h transpair_model4.h
-vdebug/model3.o: model3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h collCounts.h transpair_model4.h utility.h D5Tables.h \
-  transpair_model5.h Parameter.h Pointer.h
-vdebug/model3_viterbi.o: model3_viterbi.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h utility.h
-vdebug/model3_viterbi_with_tricks.o: model3_viterbi_with_tricks.cpp mystl.h \
-  myassert.h mymath.h Array2.h model3.h Vector.h MoveSwapMatrix.h \
-  alignment.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  getSentence.h model2.h model1.h Perplexity.h Dictionary.h \
-  transpair_modelhmm.h ForwardBackward.h Array.h hmm.h WordClasses.h \
-  HMMTables.h FlexArray.h D4Tables.h AlignTables.h collCounts.h \
-  transpair_model4.h utility.h D5Tables.h transpair_model5.h Parameter.h \
-  Pointer.h collCounts.cpp
-vdebug/MoveSwapMatrix.o: MoveSwapMatrix.cpp MoveSwapMatrix.h alignment.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h transpair_model4.h D4Tables.h \
-  WordClasses.h transpair_model5.h D5Tables.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h
-vdebug/myassert.o: myassert.cpp mystl.h myassert.h mymath.h Array2.h
-vdebug/NTables.o: NTables.cpp NTables.h Array2.h mystl.h myassert.h mymath.h \
-  Vector.h defs.h vocab.h Parameter.h Pointer.h Globals.h
-vdebug/Parameter.o: Parameter.cpp Parameter.h mystl.h myassert.h mymath.h \
-  Array2.h Pointer.h Globals.h defs.h Vector.h
-vdebug/parse.o: parse.cpp defs.h utility.h Perplexity.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h TTables.h vocab.h getSentence.h \
-  D4Tables.h WordClasses.h D5Tables.h ATables.h Array4.h Parameter.h \
-  Pointer.h
-vdebug/Perplexity.o: Perplexity.cpp Perplexity.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h Globals.h
-vdebug/plain2snt.o: plain2snt.cpp
-vdebug/reports.o: reports.cpp defs.h vocab.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h Perplexity.h Globals.h getSentence.h TTables.h Parameter.h \
-  Pointer.h
-vdebug/snt2cooc.o: snt2cooc.cpp
-vdebug/snt2plain.o: snt2plain.cpp
-vdebug/transpair_model3.o: transpair_model3.cpp transpair_model3.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h transpair_model2.h \
-  transpair_model1.h
-vdebug/transpair_model4.o: transpair_model4.cpp transpair_model4.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D4Tables.h WordClasses.h \
-  transpair_model3.h transpair_model2.h transpair_model1.h Parameter.h \
-  Pointer.h
-vdebug/transpair_model5.o: transpair_model5.cpp transpair_model5.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D5Tables.h D4Tables.h \
-  WordClasses.h transpair_model4.h transpair_model3.h transpair_model2.h \
-  transpair_model1.h Parameter.h Pointer.h
-vdebug/TTables.o: TTables.cpp TTables.h defs.h vocab.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h Parameter.h Pointer.h
-vdebug/utility.o: utility.cpp mymath.h
-vdebug/vocab.o: vocab.cpp vocab.h defs.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h
-#Automatically generated dependecy list
-norm/alignment.o: alignment.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h
-norm/AlignTables.o: AlignTables.cpp AlignTables.h defs.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h transpair_model1.h NTables.h vocab.h \
-  ATables.h Array4.h TTables.h Globals.h alignment.h
-norm/ATables.o: ATables.cpp ATables.h defs.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h Array4.h Globals.h Parameter.h Pointer.h
-norm/collCounts.o: collCounts.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  collCounts.h MoveSwapMatrix.h D4Tables.h WordClasses.h \
-  transpair_model4.h D5Tables.h transpair_model5.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h Parameter.h Pointer.h
-norm/Dictionary.o: Dictionary.cpp Dictionary.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h
-norm/ForwardBackward.o: ForwardBackward.cpp ForwardBackward.h myassert.h \
-  Array.h Vector.h mystl.h mymath.h Array2.h Globals.h defs.h HMMTables.h \
-  FlexArray.h
-norm/getSentence.o: getSentence.cpp getSentence.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h vocab.h Globals.h Parameter.h Pointer.h
-norm/hmm.o: hmm.cpp hmm.h Vector.h mystl.h myassert.h mymath.h Array2.h \
-  TTables.h defs.h vocab.h Globals.h ATables.h Array4.h getSentence.h \
-  model2.h model1.h Perplexity.h Dictionary.h WordClasses.h HMMTables.h \
-  FlexArray.h Array.h ForwardBackward.h utility.h Parameter.h Pointer.h \
-  HMMTables.cpp
-norm/HMMTables.o: HMMTables.cpp HMMTables.h FlexArray.h Array.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h Globals.h defs.h Parameter.h \
-  Pointer.h
-norm/logprob.o: logprob.cpp logprob.h
-norm/main.o: main.cpp getSentence.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h defs.h vocab.h Globals.h TTables.h model1.h Perplexity.h \
-  Dictionary.h model2.h ATables.h Array4.h model3.h MoveSwapMatrix.h \
-  alignment.h transpair_model3.h NTables.h transpair_model2.h \
-  transpair_model1.h transpair_modelhmm.h ForwardBackward.h Array.h hmm.h \
-  WordClasses.h HMMTables.h FlexArray.h D4Tables.h AlignTables.h \
-  file_spec.h utility.h Parameter.h Pointer.h D5Tables.h \
-  transpair_model4.h transpair_model5.h
-norm/model1.o: model1.cpp model1.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h vocab.h defs.h TTables.h Globals.h getSentence.h Perplexity.h \
-  Dictionary.h utility.h Parameter.h Pointer.h
-norm/model2.o: model2.cpp model2.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h TTables.h defs.h vocab.h Globals.h ATables.h Array4.h \
-  getSentence.h model1.h Perplexity.h Dictionary.h utility.h Parameter.h \
-  Pointer.h
-norm/model2to3.o: model2to3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h utility.h
-norm/model345-peg.o: model345-peg.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h collCounts.h transpair_model4.h
-norm/model3.o: model3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h collCounts.h transpair_model4.h utility.h D5Tables.h \
-  transpair_model5.h Parameter.h Pointer.h
-norm/model3_viterbi.o: model3_viterbi.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h utility.h
-norm/model3_viterbi_with_tricks.o: model3_viterbi_with_tricks.cpp mystl.h \
-  myassert.h mymath.h Array2.h model3.h Vector.h MoveSwapMatrix.h \
-  alignment.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  getSentence.h model2.h model1.h Perplexity.h Dictionary.h \
-  transpair_modelhmm.h ForwardBackward.h Array.h hmm.h WordClasses.h \
-  HMMTables.h FlexArray.h D4Tables.h AlignTables.h collCounts.h \
-  transpair_model4.h utility.h D5Tables.h transpair_model5.h Parameter.h \
-  Pointer.h collCounts.cpp
-norm/MoveSwapMatrix.o: MoveSwapMatrix.cpp MoveSwapMatrix.h alignment.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h transpair_model4.h D4Tables.h \
-  WordClasses.h transpair_model5.h D5Tables.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h
-norm/myassert.o: myassert.cpp mystl.h myassert.h mymath.h Array2.h
-norm/NTables.o: NTables.cpp NTables.h Array2.h mystl.h myassert.h mymath.h \
-  Vector.h defs.h vocab.h Parameter.h Pointer.h Globals.h
-norm/Parameter.o: Parameter.cpp Parameter.h mystl.h myassert.h mymath.h \
-  Array2.h Pointer.h Globals.h defs.h Vector.h
-norm/parse.o: parse.cpp defs.h utility.h Perplexity.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h TTables.h vocab.h getSentence.h \
-  D4Tables.h WordClasses.h D5Tables.h ATables.h Array4.h Parameter.h \
-  Pointer.h
-norm/Perplexity.o: Perplexity.cpp Perplexity.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h Globals.h
-norm/plain2snt.o: plain2snt.cpp
-norm/reports.o: reports.cpp defs.h vocab.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h Perplexity.h Globals.h getSentence.h TTables.h Parameter.h \
-  Pointer.h
-norm/snt2cooc.o: snt2cooc.cpp
-norm/snt2plain.o: snt2plain.cpp
-norm/transpair_model3.o: transpair_model3.cpp transpair_model3.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h transpair_model2.h \
-  transpair_model1.h
-norm/transpair_model4.o: transpair_model4.cpp transpair_model4.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D4Tables.h WordClasses.h \
-  transpair_model3.h transpair_model2.h transpair_model1.h Parameter.h \
-  Pointer.h
-norm/transpair_model5.o: transpair_model5.cpp transpair_model5.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D5Tables.h D4Tables.h \
-  WordClasses.h transpair_model4.h transpair_model3.h transpair_model2.h \
-  transpair_model1.h Parameter.h Pointer.h
-norm/TTables.o: TTables.cpp TTables.h defs.h vocab.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h Parameter.h Pointer.h
-norm/utility.o: utility.cpp mymath.h
-norm/vocab.o: vocab.cpp vocab.h defs.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h
-#Automatically generated dependecy list
-profile/alignment.o: alignment.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h
-profile/AlignTables.o: AlignTables.cpp AlignTables.h defs.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h transpair_model1.h NTables.h vocab.h \
-  ATables.h Array4.h TTables.h Globals.h alignment.h
-profile/ATables.o: ATables.cpp ATables.h defs.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h Array4.h Globals.h Parameter.h Pointer.h
-profile/collCounts.o: collCounts.cpp alignment.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  collCounts.h MoveSwapMatrix.h D4Tables.h WordClasses.h \
-  transpair_model4.h D5Tables.h transpair_model5.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h Parameter.h Pointer.h
-profile/Dictionary.o: Dictionary.cpp Dictionary.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h
-profile/ForwardBackward.o: ForwardBackward.cpp ForwardBackward.h myassert.h \
-  Array.h Vector.h mystl.h mymath.h Array2.h Globals.h defs.h HMMTables.h \
-  FlexArray.h
-profile/getSentence.o: getSentence.cpp getSentence.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h vocab.h Globals.h Parameter.h Pointer.h
-profile/hmm.o: hmm.cpp hmm.h Vector.h mystl.h myassert.h mymath.h Array2.h \
-  TTables.h defs.h vocab.h Globals.h ATables.h Array4.h getSentence.h \
-  model2.h model1.h Perplexity.h Dictionary.h WordClasses.h HMMTables.h \
-  FlexArray.h Array.h ForwardBackward.h utility.h Parameter.h Pointer.h \
-  HMMTables.cpp
-profile/HMMTables.o: HMMTables.cpp HMMTables.h FlexArray.h Array.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h Globals.h defs.h Parameter.h \
-  Pointer.h
-profile/logprob.o: logprob.cpp logprob.h
-profile/main.o: main.cpp getSentence.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h defs.h vocab.h Globals.h TTables.h model1.h Perplexity.h \
-  Dictionary.h model2.h ATables.h Array4.h model3.h MoveSwapMatrix.h \
-  alignment.h transpair_model3.h NTables.h transpair_model2.h \
-  transpair_model1.h transpair_modelhmm.h ForwardBackward.h Array.h hmm.h \
-  WordClasses.h HMMTables.h FlexArray.h D4Tables.h AlignTables.h \
-  file_spec.h utility.h Parameter.h Pointer.h D5Tables.h \
-  transpair_model4.h transpair_model5.h
-profile/model1.o: model1.cpp model1.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h vocab.h defs.h TTables.h Globals.h getSentence.h Perplexity.h \
-  Dictionary.h utility.h Parameter.h Pointer.h
-profile/model2.o: model2.cpp model2.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h TTables.h defs.h vocab.h Globals.h ATables.h Array4.h \
-  getSentence.h model1.h Perplexity.h Dictionary.h utility.h Parameter.h \
-  Pointer.h
-profile/model2to3.o: model2to3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h utility.h
-profile/model345-peg.o: model345-peg.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h collCounts.h transpair_model4.h
-profile/model3.o: model3.cpp model3.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h MoveSwapMatrix.h alignment.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h transpair_modelhmm.h ForwardBackward.h \
-  Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h D4Tables.h \
-  AlignTables.h collCounts.h transpair_model4.h utility.h D5Tables.h \
-  transpair_model5.h Parameter.h Pointer.h
-profile/model3_viterbi.o: model3_viterbi.cpp model3.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h MoveSwapMatrix.h alignment.h defs.h \
-  transpair_model3.h NTables.h vocab.h ATables.h Array4.h TTables.h \
-  Globals.h transpair_model2.h transpair_model1.h getSentence.h model2.h \
-  model1.h Perplexity.h Dictionary.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h WordClasses.h HMMTables.h FlexArray.h \
-  D4Tables.h AlignTables.h utility.h
-profile/model3_viterbi_with_tricks.o: model3_viterbi_with_tricks.cpp mystl.h \
-  myassert.h mymath.h Array2.h model3.h Vector.h MoveSwapMatrix.h \
-  alignment.h defs.h transpair_model3.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h transpair_model2.h transpair_model1.h \
-  getSentence.h model2.h model1.h Perplexity.h Dictionary.h \
-  transpair_modelhmm.h ForwardBackward.h Array.h hmm.h WordClasses.h \
-  HMMTables.h FlexArray.h D4Tables.h AlignTables.h collCounts.h \
-  transpair_model4.h utility.h D5Tables.h transpair_model5.h Parameter.h \
-  Pointer.h collCounts.cpp
-profile/MoveSwapMatrix.o: MoveSwapMatrix.cpp MoveSwapMatrix.h alignment.h Vector.h \
-  mystl.h myassert.h mymath.h Array2.h defs.h transpair_model3.h \
-  NTables.h vocab.h ATables.h Array4.h TTables.h Globals.h \
-  transpair_model2.h transpair_model1.h transpair_model4.h D4Tables.h \
-  WordClasses.h transpair_model5.h D5Tables.h transpair_modelhmm.h \
-  ForwardBackward.h Array.h hmm.h getSentence.h model2.h model1.h \
-  Perplexity.h Dictionary.h HMMTables.h FlexArray.h
-profile/myassert.o: myassert.cpp mystl.h myassert.h mymath.h Array2.h
-profile/NTables.o: NTables.cpp NTables.h Array2.h mystl.h myassert.h mymath.h \
-  Vector.h defs.h vocab.h Parameter.h Pointer.h Globals.h
-profile/Parameter.o: Parameter.cpp Parameter.h mystl.h myassert.h mymath.h \
-  Array2.h Pointer.h Globals.h defs.h Vector.h
-profile/parse.o: parse.cpp defs.h utility.h Perplexity.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h TTables.h vocab.h getSentence.h \
-  D4Tables.h WordClasses.h D5Tables.h ATables.h Array4.h Parameter.h \
-  Pointer.h
-profile/Perplexity.o: Perplexity.cpp Perplexity.h Vector.h mystl.h myassert.h \
-  mymath.h Array2.h defs.h Globals.h
-profile/plain2snt.o: plain2snt.cpp
-profile/reports.o: reports.cpp defs.h vocab.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h Perplexity.h Globals.h getSentence.h TTables.h Parameter.h \
-  Pointer.h
-profile/snt2cooc.o: snt2cooc.cpp
-profile/snt2plain.o: snt2plain.cpp
-profile/transpair_model3.o: transpair_model3.cpp transpair_model3.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h transpair_model2.h \
-  transpair_model1.h
-profile/transpair_model4.o: transpair_model4.cpp transpair_model4.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D4Tables.h WordClasses.h \
-  transpair_model3.h transpair_model2.h transpair_model1.h Parameter.h \
-  Pointer.h
-profile/transpair_model5.o: transpair_model5.cpp transpair_model5.h Array2.h \
-  mystl.h myassert.h mymath.h defs.h Vector.h NTables.h vocab.h ATables.h \
-  Array4.h TTables.h Globals.h alignment.h D5Tables.h D4Tables.h \
-  WordClasses.h transpair_model4.h transpair_model3.h transpair_model2.h \
-  transpair_model1.h Parameter.h Pointer.h
-profile/TTables.o: TTables.cpp TTables.h defs.h vocab.h Vector.h mystl.h \
-  myassert.h mymath.h Array2.h Globals.h Parameter.h Pointer.h
-profile/utility.o: utility.cpp mymath.h
-profile/vocab.o: vocab.cpp vocab.h defs.h Vector.h mystl.h myassert.h mymath.h \
-  Array2.h

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/file_spec.h
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/file_spec.h b/ext/giza-pp/GIZA++-v2/file_spec.h
deleted file mode 100644
index 2d43295..0000000
--- a/ext/giza-pp/GIZA++-v2/file_spec.h
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-#ifndef FILE_SPEC_H
-#define FILE_SPEC_H
-
-#include <time.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-
-/* This function returns a string, locally called file_spec. This
-   string is the concatenation of the date and time of execution
-   and the user who is performing the execution */
-/* Originally implemented in C by Yaser Al-Onaizan; 
-   editions for C++ and formatting by Noah A. Smith, 9 July 1999 */
-
-char *Get_File_Spec (){
-  struct tm *local;
-  time_t t;
-  char *user;
-  char time_stmp[19];
-  char *file_spec = 0;
-  
-  t = time(NULL);
-  local = localtime(&t);
-  
-  sprintf(time_stmp, "%02d-%02d-%02d.%02d%02d%02d.", local->tm_year, 
-	  (local->tm_mon + 1), local->tm_mday, local->tm_hour, 
-	  local->tm_min, local->tm_sec);
-  user = getenv("USER");
-
-  file_spec = (char *)malloc(sizeof(char) * 
-			     (strlen(time_stmp) + strlen(user) + 1));
-  file_spec[0] = '\0';
-  strcat(file_spec, time_stmp) ;
-  strcat(file_spec, user);
-  return file_spec;
-}
-
-#endif

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/getSentence.cpp
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/getSentence.cpp b/ext/giza-pp/GIZA++-v2/getSentence.cpp
deleted file mode 100644
index 125a6f7..0000000
--- a/ext/giza-pp/GIZA++-v2/getSentence.cpp
+++ /dev/null
@@ -1,340 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-/* --------------------------------------------------------------------------*
- *                                                                           *
- * Module : getSentece                                                       *
- *                                                                           *
- * Method Definitions File: getSentence.cc                                   *
- *                                                                           *
- * Objective: Defines clases and methods for handling I/O for the parallel   *
- *            corpus.                                                        *
- *****************************************************************************/
-
-
-#include "getSentence.h"
-#include <iostream>
-#include <sstream>
-#include "Parameter.h"
-#include "errno.h"
-
-int PrintedTooLong=0;
-
-/* -------------- Method Defnitions for Class sentenceHandler ---------------*/
-
-GLOBAL_PARAMETER(double,ManlexMAX_MULTIPLICITY,"manlexMAX_MULTIPLICITY","",PARLEV_EM,20.0);
-GLOBAL_PARAMETER(double,Manlexfactor1,"manlexfactor1","",PARLEV_EM,0.0);
-GLOBAL_PARAMETER(double,Manlexfactor2,"manlexfactor2","",PARLEV_EM,0.0);
-
-sentenceHandler::sentenceHandler(const char*  filename, vcbList* elist, 
-				 vcbList*  flist) : realCount(0)
-  // This method is the constructor of the class, it also intitializes the 
-  // sentence pair sequential number (count) to zero.
-
-{
-  readflag = false ;
-  allInMemory = false ;
-  inputFilename = filename ;
-  inputFile = new ifstream(filename);
-  pair_no = 0 ;
-  if(!(*inputFile)){
-    cerr << "\nERROR:(a) Cannot open " << filename;
-    exit(1);
-  }
-  currentSentence = 0;
-  totalPairs1 = 0 ;
-  totalPairs2 =0;
-  pair_no = 0 ;
-  noSentInBuffer = 0 ;
-  Buffer.clear();
-  bool isNegative=0;
-  if (elist && flist){
-    cout << "Calculating vocabulary frequencies from corpus " << filename << '\n';
-    sentPair s ;
-    while (getNextSentence(s, elist, flist))
-      {
-	totalPairs1++;
-	totalPairs2+=s.realCount; 
-	// NOTE: this value might change during training 
-	// for words from the manual dictionary, yet this is ignored!
-
-	if( s.noOcc<0 )
-	  isNegative=1;
-      }
-  }
-  if( isNegative==1 )
-    {
-      cerr << "WARNING: corpus contains negative occurrency frequencies => these are interpreted as entries of a manual dictionary.\n";
-      realCount=new Vector<double>(totalPairs1,1.0);
-    }
-  else
-    realCount=0;
-}
-
-void sentenceHandler::rewind()
-{
-  currentSentence = 0;
-  readflag = false ;
-  if (!allInMemory || 
-      !(Buffer.size() >= 1 && Buffer[currentSentence].sentenceNo == 1)){
-    // check if the buffer doe not already has the first chunk of pairs 
-    if (Buffer.size() > 0)
-      cerr << ' ' <<  Buffer[currentSentence].sentenceNo << '\n';
-    //    totalPairs = 0 ;
-    pair_no = 0 ;
-    noSentInBuffer = 0 ;
-    Buffer.clear();
-  }
-  if (!allInMemory){
-    delete inputFile;
-    inputFile = new ifstream(inputFilename);
-    if(!(*inputFile)){
-      cerr << "\nERROR:(b) Cannot open " << inputFilename << " " << (int)errno;
-    }
-  }
-}
-
-  
-bool sentenceHandler::getNextSentence(sentPair& sent, vcbList* elist, vcbList* flist)
-{
-  sentPair s ;
-  if (readflag){
-    cerr << "Attempting to read from the end of corpus, rewinding\n";
-    rewind();
-    return(false);
-  } 
-  if (currentSentence >= noSentInBuffer){
-    if (allInMemory)
-      return(false);
-    /* no more sentences in buffer */
-    noSentInBuffer = 0 ;
-    currentSentence = 0 ;
-    Buffer.clear();
-    cout << "Reading more sentence pairs into memory ... \n";
-    while((noSentInBuffer < TRAIN_BUFFER_SIZE) && readNextSentence(s)){
-      if ((s.fSent.size()-1) > (MAX_FERTILITY-1) * (s.eSent.size()-1)){
-	cerr << "WARNING: The following sentence pair has source/target sentence length ration more than\n"<<
-	  "the maximum allowed limit for a source word fertility\n"<<
-	  " source length = " << s.eSent.size()-1 << " target length = " << s.fSent.size()-1 <<
-	  " ratio " << double(s.fSent.size()-1)/  (s.eSent.size()-1) << " ferility limit : " <<
-	  MAX_FERTILITY-1 << '\n';
-	cerr << "Shortening sentence \n";
-	cerr << s;
-	s.eSent.resize(min(s.eSent.size(),s.fSent.size()));
-	s.fSent.resize(min(s.eSent.size(),s.fSent.size()));
-      }
-      Buffer.push_back(s) ;
-      if (elist && flist){
-	if ((*elist).size() > 0)
-	  for (WordIndex i= 0 ; i < s.eSent.size() ; i++){
-	    if (s.eSent[i] >= (*elist).uniqTokens()){
-	      if( PrintedTooLong++<100)
-		cerr << "ERROR: source word " << s.eSent[i] << " is not in the vocabulary list \n";
-	      exit(-1);
-	    }
-	    (*elist).incFreq(s.eSent[i], s.realCount);
-	  }
-	if ((*flist).size() > 0)
-	  for (WordIndex j= 1 ; j < s.fSent.size() ; j++){
-	    if (s.fSent[j] >= (*flist).uniqTokens()){
-	      cerr << "ERROR: target word " << s.fSent[j] << " is not in the vocabulary list \n";
-	      exit(-1);
-	    }
-	    (*flist).incFreq(s.fSent[j], s.realCount);
-	  }
-      }
-      noSentInBuffer++;
-    }
-    if (inputFile->eof()){
-      allInMemory = (Buffer.size() >= 1 && 
-		     Buffer[currentSentence].sentenceNo == 1) ;
-      if (allInMemory)
-	cout << "Corpus fits in memory, corpus has: " << Buffer.size() <<
-	  " sentence pairs.\n";
-    }
-  }
-  if(noSentInBuffer <= 0 ){
-    //cerr << "# sent in buffer " << noSentInBuffer << '\n';
-    readflag = true ;
-    return(false);
-  }
-  sent = Buffer[currentSentence++] ;
-  if( sent.noOcc<0 && realCount )
-    {
-      if( Manlexfactor1 && sent.noOcc==-1.0 )
-	sent.realCount=Manlexfactor1;
-      else if( Manlexfactor2 && sent.noOcc==-2.0 )
-	sent.realCount=Manlexfactor2;
-      else
-	sent.realCount=(*realCount)[sent.getSentenceNo()-1];
-    }
-  return true ;
-}
-bool sentenceHandler::readNextSentence(sentPair& sent)
-  /* This method reads in a new pair of sentences, each pair is read from the 
-     corpus file as line triples. The first line the no of times this line 
-     pair occured in the corpus, the second line is the source sentence and 
-     the third is the target sentence. The sentences are represented by a space
-     separated positive integer token ids. */
-{
-
-  string line;
-  bool fail(false) ;
-  
-  sent.clear();
-  if (getline(*inputFile, line)){
-    istringstream buffer(line);
-    buffer >> sent.noOcc;
-    if( sent.noOcc<0 )
-      {
-	if( realCount )
-	  {
-	    if( Manlexfactor1 && sent.noOcc==-1.0 )
-	      sent.realCount=Manlexfactor1;
-	    else if( Manlexfactor2 && sent.noOcc==-2.0 )
-	      sent.realCount=Manlexfactor2;
-	    else
-	      {
-		sent.realCount=(*realCount)[pair_no];
-	      }
-	  }
-	else
-	  sent.realCount=1.0;
-      }
-    else
-      sent.realCount=sent.noOcc;
-  }
-  else {
-    fail = true ;;
-  }
-  if (getline(*inputFile, line)){
-    istringstream buffer(line);
-    WordIndex w;  // w is a local variabe for token id
-    sent.eSent.push_back(0); // each source word is assumed to have 0 == 
-    // a null word (id 0) at the begining of the sentence. 
-    while(buffer>>w){ // read source sentece , word by word .
-      if (sent.eSent.size() < MAX_SENTENCE_LENGTH)
-	sent.eSent.push_back(w);
-      else {
-	if( PrintedTooLong++<100)
-	  cerr << "{WARNING:(a)truncated sentence "<<pair_no<<"}";
-	//cerr << "ERROR: getSentence.cc:getNextSentence(): sentence exceeds preset length limit of : " << MAX_SENTENCE_LENGTH << '\n';
-	//cerr << "The following sentence will be truncated\n" << line;
-	break ;
-      }
-    }
-  }
-  else {
-    fail = true ;
-  }
-  if (getline(*inputFile, line)){
-    istringstream buffer(line);
-    WordIndex w;  // w is a local variabe for token id
-    sent.fSent.push_back(0); //0 is inserted for program uniformity
-    while(buffer>>w){ // read target sentece , word by word .
-      if (sent.fSent.size() < MAX_SENTENCE_LENGTH)
-	sent.fSent.push_back(w);
-      else {
-	if( PrintedTooLong++<100)
-	  cerr << "{WARNING:(b)truncated sentence "<<pair_no<<"}";
-	//cerr << "ERROR: getSentence.cc:getNextSentence(): sentence exceeds preset length limit of : " << MAX_SENTENCE_LENGTH << '\n';
-	//cerr << "The following sentence will be truncated\n" << line;
-	break ;
-      }
-    }
-  }
-  else {
-    fail = true ;
-  }
-  if (fail){
-    sent.eSent.clear();
-    sent.fSent.clear();
-    sent.sentenceNo = 0 ;
-    sent.noOcc = 0 ;
-    sent.realCount=0;
-    return(false);
-  }  
-  if( sent.eSent.size()==1||sent.fSent.size()==1 )
-    cerr << "ERROR: Forbidden zero sentence length " << sent.sentenceNo << endl;
-  sent.sentenceNo = ++pair_no;
-  if(pair_no % 100000 == 0) 
-    cout << "[sent:" << sent.sentenceNo  << "]"<< '\n';
-  return true;
-}
-
-double optimize_lambda(Vector<double>&vd)
-{
-  Vector<double> l;
-  for(double lambda=1.0;lambda<ManlexMAX_MULTIPLICITY;lambda+=0.33)
-    {
-      double prod=0.0;
-      for(unsigned int i=0;i<vd.size();++i)
-	{
-	  prod += vd[i]*exp(lambda*vd[i])/(exp(lambda*vd[i])-1.0);
-	}
-      l.push_back(fabs(prod-1.0));
-    }
-  double lam=double(min_element(l.begin(),l.end())-l.begin())*0.33+1.0;
-  if( lam<1.0 )
-    {
-      cerr << "ERROR: lambda is smaller than one: " << lam << endl;
-      for(unsigned int i=0;i<vd.size();++i)
-	cerr << vd[i] << ' ';
-      cerr << endl;
-    }
-  return lam;
-}
-
-void sentenceHandler::setProbOfSentence(const sentPair&s,double d)
-{
-  if( realCount==0 )
-    return;
-  else
-    {
-      if( s.noOcc<=0 )
-	{
-	  double ed=exp(d);
-	  if( oldPairs.size()>0&&(oldPairs.back().get_eSent()!=s.get_eSent()||oldPairs.back().getSentenceNo()>=s.getSentenceNo()) )
-	    {
-	      double lambda=optimize_lambda(oldProbs);
-	      for(unsigned int i=0;i<oldPairs.size();++i)
-		{
-		  if( oldProbs[i]<1e-5 )
-		    (*realCount)[oldPairs[i].getSentenceNo()-1]=1.0;
-		  else
-		    (*realCount)[oldPairs[i].getSentenceNo()-1]=lambda*oldProbs[i]/(1-exp(-lambda*oldProbs[i]));		    
-		}
-	      oldPairs.clear();
-	      oldProbs.clear();
-	    }
-	  oldPairs.push_back(s);
-	  oldProbs.push_back(ed);
-	}
-    }
-}
-
-/* ------------- End of Method Definition of Class sentenceHandler ----------*/
-
-
-
-
-
-

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/getSentence.h
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/getSentence.h b/ext/giza-pp/GIZA++-v2/getSentence.h
deleted file mode 100644
index 246ae1c..0000000
--- a/ext/giza-pp/GIZA++-v2/getSentence.h
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-/* --------------------------------------------------------------------------*
- *                                                                           *
- * Module : getSentence                                                      *
- *                                                                           *
- * Prototypes File: getSentence.h                                            *
- *                                                                           *
- * Objective: Defines clases and methods for handling I/O for the parallel   *
- *            corpus.                                                        *
- *****************************************************************************/
-
-
-
-
-
-#ifndef _sentenceHandler_h
-#define _sentenceHandler_h 1
-
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include "Vector.h"
-#include "defs.h"
-#include "vocab.h"
-#include "Globals.h"
-/*----------------------- Class Prototype Definition ------------------------*
- Class Name: sentenceHandleer 
- Objective: This class is defined to handle training sentece pairs from the 
- parallel corpus. Each pair has: a target sentece, called here French; a 
- source sentece, called here English sentece; and an integer number denoting
- the number of times this pair occured in trining corpus. Both source and 
- target senteces are represented as integer vector (variable size arrays), 
- each entry is a numeric value which is the token id for the particular token
- in the sentece.
-
- *---------------------------------------------------------------------------*/
-
-class sentPair{
- public:
-  int sentenceNo ;
-  float noOcc;
-  float realCount;
-  Vector<WordIndex> eSent ;
-  Vector<WordIndex> fSent;
-
- public:
-  sentPair(){};
-  void clear(){ eSent.clear(); fSent.clear(); noOcc=0; realCount=0; sentenceNo=0;};
-  const Vector<WordIndex>&get_eSent()const
-    { return eSent; }
-  const Vector<WordIndex>&get_fSent()const
-    { return fSent; }
-  int getSentenceNo()const
-    { return sentenceNo; }
-  double getCount()const
-    { return realCount; }
-};
-
-inline ostream&operator<<(ostream&of,const sentPair&s)
-{
-  of << "Sent No: " << s.sentenceNo << " , No. Occurrences: " << s.noOcc << '\n';
-  if( s.noOcc!=s.realCount )
-    of << " Used No. Occurrences: " << s.realCount << '\n';
-  unsigned int i;
-  for(i=0; i < s.eSent.size(); i++)
-    of << s.eSent[i] << ' ';
-  of <<  '\n';
-  for(i=1; i < s.fSent.size(); i++)
-    of << s.fSent[i] << ' ';
-  of << '\n';
-  return of;
-}
-
-class sentenceHandler{
-public:
-  const char * inputFilename;   // parallel corpus file name, similar for all 
-                            // sentence pair objects
-  ifstream *inputFile;     // parallel corpus file handler
-  Vector<sentPair> Buffer;
-  int noSentInBuffer ;
-  int currentSentence ;
-  int totalPairs1 ;
-  double totalPairs2;
-  bool readflag ; // true if you reach the end of file
-  bool allInMemory ;
-  int pair_no ;
-  Vector<double> *realCount;
-
-  Vector<sentPair> oldPairs;
-  Vector<double> oldProbs;
-  sentenceHandler(const char* filename, vcbList* elist=0, vcbList* flist=0);
-  void rewind();
-  bool getNextSentence(sentPair&, vcbList* = 0, vcbList* = 0);  // will be defined in the definition file, this
-  int getTotalNoPairs1()const {return totalPairs1;};
-  double getTotalNoPairs2()const {return totalPairs2;};
-  // method will read the next pair of sentence from memory buffer
-  bool readNextSentence(sentPair&);  // will be defined in the definition file, this
-  void setProbOfSentence(const sentPair&s,double d);
-};
-
-#endif
-  

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/hmm.cpp
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/hmm.cpp b/ext/giza-pp/GIZA++-v2/hmm.cpp
deleted file mode 100644
index fc4284c..0000000
--- a/ext/giza-pp/GIZA++-v2/hmm.cpp
+++ /dev/null
@@ -1,405 +0,0 @@
-/*
-
-Copyright (C) 1998,1999,2000,2001  Franz Josef Och (RWTH Aachen - Lehrstuhl fuer Informatik VI)
-
-This file is part of GIZA++ ( extension of GIZA ).
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-#include "hmm.h"
-#include "Globals.h"
-#include "utility.h"
-#include "HMMTables.h"
-#include "ForwardBackward.h"
-#include "Parameter.h"
-
-#define CLASSIFY(i,empty,ianf) bool empty=(i>=l); unsigned int ianf=(i%l);
-#define CLASSIFY2(i,ianf) unsigned int ianf=(i%l);
-
-
-short PredictionInAlignments=0;
-short UniformEntryExit=3;
-short HMMTrainingSpecialFlags=0;
-
-GLOBAL_PARAMETER2(int,ModelH_Dump_Freq,"HMM DUMP FREQUENCY","th","dump frequency of HMM",PARLEV_OUTPUT,0);
-
-GLOBAL_PARAMETER(short,CompareAlDeps,"emAlignmentDependencies",
-		 "lextrain: dependencies in the HMM alignment model. "
-		 " &1: sentence length; &2: previous class; &4: previous position; "
-		 " &8: French position; &16: French class"
-		 ,PARLEV_MODELS,2);
-GLOBAL_PARAMETER(double,GLOBALProbabilityForEmpty,"emProbForEmpty",
-		 "f-b-trn: probability for empty word",PARLEV_MODELS,0.4);
-GLOBAL_PARAMETER(short,SmoothHMM,"emSmoothHMM",
-		 "f-b-trn: smooth HMM model &1: modified counts; &2:perform smoothing with -emAlSmooth",PARLEV_SPECIAL,2);
-GLOBAL_PARAMETER(double,HMMAlignmentModelSmoothFactor,"emAlSmooth",
-		 "f-b-trn: smoothing factor for HMM alignment model (can be ignored by -emSmoothHMM)",PARLEV_SMOOTH,0.2);
-
-
-/*template<class T>
-void smooth_standard(T*a,T*b,double p)
-{
-  int n=b-a;
-  if( n==0 ) 
-    return;
-  double pp=p/n;
-  for(T*i=a;i!=b;++i)
-    *i = (1.0-p)*(*i)+pp;
-}*/
-
-
-hmm::hmm(model2& m)
-  : model2(m),counts(GLOBALProbabilityForEmpty,ewordclasses,fwordclasses),
-    probs(GLOBALProbabilityForEmpty,ewordclasses,fwordclasses)
-{  }
-
-void hmm::initialize_table_uniformly(sentenceHandler&){}
-
-int hmm::em_with_tricks(int noIterations)
-{
-  double minErrors=1.0;int minIter=0;
-  string modelName="Hmm",shortModelName="hmm";
-  int dumpFreq=ModelH_Dump_Freq;
-  time_t it_st, st, it_fn, fn;
-  string tfile, afile,afileh, number, alignfile, test_alignfile;
-  int pair_no = 0;
-  bool dump_files = false ;
-  ofstream of2 ;
-  st = time(NULL) ;
-  sHandler1.rewind();
-  cout << "\n==========================================================\n";
-  cout << modelName << " Training Started at: " << ctime(&st);
-  for(int it=1; it <= noIterations ; it++){
-    pair_no = 0;
-    it_st = time(NULL) ;
-    cout << endl << "-----------\n" << modelName << ": Iteration " << it << '\n';
-    dump_files = (dumpFreq != 0) && ((it % dumpFreq) == 0) && !NODUMPS;
-    number = "";
-    int n = it;
-    do{
-      number.insert((size_t)0, 1, (char)(n % 10 + '0'));
-    } while((n /= 10) > 0);
-    tfile = Prefix + ".t" + shortModelName + "." + number ;
-    afile = Prefix + ".a" + shortModelName + "." + number ;
-    afileh = Prefix + ".h" + shortModelName + "." + number ;
-    alignfile = Prefix + ".A" + shortModelName + "." + number ;
-    test_alignfile = Prefix + ".tst.A" + shortModelName + "." + number ;
-    counts=HMMTables<int,WordClasses>(GLOBALProbabilityForEmpty,ewordclasses,fwordclasses);
-    aCountTable.clear();
-    initAL();
-    em_loop(perp, sHandler1,  dump_files , alignfile.c_str(), trainViterbiPerp, false,it==1,it);
-    if( errorsAL()<minErrors )
-      {
-	minErrors=errorsAL();
-        minIter=it;
-      }
-    if (testPerp && testHandler)
-      em_loop(*testPerp, *testHandler, dump_files, test_alignfile.c_str(), *testViterbiPerp,  true,it==1,it); 
-    if (dump_files&&OutputInAachenFormat==1)
-      tTable.printCountTable(tfile.c_str(),Elist.getVocabList(),Flist.getVocabList(),1);
-    tTable.normalizeTable(Elist, Flist);
-    aCountTable.normalize(aTable);
-    probs=counts;
-    cout << modelName << ": ("<<it<<") TRAIN CROSS-ENTROPY " << perp.cross_entropy()
-	 << " PERPLEXITY " << perp.perplexity() << '\n';
-     if (testPerp && testHandler)
-       cout << modelName << ": ("<<it<<") TEST CROSS-ENTROPY " << (*testPerp).cross_entropy()
-	    << " PERPLEXITY " << (*testPerp).perplexity() 
-	    << '\n';
-     cout << modelName << ": ("<<it<<") VITERBI TRAIN CROSS-ENTROPY " << trainViterbiPerp.cross_entropy()
-	 << " PERPLEXITY " << trainViterbiPerp.perplexity() << '\n';
-    if (testPerp && testHandler)
-       cout << modelName << ": ("<<it<<") VITERBI TEST CROSS-ENTROPY " << testViterbiPerp->cross_entropy()
-	    << " PERPLEXITY " << testViterbiPerp->perplexity() 
-	    << '\n';
-    if (dump_files){
-      if( OutputInAachenFormat==0)
-	tTable.printProbTable(tfile.c_str(),Elist.getVocabList(),Flist.getVocabList(),OutputInAachenFormat);
-      ofstream afilestream(afileh.c_str());
-      probs.writeJumps(afilestream);
-      aCountTable.printTable(afile.c_str());
-    }
-    it_fn = time(NULL) ;
-    cout << "\n" << modelName << " Iteration: " << it<< " took: " <<
-      difftime(it_fn, it_st) << " seconds\n";
-  } // end of iterations 
-  fn = time(NULL) ;
-  cout << endl << "Entire " << modelName << " Training took: " << difftime(fn, st) << " seconds\n";
-  //cout << "tTable contains " << tTable.getHash().bucket_count() 
-  //     << " buckets and  " << tTable.getHash().size() << " entries." ;
-  cout << "==========================================================\n";
-  return minIter;
-}
-
-/*template<class T>
-T normalize_if_possible_with_increment(T*a,T*b,int increment)
-{
-  T sum=0;
-  for(T*i=a;i!=b;i+=increment)
-    sum+=*i;
-  if( sum )
-    for(T*i=a;i!=b;i+=increment)
-      *i/=sum;
-  else
-    {
-      T factor=increment/(b-a);
-      for(T*i=a;i!=b;i+=increment)
-	*i=factor;
-    }
-  return sum;
-}*/
-
-void hmm::load_table(const char* aname){
-  cout << "Hmm: loading a table not implemented.\n";
-  abort();
-  ifstream anamefile(aname);
-  probs.readJumps(anamefile);
-}
-
-HMMNetwork *hmm::makeHMMNetwork(const Vector<WordIndex>& es,const Vector<WordIndex>&fs,bool doInit)const
-{
-  unsigned int i,j;
-  unsigned int l = es.size() - 1;
-  unsigned int m = fs.size() - 1;
-  unsigned int I=2*l,J=m;
-  int IJ=I*J;
-  bool DependencyOfJ=(CompareAlDeps&(16|8))||(PredictionInAlignments==2);
-  bool DependencyOfPrevAJ=(CompareAlDeps&(2|4))||(PredictionInAlignments==0);
-  HMMNetwork *net = new HMMNetwork(I,J);
-  fill(net->alphainit.begin(),net->alphainit.end(),0.0);
-  fill(net->betainit.begin(),net->betainit.end(),0.0);
-  for(j=1;j<=m;j++)
-    {
-      for(i=1;i<=l;i++)
-	net->n(i-1,j-1)=tTable.getProb(es[i], fs[j]) ;
-      double emptyContribution=0;  
-      emptyContribution=tTable.getProb(es[0],fs[j]) ;
-      for(i=1;i<=l;i++)
-	net->n(i+l-1,j-1)=emptyContribution;
-      net->finalMultiply*=max(normalize_if_possible_with_increment(&net->n(0,j-1),&net->n(0,j-1)+IJ,J),double(1e-12));
-    }
-  if( DependencyOfJ )
-    net->e.resize(m-1);
-  else
-    net->e.resize(J>1);
-  for(j=0;j<net->e.size();j++)
-    {
-      int frenchClass=fwordclasses.getClass(fs[1+min(int(m)-1,int(j)+1)]);
-      net->e[j].resize(I,I,0);
-      for(unsigned int i1=0;i1<I;++i1) {
-	Array<double> al(l);
-	CLASSIFY2(i1,i1real);
-	for(unsigned int i2=0;i2<l;i2++)
-	  al[i2]=probs.getAlProb(i1real,i2,l,m,ewordclasses.getClass(es[1+i1real]),frenchClass
-				 ,j+1);
-	normalize_if_possible(conv<double>(al.begin()),conv<double>(al.end()));
-	if( SmoothHMM&2 )
-	  smooth_standard(conv<double>(al.begin()),conv<double>(al.end()),HMMAlignmentModelSmoothFactor);
-	for(unsigned int i2=0;i2<I;i2++) {
-	  CLASSIFY(i2,empty_i2,i2real);
-	  net->e[j](i1,i2)	    = al[i2real];
-	  
-	  if( empty_i2 )
-	    if(i1real!=i2real)
-	      {
-		net->e[j](i1,i2)=0;
-	      }
-	    else
-	      {
-		net->e[j](i1,i2)=doInit?al[0]:(probs.getProbabilityForEmpty()); // make first HMM iteration like IBM-1
-	      }
-	}
-	normalize_if_possible(&net->e[j](i1,0),&net->e[j](i1,0)+I);
-      }
-    }
-  if( doInit )
-    {
-      for(unsigned int i=0;i<I;++i)
-	{
-	  net->alphainit[i]=net->betainit[i]=(i<I/2)?1:(2.0/I);
-	  net->betainit[i]=1.0;
-	}
-    }
-  else
-    {
-      if( DependencyOfPrevAJ==0 )
-	{
-	  for(i=0;i<I;i++)
-	    {
-	      CLASSIFY2(i,ireal);
-	      net->alphainit[i]=probs.getAlProb(-1,ireal,l,m,0,fwordclasses.getClass(fs[1+0]),0);
-	    }
-	}
-      else
-	{
-	  if( UniformEntryExit&2 )probs.getBetaInit(I,net->betainit);
-	  if( UniformEntryExit&1 )probs.getAlphaInit(I,net->alphainit);
-	}
-    }
-  massert( net->alphainit.size()==I );massert( net->betainit.size()==I );
-  normalize_if_possible(conv<double>(net->alphainit.begin()),conv<double>(net->alphainit.end()));
-  normalize_if_possible(conv<double>(net->betainit.begin()),conv<double>(net->betainit.end()));
-  transform(net->betainit.begin(),net->betainit.end(),net->betainit.begin(),bind1st(multiplies<double>(),2*l));
-  return net;
-}
-extern float MINCOUNTINCREASE;
-
-void hmm::em_loop(Perplexity& perp, sentenceHandler& sHandler1, 
-		  bool dump_alignment, const char* alignfile, Perplexity& viterbi_perp, 
-		     bool test,bool doInit,int 
-)
-{
-  WordIndex i, j, l, m ;
-  double cross_entropy;
-  int pair_no=0 ;
-  perp.clear();
-  viterbi_perp.clear();
-  ofstream of2;
-  // for each sentence pair in the corpus
-  if (dump_alignment||FEWDUMPS )
-    of2.open(alignfile);
-  sentPair sent ;
-  sHandler1.rewind();
-  while(sHandler1.getNextSentence(sent)){
-    const Vector<WordIndex>& es = sent.get_eSent();
-    const Vector<WordIndex>& fs = sent.get_fSent();
-    const float so  = sent.getCount();
-    l = es.size() - 1;
-    m = fs.size() - 1;
-    cross_entropy = log(1.0);
-    Vector<WordIndex> viterbi_alignment(fs.size());
-
-    unsigned int I=2*l,J=m;
-    bool DependencyOfJ=(CompareAlDeps&(16|8))||(PredictionInAlignments==2);
-    bool DependencyOfPrevAJ=(CompareAlDeps&(2|4))||(PredictionInAlignments==0);
-    HMMNetwork *net=makeHMMNetwork(es,fs,doInit);
-    Array<double> gamma;
-    Array<Array2<double> > epsilon(DependencyOfJ?(m-1):1);
-    double trainProb;
-      trainProb=ForwardBackwardTraining(*net,gamma,epsilon);
-    if( !test )
-      {
-	double *gp=conv<double>(gamma.begin());
-	for(unsigned int i2=0;i2<J;i2++)for(unsigned int i1=0;i1<I;++i1,++gp)
-	  if( *gp>MINCOUNTINCREASE )
-	    {
-	      COUNT add= *gp*so;
-	      if( i1>=l )
-		{
-		  tTable.incCount(es[0],fs[1+i2],add);
-		  aCountTable.getRef(0,i2+1,l,m)+=add;
-		}
-	      else
-		{
-		  tTable.incCount(es[1+i1],fs[1+i2],add);
-		  aCountTable.getRef(1+i1,1+i2,l,m)+=add;
-		}
-	    }
-	double p0c=0.0,np0c=0.0;
-	for(unsigned int jj=0;jj<epsilon.size();jj++)
-	  {
-	    int frenchClass=fwordclasses.getClass(fs[1+min(int(m)-1,int(jj)+1)]);
-	    double *ep=epsilon[jj].begin();
-	    if( ep )
-	      {
-		//for(i=0;i<I;i++)
-		//  normalize_if_possible_with_increment(ep+i,ep+i+I*I,I);
-		//		for(i=0;i<I*I;++i)
-		//  ep[i] *= I;
-		//if( DependencyOfJ )
-		//  if( J-1 )
-		//    for(i=0;i<I*I;++i)
-		//      ep[i] /= (J-1);
-		double mult=1.0;
-		mult*=l;
-		//if( DependencyOfJ && J-1)
-		//  mult/=(J-1);
-		for(i=0;i<I;i++)
-		  {
-		    for(unsigned int i_bef=0;i_bef<I;i_bef++,ep++)
-		      {
-			CLASSIFY(i,i_empty,ireal);
-			CLASSIFY2(i_bef,i_befreal);
-			if( i_empty )
-			  p0c+=*ep * mult;
-			else
-			  {
-			    counts.addAlCount(i_befreal,ireal,l,m,ewordclasses.getClass(es[1+i_befreal]),
-					      frenchClass ,jj+1,*ep * mult,0.0);
-			    np0c+=*ep * mult; 
-			  }
-			massert( &epsilon[jj](i,i_bef)== ep);
-		      }
-		  }
-	      }
-	  }
-	double *gp1=conv<double>(gamma.begin()),*gp2=conv<double>(gamma.end())-I;
-	Array<double>&ai=counts.doGetAlphaInit(I);
-	Array<double>&bi=counts.doGetBetaInit(I);
-	int firstFrenchClass=(fs.size()>1)?(fwordclasses.getClass(fs[1+0])):0;
-	for(i=0;i<I;i++,gp1++,gp2++)
-	  {
-	    CLASSIFY(i,i_empty,ireal);
-	    ai[i]+= *gp1;
-	    bi[i]+= *gp2;
-	    if( DependencyOfPrevAJ==0 )
-	      {
-		if( i_empty )
-		  p0c+=*gp1;
-		else
-		  {
-		    counts.addAlCount(-1,ireal,l,m,0,firstFrenchClass,0,*gp1,0.0);
-		    np0c+=*gp1;
-		  }
-	      }
-	  }
-    if( Verbose )
-      cout << "l: " << l << "m: " << m << " p0c: " << p0c << " np0c: " << np0c << endl;
-      }
-    cross_entropy+=log(max(trainProb,1e-100))+log(max(net->finalMultiply,1e-100));
-    Array<int>vit;
-    double viterbi_score=1.0;
-    if( (HMMTrainingSpecialFlags&1) )
-      HMMViterbi(*net,gamma,vit);
-    else
-      viterbi_score=HMMRealViterbi(*net,vit);
-    for(j=1;j<=m;j++)
-      {
-	viterbi_alignment[j]=vit[j-1]+1;
-	if( viterbi_alignment[j]>l)
-	  viterbi_alignment[j]=0;
-      }
-    sHandler1.setProbOfSentence(sent,cross_entropy);
-    perp.addFactor(cross_entropy, so, l, m,1);
-    viterbi_perp.addFactor(log(viterbi_score)+log(max(net->finalMultiply,1e-100)), so, l, m,1);
-    if( Verbose )
-      cout << "Viterbi-perp: " << log(viterbi_score) << ' ' << log(max(net->finalMultiply,1e-100)) << ' ' << viterbi_score << ' ' << net->finalMultiply << ' ' << *net << "gamma: " << gamma << endl;
-    delete net;net=0;
-    if (dump_alignment||(FEWDUMPS&&sent.getSentenceNo()<1000) )
-      printAlignToFile(es, fs, Elist.getVocabList(), Flist.getVocabList(), of2, viterbi_alignment, sent.getSentenceNo(), viterbi_score);
-    addAL(viterbi_alignment,sent.getSentenceNo(),l);    
-    pair_no++;
-  } /* of while */
-  sHandler1.rewind();
-  perp.record("HMM");
-  viterbi_perp.record("HMM");
-  errorReportAL(cout,"HMM");
-}
-
-#include "HMMTables.cpp"
-template class HMMTables<int,WordClasses>;
- 

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/hmm.h
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/hmm.h b/ext/giza-pp/GIZA++-v2/hmm.h
deleted file mode 100644
index 6909bea..0000000
--- a/ext/giza-pp/GIZA++-v2/hmm.h
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-#ifndef _hmm_h
-#define _hmm_h 1
-
-#include <cassert>
- 
-#include <iostream>
-#include <algorithm>
-#include <functional>
-#include <map>
-#include <set>
-#include "Vector.h"
-#include <utility>
-
-#include <fstream>
-#include <cmath>
-#include <ctime>
-
-#include "TTables.h"
-#include "ATables.h" 
-#include "getSentence.h"
-#include "defs.h"
-#include "model2.h"
-#include "Perplexity.h"
-#include "vocab.h"
-#include "WordClasses.h"
-#include "HMMTables.h"
-#include "ForwardBackward.h"
-
-class hmm : public model2
-{
- private:
-  WordClasses ewordclasses;
-  WordClasses fwordclasses;
-  HMMTables<int,WordClasses> counts,probs;
- public:
-  template<class MAPPER>
-  void makeWordClasses(const MAPPER&m1,const MAPPER&m2,string efile,string ffile)
-    {
-      ifstream estrm(efile.c_str()),fstrm(ffile.c_str());
-      if( !estrm )
-	{
-	  cerr << "ERROR: can not read " << efile << endl;
-	}
-      else
-	ewordclasses.read(estrm,m1);
-      if( !fstrm )
-	cerr << "ERROR: can not read " << ffile << endl;
-      else
-	fwordclasses.read(fstrm,m2);
-    }
-  hmm(model2&m2);
-  void initialize_table_uniformly(sentenceHandler&);
-  int em_with_tricks(int);
-  void load_table(const char* aname);
-  void em_loop(Perplexity& perp, sentenceHandler& sHandler1, bool dump_files, 
-	       const char* alignfile, Perplexity&, bool test,bool doInit,int iter);
-  HMMNetwork *makeHMMNetwork(const Vector<WordIndex>& es,const Vector<WordIndex>&fs,bool doInit)const;
-  friend class model3;
-};
-
-#endif

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/logprob.cpp
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/logprob.cpp b/ext/giza-pp/GIZA++-v2/logprob.cpp
deleted file mode 100644
index 9035f80..0000000
--- a/ext/giza-pp/GIZA++-v2/logprob.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-
-//  Routines to perform integer exponential arithmetic.
-//  A number x is represented as n, where x = b**n.
-//  It is assumed that b > 1, something like b = 1.001;
-
-#include "logprob.h"
-#include <stdlib.h>
-#include <stdio.h>
-#include <iostream>
-#include <fstream>
-#include <string>
-double *LogProb::ntof  = NULL; // Tables will be initialized
-int   *LogProb::addtbl = NULL; // in Initialize function.
-int   *LogProb::subtbl = NULL; //
-
-const int    LogProb::max_2byte_integer =  32767;
-const int    LogProb::min_2byte_integer = -32768;
-const double LogProb::b      = 1.001;   // a logarithm basis
-const double LogProb::logb2  = log(b);
-//const int    LogProb::nmax   = round(78.0E0 * log(1.0E1) / logb2);
-const int    LogProb::nmax   = round(300.0E0 * log(1.0E1) / logb2);
-const int    LogProb::nmin   = -nmax;
-const int    LogProb::tblbnd = round(log((b-1.0E0)/2.0E0)/logb2);
-const int    LogProb::zeron  = round(pow(-2, 23));
-const int    LogProb::onen   = 0;
-const int    LogProb::infn   = onen - zeron;
-
-const int LogProb::initialized = LogProb::Initialize();
-const LogProb LogProb::zero(0);
-const LogProb LogProb::one(1);
-const LogProb LogProb::minus2(1e-2);
-const LogProb LogProb::minus4(1e-4);
-const LogProb LogProb::minus6(1e-6);
-const LogProb LogProb::minus8(1e-8);
-const LogProb LogProb::minus10(1e-10);
-const LogProb LogProb::minus12(1e-12);
-const LogProb LogProb::minus14(1e-14);
-const LogProb LogProb::minus16(1e-16);
-
-// static table initialization function
-int LogProb::Initialize()
-{
-  int nbytes = sizeof(double)*(nmax-nmin+1) + sizeof(int)*(0-tblbnd+1);
-  std::cerr << nbytes << " bytes used for LogProb tables (C++ version)\n";
-  ntof   = new double[nmax-nmin+1];
-  addtbl = new int[-tblbnd+1];
-  subtbl = new int[-tblbnd+1];
-
-  //  char filename[257];
-  //  string filename ;
-  //  ifstream ifs;
-  //  ifs.open(filename.c_str());
-  //  if (!ifs)
-  //    {
-  int i;
-  std::cerr << "Building integer logs conversion tables\n";
-  ntof[0] = 0 ;
-  
-  for (i=nmin+1; i<=nmax; ++i) 
-    {
-      double x = i;
-      ntof[i-nmin] = exp(x*logb2);
-      
-    }
-  for (i=tblbnd; i<=0; ++i) 
-    {
-      double x = 1.0 + pow(b, i);
-      addtbl[i-tblbnd] = round(log(x)/logb2);
-    }
-  double sqrtb = exp(0.5*logb2);
-  for (i=0; i<=-tblbnd; ++i) 
-    {
-      double x = sqrtb * pow(b, i) - 1.0;
-      subtbl[i] = round(log(x)/logb2);
-    }
-  //      if (toolsRoot)
-  //	{
-  //      ofstream ofs(filename.c_str());
-  //      if (!ofs)
-  //	cerr << "Could not write LogProb data to " << filename << endl;
-  //      else
-  //	{
-  //	  ofs.write((const char *)ntof, sizeof(double) * (nmax-nmin+1));
-  //	  ofs.write((const char *)addtbl, sizeof(int) * (-tblbnd+1));
-  //	  ofs.write((const char *)subtbl, sizeof(int) * (-tblbnd+1));
-  //	}
-  //    }
-  //    }
-  //  else
-  //    {
-  //      ifs.read((char *)ntof,   sizeof(double) * (nmax - nmin + 1));
-  //      ifs.read((char *)addtbl, sizeof(int) * (-tblbnd+1));
-  //      ifs.read((char *)subtbl, sizeof(int) * (-tblbnd+1));
-  //    }
-  return 1;
-}
-
-void LogProb::FreeTables()
-{
-   delete [] addtbl;
-   delete [] subtbl;
-   delete [] ntof;
-}
-
-//---------------------------------------------------------------------------
-//            Aritmetic operators
-//---------------------------------------------------------------------------
-
-
-// Subtract two logarithm numbers. Use the following method:
-// b**n - b**m = b**m( b**(n-m) - 1 ), assuming n >= m. 
-LogProb& LogProb::operator-=(const LogProb &subs) 
-{
-  if (subs.logr == zeron)
-    return *this;
-  int a = logr - subs.logr;
-  if (a <= 0)
-    {
-      if (a < 0)
-	{
-	  std::cerr << "WARNING(logprob): Invalid arguments to nsub" <<(*this)<< " " << subs << std::endl;
-	  //abort();
-	}
-      logr = zeron;
-      return *this;
-    }
-  if (a > -tblbnd)
-    return *this;
-  logr = subs.logr + subtbl[a];
-  return *this;
-}
-
-

http://git-wip-us.apache.org/repos/asf/incubator-joshua/blob/ef91969a/ext/giza-pp/GIZA++-v2/logprob.h
----------------------------------------------------------------------
diff --git a/ext/giza-pp/GIZA++-v2/logprob.h b/ext/giza-pp/GIZA++-v2/logprob.h
deleted file mode 100644
index 14696ac..0000000
--- a/ext/giza-pp/GIZA++-v2/logprob.h
+++ /dev/null
@@ -1,217 +0,0 @@
-/*
-
-EGYPT Toolkit for Statistical Machine Translation
-Written by Yaser Al-Onaizan, Jan Curin, Michael Jahr, Kevin Knight, John Lafferty, Dan Melamed, David Purdy, Franz Och, Noah Smith, and David Yarowsky.
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 
-USA.
-
-*/
-#ifndef _LOGPROB_H
-#define _LOGPROB_H
-
-// Routines to perform integer exponential arithmetic.
-// A number x is represented as n, where x = b**n
-// It is assumed that b > 1, something like b = 1.001
-
-#include <iostream>
-#include <math.h>
-#include <algorithm>
-
-//#define  MAX(A,B) ((A) > (B) ? (A) : (B))
-//#define  MIN(A,B) ((A) > (B) ? (B) : (A))
-
-
-class LogProb {
-public:
-  // mj for cross entropy
-  double base2() const {
-    return (logr * logb2 / log(2));
-  }
-  
-  // Constructors
-  LogProb() : logr(zeron) {}
-  LogProb(const LogProb &obj) : logr(obj.logr) {}
-  LogProb(double x) : logr(x == 0.0 ? zeron : round(log(x)/logb2)) {}
-  // destructor
-  ~LogProb() {}                  // default destructor
-
-  operator double() const    // converts logr to (double) b**logr
-    {
-      if (logr < nmin) return ntof[0];
-      if (logr > nmax) return ntof[nmax-nmin];
-      return ntof[logr-nmin];
-    }
-
-  LogProb &operator=(const LogProb &obj) { logr = obj.logr; return *this; }
-  int operator!() const { return logr == zeron; }
-  
-  // iostream friend specifications
-  friend std::ostream& operator<<(std::ostream& os, const LogProb &obj);
-  friend std::istream& operator>>(std::istream& is, LogProb &obj);
-  friend std::ostream& operator<<=(std::ostream& os, const LogProb &obj);
-  friend std::istream& operator>>=(std::istream& is, LogProb &obj);
-
-  // arithmetic operators 
-  LogProb &operator+=(const LogProb &add)   // logr2 = logb ( b**logr2 + b**logr1 )
-    // Add two numbers represented as logarithms. Use the following method:
-    //   b**n + b**m = b**n(1 + b**(m-n)), assuming n >= m.
-    {
-      if (add.logr == zeron)
-	return *this;
-      if (logr == zeron)
-	{
-	  logr = add.logr;
-	  return *this;
-	}
-      int a = add.logr - logr;
-      if (a > 0)
-	{
-	  a = -a;
-	  logr = add.logr;
-	}
-      if (a < tblbnd)
-	return *this;
-      logr += addtbl[a-tblbnd];
-      return *this;
-    }
-
-  LogProb &operator-=(const LogProb &);   // logr2 = logb ( b**logr2 + b**logr1 )
-  LogProb operator*(const LogProb &mul) const  // logr3 = logr2 + logr1
-    {
-      LogProb result;		// start out with result == 0
-      if ((logr != zeron) && (mul.logr != zeron))
-	result.logr = std::max(logr+mul.logr, zeron);
-      return result;
-    }
-  LogProb operator*(double x) const  // logr3 = logr2 + logr1
-    {
-      return (*this)*(LogProb)x;
-    }
-  LogProb operator^(const int i) const  // logr2 = logr1 * i
-    {
-      LogProb result;		// start out with result == 0
-      //      if ((logr != zeron) && (mul.logr != zeron))
-      	result.logr = logr * i ;
-	return result;
-    }
-  LogProb &operator*=(const LogProb &mul) // logr2 += logr1
-    { 
-      if ((logr == zeron) || (mul.logr == zeron))
-	logr = zeron;
-      else
-	logr = std::max(logr+mul.logr, zeron);
-      return *this;
-    }
-  LogProb operator/(const LogProb &div) const  // logr3 = logr2 -logr1
-    {
-      LogProb result;
-      if (logr != zeron)
-	result.logr = std::max(logr - div.logr, zeron);
-      return result;
-    }
-  LogProb &operator/=(const LogProb &div) // logr2 -= logr1
-    {
-      if (logr != zeron)
-	logr = std::max(logr - div.logr, zeron);
-      return *this;
-    }
-  LogProb operator+(const LogProb &l) const // logr3 = logb ( b**logr2 + b**logr1 )
-    { LogProb result(*this); result += l; return result; }
-  LogProb operator-(const LogProb &l) const // logr3 = logb ( b**logr2 - b**logr1 )
-    { LogProb result(*this); result -= l; return result; }
-  LogProb power(const int n) const // logr2 = logr1 * int
-    { LogProb result(*this); result.logr *= n; return result; }
-  
-  // Conditional operators
-  int operator<(const LogProb &obj)  const { return logr <  obj.logr; }
-  int operator<=(const LogProb &obj) const { return logr <= obj.logr; }
-  int operator>(const LogProb &obj)  const { return logr >  obj.logr; }
-  int operator>=(const LogProb &obj) const { return logr >= obj.logr; }
-  int operator==(const LogProb &obj) const { return logr == obj.logr; }
-  int operator!=(const LogProb &obj) const { return logr != obj.logr; }
-  int operator<(double d)  const { return ((double)*this) < d;  }
-  int operator<=(double d) const { return ((double)*this) <= d; }
-  int operator>(double d)  const { return ((double)*this) >  d; }
-  int operator>=(double d) const { return ((double)*this) >= d; }
-  int operator==(double d) const { return ((double)*this) == d; }
-  int operator!=(double d) const { return ((double)*this) != d; }
-  
-
-  LogProb &SetZero() { logr = zeron; return *this; } // representation of 0,
-  LogProb &SetOne() { logr = onen; return *this; }   // 1, and
-  LogProb &SetInf() { logr = infn; return *this; }   // inf in logarithm domain 
-
-private:
-  int logr;			// a representation of logarithm
-  // static constants
-  static const  int    initialized; // initialization flag
-  static const  double b;
-  static const  double logb2;
-  static const  int    nmin, nmax;
-  static const  int    tblbnd;
-  static const  int    zeron, onen, infn;  // zero, one, and inf in log domain
-  static const  int    max_2byte_integer, min_2byte_integer;
-  
-  // Arithmetic computation Tables
-  static double *ntof;
-  static int   *addtbl;
-  static int   *subtbl;
-
-  static int Initialize();
-
-public:
-  static void FreeTables();
-  // constants for initializing LogProbs to 0 or 1
-  static const LogProb zero;
-  static const LogProb one;
-  static const LogProb minus2;
-  static const LogProb minus4;
-  static const LogProb minus6;
-  static const LogProb minus8;
-  static const LogProb minus10;
-  static const LogProb minus12;
-  static const LogProb minus14;
-  static const LogProb minus16;
-};
-
-// iostream friend operators
-inline std::ostream &operator<<(std::ostream& os, const LogProb &obj)
-{
-  return os << (double) obj;         // output in linear domain, b**logr
-}
-
-inline std::istream &operator>>(std::istream& is, LogProb &obj)
-{
-  double d;
-  is >> d;
-  obj = d;
-  return is;
-}
-
-inline std::ostream &operator<<=(std::ostream& os, const LogProb &obj) // write binary
-{
-  os.write((const char *)&obj.logr, sizeof(obj.logr));
-  return os;
-}
-
-inline std::istream &operator>>=(std::istream& is, LogProb &obj)
-{
-  is.read((char *)&obj.logr, sizeof(obj.logr));
-  return is;
-}
-
-#endif
-