openalea · pradal · May 4, 2017 · May 3, 2017 · May 4, 2017
diff --git a/sequence_analysis/SConstruct b/sequence_analysis/SConstruct
@@ -9,7 +9,7 @@ options = Variables(['../options.py', 'options.py'], ARGUMENTS)
 options.Add(BoolVariable('with_efence', 'build tests with efence library', 0))
 options.Add(BoolVariable('DEBUG', 'my debug', 0))
 
-tools = ['boost_python', 'qt4', 'vplants.tool', 'install', 'vplants.stat_tool']
+tools = ['boost_python', 'vplants.stat_tool'] #'qt4', 'vplants.tool', 'install',
 
 env = ALEASolution(options, tools)
 env.AppendUnique(CXXFLAGS=['-x', 'c++', '-std=c++0x'])

diff --git a/sequence_analysis/src/cpp/SConscript b/sequence_analysis/src/cpp/SConscript
@@ -6,7 +6,7 @@ bn = os.path.basename
 Import( "env" )
 
 lib_env = env.Clone()
-lib_env.EnableQt4Modules(['QtCore','QtOpenGL', 'QtGui'])
+#lib_env.EnableQt4Modules(['QtCore','QtOpenGL', 'QtGui'])
 
 # Import / Export symbols for windows dll
 if lib_env['compiler'] == 'mingw':
@@ -15,7 +15,7 @@ if lib_env['compiler'] == 'mingw':
                "-enable-runtime-pseudo-reloc",
                "-s"]
     lib_env.AppendUnique(LINKFLAGS=LINKFLAGS)
-    
+
 
 includes= lib_env.ALEAGlob('*.h')
 includes += lib_env.ALEAGlob('*.hpp')
@@ -25,15 +25,16 @@ sources = lib_env.ALEAGlob('*.cpp')
 excludes = Split( """
 """)
 
-for f in excludes: 
+for f in excludes:
     for cpp in sources:
 	if f in cpp:
             sources.remove(cpp)
 	    break
 
 # Add defines to export symbols
 lib_env.AppendUnique(CPPDEFINES=['MESSAGE'])
-lib_env.AppendUnique(LIBS=['vptool', 'vpstat_tool'])
+#lib_env.AppendUnique(LIBS=['vptool', 'vpstat_tool'])
+lib_env.AppendUnique(LIBS=['vpstat_tool'])
 
 if lib_env['DEBUG']:
     lib_env.Append(CPPDEFINES= ['DEBUG'])

diff --git a/sequence_analysis/src/wrapper/SConscript b/sequence_analysis/src/wrapper/SConscript
@@ -4,7 +4,7 @@ import os
 
 Import("env")
 
-env.EnableQt4Modules(['QtCore','QtOpenGL', 'QtGui'])
+#env.EnableQt4Modules(['QtCore','QtOpenGL', 'QtGui'])
 
 # Export symbols under windows
 if env['compiler'] == 'mingw':
@@ -20,11 +20,13 @@ if env['compiler'] == 'mingw':
 sources = env.ALEAGlob('*.h')
 sources = env.ALEAGlob('*.cpp')
 
-LIBS = ['vptool', 'vpstat_tool', 'vpsequence']
+#LIBS = ['vptool', 'vpstat_tool', 'vpsequence']
+LIBS = ['vpstat_tool', 'vpsequence']
 env.AppendUnique(LIBS=LIBS)
 
 env.AppendUnique(CPPDEFINES=['MESSAGE'])
-env.AppendUnique(LIBS=['vptool', 'vpstat_tool', 'vpsequence'])
+#env.AppendUnique(LIBS=['vptool', 'vpstat_tool', 'vpsequence'])
+env.AppendUnique(LIBS=['vpstat_tool', 'vpsequence'])
 
 env.ALEAWrapper("../sequence_analysis", "_sequence_analysis", sources)
 
diff --git a/sequence_analysis/src/wrapper/boost_python_aliases.h b/sequence_analysis/src/wrapper/boost_python_aliases.h
@@ -47,7 +47,7 @@
 #define FOOTER_OS \
     if (!ret) \
       sequence_analysis::wrap_util::throw_error(error);\
-    cout << os.str() << endl;\
+    //cout << os.str() << endl;\
     return ret;\
 
 #define FOOTER \
@@ -64,7 +64,8 @@
 #define HEADER_OS(TYPE) \
     StatError error; \
     TYPE* ret;\
-    std::stringstream os;\
+    bool os = true; \
+    //std::stringstream os;\
 
 
 

diff --git a/sequence_analysis/src/wrapper/export_correlation.cpp b/sequence_analysis/src/wrapper/export_correlation.cpp
@@ -25,7 +25,6 @@
 
 #include "sequence_analysis/sequences.h"
 #include "sequence_analysis/sequence_label.h"
-#include "tool/config.h"
 
 #include <boost/python.hpp>
 #include <boost/python/extract.hpp>

diff --git a/sequence_analysis/src/wrapper/export_function.cpp b/sequence_analysis/src/wrapper/export_function.cpp
@@ -24,11 +24,6 @@
 #include <math.h>
 #include <iomanip>
 #include <sstream>
-#include <tool/rw_tokenizer.h>
-#include <tool/rw_cstring.h>
-#include <tool/rw_locale.h>
-
-#include "tool/config.h"
 
 #include "stat_tool/stat_label.h"
 

diff --git a/sequence_analysis/src/wrapper/export_hidden_semi_markov.cpp b/sequence_analysis/src/wrapper/export_hidden_semi_markov.cpp
@@ -21,8 +21,6 @@
 
 #include "wrapper_util.h"
 
-#include "tool/config.h"
-
 #include "stat_tool/stat_label.h"
 
 #include "sequence_analysis/hidden_semi_markov.h"
@@ -82,7 +80,8 @@ class WRAP {
   state_sequence_computation(const HiddenSemiMarkov &input,
       const MarkovianSequences &seq, bool characteristic_flag = true)
   {
-    std:stringstream os;
+    //std:stringstream os;
+    bool os = true; // display
     SIMPLE_METHOD_TEMPLATE_1(input, state_sequence_computation,
         SemiMarkovData, os, seq, characteristic_flag);
   }

diff --git a/sequence_analysis/src/wrapper/export_hidden_variable_order_markov.cpp b/sequence_analysis/src/wrapper/export_hidden_variable_order_markov.cpp
@@ -21,8 +21,6 @@
 
 #include "wrapper_util.h"
 
-#include "tool/config.h"
-
 #include "stat_tool/stat_label.h"
 
 #include "sequence_analysis/hidden_variable_order_markov.h"

diff --git a/sequence_analysis/src/wrapper/export_markovian_sequences.cpp b/sequence_analysis/src/wrapper/export_markovian_sequences.cpp
@@ -102,9 +102,9 @@ class WRAP {
   cluster_step(const MarkovianSequences &seq, int variable, int step, int imode)
   {
     StatError error;
-      
+
     MarkovianSequences *ret = NULL;
-    
+
     rounding rmode = rounding(imode);
     ret = seq.cluster(error, variable, step, rmode);
     if (!ret)
@@ -231,7 +231,8 @@ class WRAP {
 		  const char *path = 0)
   {
     StatError error;
-    std::stringstream os;
+    // std::stringstream os;
+    bool os = true; // display
     bool ret = true;
 
     ret = input.transition_count(error, os,
@@ -244,7 +245,8 @@ class WRAP {
 		  int begin_state, int end_state, int min_frequency)
   {
     StatError error;
-    std::stringstream os;
+    //std::stringstream os;
+    bool os = true; //display
     bool ret = true;
 
     ret = input.word_count(error, os ,variable, word_length,
@@ -253,7 +255,7 @@ class WRAP {
     if (!ret)
       sequence_analysis::wrap_util::throw_error(error);
     //todo if this what we want to return ?
-    return os.str();
+    return string();
   }
 
 
@@ -266,7 +268,7 @@ class WRAP {
     process_type itype = process_type(iitype);
     memory_tree_selection algorithm = memory_tree_selection(ialgorithm);
     transition_estimator estimator = transition_estimator(iestimator);
-    
+
     HEADER_OS(VariableOrderMarkov);
     ret = input.variable_order_markov_estimation(error, os, itype,
         min_order, max_order, algorithm, threshold, estimator,
@@ -354,7 +356,8 @@ class WRAP {
   {
     StatError error;
     bool ret = false;
-    std::stringstream os;
+    //std::stringstream os;
+    bool os = true; // display
 
     CREATE_ARRAY(input_markov, const VariableOrderMarkov*, data);
     ret = input.comparison(error, os, data_size, data.get(), filename);
@@ -366,7 +369,8 @@ class WRAP {
       boost::python::list &input_markov, char *filename)
   {
     StatError error;
-    std::stringstream os;
+    //std::stringstream os;
+    bool os = true; // display
     bool ret = false;
 
     CREATE_ARRAY(input_markov, const SemiMarkov*, data);
@@ -379,7 +383,8 @@ class WRAP {
       boost::python::list &input_markov, latent_structure_algorithm algorithm, const char *filename)
   {
     StatError error;
-    std::stringstream os;
+    //std::stringstream os;
+    bool os = true; // display
     bool ret = false;
 
     CREATE_ARRAY(input_markov, const HiddenVariableOrderMarkov*, data);
@@ -394,7 +399,8 @@ class WRAP {
       const char *filename)
   {
     StatError error;
-    std::stringstream os;
+    //std::stringstream os;
+    bool os = true; // display
     bool ret = false;
 
     CREATE_ARRAY(input_markov, const HiddenSemiMarkov*, markov);
@@ -508,8 +514,8 @@ class WRAP {
   {
     StatError error;
     bool ret;
-    std::stringstream os;
-
+    // std::stringstream os;
+    bool os = true; // display
     CREATE_ARRAY(input_values, int, data);
     ret = input.lumpability_test(error, os, data.get(), order);
     FOOTER_OS;
@@ -526,7 +532,7 @@ class WRAP {
   static SequenceCharacteristics *
   get_characteristics(const MarkovianSequences &input, const int variable)
   {
-    // todo : shall we return something ? 
+    // todo : shall we return something ?
     HEADER(SequenceCharacteristics);
     ret = input.get_characteristics(variable);
     FOOTER;
@@ -542,7 +548,7 @@ class WRAP {
     return ret;
   }
 
-  static MarkovianSequences* 
+  static MarkovianSequences*
   initial_run_computation(const MarkovianSequences &input)
   {
     HEADER(MarkovianSequences);

diff --git a/sequence_analysis/src/wrapper/export_nonhomogeneous_markov.cpp b/sequence_analysis/src/wrapper/export_nonhomogeneous_markov.cpp
@@ -21,8 +21,6 @@
 
 #include "wrapper_util.h"
 
-#include "tool/config.h"
-
 #include "stat_tool/stat_label.h"
 
 #include "sequence_analysis/nonhomogeneous_markov.h"

diff --git a/sequence_analysis/src/wrapper/export_semi_markov.cpp b/sequence_analysis/src/wrapper/export_semi_markov.cpp
@@ -21,8 +21,6 @@
 
 #include "wrapper_util.h"
 
-#include "tool/config.h"
-
 #include "stat_tool/stat_label.h"
 
 #include "sequence_analysis/semi_markov.h"