only include moses root when compiling

Jamroot

@@ -111,6 +111,7 @@ project : requirements
   <threading>multi:<library>boost_thread
   <define>_FILE_OFFSET_BITS=64 <define>_LARGE_FILES
   $(requirements)
+  <include>.
   ;
 
 #Add directories here if you want their incidental targets too (i.e. tests).

mert/Jamfile

@@ -49,7 +49,7 @@ SentenceLevelScorer.cpp
 Permutation.cpp
 PermutationScorer.cpp
 StatisticsBasedScorer.cpp
-../util//kenutil m ..//z : <include>. : : <include>. ;
+../util//kenutil m ..//z ;
 
 exe mert : mert.cpp mert_lib ../moses//ThreadPool ;
 

moses-cmd/Jamfile

@@ -1,6 +1,6 @@
 alias deps : IOWrapper.cpp mbr.cpp LatticeMBR.cpp TranslationAnalysis.cpp ../moses//moses ;
 
-exe moses : Main.cpp deps : <include>. ;
-exe lmbrgrid : LatticeMBRGrid.cpp deps : <include>. ;
+exe moses : Main.cpp deps ;
+exe lmbrgrid : LatticeMBRGrid.cpp deps ;
 
 alias programs : moses lmbrgrid ;

moses/Jamfile

@@ -3,7 +3,7 @@ path-constant FACTOR-LOG : bin/factor.log ;
 update-if-changed $(FACTOR-LOG) $(max-factors) ;
 max-factors = <define>MAX_NUM_FACTORS=$(max-factors) <dependency>$(FACTOR-LOG) ;
 
-alias headers : ../util//kenutil : : : <include>. $(max-factors) ;
+alias headers : ../util//kenutil : : : $(max-factors) ;
 
 alias ThreadPool : ThreadPool.cpp ;
 

moses/LM/SRI.cpp

@@ -24,12 +24,12 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <iostream>
 #include <fstream>
 
-#include "LM/SRI.h"
-#include "TypeDef.h"
-#include "Util.h"
-#include "FactorCollection.h"
-#include "Phrase.h"
-#include "StaticData.h"
+#include "SRI.h"
+#include "moses/TypeDef.h"
+#include "moses/Util.h"
+#include "moses/FactorCollection.h"
+#include "moses/Phrase.h"
+#include "moses/StaticData.h"
 
 #include "Vocab.h"
 #include "Ngram.h"

moses/LM/SRI.h

@@ -24,9 +24,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include <string>
 #include <vector>
-#include "Factor.h"
-#include "TypeDef.h"
-#include "LM/SingleFactor.h"
+#include "moses/Factor.h"
+#include "moses/TypeDef.h"
+#include "SingleFactor.h"
 
 class Factor;
 class Phrase;

moses/Parameter.cpp

@@ -54,7 +54,6 @@ Parameter::Parameter()
   AddParam("input-file", "i", "location of the input file to be translated");
   AddParam("inputtype", "text (0), confusion network (1), word lattice (2) (default = 0)");
   AddParam("labeled-n-best-list", "print out labels for each weight type in n-best list. default is true");
-  AddParam("include-alignment-in-n-best", "include word alignment in the n-best list. default is false");
   AddParam("lmodel-file", "location and properties of the language models");
   AddParam("lmodel-dub", "dictionary upper bounds of language models");
   AddParam("lmodel-oov-feature", "add language model oov feature, one per model");
@@ -70,7 +69,6 @@ Parameter::Parameter()
   AddParam("phrase-drop-allowed", "da", "if present, allow dropping of source words"); //da = drop any (word); see -du for comparison
   AddParam("report-all-factors", "report all factors in output, not just first");
   AddParam("report-all-factors-in-n-best", "Report all factors in n-best-lists. Default is false");
-  AddParam("report-segmentation", "t", "report phrase segmentation in the output");
 #ifdef HAVE_SYNLM
 	AddParam("slmodel-file", "location of the syntactic language model file(s)");
 	AddParam("weight-slm", "slm", "weight(s) for syntactic language model");
@@ -141,9 +139,6 @@ Parameter::Parameter()
 	AddParam("cube-pruning-diversity", "cbd", "How many hypotheses should be created for each coverage. (default = 0)");
 	AddParam("search-algorithm", "Which search algorithm to use. 0=normal stack, 1=cube pruning, 2=cube growing. (default = 0)");
 	AddParam("constraint", "Location of the file with target sentences to produce constraining the search");
-	AddParam("use-alignment-info", "Use word-to-word alignment: actually it is only used to output the word-to-word alignment. Word-to-word alignments are taken from the phrase table if any. Default is false.");
-	AddParam("print-alignment-info", "Output word-to-word alignment into the log file. Word-to-word alignments are taken from the phrase table if any. Default is false");
-	AddParam("print-alignment-info-in-n-best", "Include word-to-word alignment in the n-best list. Word-to-word alignments are takne from the phrase table if any. Default is false");
 	AddParam("link-param-count", "Number of parameters on word links when using confusion networks or lattices (default = 1)");
 	AddParam("description", "Source language, target language, description");
 	AddParam("max-chart-span", "maximum num. of source word chart rules can consume (default 10)");
@@ -165,9 +160,6 @@ Parameter::Parameter()
   AddParam("parsing-algorithm", "Which parsing algorithm to use. 0=CYK+, 1=scope-3. (default = 0)");
   AddParam("search-algorithm", "Which search algorithm to use. 0=normal stack, 1=cube pruning, 2=cube growing, 4=stack with batched lm requests (default = 0)");
   AddParam("constraint", "Location of the file with target sentences to produce constraining the search");
-  AddParam("use-alignment-info", "Use word-to-word alignment: actually it is only used to output the word-to-word alignment. Word-to-word alignments are taken from the phrase table if any. Default is false.");
-  AddParam("print-alignment-info", "Output word-to-word alignment into the log file. Word-to-word alignments are takne from the phrase table if any. Default is false");
-  AddParam("print-alignment-info-in-n-best", "Include word-to-word alignment in the n-best list. Word-to-word alignments are takne from the phrase table if any. Default is false");
   AddParam("link-param-count", "Number of parameters on word links when using confusion networks or lattices (default = 1)");
   AddParam("description", "Source language, target language, description");
 
@@ -179,8 +171,6 @@ Parameter::Parameter()
   AddParam("unknown-lhs", "file containing target lhs of unknown words. 1 per line: LHS prob");
   AddParam("translation-systems", "specify multiple translation systems, each consisting of an id, followed by a set of models ids, eg '0 T1 R1 L0'");
   AddParam("show-weights", "print feature weights and exit");
-  AddParam("alignment-output-file", "print output word alignments into given file");
-  AddParam("sort-word-alignment", "Sort word alignments for more consistent display. 0=no sort (default), 1=target order");
   AddParam("start-translation-id", "Id of 1st input. Default = 0");
   AddParam("text-type", "should be one of dev/devtest/test, used for domain adaptation features");
   AddParam("output-unknowns", "Output the unknown (OOV) words to the given file, one line per sentence");
@@ -188,6 +178,15 @@ Parameter::Parameter()
   // Compact phrase table and reordering table.                                                                                  
   AddParam("minlexr-memory", "Load lexical reordering table in minlexr format into memory");                                          
   AddParam("minphr-memory", "Load phrase table in minphr format into memory");
+
+  AddParam("include-alignment-in-n-best", "include word alignment in the n-best list. default is false");
+  AddParam("use-alignment-info", "Use word-to-word alignment: actually it is only used to output the word-to-word alignment. Word-to-word alignments are taken from the phrase table if any. Default is false.");
+  AddParam("print-alignment-info", "Output word-to-word alignment into the log file. Word-to-word alignments are taken from the phrase table if any. Default is false");
+  AddParam("print-alignment-info-in-n-best", "Include word-to-word alignment in the n-best list. Word-to-word alignments are takne from the phrase table if any. Default is false");
+  AddParam("alignment-output-file", "print output word alignments into given file");
+  AddParam("sort-word-alignment", "Sort word alignments for more consistent display. 0=no sort (default), 1=target order");
+
+  AddParam("report-segmentation", "t", "report phrase segmentation in the output");
 }
 
 Parameter::~Parameter()

phrase-extract/Jamfile

@@ -1,10 +1,10 @@
 local most-deps = [ glob *.cpp : PhraseAlignment.cpp *Test.cpp *-main.cpp ] ;
 #Build .o files with include path setting, reused. 
 for local d in $(most-deps) {
-  obj $(d:B).o : $(d) : <include>. <include>.. ;
+  obj $(d:B).o : $(d) ;
 }
 #and stuff them into an alias.
-alias deps : $(most-deps:B).o ..//z ..//boost_iostreams ../moses//ThreadPool ../util//kenutil : <include>. <include>.. ;
+alias deps : $(most-deps:B).o ..//z ..//boost_iostreams ../moses//ThreadPool ../util//kenutil ;
 
 #PhraseAlignment.cpp requires that main define some global variables.  
 #Build the mains that do not need these global variables.