Add support of Cmake

10 files changed, 496 insertions, 11 deletions

diff --git a/mgizapp/CMakeLists.txt b/mgizapp/CMakeLists.txt
new file mode 100644
index 0000000..6f9955f
--- /dev/null
+++ b/mgizapp/CMakeLists.txt
@@ -0,0 +1,67 @@
+PROJECT (srlextract)
+
+SET(MGIZA_VERSION_MAJOR "0")
+SET(MGIZA_VERSION_MINOR "6")
+SET(MGIZA_VERSION_PATCH "7")
+
+MATH(EXPR MGIZA_INT_VERSION "(${MGIZA_VERSION_MAJOR} * 10000) + (${MGIZA_VERSION_MINOR} * 100) + (${MGIZA_VERSION_PATCH} * 1)" )
+
+SET(MGIZA_VERSION "${MGIZA_VERSION_MAJOR}.${MGIZA_VERSION_MINOR}.${MGIZA_VERSION_PATCH}")
+
+#CMake 2.6+ is recommended to an improved Boost module
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6.0 FATAL_ERROR)
+
+IF(COMMAND cmake_policy)
+  cmake_policy(SET CMP0003 NEW)
+ENDIF(COMMAND cmake_policy)
+
+IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+    SET(CMAKE_INSTALL_PREFIX
+        "inst" CACHE PATH "MGIZA install prefix" FORCE
+        )
+    MESSAGE(STATUS "You have not set the install dir, default to './inst', if
+    you want to set it, use cmake -DCMAKE_INSTALL_PREFIX to do so")
+ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+
+#set various platform specific global options
+IF(WIN32)
+ SET(CMAKE_DEBUG_POSTFIX "d")
+ENDIF(WIN32)
+
+INCLUDE(cmake/FindTR1.cmake)
+
+# include specific modules
+SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+
+# Find Boost library, specify
+# BOOST_ROOT=/e/programs/boost_1_35_0
+# BOOST_LIBRARYDIR=$BOOST_ROOT/stage/lib
+
+set(Boost_USE_STATIC_LIBS        ON)
+set(Boost_USE_MULTITHREADED      ON)
+set(Boost_USE_STATIC_RUNTIME    OFF)
+
+
+FIND_PACKAGE( Boost 1.46)
+
+ IF(Boost_FOUND)
+    IF (NOT _boost_IN_CACHE)
+     MESSAGE( "Boost found" )
+     message(STATUS "Boost_INCLUDE_DIR    : ${Boost_INCLUDE_DIR}")
+    ENDIF (NOT _boost_IN_CACHE)
+	LINK_DIRECTORIES ( ${Boost_LIBRARY_DIRS} )
+	INCLUDE_DIRECTORIES ( ${Boost_INCLUDE_DIRS} )
+ELSE()
+    MESSAGE(FATAL_ERROR "Boost not found, please set the BOOST_ROOT and BOOST_LIBRARYDIR environment variables " )
+ENDIF()
+
+ADD_SUBDIRECTORY (src)
+ADD_SUBDIRECTORY (src/mkcls)
+ADD_SUBDIRECTORY (scripts)
+
+
+
+
+
+
diff --git a/mgizapp/cmake/CheckCXXSourceCompiles.cmake b/mgizapp/cmake/CheckCXXSourceCompiles.cmake
new file mode 100644
index 0000000..3921c89
--- /dev/null
+++ b/mgizapp/cmake/CheckCXXSourceCompiles.cmake
@@ -0,0 +1,60 @@
+# - Check if the source code provided in the SOURCE argument compiles.
+# CHECK_CXX_SOURCE_COMPILES(SOURCE VAR)
+# - macro which checks if the source code compiles
+#  SOURCE - source code to try to compile
+#  VAR    - variable to store whether the source code compiled
+#
+# The following variables may be set before calling this macro to
+# modify the way the check is run:
+#
+#  CMAKE_REQUIRED_FLAGS = string of compile command line flags
+#  CMAKE_REQUIRED_DEFINITIONS = list of macros to define (-DFOO=bar)
+#  CMAKE_REQUIRED_INCLUDES = list of include directories
+#  CMAKE_REQUIRED_LIBRARIES = list of libraries to link
+
+MACRO(CHECK_CXX_SOURCE_COMPILES SOURCE VAR)
+  IF("${VAR}" MATCHES "^${VAR}$")
+    SET(MACRO_CHECK_FUNCTION_DEFINITIONS 
+      "-D${VAR} ${CMAKE_REQUIRED_FLAGS}")
+    IF(CMAKE_REQUIRED_LIBRARIES)
+      SET(CHECK_CXX_SOURCE_COMPILES_ADD_LIBRARIES
+        "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+    ELSE(CMAKE_REQUIRED_LIBRARIES)
+      SET(CHECK_CXX_SOURCE_COMPILES_ADD_LIBRARIES)
+    ENDIF(CMAKE_REQUIRED_LIBRARIES)
+    IF(CMAKE_REQUIRED_INCLUDES)
+      SET(CHECK_CXX_SOURCE_COMPILES_ADD_INCLUDES
+        "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}")
+    ELSE(CMAKE_REQUIRED_INCLUDES)
+      SET(CHECK_CXX_SOURCE_COMPILES_ADD_INCLUDES)
+    ENDIF(CMAKE_REQUIRED_INCLUDES)
+    FILE(WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src.cxx"
+      "${SOURCE}\n")
+
+    MESSAGE(STATUS "Performing Test ${VAR}")
+    TRY_COMPILE(${VAR}
+      ${CMAKE_BINARY_DIR}
+      ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src.cxx
+      COMPILE_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS}
+      CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS}
+      "${CHECK_CXX_SOURCE_COMPILES_ADD_LIBRARIES}"
+      "${CHECK_CXX_SOURCE_COMPILES_ADD_INCLUDES}"
+      OUTPUT_VARIABLE OUTPUT)
+    IF(${VAR})
+      SET(${VAR} 1 CACHE INTERNAL "Test ${VAR}")
+      MESSAGE(STATUS "Performing Test ${VAR} - Success")
+      FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeOutput.log 
+        "Performing C++ SOURCE FILE Test ${VAR} succeded with the following output:\n"
+        "${OUTPUT}\n"
+        "Source file was:\n${SOURCE}\n")
+    ELSE(${VAR})
+      MESSAGE(STATUS "Performing Test ${VAR} - Failed")
+      SET(${VAR} "" CACHE INTERNAL "Test ${VAR}")
+      FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log 
+        "Performing C++ SOURCE FILE Test ${VAR} failed with the following output:\n"
+        "${OUTPUT}\n"
+        "Source file was:\n${SOURCE}\n")
+    ENDIF(${VAR})
+  ENDIF("${VAR}" MATCHES "^${VAR}$")
+ENDMACRO(CHECK_CXX_SOURCE_COMPILES)
+
diff --git a/mgizapp/cmake/FindTR1.cmake b/mgizapp/cmake/FindTR1.cmake
new file mode 100644
index 0000000..3ef2b44
--- /dev/null
+++ b/mgizapp/cmake/FindTR1.cmake
@@ -0,0 +1,84 @@
+# Check availability of C++ TR1 contents.
+
+# Sets the following variables:
+#
+# TR1_SHARED_PTR_FOUND          -- std::tr1::shared_ptr1<T> available
+# TR1_SHARED_PTR_USE_TR1_MEMORY -- #include <tr1/memory>
+# TR1_SHARED_PTR_USE_MEMORY     -- #include <memory>
+ 
+# We need to have at least this version to support the VERSION_LESS argument to 'if' (2.6.2) and unset (2.6.3)
+cmake_policy(PUSH)
+    cmake_minimum_required(VERSION 2.6.3)
+cmake_policy(POP)
+
+INCLUDE(${PROJECT_SOURCE_DIR}/cmake/CheckCXXSourceCompiles.cmake)
+# ---------------------------------------------------------------------------
+# std::tr1::shared_ptr<T>
+# ---------------------------------------------------------------------------
+   
+check_cxx_source_compiles(
+   "
+   #include <tr1/memory>
+   int main() {
+      std::tr1::shared_ptr<int> ptr;
+      return 0;
+   }
+  "
+TR1_SHARED_PTR_USE_TR1_MEMORY)
+check_cxx_source_compiles(
+        "
+        #include <memory>
+        int main() {
+           std::tr1::shared_ptr<int> ptr;
+           return 0;
+        }
+       "
+TR1_SHARED_PTR_USE_MEMORY)
+   
+set (TR1_SHARED_PTR -NOTFOUND)
+if (TR1_SHARED_PTR_USE_TR1_MEMORY)
+set (TR1_SHARED_PTR_FOUND TRUE)
+endif (TR1_SHARED_PTR_USE_TR1_MEMORY)
+if (TR1_SHARED_PTR_USE_MEMORY)
+set (TR1_SHARED_PTR_FOUND TRUE)
+endif (TR1_SHARED_PTR_USE_MEMORY)
+    
+mark_as_advanced (TR1_SHARED_PTR_FOUND)
+mark_as_advanced (TR1_SHARED_PTR_USE_TR1_MEMORY)
+mark_as_advanced (TR1_SHARED_PTR_USE_MEMORY)
+    
+# ---------------------------------------------------------------------------
+# std::tr1::unordered_map<K, V>
+# ---------------------------------------------------------------------------
+    
+check_cxx_source_compiles(
+        "
+        #include <tr1/unordered_map>
+        int main() {
+             std::tr1::unordered_map<int, int> m;
+             return 0;
+        }
+        "
+        TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP)
+check_cxx_source_compiles(
+        "
+        #include <unordered_map>
+        int main() {
+        std::tr1::unordered_map<int, int> m;
+        return 0;
+        }
+       "
+       TR1_UNORDERED_MAP_USE_UNORDERED_MAP)
+    
+set (TR1_UNORDERED_MAP -NOTFOUND)
+if (TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP)
+set (TR1_UNORDERED_MAP_FOUND TRUE)
+endif (TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP)
+if (TR1_UNORDERED_MAP_USE_UNORDERED_MAP)
+set (TR1_UNORDERED_MAP_FOUND TRUE)
+endif (TR1_UNORDERED_MAP_USE_UNORDERED_MAP)
+   
+mark_as_advanced (TR1_UNORDERED_MAP_FOUND)
+mark_as_advanced (TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP)
+mark_as_advanced (TR1_UNORDERED_MAP_USE_UNORDERED_MAP)
+
diff --git a/mgizapp/cmake/SRLBoost.cmake b/mgizapp/cmake/SRLBoost.cmake
new file mode 100644
index 0000000..af3a956
--- /dev/null
+++ b/mgizapp/cmake/SRLBoost.cmake
@@ -0,0 +1,21 @@
+#Locate Boost libs. Windows users: make sure BOOST_ROOT and BOOST_PATH are set correctly on your environment.
+#See the site FAQ for more details.
+
+MACRO (GET_BOOST_INCLUDE_PATH path libs)
+  #todo: allow this to fall back on a local distributed copy, so user doesn't have to d/l Boost seperately
+  
+  #todo: limit Boost version?
+  #todo: use COMPONENTS threads to locate boost_threads without breaking the current support
+  IF(Boost_FOUND)
+    IF (NOT _boost_IN_CACHE)
+      MESSAGE( "Boost found" )
+      message(STATUS "Boost_INCLUDE_DIR    : ${Boost_INCLUDE_DIR}")
+    ENDIF (NOT _boost_IN_CACHE)
+    SET(${path} ${Boost_INCLUDE_DIRS} )
+	SET(${libs} ${Boost_LIBRARIES} )
+	link_directories ( ${Boost_LIBRARY_DIRS} )
+  ELSE()
+    MESSAGE(FATAL_ERROR "Boost not found, please set the BOOST_ROOT environment variable " )
+  ENDIF()
+ENDMACRO (GET_BOOST_INCLUDE_PATH path libs)
+
diff --git a/mgizapp/scripts/CMakeLists.txt b/mgizapp/scripts/CMakeLists.txt
new file mode 100644
index 0000000..afa694e
--- /dev/null
+++ b/mgizapp/scripts/CMakeLists.txt
@@ -0,0 +1,4 @@
+INSTALL(PROGRAMS force-align-moses.sh  giza2bal.pl  merge_alignment.py  plain2snt-hasvcb.py  sntpostproc.py force-align-moses-old.sh run.sh
+    DESTINATION scripts
+    PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE
+    )
diff --git a/mgizapp/scripts/force-align-moses-old.sh b/mgizapp/scripts/force-align-moses-old.sh
new file mode 100755
index 0000000..fd4cf12
--- /dev/null
+++ b/mgizapp/scripts/force-align-moses-old.sh
@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+
+MGIZA=${QMT_HOME}/bin/mgiza
+
+if [ $# -lt 4 ]; then
+	echo "OK, this is simple, put me into your Moses training directory, link your source/target corpus" 1>&2
+	echo "and run " $0 " PREFIX src_tag tgt_tag root-dir." 1>&2
+	echo "and get force-aligned data: root-dir/giza.[src-tgt|tgt-src]/*.A3.final.* " 1>&2
+	echo "make sure I can find PREFIX.src_tag-tgt_tag and PREFIX.tgt_tag-src_tag, and \${QMT_HOME} is set" 1>&2
+	exit
+fi
+
+PRE=$1
+SRC=$2
+TGT=$3
+ROOT=$4
+
+mkdir -p $ROOT/giza.${SRC}-${TGT}
+mkdir -p $ROOT/giza.${TGT}-${SRC}
+mkdir -p $ROOT/corpus
+
+echo "Generating corpus file " 1>&2
+
+${QMT_HOME}/scripts/plain2snt-hasvcb.py corpus/$SRC.vcb corpus/$TGT.vcb ${PRE}.${SRC} ${PRE}.${TGT} $ROOT/corpus/${TGT}-${SRC}.snt $ROOT/corpus/${SRC}-${TGT}.snt $ROOT/corpus/$SRC.vcb $ROOT/corpus/$TGT.vcb
+
+ln -sf $PWD/corpus/$SRC.vcb.classes $PWD/corpus/$TGT.vcb.classes $ROOT/corpus/
+
+echo "Generating co-occurrence file " 1>&2
+
+${QMT_HOME}/bin/snt2cooc $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC}.cooc $ROOT/corpus/$SRC.vcb $ROOT/corpus/$TGT.vcb $ROOT/corpus/${TGT}-${SRC}.snt
+${QMT_HOME}/bin//snt2cooc $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT}.cooc $ROOT/corpus/$TGT.vcb $ROOT/corpus/$SRC.vcb $ROOT/corpus/${SRC}-${TGT}.snt
+
+echo "Running force alignment " 1>&2
+
+$MGIZA giza.$TGT-$SRC/$TGT-$SRC.gizacfg -c $ROOT/corpus/$TGT-$SRC.snt -o $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC} \
+-s $ROOT/corpus/$SRC.vcb -t $ROOT/corpus/$TGT.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC}.cooc \
+-restart 11 -previoust giza.$TGT-$SRC/$TGT-$SRC.t3.final \
+-previousa giza.$TGT-$SRC/$TGT-$SRC.a3.final -previousd giza.$TGT-$SRC/$TGT-$SRC.d3.final \
+-previousn giza.$TGT-$SRC/$TGT-$SRC.n3.final -previousd4 giza.$TGT-$SRC/$TGT-$SRC.d4.final \
+-previousd42 giza.$TGT-$SRC/$TGT-$SRC.D4.final -m3 0 -m4 1
+
+$MGIZA giza.$SRC-$TGT/$SRC-$TGT.gizacfg -c $ROOT/corpus/$SRC-$TGT.snt -o $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT} \
+-s $ROOT/corpus/$TGT.vcb -t $ROOT/corpus/$SRC.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT}.cooc \
+-restart 11 -previoust giza.$SRC-$TGT/$SRC-$TGT.t3.final \
+-previousa giza.$SRC-$TGT/$SRC-$TGT.a3.final -previousd giza.$SRC-$TGT/$SRC-$TGT.d3.final \
+-previousn giza.$SRC-$TGT/$SRC-$TGT.n3.final -previousd4 giza.$SRC-$TGT/$SRC-$TGT.d4.final \
+-previousd42 giza.$SRC-$TGT/$SRC-$TGT.D4.final -m3 0 -m4 1
+
diff --git a/mgizapp/scripts/force-align-moses.sh b/mgizapp/scripts/force-align-moses.sh
index fd4cf12..ac95bcb 100755
--- a/mgizapp/scripts/force-align-moses.sh
+++ b/mgizapp/scripts/force-align-moses.sh
@@ -14,33 +14,34 @@ PRE=$1
 SRC=$2
 TGT=$3
 ROOT=$4
+NUM=$5
 
-mkdir -p $ROOT/giza.${SRC}-${TGT}
-mkdir -p $ROOT/giza.${TGT}-${SRC}
-mkdir -p $ROOT/corpus
+mkdir -p $ROOT/giza-inverse.${NUM}
+mkdir -p $ROOT/giza.${NUM}
+mkdir -p $ROOT/prepared.${NUM}
 
 echo "Generating corpus file " 1>&2
 
-${QMT_HOME}/scripts/plain2snt-hasvcb.py corpus/$SRC.vcb corpus/$TGT.vcb ${PRE}.${SRC} ${PRE}.${TGT} $ROOT/corpus/${TGT}-${SRC}.snt $ROOT/corpus/${SRC}-${TGT}.snt $ROOT/corpus/$SRC.vcb $ROOT/corpus/$TGT.vcb
+${QMT_HOME}/scripts/plain2snt-hasvcb.py prepared.${NUM}/$SRC.vcb prepared.${NUM}/$TGT.vcb ${PRE}.${SRC} ${PRE}.${TGT} $ROOT/prepared.${NUM}/${TGT}-${SRC}.snt $ROOT/prepared.${NUM}/${SRC}-${TGT}.snt $ROOT/prepared.${NUM}/$SRC.vcb $ROOT/prepared.${NUM}/$TGT.vcb
 
-ln -sf $PWD/corpus/$SRC.vcb.classes $PWD/corpus/$TGT.vcb.classes $ROOT/corpus/
+ln -sf $PWD/prepared.${NUM}/$SRC.vcb.classes $PWD/prepared.${NUM}/$TGT.vcb.classes $ROOT/prepared.${NUM}/
 
 echo "Generating co-occurrence file " 1>&2
 
-${QMT_HOME}/bin/snt2cooc $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC}.cooc $ROOT/corpus/$SRC.vcb $ROOT/corpus/$TGT.vcb $ROOT/corpus/${TGT}-${SRC}.snt
-${QMT_HOME}/bin//snt2cooc $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT}.cooc $ROOT/corpus/$TGT.vcb $ROOT/corpus/$SRC.vcb $ROOT/corpus/${SRC}-${TGT}.snt
+${QMT_HOME}/bin/snt2cooc $ROOT/giza.${NUM}/$TGT-${SRC}.cooc $ROOT/prepared.${NUM}/$SRC.vcb $ROOT/prepared.${NUM}/$TGT.vcb $ROOT/prepared.${NUM}/${TGT}-${SRC}.snt
+${QMT_HOME}/bin//snt2cooc $ROOT/giza-inverse.${NUM}/$SRC-${TGT}.cooc $ROOT/prepared.${NUM}/$TGT.vcb $ROOT/prepared.${NUM}/$SRC.vcb $ROOT/prepared.${NUM}/${SRC}-${TGT}.snt
 
 echo "Running force alignment " 1>&2
 
-$MGIZA giza.$TGT-$SRC/$TGT-$SRC.gizacfg -c $ROOT/corpus/$TGT-$SRC.snt -o $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC} \
--s $ROOT/corpus/$SRC.vcb -t $ROOT/corpus/$TGT.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza.${TGT}-${SRC}/$TGT-${SRC}.cooc \
+$MGIZA giza.$TGT-$SRC/$TGT-$SRC.gizacfg -c $ROOT/prepared.${NUM}/$TGT-$SRC.snt -o $ROOT/giza.${NUM}/$TGT-${SRC} \
+-s $ROOT/prepared.${NUM}/$SRC.vcb -t $ROOT/prepared.${NUM}/$TGT.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza.${NUM}/$TGT-${SRC}.cooc \
 -restart 11 -previoust giza.$TGT-$SRC/$TGT-$SRC.t3.final \
 -previousa giza.$TGT-$SRC/$TGT-$SRC.a3.final -previousd giza.$TGT-$SRC/$TGT-$SRC.d3.final \
 -previousn giza.$TGT-$SRC/$TGT-$SRC.n3.final -previousd4 giza.$TGT-$SRC/$TGT-$SRC.d4.final \
 -previousd42 giza.$TGT-$SRC/$TGT-$SRC.D4.final -m3 0 -m4 1
 
-$MGIZA giza.$SRC-$TGT/$SRC-$TGT.gizacfg -c $ROOT/corpus/$SRC-$TGT.snt -o $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT} \
--s $ROOT/corpus/$TGT.vcb -t $ROOT/corpus/$SRC.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza.${SRC}-${TGT}/$SRC-${TGT}.cooc \
+$MGIZA giza.$SRC-$TGT/$SRC-$TGT.gizacfg -c $ROOT/prepared.${NUM}/$SRC-$TGT.snt -o $ROOT/giza-inverse.${NUM}/$SRC-${TGT} \
+-s $ROOT/prepared.${NUM}/$TGT.vcb -t $ROOT/prepared.${NUM}/$SRC.vcb -m1 0 -m2 0 -mh 0 -coocurrence $ROOT/giza-inverse.${NUM}/$SRC-${TGT}.cooc \
 -restart 11 -previoust giza.$SRC-$TGT/$SRC-$TGT.t3.final \
 -previousa giza.$SRC-$TGT/$SRC-$TGT.a3.final -previousd giza.$SRC-$TGT/$SRC-$TGT.d3.final \
 -previousn giza.$SRC-$TGT/$SRC-$TGT.n3.final -previousd4 giza.$SRC-$TGT/$SRC-$TGT.d4.final \
diff --git a/mgizapp/scripts/run.sh b/mgizapp/scripts/run.sh
new file mode 100755
index 0000000..2bb3972
--- /dev/null
+++ b/mgizapp/scripts/run.sh
@@ -0,0 +1,23 @@
+PRE=test
+SRC=fr
+TGT=en
+NUM=1
+SCRIPT_DIR=/opt/AO/sw/edinburgh-code/scripts-20110926-1425
+
+export QMT_HOME=/root/workspace/mgizapp
+
+rm -rf out
+
+$QMT_HOME/scripts/force-align-moses.sh $PRE $SRC $TGT out 1
+
+echo "FINISHED forced alignment"
+
+$SCRIPT_DIR/../merge_alignment.py out/giza-inverse.$NUM/$SRC-$TGT.A3.final.part* | gzip -c > out/giza-inverse.$NUM/$SRC-$TGT.A3.final.gz
+$SCRIPT_DIR/../merge_alignment.py out/giza.$NUM/$TGT-$SRC.A3.final.part* | gzip -c > out/giza.$NUM/$TGT-$SRC.A3.final.gz
+
+$SCRIPT_DIR/training/symal/giza2bal.pl -d "gzip -cd out/giza.$NUM/$TGT-$SRC.A3.final.gz" -i "gzip -cd out/giza-inverse.$NUM/$SRC-$TGT.A3.final.gz" | $SCRIPT_DIR/training/symal/symal -alignment="grow" -diagonal="yes" -final="yes" -both="yes" > out/aligned.1.grow-diag-final-and
+
+echo "FINISHED giza2bal & symal"
+
+$SCRIPT_DIR/training/phrase-extract/extract $PRE.$TGT $PRE.$SRC out/aligned.1.grow-diag-final-and out/extract.1 7 orientation --model wbe-msd
+
diff --git a/mgizapp/src/CMakeLists.txt b/mgizapp/src/CMakeLists.txt
new file mode 100644
index 0000000..b4b4f65
--- /dev/null
+++ b/mgizapp/src/CMakeLists.txt
@@ -0,0 +1,105 @@
+
+# Set output directory
+
+FIND_PACKAGE(Threads)
+
+
+SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+
+ADD_DEFINITIONS("-DNDEBUG")
+ADD_DEFINITIONS("-DWORDINDEX_WITH_4_BYTE")
+ADD_DEFINITIONS("-DBINARY_SEARCH_FOR_TTABLE")
+ADD_DEFINITIONS("-DDEBUG")
+ADD_DEFINITIONS("-Wno-deprecated")
+ADD_DEFINITIONS("-Wno-write-strings")
+
+SET( LIBMGIZA_SRC
+    alignment.cpp alignment.h
+    AlignTables.cpp AlignTables.h
+    Array2.h Array4.h
+    Array.h ATables.cpp
+    ATables.h cmd.c
+    cmd.h collCounts.cpp
+    collCounts.h common.h
+    D4Tables.h
+    D5Tables.h defs.h
+    Dictionary.cpp Dictionary.h
+    file_spec.h FlexArray.h
+    ForwardBackward.cpp ForwardBackward.h
+    getSentence.cpp getSentence.h
+    Globals.h hmm.cpp
+    hmm.h 
+    HMMTables.cpp HMMTables.h
+    logprob.cpp logprob.h
+    model1.cpp
+    model1.h model2.cpp
+    model2.h model2to3.cpp
+    model345-peg.cpp model3.cpp
+    model3.h model3_viterbi.cpp
+    model3_viterbi_with_tricks.cpp MoveSwapMatrix.cpp
+    MoveSwapMatrix.h myassert.cpp
+    myassert.h mymath.h
+    mystl.h NTables.cpp
+    NTables.h Parameter.cpp
+    Parameter.h parse.cpp
+    Perplexity.cpp Perplexity.h
+    Pointer.h
+    reports.cpp SetArray.cpp
+    SetArray.h
+    syncObj.h transpair_model1.h
+    transpair_model2.h transpair_model3.cpp
+    transpair_model3.h transpair_model4.cpp
+    transpair_model4.h transpair_model5.cpp
+    transpair_model5.h transpair_modelhmm.h
+    ttableDiff.hpp TTables.cpp
+    TTables.h types.h
+    utility.cpp utility.h
+    Vector.h vocab.cpp
+    vocab.h WordClasses.h
+)
+
+ADD_LIBRARY(mgiza STATIC ${LIBMGIZA_SRC})
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR} )
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/src/ )
+LINK_DIRECTORIES ( ${LIBRARY_OUTPUT_PATH} )
+
+SET( MGIZA_SRC main.cpp )
+
+ADD_EXECUTABLE( mgizapp ${MGIZA_SRC} )
+
+TARGET_LINK_LIBRARIES (
+    mgizapp
+    mgiza
+    ${Boost_LIBRARIES}
+    ${CMAKE_THREAD_LIBS_INIT}
+    )
+
+
+ADD_EXECUTABLE(snt2cooc snt2cooc.cpp)
+ADD_EXECUTABLE(snt2plain snt2plain.cpp)
+ADD_EXECUTABLE(plain2snt plain2snt.cpp)
+ADD_EXECUTABLE(symal symal.cpp cmd.c)
+ADD_EXECUTABLE(hmmnorm hmmnorm.cxx)
+ADD_EXECUTABLE(d4norm d4norm.cxx)
+TARGET_LINK_LIBRARIES (
+    hmmnorm
+    mgiza
+    ${Boost_LIBRARIES}
+    ${CMAKE_THREAD_LIBS_INIT}
+    )
+TARGET_LINK_LIBRARIES (
+    d4norm
+    mgiza
+    ${Boost_LIBRARIES}
+    ${CMAKE_THREAD_LIBS_INIT}
+    )
+
+INSTALL(TARGETS mgiza mgizapp snt2cooc snt2plain plain2snt symal hmmnorm d4norm
+    RUNTIME DESTINATION bin
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib
+    )
+
+
+
diff --git a/mgizapp/src/mkcls/CMakeLists.txt b/mgizapp/src/mkcls/CMakeLists.txt
new file mode 100644
index 0000000..3554fb7
--- /dev/null
+++ b/mgizapp/src/mkcls/CMakeLists.txt
@@ -0,0 +1,72 @@
+
+# Set output directory
+
+FIND_PACKAGE(Threads)
+
+
+SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+
+ADD_DEFINITIONS("-DNDEBUG")
+ADD_DEFINITIONS("-Wno-deprecated")
+ADD_DEFINITIONS("-Wno-write-strings")
+
+SET( MKCLS_SRC
+    Array.h
+    FixedArray.h 
+    FlexArray.h 
+    GDAOptimization.cpp 
+    GDAOptimization.h 
+    general.cpp 
+    general.h 
+    HCOptimization.cpp 
+    HCOptimization.h 
+    IterOptimization.cpp 
+    IterOptimization.h 
+    KategProblem.cpp 
+    KategProblem.h 
+    KategProblemKBC.cpp 
+    KategProblemKBC.h 
+    KategProblemTest.cpp 
+    KategProblemTest.h 
+    KategProblemWBC.cpp 
+    KategProblemWBC.h 
+    mkcls.cpp 
+    my.h 
+    myassert.h 
+    myleda.h 
+    MYOptimization.cpp 
+    MYOptimization.h 
+    mystl.h 
+    Optimization.cpp 
+    Optimization.h 
+    Problem.cpp 
+    Problem.h 
+    ProblemTest.cpp 
+    ProblemTest.h 
+    RRTOptimization.cpp 
+    RRTOptimization.h 
+    SAOptimization.cpp 
+    SAOptimization.h 
+    StatVar.cpp 
+    StatVar.h 
+    TAOptimization.cpp 
+    TAOptimization.h
+
+    )
+
+ADD_EXECUTABLE(mkcls ${MKCLS_SRC})
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR} )
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/src/ )
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/src/mkcls )
+LINK_DIRECTORIES ( ${LIBRARY_OUTPUT_PATH} )
+
+
+INSTALL(TARGETS mkcls 
+    RUNTIME DESTINATION bin
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib
+    )
+
+
+