Merge branch 'master' of ssh://eodev.git.sourceforge.net/gitroot/eodev/eodev

edo/AUTHORS

@@ -1,6 +1,5 @@
-
+The Evolving Distribution Objects framework (EDO) is a template-based,
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+ANSI-C++ evolutionary computation library which helps you to write your
-ANSI-C++ evolutionary computation library which helps you to write your 
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/CMakeLists.txt

@@ -1,5 +1,14 @@
+############################################################################
+##########
+### 1) If you want to set your own variables in install.cmake and avoid the cmd line
 ######################################################################################
-### 1) Set the application properties
+
+INCLUDE(install.cmake OPTIONAL)
+
+######################################################################################
+
+######################################################################################
+### 2) Project properties
 ######################################################################################
 
 # Checks cmake version compatibility
@@ -16,15 +25,12 @@ SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT
 
 
 ######################################################################################
-### 2) Include useful features
+### 3) Include useful features
 ######################################################################################
 
 INCLUDE(FindDoxygen)
 INCLUDE(FindPkgConfig)
 
-PKG_CHECK_MODULES(EO eo REQUIRED)
-PKG_CHECK_MODULES(MO mo REQUIRED)
-
 FIND_PACKAGE(Boost 1.33.0)
 
 INCLUDE_DIRECTORIES(
@@ -34,11 +40,16 @@ INCLUDE_DIRECTORIES(
   #  /Dev/ometah-0.3/common
   )
 
+LINK_DIRECTORIES(
+  ${EO_LIBRARY_DIRS}
+  ${MO_LIBRARY_DIRS}
+  )
+
 ######################################################################################
 
 
 ######################################################################################
-### 3) Include header files path
+### 4) Include header files path
 ######################################################################################
 
 INCLUDE_DIRECTORIES(
@@ -49,7 +60,7 @@ INCLUDE_DIRECTORIES(
 
 
 ######################################################################################
-### 4) Set compiler definitions
+### 5) Set compiler definitions
 ######################################################################################
 
 IF(UNIX)
@@ -63,7 +74,7 @@ ENDIF()
 
 
 ######################################################################################
-### 5) Prepare some variables for CMAKE usage
+### 6) Prepare some variables for CMAKE usage
 ######################################################################################
 
 SET(SAMPLE_SRCS)
@@ -72,7 +83,7 @@ SET(SAMPLE_SRCS)
 
 
 ######################################################################################
-### 6) Now where we go ?
+### 7) Now where we go ?
 ######################################################################################
 
 ADD_SUBDIRECTORY(src)
@@ -85,7 +96,7 @@ ADD_SUBDIRECTORY(doc)
 
 
 ######################################################################################
-### 7) Create executable, link libraries and prepare target
+### 8) Create executable, link libraries and prepare target
 ######################################################################################
 
 SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
@@ -99,7 +110,7 @@ INSTALL(TARGETS edo ARCHIVE DESTINATION lib COMPONENT libraries)
 
 
 ######################################################################################
-### 8) Install pkg-config config file for EO
+### 9) Install pkg-config config file for EO
 ######################################################################################
 
 INSTALL(FILES edo.pc DESTINATION lib/pkgconfig COMPONENT headers)
@@ -108,7 +119,7 @@ INSTALL(FILES edo.pc DESTINATION lib/pkgconfig COMPONENT headers)
 
 
 ######################################################################################
-### 9) Include packaging
+### 10) Include packaging
 ######################################################################################
 
 INCLUDE(Packaging.cmake)

edo/COPYING

@@ -1,5 +1,5 @@
-                  GNU LESSER GENERAL PUBLIC LICENSE
+		  GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 2.1, February 1999
+		       Version 2.1, February 1999
 
  Copyright (C) 1991, 1999 Free Software Foundation, Inc.
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -10,7 +10,7 @@
  as the successor of the GNU Library Public License, version 2, hence
  the version number 2.1.]
 
-                            Preamble
+			    Preamble
 
   The licenses for most software are designed to take away your
 freedom to share and change it.  By contrast, the GNU General Public
@@ -112,7 +112,7 @@ modification follow.  Pay close attention to the difference between a
 former contains code derived from the library, whereas the latter must
 be combined with the library in order to run.
 
-                  GNU LESSER GENERAL PUBLIC LICENSE
+		  GNU LESSER GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
   0. This License Agreement applies to any software library or other
@@ -432,7 +432,7 @@ decision will be guided by the two goals of preserving the free status
 of all derivatives of our free software and of promoting the sharing
 and reuse of software generally.
 
-                            NO WARRANTY
+			    NO WARRANTY
 
   15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
 WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
@@ -455,9 +455,9 @@ FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
 SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 
-                     END OF TERMS AND CONDITIONS
+		     END OF TERMS AND CONDITIONS
 
-           How to Apply These Terms to Your New Libraries
+	   How to Apply These Terms to Your New Libraries
 
   If you develop a new library, and you want it to be of the greatest
 possible use to the public, we recommend making it free software that

edo/application/common/CMakeLists.txt

@@ -10,6 +10,6 @@ FOREACH(file ${RESOURCES})
   EXECUTE_PROCESS(
     COMMAND ${CMAKE_COMMAND} -E copy_if_different
     ${CMAKE_CURRENT_SOURCE_DIR}/${file}
-    ${DO_BINARY_DIR}/${file}
+    ${EDO_BINARY_DIR}/${file}
     )
 ENDFOREACH(file)

edo/application/eda/main.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/install.cmake-dist

@@ -0,0 +1,20 @@
+# Variables to set
+
+#  directory we need to build project
+SET(EO_DIR "<<PATH_TO_EO>>" CACHE PATH "EO directory" FORCE)
+SET(MO_DIR "<<PATH_TO_MO>>" CACHE PATH "MO directory" FORCE)
+
+# automagically set parameters, do not edit
+
+SET(EO_INCLUDE_DIRS "${EO_DIR}/src" CACHE PATH "EO include directory" FORCE)
+SET(EO_LIBRARY_DIRS "${EO_DIR}/release/lib" CACHE PATH "EO library directory" FORCE)
+SET(EO_LIBRARIES "eoutils eo es ga cma gcov")
+
+SET(MO_INCLUDE_DIRS "${MO_DIR}/src" CACHE PATH "MO include directory" FORCE)
+SET(MO_LIBRARY_DIRS "${MO_DIR}/release/lib" CACHE PATH "MO library directory" FORCE)
+SET(MO_LIBRARIES "mo")
+
+# ... or rather use pkg-config (dont forget to comment the code above)
+
+#PKG_CHECK_MODULES(EO eo REQUIRED)
+#PKG_CHECK_MODULES(MO mo REQUIRED)

edo/src/edo

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edo.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -25,4 +25,3 @@ Authors:
 */
 
 #include "edo"
-

edo/src/edoAlgo.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoBounder.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoBounderBound.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoBounderNo.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoBounderRng.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -60,4 +60,3 @@ private:
 };
 
 #endif // !_edoBounderRng_h
-

edo/src/edoBounderUniform.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -39,16 +39,16 @@ public:
 
     void operator()( EOT& sol )
     {
-        unsigned int size = sol.size();
+	unsigned int size = sol.size();
-        assert(size > 0);
+	assert(size > 0);
 
-        for (unsigned int d = 0; d < size; ++d) {
+	for (unsigned int d = 0; d < size; ++d) {
 
-            if ( sol[d] < this->min()[d] || sol[d] > this->max()[d]) {
+	    if ( sol[d] < this->min()[d] || sol[d] > this->max()[d]) {
-                // use EO's global "rng"
+		// use EO's global "rng"
-                sol[d] = rng.uniform( this->min()[d], this->max()[d] );
+		sol[d] = rng.uniform( this->min()[d], this->max()[d] );
-            }
+	    }
-        } // for d in size
+	} // for d in size
     }
 };
 

edo/src/edoContinue.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoDistrib.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoEDA.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -108,7 +108,7 @@ public:
     */
     void operator ()(eoPop< EOT > & pop)
     {
-        assert(pop.size() > 0);
+	assert(pop.size() > 0);
 
 	//double temperature = _initial_temperature;
 

edo/src/edoEDASA.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -108,7 +108,7 @@ public:
     */
     void operator ()(eoPop< EOT > & pop)
     {
-        assert(pop.size() > 0);
+	assert(pop.size() > 0);
 
 	double temperature = _initial_temperature;
 

edo/src/edoEstimator.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoEstimatorNormalMono.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoEstimatorNormalMulti.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -73,7 +73,7 @@ public:
 	    //-------------------------------------------------------------
 
 
-	    _varcovar.resize(s_size, s_size);
+	    _varcovar.resize(s_size);
 
 
 	    //-------------------------------------------------------------

edo/src/edoEstimatorUniform.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoModifier.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -38,4 +38,3 @@ public:
 };
 
 #endif // !_edoModifier_h
-

edo/src/edoModifierDispersion.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoModifierMass.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -42,4 +42,3 @@ public:
 };
 
 #endif // !_edoModifierMass_h
-

edo/src/edoNormalMono.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoNormalMonoCenter.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -44,4 +44,3 @@ public:
 };
 
 #endif // !_edoNormalMonoCenter_h
-

edo/src/edoNormalMulti.h

@@ -1,8 +1,8 @@
 // (c) Thales group, 2010
 /*
     Authors:
-             Johann Dreo <johann.dreo@thalesgroup.com>
+	     Johann Dreo <johann.dreo@thalesgroup.com>
-             Caner Candan <caner.candan@thalesgroup.com>
+	     Caner Candan <caner.candan@thalesgroup.com>
 */
 
 #ifndef _edoNormalMulti_h

edo/src/edoNormalMultiCenter.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoSampler.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoSamplerNormalMono.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -74,7 +74,7 @@ public:
 	    {
 		AtomType mean = distrib.mean()[i];
 		AtomType variance = distrib.variance()[i];
-	        AtomType random = rng.normal(mean, variance);
+		AtomType random = rng.normal(mean, variance);
 
 		assert(variance >= 0);
 

edo/src/edoSamplerNormalMulti.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -53,7 +53,7 @@ public:
 
 	    assert( Vl == Vc );
 
-	    _L.resize(Vl, Vc);
+	    _L.resize(Vl);
 
 	    unsigned int i,j,k;
 

edo/src/edoSamplerUniform.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoUniform.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoUniformCenter.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/edoVectorBounds.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoCheckPoint.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoFileSnapshot.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoFileSnapshot.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoHyperVolume.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoPopStat.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoStat.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoStatNormalMono.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoStatNormalMulti.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/src/utils/edoStatUniform.h

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/test/t-bounderno.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/test/t-continue.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/test/t-edoEstimatorNormalMulti.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/test/t-mean-distance.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or
@@ -41,7 +41,7 @@ Authors:
 #include <edo>
 
 #include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/symmetric_matrix.hpp>
+#include <boost/numeric/ublas/symmetric.hpp>
 
 #include "Rosenbrock.h"
 #include "Sphere.h"

edo/test/t-uniform.cpp

@@ -1,6 +1,6 @@
 /*
-The Evolving Distribution Objects framework (EDO) is a template-based, 
+The Evolving Distribution Objects framework (EDO) is a template-based,
-ANSI-C++ evolutionary computation library which helps you to write your 
+ANSI-C++ evolutionary computation library which helps you to write your
 own estimation of distribution algorithms.
 
 This library is free software; you can redistribute it and/or

edo/test/test_cov_parameters.py

@@ -10,9 +10,9 @@ from numpy import arange
 if __name__ == '__main__':
 
     for p1 in list(arange(0.1, 1.1, 0.1)):
-        for p2 in list(arange(-1., 0., 0.1)) + list(arange(0., 1.1, 0.1)):
+	for p2 in list(arange(-1., 0., 0.1)) + list(arange(0., 1.1, 0.1)):
-            for p3 in list(arange(0.1, 1.1, 0.1)):
+	    for p3 in list(arange(0.1, 1.1, 0.1)):
-                gen = '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3)
+		gen = '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3)
-                cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, gen, gen )
+		cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, gen, gen )
-                print cmd
+		print cmd
-                system( cmd )
+		system( cmd )

eo/CHANGELOG

@@ -1274,11 +1274,11 @@ Date:   Thu Feb 22 08:27:32 2007 +0000
 
     * mutation.tmpl, quadCrossover.tmpl, stat.tmpl: Initialize formerly
     uninitialized variables.
-    
+
     * README.tmpl: Hint to regular Templates/README for details.
-    
+
     * README: Add documentation for adding new source-files.
-    
+
     * Makefile.am.src-tmpl (noinst_HEADERS): Add
     (MyStruct_SOURCES): Move header files from here to the new
     noinst_HEADERS variable.
@@ -1315,7 +1315,7 @@ Date:   Sun Jan 14 18:56:31 2007 +0000
     for automake finding the scripts of eo itself if we run it in a embedded
     subdirectory.
     (COPYING, INSTALL): create.
-    
+
     * README: State more explicitly what a "complete installation" means.
     Give build-instructions for moved directories.
 
@@ -1359,9 +1359,9 @@ Author: kuepper <kuepper>
 Date:   Mon Dec 18 11:17:55 2006 +0000
 
     * TODO.html, README.html: Remove these old files.
-    
+
     * AUTHORS, COPYING, ForRelease, NEWS, ToDo: Update for release.
-    
+
     * eo.cfg (PROJECT_NUMBER): Bump version to 1.0
 
 Author: kuepper <kuepper>
@@ -1373,7 +1373,7 @@ Author: kuepper <kuepper>
 Date:   Sun Dec 17 22:59:53 2006 +0000
 
     * README: Better links to Templates/
-    
+
     * configure.in: Bump version to 1.0-beta2.
 
 Author: kuepper <kuepper>
@@ -1402,11 +1402,11 @@ Date:   Sat Dec 16 21:55:03 2006 +0000
 
     * EO.tpl, MyStructEA.cpp, MyStructSEA.cpp, make_MyStruct.cpp: Use
     correct names for includes.
-    
+
     * README.manual: This is a copy of the old README.
-    
+
     * README: Describe the new way and setup of creating a new EO project.
-    
+
     * createEOproject.sh, Makefile.am.src-tmpl, Makefile.am.top-tmpl:
     * configure.ac.tmpl: New files to create a standalone EO project from
     templates.
@@ -1435,7 +1435,7 @@ Author: kuepper <kuepper>
 Date:   Mon Dec 4 22:27:41 2006 +0000
 
     * Makefile.am: Add t-eoRNG
-    
+
     * t-eoRNG.cpp: Start test for random number generator.
 
 Author: kuepper <kuepper>
@@ -1472,11 +1472,11 @@ Author: kuepper <kuepper>
 Date:   Sun Dec 3 10:41:54 2006 +0000
 
     * mainpage.html: update, add link to Niko Hansen's comparison
-    
+
     * README: Add more specific note about tutorial.
-    
+
     * configure.in: Bump version to 1.0-beta1
-    
+
     * tutorial/Makefile.am: Add all necessary files, including html and
     Templates to distribution.
 
@@ -1517,13 +1517,13 @@ Author: kuepper <kuepper>
 Date:   Sat Dec 2 10:18:57 2006 +0000
 
     * eoTimedMonitor.h (eoTimedMonitor::seconds): Make unsigned.
-    
+
     * eoRNG.cpp, eoRNG.h (K, M, N): Declare static and initialize in cpp.
-    
+
     * t-eoGenOp.cpp (init): Do not add std::ends to end of string, as this
     results in escape-codes (^@) to be printed at runtime and is not
     necessary anyway.
-    
+
     * test/t-eoSymreg.cpp (SymregNode::operator()): Initialize r1 and r2 to
     avoid compiler warnings.
 
@@ -1531,7 +1531,7 @@ Author: kuepper <kuepper>
 Date:   Sat Dec 2 09:39:13 2006 +0000
 
     * eoRNG.h: Cleanup docs and document /all/ members.
-    
+
     * eoRNG.cpp, eoRNG.h (K, M, N): Declare static and initialize in cpp.
 
 Author: kuepper <kuepper>
@@ -1548,9 +1548,9 @@ Author: kuepper <kuepper>
 Date:   Fri Dec 1 20:08:51 2006 +0000
 
     * Makefile.am: Update for release-distribution.
-    
+
     * Makefile.am: Add missing CMA header for distribution.
-    
+
     * Makefile.am: Add missing header for distribution.
 
 Author: kuepper <kuepper>
@@ -1603,7 +1603,7 @@ Author: kuepper <kuepper>
 Date:   Thu Nov 16 12:52:46 2006 +0000
 
     * configure.in (AC_DEBUG): add test
-    
+
     * acinclude.m4 (AC_DEBUG): Define debug-feature and set DEBUG, NODEBUG,
     or NDEBUG according to its value.
 
@@ -1613,10 +1613,10 @@ Date:   Thu Nov 16 12:35:46 2006 +0000
     * make_genotype_real.h (eoEsChromInit): Rewrite vecSigmaInit-handling:
     If sigmaInit is relative (%), do not read vecSigmaInit. Otherwise
     always use vecSigmaInit with default all values of sigmaInit.
-    
+
     * eoParser.h (eoParser::getORcreateParam): Make this a real if-then-else
     clause around ptParam (found or not).
-    
+
     * eoParam.h (eoValueParam::setValue): Document.
     (eoValueParam<std::vector<double> >::setValue): Allow delimiters ',' and
     ';'. A plain ' ' does not work, as it is not correctly read by
@@ -1973,9 +1973,9 @@ Date:   Sun Oct 2 21:42:08 2005 +0000
     - add a user-option for gnuplot-support
     - separate gnuplot-code into declaration and implementation,
       so we can define at EO-build-time whether to use it or not.
-    
+
     Adopt code and Makefiles to above changes.
-    
+
     Some minor fixes.
 
 Author: kuepper <kuepper>
@@ -2311,7 +2311,7 @@ Date:   Thu Dec 23 15:29:07 2004 +0000
 
     Adjust code to perform to C++ standard according to gcc-3.4
     interpretation... (Have not compiled/checked/changed paradisEO.)
-    
+
     That is, the current code compiles with gcc-3.4 and the checks
     (besides t-MGE1bit) all pass.
 
@@ -2362,7 +2362,7 @@ Date:   Fri Nov 5 08:57:34 2004 +0000
     easily read as a parameter)
     - eoIntBound and all other integer-equivalent of the classes in eoRealBound.h
     Note that there is no equivalent to eoRealVectorBounds for vector of integers
-    
+
     In file eo, I have added the 2 includes of eoRealBounds.h and eoIntBounds.h
     The first one was already there by chance, through eoUniformInit.h
 
@@ -2569,13 +2569,13 @@ Author: kuepper <kuepper>
 Date:   Fri Sep 17 16:53:31 2004 +0000
 
     Updated build-prcess to be completely under automake control.
-    
+
     For the tutorial the old Makefiles are saved as Makefile.simple in all
     the respective directories.
-    
+
     Use generated config.h instead of command-line passing of preprocessor
     flags.
-    
+
     Updated support files from current automake.
 
 Author: kuepper <kuepper>
@@ -3300,7 +3300,7 @@ Date:   Sun Jan 5 16:31:50 2003 +0000
 
     Added pyeo. Some changes needed to be made for include files and the like
     in some files (and some bugs were fixed as well [Marc: eoOneToOneBreeder was a mess])
-    
+
     eoFunctor.h now contains static functor_category members, this shouldn't hurt anyone.
 
 Author: maartenkeijzer <maartenkeijzer>
@@ -3398,7 +3398,7 @@ Date:   Wed Sep 18 12:40:46 2002 +0000
 
     A new readFrom & printOn function for EO.h
     Now it CAN handle VALID/INVALID fitnesses.
-    
+
     The problems are over at last
 
 Author: cahon <cahon>
@@ -3592,7 +3592,7 @@ Date:   Mon Jun 17 04:13:45 2002 +0000
 
     Adding the truncation selectors.
     2 versions: eoTruncatedSelectOne is an eoSelectOne, and
-                eoTruncatedSelectMany works like an eoSelectMany (but is NOT)
+		eoTruncatedSelectMany works like an eoSelectMany (but is NOT)
 
 Author: jeggermo <jeggermo>
 Date:   Mon Jun 10 14:10:35 2002 +0000
@@ -3609,7 +3609,7 @@ Date:   Mon May 13 11:31:32 2002 +0000
 
     EO::printOn has been changed so that the printOn function will
     always print a valid fitness value even if the fitness is invalid
-    
+
     Jeroen
 
 Author: jeggermo <jeggermo>
@@ -3827,7 +3827,7 @@ Date:   Mon Apr 15 12:56:35 2002 +0000
 
     eoParseTree printOn and readFrom functions changed for
     compatibility with paradisEO
-    
+
     The fitness is now printed in the same way as in eoBit
 
 Author: evomarc <evomarc>
@@ -4138,9 +4138,9 @@ Date:   Mon Feb 4 14:28:00 2002 +0000
 
     the gpsymreg code has been slightly altered to allow compilation using the
     Intel C++ Compiler for Linux.
-    
+
     Other compilers should not be affected.
-    
+
     A slightly different makefile is needed
 
 Author: jeggermo <jeggermo>
@@ -4317,7 +4317,7 @@ Date:   Tue Dec 4 21:15:16 2001 +0000
     some template classes and functions which did not need
     to be templates have been changed to normal classes and functions
     with hard coded typed
-    
+
     This might help with M$VC++ 6.0 compatibility
 
 Author: jeggermo <jeggermo>
@@ -4537,8 +4537,8 @@ Date:   Sat Nov 10 09:02:17 2001 +0000
 
     Small modifications here and there to be MSVC++ compatible
     Mainly, time.h -> ctime
-            definition of loop index out of loops when multiply used
+	    definition of loop index out of loops when multiply used
-            no typename in declaration using template typename
+	    no typename in declaration using template typename
 
 Author: evomarc <evomarc>
 Date:   Sat Nov 10 06:59:02 2001 +0000
@@ -4628,15 +4628,15 @@ Date:   Sat Nov 3 22:10:11 2001 +0000
 
     the name of the eoGpDepthInitializer class (initializer for
     parse_tree's has been changed to
-    
+
     eoParseTreeDepthInit but backward compatibility is maintained by
     using a #define statement:
-    
+
     #define eoGpDepthInitializer eoParseTreeDepthInit
-    
+
     The initializer for strongly typed GP has been changed to
     eoStParseTreeDepthInit
-    
+
     the gpsymreg application has been changed to use the new name
 
 Author: jeggermo <jeggermo>
@@ -4839,7 +4839,7 @@ Author: jeggermo <jeggermo>
 Date:   Tue Jul 17 08:58:52 2001 +0000
 
     small documentation change for eoParseTree.h.
-    
+
     added a depth initializer for strongly typed genetic programming
     added subtree xover for strongly typed genetic programming
     added branch mutation for strongly typed genetic programming
@@ -4862,7 +4862,7 @@ Date:   Wed Jul 4 04:44:30 2001 +0000
     Adding eoPopEvalFunc, that handles evaluation globally: it receives
     two populations, parents and offspring, and does whatever necessary.
     The subclass eoPopLoopEval does the simple loop on the offspring.
-    
+
     eoEasyEA was subsequently modified to handle an eoPopEval passed in Ctor,
     but also to encapsulate an eoEvalFunc into an eoPopLoopEval tranparently.
 
@@ -4874,7 +4874,7 @@ Date:   Tue Jul 3 12:56:44 2001 +0000
     Modified eoEaseyEA accordingly - you can either pass an eoEvalFunc, as
     before (it is then encapsulated into an eoPopLoopEval that does the good
     old loop on the offspring - or directly pass a full eoPopEvalFunc
-    
+
     Small modification also in make_op_es -> keyword "none" is now recognized
     for one of the crossover of either object variables or stdev's
 
@@ -4883,9 +4883,9 @@ Date:   Mon Jul 2 13:31:04 2001 +0000
 
     Changed the directory structure for gp
     now: eoParseTree <-- the eoParseTree class
-         eoParseTreeDepthInit <-- the eoParseTree depth initializer (eoGpDepthInitializer)
+	 eoParseTreeDepthInit <-- the eoParseTree depth initializer (eoGpDepthInitializer)
-         eoParseTreeOp <-- the operators (xover and mutation)
+	 eoParseTreeOp <-- the operators (xover and mutation)
-    
+
     base documentation written for:
     * eoParseTree
     * eoGpDepthInitializer
@@ -4895,9 +4895,9 @@ Date:   Mon Jul 2 13:31:04 2001 +0000
     * eoExpansionMutation
     * eoCollapseSubtreeMutation
     * eoHoistMutation
-    
+
     I also created a group ParseTree which contains all classes related to eoParseTree
-    
+
     eoGpMutate.h has been removed (merged with eoParseTree operators into eoParseTreeOp
 
 Author: jeggermo <jeggermo>
@@ -4978,16 +4978,16 @@ Author: jeggermo <jeggermo>
 Date:   Thu Jun 28 14:03:59 2001 +0000
 
     new Mutation operators for eoParseTree in src/gp/eoGpMutate.h
-    
+
     a symbolic regression example program added to the app-dir
-    
+
     configure.in and Makefile(s).am changed
 
 Author: jeggermo <jeggermo>
 Date:   Thu Jun 28 13:55:14 2001 +0000
 
     Additional mutation operators for eoParseTree
-    
+
     * Point Mutation
     * Expansion Mutation
     * Collapse Subtree Mutation
@@ -5195,7 +5195,7 @@ Date:   Wed May 2 10:42:32 2001 +0000
     src/es/eoEsGlobalXover.h and src/es/eoEsLocalXover.h for crossover
     src/es/make_XXX_es.h for user-input
     test/t-eoEsAll.cpp to test
-    
+
     However, an old bug appeared: className was not const in eoGenOp (and derived classes)
     so I had to change that throughtout the hierarchy
 
@@ -5212,7 +5212,7 @@ Date:   Mon Apr 30 13:24:42 2001 +0000
     Changed the interface of make_genotype - now templatized by the EOT
     and not the fitness - this is mandatory for ES genoptypes as it allows to
     choose the type of gentype at run-time (from existing types, of course!)
-    
+
     Also moved make_help.cpp into utils dir (otherwise you'd had to maintain
     a copy into each representation dir!).
 
@@ -5224,7 +5224,7 @@ Date:   Mon Apr 30 13:01:07 2001 +0000
     Changed the interface of make_genotype - now templatized by the EOT
     and not the fitness - this is mandatory for ES genoptypes as it allows to
     choose the type of gentype at run-time (from existing types, of course!)
-    
+
     Also moved make_help.cpp into utils dir (otherwise you'd had to maintain
     a copy into each representation dir!).
 
@@ -5427,7 +5427,7 @@ Date:   Wed Apr 4 03:47:33 2001 +0000
 
     Added the signal handling - see eoCtrlCContinue.h
     I've disabled it in case of MSC as I don't know if this works there ...
-    
+
     Also added a couple of "virtual" in the ga dir
 
 Author: evomarc <evomarc>
@@ -5455,7 +5455,7 @@ Date:   Wed Mar 28 09:00:54 2001 +0000
     FDCStat and FileSnapshot: better error messageing
     Scalar fitness: is now a vector of doubles
     exercise3.1 added gnuplot again
-    
+
     Don't know about eoCombinedContinue
 
 Author: evomarc <evomarc>
@@ -5646,7 +5646,7 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Mon Mar 12 16:00:58 2001 +0000
 
     EO: added overloaded printing of fitness (for vectors and pairs)
-    
+
     Various bugs and ommissions in eoPerf2Worth and eoSelectFromWorth
 
 Author: maartenkeijzer <maartenkeijzer>
@@ -5658,12 +5658,12 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Sat Mar 10 14:02:23 2001 +0000
 
     Changed the populator to be a) more efficient and b) more useable
-    
+
     It is no longer derived from eoPop, it now gets a destination population.
     This saves a lot of copying. The semantics has changed a little as well. It is
     now an _infinite_ iterator. operator++ will *not* dispense new individuals, but
     will merely stay at the end. To get a new indy, use operator*() as before.
-    
+
     eoEasyEA now checks the checkpoint *after* making a generation and clears the offspring
     eoGeneralBreeder is changed to reflect the changes in eoPopulator
     eoSequentialSelect now uses setup() rather than init()
@@ -5717,7 +5717,7 @@ Date:   Mon Feb 19 12:23:13 2001 +0000
     To be able to use the primitive std::generate function, added a
     set of wrappers in eoSTLFunctor.h that have the copy semantics most
     STL functions expect (namely pass-by-value rather then pass-by-reference).
-    
+
     Updated test/Makefile.am to also test t-eoRandom
 
 Author: evomarc <evomarc>
@@ -5736,14 +5736,14 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Sat Feb 17 10:51:31 2001 +0000
 
     eoVector is back (eoFixedLength and eoVariableLength are gone)
-    
+
     Also: introducing eoRndGenerators.h for eoRndGenerator derived classes:
-    
+
       eoNormalGenerator
       eoUniformGenerator
       eoBooleanGenerator
       eoNegExpGenerator
-    
+
     Note the suffix that are added to aid in determining what these classes do
 
 Author: evomarc <evomarc>
@@ -5829,13 +5829,13 @@ Date:   Wed Feb 14 14:09:16 2001 +0000
 Author: maartenkeijzer <maartenkeijzer>
 Date:   Wed Feb 14 10:35:26 2001 +0000
 
-    
+
     Changed the signature of eoMon, eoBin and eoQuadOp to return a bool,
     without invalidating fitness. Added a set of invalidators to take over
     that job (see for instance eoSGA and eoSGATransform how this can transparantly used)
-    
+
     Derived eoState from eoFunctorStore (for convenience, from a design perspective this may sound wrong)
-    
+
     Added a wrap_op function that does the wrapping for you (see eoOpContainer how this made this functor
     exceedingly less hairy). Checked all the tests removed the eoGeneric*Op family (not needed anymore)
     and of course changed all the operators to reflect the change (and found a few that didn't
@@ -5865,24 +5865,24 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Tue Feb 13 12:38:19 2001 +0000
 
     fixed a bug: the parser now correctly parses parameters of the form
-    
+
     -Pvalue
-    
+
     This will now produce 'value'. The buggy parser would parse 'alue' here. I am truly and deeply
     ashamed to have created such an off-by-one error.
-    
+
     Marc assumed this was wanted behaviour (so that it should read: -P=value)
     I must admit that this is a logical conclusion, though it was merely a side-effect
     of the error. To not force Marc to rewrite the tutorial and his way of working with
     EO, I decided to make a feature out of the bug, so that now the parser will parse:
-    
+
     -Pvalue
     -P=value
-    
+
     and of course the true and blue:
-    
+
     -Parameter=value
-    
+
     I will now go and check if I sent out some crappy papers caused by this bug (as I've been using eo!)
 
 Author: maartenkeijzer <maartenkeijzer>
@@ -5894,14 +5894,14 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Mon Feb 12 13:58:51 2001 +0000
 
     Ok, updated the Makefile.am again to use the
-    
+
     make check
-    
+
     Command I picked up in the automake documentation (RTFM, you know)
-    
+
     Tagged a lot of header functions in the GnuPlot files with 'inline',
     so they can be used from more than one sourcefile.
-    
+
     Ok, now the interesting news. Started a new library libga (not to be confused
     with Matthew's GaLib). Here I suggest we put a fairly complete and configurable
     genetic algorithm. Just to see how far we can stretch ourselves and also to have
@@ -5920,7 +5920,7 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Sun Feb 11 16:25:03 2001 +0000
 
     Removed small bug in reading outside a buffer in eoParser::readFrom
-    
+
     This caused the parser to crash when a simple flag of the form program -f
     was given.
 
@@ -6014,8 +6014,8 @@ Date:   Fri Feb 9 05:09:26 2001 +0000
     I also changed
       - the eoQuadratic into eoQuad (as dicussed with Maarten)
       - the eoBin into eoBit, with more appropriate names for the "binary"
-        operators (that can be unary!) as no one protested when I posted on
+	operators (that can be unary!) as no one protested when I posted on
-        eodev list
+	eodev list
 
 Author: evomarc <evomarc>
 Date:   Wed Feb 7 05:15:18 2001 +0000
@@ -6039,7 +6039,7 @@ Date:   Wed Feb 7 05:04:24 2001 +0000
     Added selection methods
     eoBestSelect            always return the best individual
     eoSequentialSelect      a selectOne version of eoDetSelect (uses an index to
-                            return next offspring from sorted pop)
+			    return next offspring from sorted pop)
 
 Author: evomarc <evomarc>
 Date:   Thu Feb 1 05:27:36 2001 +0000
@@ -6061,7 +6061,7 @@ Date:   Wed Jan 31 18:38:39 2001 +0000
     every generation) which is different from the continuous monitoring (same file/plot is
     angemented every generation).
     This lead to a number of modifications in many files in utils dir
-    
+
     But now we can watch on-line
     - fitness spreadout
     - FDC plots
@@ -6078,7 +6078,7 @@ Date:   Mon Jan 29 10:25:44 2001 +0000
     Added the truncate and the hasNoBoundAtAll methods in eoRealBounds.
     The former simply set values to the boundary values in case they are out
     The latter allows to short-cut all bound-checks when no need
-    
+
     SOme day I will put this in utils, and have a eoRealBounds.cpp in the
     pre-compiled library
 
@@ -6129,12 +6129,12 @@ Date:   Sat Jan 27 07:43:58 2001 +0000
        eo   everything that is general to any representation
        es.h everything about real representation (in es dir)
        ga.h everything related to bitstring representation (in ga dir)
-    
+
     To be continued by gp.h, and ...
-    
+
     This has lead to some slight modifications in test file eobin and all tutorial
     examples files...
-    
+
     I've also added in utils eoDistance, generic functor to compute distances,
     including also the generic Euclidian distance
 
@@ -6145,9 +6145,9 @@ Date:   Sat Jan 27 07:41:46 2001 +0000
        eo   everything that is general to any representation
        es.h everything about real representation (in es dir)
        ga.h everything related to bitstring representation (in ga dir)
-    
+
     To be continued by gp.h, and ...
-    
+
     This has lead to some slight modifications in test file eobin and all tutorial
     examples files...
 
@@ -6405,7 +6405,7 @@ Date:   Tue Jan 2 07:03:57 2001 +0000
       permanent parameters (eoParser only holds references), and egcs did not allow
       to create them by reference, i.e. in the line
       eoValueParam<xxx> & blablaParam(...);
-    
+
     So now everything is done in the main_function, and 3 lines are needed to create
     and read every paramter (sigh ...)
 
@@ -6483,16 +6483,16 @@ Date:   Tue Dec 19 18:41:19 2000 +0000
     THe big eoReplacement update:
     The interface for eoReplacement is now eoPop<EOT>&, eoPop<EOT>&
     (i.e. no const) and the result must be in the first argument in the end.
-    
+
     Hence it is possible to do SSGA and all intermediate replacmeent procedures
-    
+
     The classes derived from eoMergeReduce.h are now in a separate file
     The SSGA-like replcaement procedures are in eoReduceMerge.h
     A more general replacement can be found in eoSurviveAndDie.h
     (it could be made a littel more general - still open for upgrades).
-    
+
     Also some accessors have been added to the eoPop (best and worse individuals)
-    
+
     And include file eo has been updated
 
 Author: evomarc <evomarc>
@@ -6630,16 +6630,16 @@ Author: evomarc <evomarc>
 Date:   Mon Dec 4 06:58:43 2000 +0000
 
     Added the lastCall construct: if the stopping condition becomes true in eoCheckPoint,
-          a method called lastCall is called for everything contained in that checkpoint
+	  a method called lastCall is called for everything contained in that checkpoint
-          (stats, updaters and monitors). This can be extremely useful
+	  (stats, updaters and monitors). This can be extremely useful
-          - for stateSavers (see below)
+	  - for stateSavers (see below)
-          - for monitoring things like rates of success of operators, where what you
+	  - for monitoring things like rates of success of operators, where what you
-            are interested in is the final result only.
+	    are interested in is the final result only.
     Added of course a virtual method lastCall that does nothing by default in classes
-          eoBaseStat, eoBaseSortedStat, eoUpdater and eoMonitor
+	  eoBaseStat, eoBaseSortedStat, eoUpdater and eoMonitor
     Added a boolean to control the save of the state in method eoCountedStateSaver::lastCall
-          so you can ask that the state is saved at final population, whatever happens.
+	  so you can ask that the state is saved at final population, whatever happens.
-          I also added the corresponding constructor to take this into account.
+	  I also added the corresponding constructor to take this into account.
 
 Author: evomarc <evomarc>
 Date:   Mon Dec 4 05:55:59 2000 +0000
@@ -6822,8 +6822,8 @@ Author: evomarc <evomarc>
 Date:   Tue Nov 28 06:46:37 2000 +0000
 
     Modified the contructor: the default value for the delimiter is now " "
-         and I added a boolean argument to indicate whether or not we want to
+	 and I added a boolean argument to indicate whether or not we want to
-             overwrite an existing file with same name (default is overwrite).
+	     overwrite an existing file with same name (default is overwrite).
     Added the getFileName accessor.
 
 Author: evomarc <evomarc>
@@ -7085,7 +7085,7 @@ Author: maartenkeijzer <maartenkeijzer>
 Date:   Fri Oct 6 10:41:38 2000 +0000
 
     Added an eoSortedStatBase for more efficient statistic calculations
-    
+
     updated a few makefiles to include the html and latex docs with the
     distribution.
 
@@ -7844,12 +7844,12 @@ Author: mac <mac>
 Date:   Mon Mar 6 16:05:47 2000 +0000
 
     Fixed bug in eoGOpSelector (missing break!)
-    
+
     eoOp.h: binOp's second arg is const once more
-    
+
     all dsp and dsw files were touched by msvc, but did add some stuff (which
     will be added to eo later)
-    
+
     Hope this all works
 
 Author: mac <mac>
@@ -7879,7 +7879,7 @@ Author: marc <marc>
 Date:   Tue Feb 29 05:14:40 2000 +0000
 
     wherease the command "cvs ci" is OK.
-    
+
     Here we go:
     - added the virtual destructors of all classes,
      to suppress g++ annoying warnings when using -Wall option
@@ -7930,7 +7930,7 @@ Date:   Sat Feb 19 16:30:42 2000 +0000
 
     Moved the static eoRNG rng to an extern eoRNG
     This external object is now defined in eoPersistent.cpp
-    
+
     This should change...
 
 Author: mac <mac>

eo/CMakeLists.txt

@@ -44,6 +44,12 @@ ENABLE_LANGUAGE(C)
 ### 2) Include required modules / configuration files
 #####################################################################################
 
+FIND_PACKAGE(OpenMP REQUIRED)
+IF(OPENMP_FOUND)
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+ENDIF()
+
 INCLUDE(CMakeBackwardCompatibilityCXX)
 
 INCLUDE(FindDoxygen)
@@ -103,7 +109,7 @@ ENDIF (ENABLE_CMAKE_TESTING)
 ### 5) Where must cmake go now ?
 ######################################################################################
 
-ADD_SUBDIRECTORY(app)
+#ADD_SUBDIRECTORY(app)
 ADD_SUBDIRECTORY(doc)
 ADD_SUBDIRECTORY(src)
 ADD_SUBDIRECTORY(test)

eo/COPYING

@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-  
+
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an
@@ -457,7 +457,7 @@ DAMAGES.
 
 		     END OF TERMS AND CONDITIONS
 
-           How to Apply These Terms to Your New Libraries
+	   How to Apply These Terms to Your New Libraries
 
   If you develop a new library, and you want it to be of the greatest
 possible use to the public, we recommend making it free software that

eo/ConfigureChecks.cmake

@@ -1,4 +1,3 @@
-
 # NOTE: only add something here if it is really needed by EO
 
 include(CheckIncludeFile)
@@ -7,17 +6,17 @@ include(CheckSymbolExists)
 include(CheckFunctionExists)
 include(CheckLibraryExists)
 
-check_library_exists(m   cos "cos in libm" HAVE_LIBM) 
+check_library_exists(m   cos "cos in libm" HAVE_LIBM)
 
-check_include_files(cmath.h  "cmath.h"      HAVE_CMATH_H)               
+check_include_files(cmath.h  "cmath.h"      HAVE_CMATH_H)
-check_include_files(stdio.h  "stdio.h"      HAVE_STDIO_H)              
+check_include_files(stdio.h  "stdio.h"      HAVE_STDIO_H)
-check_include_files(stdlib.h "stdlib.h"     HAVE_STDLIB_H)                
+check_include_files(stdlib.h "stdlib.h"     HAVE_STDLIB_H)
-check_include_files(string.h  "string.h"    HAVE_STRING_H)                  
+check_include_files(string.h  "string.h"    HAVE_STRING_H)
-check_include_files(strings.h "strings.h"   HAVE_STRINGS_H)                   
+check_include_files(strings.h "strings.h"   HAVE_STRINGS_H)
-check_include_files(malloc.h  "malloc.h"    HAVE_MALLOC_H)                    
+check_include_files(malloc.h  "malloc.h"    HAVE_MALLOC_H)
-check_include_files(limits.h  "limits.h"    HAVE_LIMITS_H)                   
+check_include_files(limits.h  "limits.h"    HAVE_LIMITS_H)
-check_include_files(unistd.h  "unistd.h"    HAVE_UNISTD_H)                  
+check_include_files(unistd.h  "unistd.h"    HAVE_UNISTD_H)
-check_include_files(stdint.h  "stdint.h"    HAVE_STDINT_H) 
+check_include_files(stdint.h  "stdint.h"    HAVE_STDINT_H)
 
 
 # Use check_symbol_exists to check for symbols in a reliable
@@ -27,7 +26,4 @@ check_include_files(stdint.h  "stdint.h"    HAVE_STDINT_H)
 # specific order.  Refer to the man page for each symbol for which a
 # check is to be added to get the proper set of headers. Example :
 
-#check_symbol_exists(asymbol          "symbole.h"                 HAVE_SYMBOLE)      
+#check_symbol_exists(asymbol          "symbole.h"                 HAVE_SYMBOLE)
-
-
-

eo/INSTALL

@@ -233,4 +233,3 @@ operates.
 
 `configure' also accepts some other, not widely useful, options.  Run
 `configure --help' for more details.
-

eo/LICENSE

@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-  
+
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an
@@ -457,7 +457,7 @@ DAMAGES.
 
 		     END OF TERMS AND CONDITIONS
 
-           How to Apply These Terms to Your New Libraries
+	   How to Apply These Terms to Your New Libraries
 
   If you develop a new library, and you want it to be of the greatest
 possible use to the public, we recommend making it free software that
@@ -500,5 +500,3 @@ necessary.  Here is a sample; alter the names:
   Ty Coon, President of Vice
 
 That's all there is to it!
-
-

eo/NEWS

@@ -7,11 +7,11 @@
   - GCC 4.3 compatibility
   - new versatile log system with several nested verbose levels
   - classes using intern verbose parameters marked as deprecated, please update your code accordingly if you use one of the following files:
-        eo/src/eoCombinedInit.h
+	eo/src/eoCombinedInit.h
-        eo/src/eoGenContinue.h
+	eo/src/eoGenContinue.h
-        eo/src/eoProportionalCombinedOp.h
+	eo/src/eoProportionalCombinedOp.h
-        eo/src/utils/eoData.h
+	eo/src/utils/eoData.h
-        eo/src/utils/eoStdoutMonitor.h
+	eo/src/utils/eoStdoutMonitor.h
   - an evaluator that throw an exception if a maximum eval numbers has been reached, independently of the number of generations
   - new monitor that can write on any ostream
   - new continuator that can catch POSIX system user signals
@@ -33,10 +33,9 @@
   - Add Microsoft Visual C++ project support files (for Visual Studio 2003 and 2005)
   - Upgrade Teamplates/ script to create a complete standalone EO project (using autotools)
   - Remove support for pre-standard C++ compiler (i.e. gcc-2.x), which allows to
-    clean up the code considerably. 
+    clean up the code considerably.
     Assume availability of sstream and limits.
 
 * release 0.9.3z.1 (1. Oct. 2005)
   - Support gcc-3.4 and gcc.4.x.
   - Provide full automake/autoconf/configure support.
-

eo/README

@@ -1,8 +1,7 @@
-
+		      EO README FILE
-                      EO README FILE
 
 =======================================================================
-         check latest news at http://eodev.sourceforge.net/
+	 check latest news at http://eodev.sourceforge.net/
 =======================================================================
 
 Welcome to EO, the Evolving Objects library.
@@ -14,7 +13,7 @@ In case of any problem, please e-mail us at
     eodev-help@lists.sourceforge.net, eodev@egroups.com
 
 To get started, take a look at the tutorial, starting with
-    ./tutorial/html/eoTutorial.html  
+    ./tutorial/html/eoTutorial.html
 
 The easiest way to start programming a new genome with all EO
 evolution engines handy is to create a new standalone EO project from
@@ -23,11 +22,11 @@ an introduction;)
 
 
 ==================================================================
-                      BUILDING EO
+		      BUILDING EO
 ==================================================================
 The basic installation procedure goes the following:
 
-Go to your build-directory and run 
+Go to your build-directory and run
     $(SRCDIR)/configure
     make
     make check
@@ -50,7 +49,7 @@ specific about EO.
 
 
 ===================================================================
-                       DIRECTORY STRUCTURE
+		       DIRECTORY STRUCTURE
 ===================================================================
 After unpacking the archive file, you should end up with the following
 structure:
@@ -63,7 +62,7 @@ structure:
    |   |
    |   +- ga             bistring-genotypes source files
    |   |
-   |   +- es             real-valued-genotypes source files  
+   |   +- es             real-valued-genotypes source files
    |   |
    |   +- gp             Genetic Programming source files
    |   |
@@ -74,9 +73,9 @@ structure:
    +-- tutorial               TUTORIAL dir (indeed :-)
    |   |
    |   +- html           all html files - start by browsing index.html
-   |   | 
+   |   |
    |   +- LessonX        for X=1, 2, 3, ... : example of increasing complexity
-   | 
+   |
    |
    |
    +-- doc                    DOCUMENTATION dir (generated by Doxygen)
@@ -93,7 +92,7 @@ structure:
    |
    +-- app                    APPLICATIONS - one dir per separate application
    |   |
-   |   +- gprop            GA/backpropagation for neural nets 
+   |   +- gprop            GA/backpropagation for neural nets
    |   |
    |   +- mastermind       the wellknown MasterMind game
    |
@@ -103,7 +102,7 @@ structure:
 
 
 ===================================================================
-              NOTES
+	      NOTES
 ===================================================================
 If you extracted a fresh snapshot from the cvs-repository, remember
 to run

eo/app/gprop/CMakeLists.txt

@@ -18,15 +18,14 @@ LINK_DIRECTORIES(${EO_BINARY_DIR}/lib)
 SET (GPROP_SOURCES gprop.cpp)
 
 # especially for Visual Studio
-IF(NOT WIN32 OR CYGWIN)  
+IF(NOT WIN32 OR CYGWIN)
-  	ADD_EXECUTABLE(gprop ${GPROP_SOURCES})                             
+  	ADD_EXECUTABLE(gprop ${GPROP_SOURCES})
     ADD_DEPENDENCIES(gprop eo eoutils)
-    
+
-    TARGET_LINK_LIBRARIES(gprop eo eoutils) 
+    TARGET_LINK_LIBRARIES(gprop eo eoutils)
-    
+
     SET(GPROP_VERSION ${GLOBAL_VERSION})
   SET_TARGET_PROPERTIES(gprop PROPERTIES VERSION "${GPROP_VERSION}")
 ENDIF(NOT WIN32 OR CYGWIN)
 
 ######################################################################################
-

eo/app/gprop/gprop.h

@@ -207,12 +207,12 @@ int correct(const mlp::net& net, const mlp::set& set)
       unsigned partial = 0;
 
       for (unsigned i = 0; i < s->output.size(); ++i)
-        if ((s->output[i] < 0.5 && net(s->input)[i] < 0.5) ||
+	if ((s->output[i] < 0.5 && net(s->input)[i] < 0.5) ||
-            (s->output[i] > 0.5 && net(s->input)[i] > 0.5))
+	    (s->output[i] > 0.5 && net(s->input)[i] > 0.5))
-          ++partial;
+	  ++partial;
 
       if (partial == s->output.size())
-        ++sum;
+	++sum;
     }
 
   return sum;

eo/app/gprop/l2.h

@@ -29,7 +29,7 @@ namespace l2
   //---------------------------------------------------------------------------
   // error
   //---------------------------------------------------------------------------
-  
+
   real error(const mlp::net& net, const set& ts)
   {
     real error_ = 0.0;
@@ -37,12 +37,12 @@ namespace l2
     for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
       {
 	vector out = net(s->input);
-	
+
 	for (unsigned i = 0; i < out.size(); ++i)
 	  {
 	    real target = s->output[i];
 	    real value = out[i];
-	    error_ -= target * log(value + min_real) + 
+	    error_ -= target * log(value + min_real) +
 	      (1.0 - target) * log(1.0 - value + min_real);
 	  }
       }
@@ -53,25 +53,25 @@ namespace l2
   //-------------------------------------------------------------------------
   // l2
   //-------------------------------------------------------------------------
-  
+
   class net: public qp::net
   {
   public:
     net(mlp::net& n): qp::net(n) {}
-    
+
     real error(const set& ts)
     {
       real error_ = 0;
-      
+
       for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
 	{
 	  forward(s->input);
 	  error_ -= backward(s->input, s->output);
 	}
-      
+
       return error_;
     }
-    
+
   private:
     real backward(const vector& input, const vector& output)
     {
@@ -84,7 +84,7 @@ namespace l2
 	{
 	  neuron& n = (*current_layer)[j];
 	  real out = output[j];
-	  n.ndelta += n.delta = (out - n.out) / 
+	  n.ndelta += n.delta = (out - n.out) /
 	    (n.out * (1.0 - n.out) + min_real) * n.out * (1.0 - n.out);
 
 	  if (size() == 1)                                        // monolayer
@@ -92,21 +92,21 @@ namespace l2
 	  else                                                    // multilayer
 	    for (unsigned k = 0; k < n.dxo.size(); ++k)
 	      n.dxo[k] += n.delta * (*backward_layer)[k].out;
-	  
+
-	  error_ += out * log(n.out + min_real) + 
+	  error_ += out * log(n.out + min_real) +
 	    (1.0 - out) * log(1.0 - n.out + min_real);
 	}
-      
+
       // hidden layers
       while (++current_layer != rend())
 	{
 	  reverse_iterator forward_layer  = current_layer - 1;
-          reverse_iterator backward_layer = current_layer + 1;
+	  reverse_iterator backward_layer = current_layer + 1;
-	  
+
 	  for (unsigned j = 0; j < current_layer->size(); ++j)
 	    {
 	      neuron& n = (*current_layer)[j];
-	      real sum = 0; 
+	      real sum = 0;
 	      for (unsigned k = 0; k < forward_layer->size(); ++k)
 		{
 		  neuron& nf = (*forward_layer)[k];
@@ -114,7 +114,7 @@ namespace l2
 		}
 	      n.delta = n.out * (1.0 - n.out) * sum;
 	      n.ndelta += n.delta;
-	      
+
 	      if (backward_layer == rend())               // first hidden layer
 		n.dxo += n.delta * input;
 	      else                                     // rest of hidden layers
@@ -122,19 +122,19 @@ namespace l2
 		  n.dxo[k] += n.delta * (*backward_layer)[k].out;
 	    }
 	}
-    
+
       return error_;
     }
   };
-  
+
   //---------------------------------------------------------------------------
-  
+
 } // namespace l2
 
 //-----------------------------------------------------------------------------
 
 #endif // l2_h
 
-// Local Variables: 
+// Local Variables:
-// mode:C++ 
+// mode:C++
 // End:

eo/app/gprop/mlp.h

@@ -45,7 +45,7 @@ namespace std {
   istream& operator>>(istream& is, mlp::vector& v)
   {
     for (mlp::vector::iterator vi = v.begin() ; vi != v.end() ; vi++) {
-        is >> *vi;
+	is >> *vi;
     }
     return is;
   }
@@ -133,15 +133,15 @@ namespace mlp
     #ifdef HAVE_LIBYAML_CPP
     YAML_SERIALIZABLE_AUTO(neuron)
     void emit_yaml(YAML::Emitter&out) const {
-            out << YAML::BeginMap;
+	    out << YAML::BeginMap;
-            out << YAML::Key << "Class" << YAML::Value << "mlp::neuron";
+	    out << YAML::Key << "Class" << YAML::Value << "mlp::neuron";
-            YAML_EMIT_MEMBER(out,bias);
+	    YAML_EMIT_MEMBER(out,bias);
-            YAML_EMIT_MEMBER(out,weight);
+	    YAML_EMIT_MEMBER(out,weight);
-            out << YAML::EndMap;
+	    out << YAML::EndMap;
     }
     void load_yaml(const YAML::Node& node) {
-        YAML_LOAD_MEMBER(node, bias);
+	YAML_LOAD_MEMBER(node, bias);
-        YAML_LOAD_MEMBER(node, weight);
+	YAML_LOAD_MEMBER(node, weight);
     }
     #endif
  };
@@ -213,17 +213,17 @@ namespace mlp {
     }
     #ifdef HAVE_LIBYAML_CPP
     friend ostream& operator<<(YAML::Emitter& e, const layer &l) {
-        e << ((std::vector<neuron>)l);
+	e << ((std::vector<neuron>)l);
     }
 
     friend void operator>>(const YAML::Node& n, layer &l) {
-        // These temporary variable shenanegins are necessary because 
+	// These temporary variable shenanegins are necessary because
-        // the compiler gets very confused about which template operator>> 
+	// the compiler gets very confused about which template operator>>
-        // function to use.
+	// function to use.
-        // The following does not work:  n >> l;
+	// The following does not work:  n >> l;
-        // So we use a temporary variable thusly:
+	// So we use a temporary variable thusly:
-        std::vector<mlp::neuron> *obviously_a_vector = &l;
+	std::vector<mlp::neuron> *obviously_a_vector = &l;
-        n >> *obviously_a_vector;
+	n >> *obviously_a_vector;
     }
     #endif
 
@@ -243,7 +243,7 @@ namespace std {
   istream& operator>>(istream& is, mlp::layer& l)
   {
     for (mlp::layer::iterator li = l.begin() ; li != l.end() ; li++) {
-        is >> *li;
+	is >> *li;
     }
     return is;
   }
@@ -277,15 +277,15 @@ namespace mlp {
     #ifdef HAVE_LIBYAML_CPP
     YAML_SERIALIZABLE_AUTO(net)
     void emit_members(YAML::Emitter&out) const {
-        const std::vector<layer>* me_as_layer_vector = this;
+	const std::vector<layer>* me_as_layer_vector = this;
-        out << YAML::Key << "layers" << YAML::Value << *me_as_layer_vector;
+	out << YAML::Key << "layers" << YAML::Value << *me_as_layer_vector;
     }
 
     void load_members(const YAML::Node& node) {
-        std::vector<layer>* me_as_layer_vector = this;
+	std::vector<layer>* me_as_layer_vector = this;
-        node["layers"] >> *me_as_layer_vector;
+	node["layers"] >> *me_as_layer_vector;
     }
-    #endif // HAVE_LIBYAML_CPP  
+    #endif // HAVE_LIBYAML_CPP
 
       /** Virtual destructor */
       virtual ~net() {};
@@ -303,14 +303,14 @@ namespace mlp {
 	   is >> layer_size;
 	   layer_sizes.push_back(layer_size);
 	}
-        unsigned check_outputs;
+	unsigned check_outputs;
 	is >> check_outputs;
 	assert (check_outputs ==  num_outputs);
 	init (num_inputs,num_outputs,layer_sizes);
-        // skip forward to pass up opening '<' char
+	// skip forward to pass up opening '<' char
-        char c=' ';
+	char c=' ';
-        while (c!='<' && !is.eof()) { is >> c;}
+	while (c!='<' && !is.eof()) { is >> c;}
-        for (iterator l =begin() ; l != end(); l++) {
+	for (iterator l =begin() ; l != end(); l++) {
 	    is >> *l;
 	}
 	do { is >> c; } while (c == ' ' && !is.eof());
@@ -351,15 +351,15 @@ namespace mlp {
     }
 
     void save(ostream &os) const {
-        // Save the number of inputs, number of outputs, and number of hidden layers
+	// Save the number of inputs, number of outputs, and number of hidden layers
 	os << num_inputs() << "\n" << num_outputs() << "\n" << num_hidden_layers() << "\n";
-        for(const_iterator l = begin(); l != end(); ++l)
+	for(const_iterator l = begin(); l != end(); ++l)
 	   os << l->size() << " ";
-        os << "\n";
+	os << "\n";
-        os << "< ";
+	os << "< ";
-        for(const_iterator l = begin(); l != end(); ++l)
+	for(const_iterator l = begin(); l != end(); ++l)
 	   os << *l << " ";
-        os << ">\n";
+	os << ">\n";
     }
 
 
@@ -454,7 +454,7 @@ namespace mlp {
 
     void load(istream &is) {
 	unsigned input_size, output_size;
-        is >> input_size >> output_size;
+	is >> input_size >> output_size;
 	sample samp(input_size, output_size);;
 	while (is >> samp) { push_back(samp); }
     }

eo/app/gprop/mse.h

@@ -28,7 +28,7 @@ namespace mse
   //---------------------------------------------------------------------------
   // error
   //---------------------------------------------------------------------------
-  
+
   real error(const mlp::net& net, const set& ts)
   {
     real error_ = 0.0;
@@ -36,7 +36,7 @@ namespace mse
     for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
       {
 	vector out = net(s->input);
-	
+
 	for (unsigned i = 0; i < out.size(); ++i)
 	  {
 	    real diff = s->output[i] - out[i];
@@ -49,26 +49,26 @@ namespace mse
   //-------------------------------------------------------------------------
   // mse
   //-------------------------------------------------------------------------
-  
+
   class net: public qp::net
   {
   public:
     net(mlp::net& n): qp::net(n) {}
-    
+
     real error(const set& ts)
     {
       real error_ = 0;
-      
+
       for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
 	{
 	  forward(s->input);
 	  error_ += backward(s->input, s->output);
 	}
       error_ /= ts.size();
-	
+
       return error_;
     }
-      
+
   private:
     real backward(const vector& input, const vector& output)
     {
@@ -89,22 +89,22 @@ namespace mse
 	  else                                                    // multilayer
 	    for (unsigned k = 0; k < n.dxo.size(); ++k)
 	      n.dxo[k] += n.delta * (*backward_layer)[k].out;
-	  
+
 	  error_ += diff * diff;
 	}
-      
+
       // hidden layers
       while (++current_layer != rend())
 	{
 	  reverse_iterator forward_layer  = current_layer - 1;
 	  reverse_iterator backward_layer = current_layer + 1;
-	  
+
 	  for (unsigned j = 0; j < current_layer->size(); ++j)
 	    {
-	      
+
 	      neuron& n = (*current_layer)[j];
 	      real sum = 0;
-	      
+
 	      for (unsigned k = 0; k < forward_layer->size(); ++k)
 		{
 		  neuron& nf = (*forward_layer)[k];
@@ -113,8 +113,8 @@ namespace mse
 
 	      n.delta = n.out * (1.0 - n.out) * sum;
 	      n.ndelta += n.delta;
-	      
+
-	      
+
 	      if (backward_layer == rend())              // first hidden layer
 		n.dxo += n.delta * input;
 	      else                                     // rest of hidden layers
@@ -122,19 +122,19 @@ namespace mse
 		  n.dxo[k] += n.delta * (*backward_layer)[k].out;
 	    }
 	}
-    
+
       return error_;
     }
   };
 
   //---------------------------------------------------------------------------
-  
+
 } // namespace mse
 
 //-----------------------------------------------------------------------------
 
 #endif // mse_h
 
-// Local Variables: 
+// Local Variables:
-// mode:C++ 
+// mode:C++
 // End:

eo/app/gprop/qp.h

@@ -41,55 +41,55 @@ namespace qp
   const real backtrack_step = 0.5;
   const real me_floor       = 0.0001;
   const real mw_floor       = 0.0001;
-  
+
 
   //---------------------------------------------------------------------------
   // neuron
   //---------------------------------------------------------------------------
-  
+
   struct neuron
   {
     mlp::neuron* n;
     real out, delta, ndelta, dbias1, dbias2;
     vector dweight1, dweight2, dxo;
-    
+
-    neuron(mlp::neuron& _n): 
+    neuron(mlp::neuron& _n):
-      n(&_n), out(0), delta(0), ndelta(0), dbias1(0), dbias2(0), 
+      n(&_n), out(0), delta(0), ndelta(0), dbias1(0), dbias2(0),
-      dweight1(n->weight.size(), 0), 
+      dweight1(n->weight.size(), 0),
-      dweight2(n->weight.size(), 0), 
+      dweight2(n->weight.size(), 0),
       dxo(n->weight.size(), 0) {}
-    
+
     void reset()
     {
       // underlaying neuron
       n->reset();
-      
+
       // addons
       out = delta = ndelta = dbias1 = dbias2 = 0;
       fill(dweight1.begin(), dweight1.end(), 0);
       fill(dweight2.begin(), dweight2.end(), 0);
       fill(dxo.begin(), dxo.end(), 0);
     }
-    
+
     real operator()(const vector& input)
     {
-      return out = mlp::sigmoid(n->bias + dbias1 + 
+      return out = mlp::sigmoid(n->bias + dbias1 +
 				(n->weight + dweight1) * input);
     }
   };
-  
+
   std::ostream& operator<<(std::ostream& os, const neuron& n)
   {
-    return os << *n.n << " " << n.out << " " << n.delta << " " 
+    return os << *n.n << " " << n.out << " " << n.delta << " "
-	      << n.ndelta << " " << n.dbias1 << " " << n.dbias2 << " " 
+	      << n.ndelta << " " << n.dbias1 << " " << n.dbias2 << " "
 	      << n.dweight1 << " " << n.dweight2 << " " << n.dxo;
   }
-  
+
-  
+
   //---------------------------------------------------------------------------
   // layer
   //---------------------------------------------------------------------------
-  
+
   class layer: public std::vector<neuron>
   {
   public:
@@ -102,16 +102,16 @@ namespace qp
     void reset()
     {
       for(iterator n = begin(); n != end(); ++n)
-        n->reset();
+	n->reset();
     }
 
     vector operator()(const vector& input)
     {
       vector output(size());
-      
+
       for(unsigned i = 0; i < output.size(); ++i)
-        output[i] = (*this)[i](input);
+	output[i] = (*this)[i](input);
-      
+
       return output;
     }
   };
@@ -120,10 +120,10 @@ namespace qp
   //---------------------------------------------------------------------------
   // net
   //---------------------------------------------------------------------------
-  
+
   class net: public std::vector<layer>
   {
-  public:  
+  public:
     net(mlp::net& n) //: std::vector<layer>(n.begin(), n.end()) { reset(); }
     {
       for (mlp::net::iterator l = n.begin(); l != n.end(); ++l)
@@ -135,27 +135,27 @@ namespace qp
     void reset()
     {
       for(iterator l = begin(); l != end(); ++l)
-        l->reset();
+	l->reset();
     }
-    
+
-    real train(const set& ts, 
+    real train(const set& ts,
-	       unsigned   epochs, 
+	       unsigned   epochs,
-	       real       target_error, 
+	       real       target_error,
 	       real       tolerance,
-	       real       eta      = eta_default, 
+	       real       eta      = eta_default,
-	       real       momentum = alpha_default, 
+	       real       momentum = alpha_default,
 	       real       lambda   = lambda_default)
     {
       real error_ = max_real;
-      
+
       while (epochs-- && error_ > target_error)
 	{
 	  real last_error = error_;
-	  
+
 	  init_delta();
 
 	  error_ = error(ts);
-	  
+
 	  if (error_ < last_error + tolerance)
 	    {
 	      coeff_adapt(eta, momentum, lambda);
@@ -170,10 +170,10 @@ namespace qp
 	      error_ = last_error;
 	    }
 	}
-      
+
       return error_;
     }
-    
+
     virtual real error(const set& ts) = 0;
 
     // protected:
@@ -185,7 +185,7 @@ namespace qp
 	  input.swap(tmp);
 	}
     }
-     
+
     // private:
     void init_delta()
     {
@@ -193,11 +193,11 @@ namespace qp
 	for (layer::iterator n = l->begin(); n != l->end(); ++n)
 	  fill(n->dxo.begin(), n->dxo.end(), n->ndelta = 0.0);
     }
-    
+
     void coeff_adapt(real& eta, real& momentum, real& lambda)
     {
       real me = 0, mw = 0, ew = 0;
-      
+
       for (iterator l = begin(); l != end(); ++l)
 	for (layer::iterator n = l->begin(); n != l->end(); ++n)
 	  {
@@ -205,7 +205,7 @@ namespace qp
 	    mw += n->dweight1 * n->dweight1;
 	    ew += n->dxo * n->dweight1;
 	  }
-      
+
       me = std::max(static_cast<real>(sqrt(me)), me_floor);
       mw = std::max(static_cast<real>(sqrt(mw)), mw_floor);
       eta *= (1.0 + 0.5 * ew / ( me * mw));
@@ -213,11 +213,11 @@ namespace qp
       lambda = lambda0 * me / mw;
       momentum = eta * lambda;
 #ifdef DEBUG
-      std::cout << me << "  \t" << mw << "  \t" << ew << "  \t" 
+      std::cout << me << "  \t" << mw << "  \t" << ew << "  \t"
 	   << eta << "  \t" << momentum << "  \t" << lambda << std::endl;
 #endif // DEBUG
     }
-    
+
     void weight_update(unsigned size, bool fire, real eta, real momentum)
     {
       for (iterator l = begin(); l != end(); ++l)
@@ -239,13 +239,13 @@ namespace qp
   };
 
   //---------------------------------------------------------------------------
-  
+
 } // namespace qp
 
 //-----------------------------------------------------------------------------
 
 #endif // qp_h
 
-// Local Variables: 
+// Local Variables:
-// mode:C++ 
+// mode:C++
 // End:

eo/app/gprop/vecop.h

@@ -160,14 +160,14 @@ template<class T> std::ostream& operator<<(std::ostream& os, const std::vector<T
     {
       std::copy(v.begin(), v.end() - 1, std::ostream_iterator<T>(os, " "));
       os << v.back();
-    } 
+    }
   return os << '>';
 }
 
 template<class T> std::istream& operator>>(std::istream& is, std::vector<T>& v)
 {
   v.clear();
-  
+
   char c;
   is >> c;
   if (!is || c != '<')
@@ -186,7 +186,7 @@ template<class T> std::istream& operator>>(std::istream& is, std::vector<T>& v)
 	  }
       } while (is && c != '>');
     }
-  
+
   return is;
 }
 
@@ -194,11 +194,11 @@ template<class T> std::istream& operator>>(std::istream& is, std::vector<T>& v)
 // euclidean_distance
 //-----------------------------------------------------------------------------
 
-template<class T> T euclidean_distance(const std::vector<T>& v1, 
+template<class T> T euclidean_distance(const std::vector<T>& v1,
 				       const std::vector<T>& v2)
 {
   T sum = 0, tmp;
-  
+
   for (unsigned i = 0; i < v1.size(); ++i)
     {
       tmp = v1[i] - v2[i];
@@ -211,4 +211,3 @@ template<class T> T euclidean_distance(const std::vector<T>& v1,
 //-----------------------------------------------------------------------------
 
 #endif
-

eo/app/gpsymreg/CMakeLists.txt

@@ -18,8 +18,8 @@ LINK_DIRECTORIES(${EO_BINARY_DIR}/lib)
 SET (GPSYMREG_SOURCES main.cpp)
 
 # no matter what is the OS, hopefully
-ADD_EXECUTABLE(gpsymreg ${GPSYMREG_SOURCES}) 
+ADD_EXECUTABLE(gpsymreg ${GPSYMREG_SOURCES})
-                             
+
 ADD_DEPENDENCIES(gpsymreg eo eoutils)
 
 ######################################################################################
@@ -36,4 +36,3 @@ SET_TARGET_PROPERTIES(gpsymreg PROPERTIES VERSION "${GPSYMREG_VERSION}")
 TARGET_LINK_LIBRARIES(gpsymreg eo eoutils)
 
 ######################################################################################
-

eo/app/gpsymreg/fitness.h

@@ -14,7 +14,7 @@
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
-             jeggermo@liacs.nl
+	     jeggermo@liacs.nl
 */
 
 #ifndef _FITNESS_FUNCTION_H
@@ -225,4 +225,3 @@ class RegFitness: public eoEvalFunc< eoParseTree<FitnessType, Node> >
 };
 
 #endif
-

eo/app/gpsymreg/main.cpp

@@ -30,7 +30,7 @@
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
 
-             jeggermo@liacs.nl
+	     jeggermo@liacs.nl
 
 */
 
@@ -146,25 +146,25 @@ int main(int argc, char *argv[])
 
 	// the parameters are passed on as well
 
-        RegFitness eval(generationCounter, initSequence, parameter);
+	RegFitness eval(generationCounter, initSequence, parameter);
 
 
 
 	// Depth Initializor, set for Ramped Half and Half Initialization
 
-        eoParseTreeDepthInit<FitnessType, Node> initializer(parameter.InitMaxDepth, initSequence, true, true);
+	eoParseTreeDepthInit<FitnessType, Node> initializer(parameter.InitMaxDepth, initSequence, true, true);
 
 
 
 	// create the initial population
 
-        Pop pop(parameter.population_size, initializer);
+	Pop pop(parameter.population_size, initializer);
 
 
 
 	// and evaluate the individuals
 
-        apply<EoType>(eval, pop);
+	apply<EoType>(eval, pop);
 
 
 
@@ -335,10 +335,3 @@ int main(int argc, char *argv[])
 
 
 }
-
-
-
-
-
-
-

eo/app/gpsymreg/node.h

@@ -3,18 +3,18 @@
     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 library 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
     Lesser General Public License for more details.
- 
+
     You should have received a copy of the GNU General Public License
     along with this library; if not, write to the Free Software
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- 
+
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
-             jeggermo@liacs.nl
+	     jeggermo@liacs.nl
 */
 
 #ifndef _NODE_H
@@ -33,13 +33,13 @@ using namespace std;
 /* A new Operation and Node class for even more flexibility.
 
    Improvements over the t-eoSymreg code are:
-   
+
    * No hardcoded functions or operators. The Operation and Node class below
      allow you to specify your own unary and binary functions as well as
      binary operators (like +,-,*,/). Moreover you can detemine if you want
      to allow primitve subroutines with either one or two arguments.
-     
+
-     If a Node has a subroutine Operation it will take evaluate the first 
+     If a Node has a subroutine Operation it will take evaluate the first
      (and possible second) child branch and use them as input variables for
      the remaining second (or third) child branch.
 */
@@ -47,20 +47,20 @@ using namespace std;
 
 typedef enum {Variable, UFunction, BFunction, BOperator, Const} Type;
 
-typedef double (*BinaryFunction)(const double,const double); 
+typedef double (*BinaryFunction)(const double,const double);
 typedef double (*UnaryFunction)(const double);
 
 struct Operation
 {
 	public:
-		
+
 		typedef unsigned int VariableID;
 		typedef string Label;
 
-	
+
 		// if your compiler allows you to have nameless unions you can make this a
 		// union by removing the //'s below
-		
+
 		//union
 		//{
 			UnaryFunction uFunction;
@@ -68,34 +68,34 @@ struct Operation
 			VariableID id;
 			double constant;
 		//};
-	
+
-		
+
-	
+
 		Label label;
 		Type type;
-	
+
 		// the default constructor results in a constant with value 0
 		Operation() : constant(0),  label("0"), type(Const){};
 		// two possible constructors for Unary Functions
 		Operation(UnaryFunction _uf, Label _label): uFunction(_uf), label(_label), type(UFunction) {};
 		Operation(Label _label, UnaryFunction _uf): uFunction(_uf), label(_label), type(UFunction) {};
-		
+
 		// Watch out there are two constructors using pointers two binary functions:
 		// Binary Function (printed as label(subtree0,subtree1)  (e.g. pow(x,y))
 		// Binary Operator (printed as (subtree0 label subtree1) (e.g. x^y)
 		// The difference is purely cosmetic.
-		
+
 		// If you specify the label before the function pointer -> Binary Function
 		Operation(Label _label, BinaryFunction _bf): bFunction(_bf), label(_label), type(BFunction) {};
 		// If you specify the function pointer before the label -> Binary Operator
 		Operation(BinaryFunction _bf, Label _label): bFunction(_bf), label(_label), type(BOperator) {};
-		
+
 		// A constructor for variables
 		Operation(VariableID _id, Label _label): id(_id), label(_label), type(Variable) {};
 		// A constructor for constants
 		Operation(double _constant, Label _label): constant(_constant), label(_label), type(Const) {};
-		
+
-		
+
 		Operation(const Operation &_op)
 		{
 			switch(_op.type)
@@ -110,7 +110,7 @@ struct Operation
 			label = _op.label;
 		};
 		virtual ~Operation(){};
-	
+
 };
 
 
@@ -118,14 +118,14 @@ class Node
 {
 	private:
 		Operation op;
-		
+
 	public:
-	
+
 		Node(void): op(Operation()){};
 		Node(Operation &_op) : op(_op){};
 		virtual ~Node(void) {}
-		
+
-		int arity(void) const 
+		int arity(void) const
 		{
 			switch(op.type)
 			{
@@ -134,53 +134,53 @@ class Node
 				case BFunction: return 2;
 				case BOperator: return 2;
 				case Const: return 0;
-			}			
+			}
-			return 0;	
+			return 0;
 		}
-		
+
 		void randomize(void) {}
-		
+
 		template<class Children>
 		void operator()(double& result, Children args, vector<double> &var) const
 		{
 			double result0;
 			double result1;
-			
+
-			
+
 			switch(op.type)
 			{
 				case Variable:  result = var[op.id%var.size()]; //%var.size() used in the case of Subroutines and as a security measure
 						break;
 				case UFunction: args[0].apply(result0, var);
-						result = op.uFunction(result0); 
+						result = op.uFunction(result0);
 						break;
-				case BFunction: 
+				case BFunction:
 				case BOperator:	args[0].apply(result0, var);
-						args[1].apply(result1, var);	
+						args[1].apply(result1, var);
 						result = op.bFunction(result0,result1);
 						break;
 				case Const:	result = op.constant;
-						break;	
+						break;
-				
+
 			}
-			
+
 		}
-		
+
 		template<class Children>
 		void operator()(string& result, Children args) const
 		{
-			
+
 			string subtree0;
 			string subtree1;
 			string subtree2;
-			
+
 			switch(op.type)
 			{
-				
+
-				case Variable:	
+				case Variable:
 				case Const: 	result += op.label;
 						break;
-					
+
 				case UFunction:	result += op.label;
 						result += "(";
 						args[0].apply(subtree0);
@@ -195,7 +195,7 @@ class Node
 						args[1].apply(subtree1);
 						result += subtree1;
 						result += ")";
-						break;								
+						break;
 				case BOperator: result += "(";
 						args[0].apply(subtree0);
 						result += subtree0;
@@ -204,16 +204,16 @@ class Node
 						result += subtree1;
 						result += ")";
 						break;
-				default: result += "ERROR in Node::operator(string,...) \n"; break;		
+				default: result += "ERROR in Node::operator(string,...) \n"; break;
 			}
 		}
-		
+
 		Operation getOp(void) const {return op;}
-	
+
 };
 
-		
+
-		
+
 
 
 
@@ -230,7 +230,7 @@ class Node
 std::ostream& operator<<(std::ostream& os, const Node& eot)
 {
     Operation op(eot.getOp());
-    
+
     os << (eot.getOp()).label;
     return os;
 }

eo/app/gpsymreg/parameters.h

@@ -3,18 +3,18 @@
     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 library 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
     Lesser General Public License for more details.
- 
+
     You should have received a copy of the GNU General Public License
     along with this library; if not, write to the Free Software
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- 
+
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
-             jeggermo@liacs.nl
+	     jeggermo@liacs.nl
 */
 
 #ifndef _PARAMETERS_FUNCTION_H
@@ -28,7 +28,7 @@ using namespace std;
 
 struct Parameters{
 			unsigned int nGenerations;	// -G
-			unsigned population_size;	// -P	
+			unsigned population_size;	// -P
 			unsigned offspring_size;	// -O
 			unsigned int MaxSize;		// -S
 			unsigned int InitMaxDepth;      // -D
@@ -41,72 +41,72 @@ struct Parameters{
 			Parameters(int argc, char **argv)
 			{
 				eoParser parser(argc,argv);
-			
+
 				// generations
 				eoValueParam<unsigned int> paramGenerations(1, "generations", "Generations", 'G', false);
 				parser.processParam( paramGenerations );
 				nGenerations = paramGenerations.value();
 				cerr << "nGenerations= " << nGenerations << endl;
-	
+
 				// populationsize
 				eoValueParam<unsigned int> paramPopulationSize(10, "populationsize", "PopulationSize", 'P', false);
 				parser.processParam( paramPopulationSize );
 				population_size = paramPopulationSize.value();
 				cerr << "population_size= " << population_size << endl;
-	
+
 				// offspringsize
 				eoValueParam<unsigned int> paramOffspringSize(population_size, "offspringsize", "OffspringSize", 'O', false);
 				parser.processParam( paramOffspringSize );
 				offspring_size = paramOffspringSize.value();
 				cerr << "offspring_size= " << offspring_size << endl;
-	
+
 				// maxsize
 				eoValueParam<unsigned int> paramMaxSize(15, "maxsize", "MaxSize", 'S', false);
 				parser.processParam( paramMaxSize );
 				MaxSize = paramMaxSize.value();
 				cerr << "MaxSize= " << MaxSize << endl;
-	
+
 				// initialmaxdepth
 				eoValueParam<unsigned int> paramInitialMaxDepth(4, "initialmaxdepth", "InitialMaxDepth", 'D', false);
 				parser.processParam( paramInitialMaxDepth );
 				InitMaxDepth = paramInitialMaxDepth.value();
 				cerr << "InitMaxDepth= " << InitMaxDepth << endl;
-			
+
 				// randomseed
 				eoValueParam<unsigned int> paramRandomSeed(1, "randomseed", "Random Seed", 'R', false);
 				parser.processParam( paramRandomSeed );
 				randomseed = paramRandomSeed.value();
 				cerr << "randomseed= " << randomseed << endl;
-	
+
-				
+
 				// crossover-rate
 				eoValueParam<double> paramXover(0.75, "crossoverrate", "crossover rate", 'x', false);
 				parser.processParam(paramXover );
 				xover_rate = paramXover.value();
 				cerr << "xover_rate= " << xover_rate << endl;
-	
+
 				//mutation-rate
 				eoValueParam<double> paramMutation(0.25, "mutationrate", "mutation rate", 'm', false);
 				parser.processParam(paramMutation );
 				mutation_rate = paramMutation.value();
 				cerr << "mutation_rate= " << mutation_rate << endl;
-				
+
 				//tournament size
 				eoValueParam<unsigned int > paramTournamentSize(5, "tournamentsize", "tournament size", 't', false);
 				parser.processParam(paramTournamentSize );
 				tournamentsize = paramTournamentSize.value();
 				cerr << "Tournament Size= " << tournamentsize << endl;
-				
+
-	
+
 				if (parser.userNeedsHelp())
 			      	{
-			        	parser.printHelp(cout);
+					parser.printHelp(cout);
-			        	exit(1);
+					exit(1);
 			      	}
 
 			};
-			
+
 			~Parameters(){};
-};			
+};
 
 #endif

eo/app/mastermind/CMakeLists.txt

@@ -18,8 +18,8 @@ LINK_DIRECTORIES(${EO_BINARY_DIR}/lib)
 SET (MASTERMIND_SOURCES mastermind.cpp)
 
 # no matter what is the OS, hopefully
-ADD_EXECUTABLE(mastermind ${MASTERMIND_SOURCES}) 
+ADD_EXECUTABLE(mastermind ${MASTERMIND_SOURCES})
-                             
+
 ADD_DEPENDENCIES(mastermind eo eoutils)
 
 ######################################################################################
@@ -36,4 +36,3 @@ SET_TARGET_PROPERTIES(mastermind PROPERTIES VERSION "${MASTERMIND_VERSION}")
 TARGET_LINK_LIBRARIES(mastermind eo eoutils)
 
 ######################################################################################
-

eo/app/mastermind/mastermind.cpp

@@ -51,8 +51,8 @@ int main(int argc, char** argv)
     }
   catch (exception& e)
     {
-        cerr << argv[0] << ": " << e.what() << endl;
+	cerr << argv[0] << ": " << e.what() << endl;
-        exit(EXIT_FAILURE);
+	exit(EXIT_FAILURE);
     }
 
   return 0;

eo/config.guess

@@ -3,7 +3,7 @@
 #   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
 #   2000, 2001, 2002, 2003 Free Software Foundation, Inc.
 
-timestamp='2004-03-03'
+timestamp='2011-05-05'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -186,7 +186,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 		fi
 		;;
 	    *)
-	        os=netbsd
+		os=netbsd
 		;;
 	esac
 	# The OS release
@@ -270,7 +270,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
 		;;
 	*5.*)
-	        UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
 		;;
 	esac
 	# According to Compaq, /usr/sbin/psrinfo has been available on
@@ -342,7 +342,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 	echo i370-ibm-openedition
 	exit 0 ;;
     *:OS400:*:*)
-        echo powerpc-ibm-os400
+	echo powerpc-ibm-os400
 	exit 0 ;;
     arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
 	echo arm-acorn-riscix${UNAME_RELEASE}
@@ -419,23 +419,23 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
     # MiNT.  But MiNT is downward compatible to TOS, so this should
     # be no problem.
     atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
+	echo m68k-atari-mint${UNAME_RELEASE}
 	exit 0 ;;
     atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
 	echo m68k-atari-mint${UNAME_RELEASE}
-        exit 0 ;;
+	exit 0 ;;
     *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
+	echo m68k-atari-mint${UNAME_RELEASE}
 	exit 0 ;;
     milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
-        echo m68k-milan-mint${UNAME_RELEASE}
+	echo m68k-milan-mint${UNAME_RELEASE}
-        exit 0 ;;
+	exit 0 ;;
     hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
-        echo m68k-hades-mint${UNAME_RELEASE}
+	echo m68k-hades-mint${UNAME_RELEASE}
-        exit 0 ;;
+	exit 0 ;;
     *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
-        echo m68k-unknown-mint${UNAME_RELEASE}
+	echo m68k-unknown-mint${UNAME_RELEASE}
-        exit 0 ;;
+	exit 0 ;;
     m68k:machten:*:*)
 	echo m68k-apple-machten${UNAME_RELEASE}
 	exit 0 ;;
@@ -504,8 +504,8 @@ EOF
 	echo m88k-motorola-sysv3
 	exit 0 ;;
     AViiON:dgux:*:*)
-        # DG/UX returns AViiON for all architectures
+	# DG/UX returns AViiON for all architectures
-        UNAME_PROCESSOR=`/usr/bin/uname -p`
+	UNAME_PROCESSOR=`/usr/bin/uname -p`
 	if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
 	then
 	    if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
@@ -614,52 +614,52 @@ EOF
 	    9000/[678][0-9][0-9])
 		if [ -x /usr/bin/getconf ]; then
 		    sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
-                    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+		    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
-                    case "${sc_cpu_version}" in
+		    case "${sc_cpu_version}" in
-                      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+		      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
-                      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+		      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
-                      532)                      # CPU_PA_RISC2_0
+		      532)                      # CPU_PA_RISC2_0
-                        case "${sc_kernel_bits}" in
+			case "${sc_kernel_bits}" in
-                          32) HP_ARCH="hppa2.0n" ;;
+			  32) HP_ARCH="hppa2.0n" ;;
-                          64) HP_ARCH="hppa2.0w" ;;
+			  64) HP_ARCH="hppa2.0w" ;;
 			  '') HP_ARCH="hppa2.0" ;;   # HP-UX 10.20
-                        esac ;;
+			esac ;;
-                    esac
+		    esac
 		fi
 		if [ "${HP_ARCH}" = "" ]; then
 		    eval $set_cc_for_build
 		    sed 's/^              //' << EOF >$dummy.c
 
-              #define _HPUX_SOURCE
+	      #define _HPUX_SOURCE
-              #include <stdlib.h>
+	      #include <stdlib.h>
-              #include <unistd.h>
+	      #include <unistd.h>
 
-              int main ()
+	      int main ()
-              {
+	      {
-              #if defined(_SC_KERNEL_BITS)
+	      #if defined(_SC_KERNEL_BITS)
-                  long bits = sysconf(_SC_KERNEL_BITS);
+		  long bits = sysconf(_SC_KERNEL_BITS);
-              #endif
+	      #endif
-                  long cpu  = sysconf (_SC_CPU_VERSION);
+		  long cpu  = sysconf (_SC_CPU_VERSION);
 
-                  switch (cpu)
+		  switch (cpu)
-              	{
+		{
-              	case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+		case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
-              	case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+		case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
-              	case CPU_PA_RISC2_0:
+		case CPU_PA_RISC2_0:
-              #if defined(_SC_KERNEL_BITS)
+	      #if defined(_SC_KERNEL_BITS)
-              	    switch (bits)
+		    switch (bits)
-              		{
+			{
-              		case 64: puts ("hppa2.0w"); break;
+			case 64: puts ("hppa2.0w"); break;
-              		case 32: puts ("hppa2.0n"); break;
+			case 32: puts ("hppa2.0n"); break;
-              		default: puts ("hppa2.0"); break;
+			default: puts ("hppa2.0"); break;
-              		} break;
+			} break;
-              #else  /* !defined(_SC_KERNEL_BITS) */
+	      #else  /* !defined(_SC_KERNEL_BITS) */
-              	    puts ("hppa2.0"); break;
+		    puts ("hppa2.0"); break;
-              #endif
+	      #endif
-              	default: puts ("hppa1.0"); break;
+		default: puts ("hppa1.0"); break;
-              	}
+		}
-                  exit (0);
+		  exit (0);
-              }
+	      }
 EOF
 		    (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
 		    test -z "$HP_ARCH" && HP_ARCH=hppa
@@ -739,22 +739,22 @@ EOF
 	exit 0 ;;
     C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
 	echo c1-convex-bsd
-        exit 0 ;;
+	exit 0 ;;
     C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
 	if getsysinfo -f scalar_acc
 	then echo c32-convex-bsd
 	else echo c2-convex-bsd
 	fi
-        exit 0 ;;
+	exit 0 ;;
     C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
 	echo c34-convex-bsd
-        exit 0 ;;
+	exit 0 ;;
     C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
 	echo c38-convex-bsd
-        exit 0 ;;
+	exit 0 ;;
     C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
 	echo c4-convex-bsd
-        exit 0 ;;
+	exit 0 ;;
     CRAY*Y-MP:*:*:*)
 	echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
 	exit 0 ;;
@@ -778,14 +778,14 @@ EOF
 	exit 0 ;;
     F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
 	FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+	FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
-        echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+	echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-        exit 0 ;;
+	exit 0 ;;
     5000:UNIX_System_V:4.*:*)
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+	FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
-        echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+	echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
 	exit 0 ;;
     i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
 	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
@@ -919,7 +919,7 @@ EOF
 	  EV6)   UNAME_MACHINE=alphaev6 ;;
 	  EV67)  UNAME_MACHINE=alphaev67 ;;
 	  EV68*) UNAME_MACHINE=alphaev68 ;;
-        esac
+	esac
 	objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
 	if test "$?" = 0 ; then LIBC="-libc1" ; else LIBC="" ; fi
 	echo ${UNAME_MACHINE}-${VENDOR}-linux${LIBC}
@@ -961,7 +961,7 @@ EOF
 				    s/.*supported targets: *//
 				    s/ .*//
 				    p'`
-        case "$ld_supported_targets" in
+	case "$ld_supported_targets" in
 	  elf32-i386)
 		TENTATIVE="${UNAME_MACHINE}-${VENDOR}-linux"
 		;;
@@ -1013,11 +1013,11 @@ EOF
 	echo i386-sequent-sysv4
 	exit 0 ;;
     i*86:UNIX_SV:4.2MP:2.*)
-        # Unixware is an offshoot of SVR4, but it has its own version
+	# Unixware is an offshoot of SVR4, but it has its own version
-        # number series starting with 2...
+	# number series starting with 2...
-        # I am not positive that other SVR4 systems won't match this,
+	# I am not positive that other SVR4 systems won't match this,
 	# I just have to hope.  -- rms.
-        # Use sysv4.2uw... so that sysv4* matches it.
+	# Use sysv4.2uw... so that sysv4* matches it.
 	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
 	exit 0 ;;
     i*86:OS/2:*:*)
@@ -1076,10 +1076,10 @@ EOF
 	exit 0 ;;
     pc:*:*:*)
 	# Left here for compatibility:
-        # uname -m prints for DJGPP always 'pc', but it prints nothing about
+	# uname -m prints for DJGPP always 'pc', but it prints nothing about
-        # the processor, so we play safe by assuming i386.
+	# the processor, so we play safe by assuming i386.
 	echo i386-pc-msdosdjgpp
-        exit 0 ;;
+	exit 0 ;;
     Intel:Mach:3*:*)
 	echo i386-pc-mach3
 	exit 0 ;;
@@ -1114,8 +1114,8 @@ EOF
 	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
 	  && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;;
     3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
-        /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-          && echo i486-ncr-sysv4 && exit 0 ;;
+	  && echo i486-ncr-sysv4 && exit 0 ;;
     m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
 	echo m68k-unknown-lynxos${UNAME_RELEASE}
 	exit 0 ;;
@@ -1149,9 +1149,9 @@ EOF
 	fi
 	exit 0 ;;
     PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
-                      # says <Richard.M.Bartel@ccMail.Census.GOV>
+		      # says <Richard.M.Bartel@ccMail.Census.GOV>
-        echo i586-unisys-sysv4
+	echo i586-unisys-sysv4
-        exit 0 ;;
+	exit 0 ;;
     *:UNIX_System_V:4*:FTX*)
 	# From Gerald Hewes <hewes@openmarket.com>.
 	# How about differentiating between stratus architectures? -djm
@@ -1173,11 +1173,11 @@ EOF
 	exit 0 ;;
     R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
 	if [ -d /usr/nec ]; then
-	        echo mips-nec-sysv${UNAME_RELEASE}
+		echo mips-nec-sysv${UNAME_RELEASE}
 	else
-	        echo mips-unknown-sysv${UNAME_RELEASE}
+		echo mips-unknown-sysv${UNAME_RELEASE}
 	fi
-        exit 0 ;;
+	exit 0 ;;
     BeBox:BeOS:*:*)	# BeOS running on hardware made by Be, PPC only.
 	echo powerpc-be-beos
 	exit 0 ;;
@@ -1262,7 +1262,7 @@ EOF
 	echo pdp10-unknown-its
 	exit 0 ;;
     SEI:*:*:SEIUX)
-        echo mips-sei-seiux${UNAME_RELEASE}
+	echo mips-sei-seiux${UNAME_RELEASE}
 	exit 0 ;;
     *:DragonFly:*:*)
 	echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
@@ -1289,11 +1289,11 @@ main ()
 #include <sys/param.h>
   printf ("m68k-sony-newsos%s\n",
 #ifdef NEWSOS4
-          "4"
+	  "4"
 #else
 	  ""
 #endif
-         ); exit (0);
+	 ); exit (0);
 #endif
 #endif
 

eo/config.h.cmake

@@ -71,5 +71,3 @@
 
 /* Define to `unsigned int' if <sys/types.h> does not define. */
 #cmakedefine size_t
-
-

eo/contrib/MGE/eoInitVirus.h

@@ -19,8 +19,8 @@
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
-             Marc.Schoenauer@polytechnique.fr
+	     Marc.Schoenauer@polytechnique.fr
-             mak@dhi.dk
+	     mak@dhi.dk
  */
 //-----------------------------------------------------------------------------
 
@@ -43,7 +43,7 @@ public:
 
   eoInitVirus(unsigned _combien, eoRndGenerator<bool>& _generator )
 	: combien(_combien), generator(_generator) {}
-  
+
   virtual void operator()( eoVirus<FitT>& chrom)
   {
 	chrom.resize(combien);
@@ -54,7 +54,7 @@ public:
 	}
 	chrom.invalidate();
   }
-  
+
 private :
   unsigned combien;
   /// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics
@@ -68,7 +68,7 @@ public:
 
   eoInitVirus1bit(unsigned _combien, eoRndGenerator<bool>& _generator )
 	: combien(_combien), generator(_generator) {}
-  
+
   virtual void operator()( eoVirus<FitT>& chrom)
   {
 	chrom.resize(combien);
@@ -77,7 +77,7 @@ public:
 	chrom.virusBitSet(0, true );
 	chrom.invalidate();
   }
-  
+
 private :
   unsigned combien;
   /// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics

eo/contrib/boost/config.hpp

@@ -1,8 +1,8 @@
 //  Boost config.hpp configuration header file  ------------------------------//
 
-//  (C) Copyright John Maddock 2002. 
+//  (C) Copyright John Maddock 2002.
-//  Use, modification and distribution are subject to the 
+//  Use, modification and distribution are subject to the
-//  Boost Software License, Version 1.0. (See accompanying file 
+//  Boost Software License, Version 1.0. (See accompanying file
 //  LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 
 //  See http://www.boost.org/libs/config for most recent version.
@@ -57,14 +57,3 @@
 #include <boost/config/suffix.hpp>
 
 #endif  // BOOST_CONFIG_HPP
-
-
-
-
-
-
-
-
-
-
-

eo/contrib/boost/config/abi_prefix.hpp

@@ -1,7 +1,7 @@
 //  abi_prefix header  -------------------------------------------------------//
 
 // © Copyright John Maddock 2003
-   
+
 // Use, modification and distribution are subject to the Boost Software License,
 // Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
 // http://www.boost.org/LICENSE_1_0.txt).

eo/contrib/boost/config/abi_suffix.hpp

@@ -1,7 +1,7 @@
 //  abi_sufffix header  -------------------------------------------------------//
 
 // © Copyright John Maddock 2003
-   
+
 // Use, modification and distribution are subject to the Boost Software License,
 // Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
 // http://www.boost.org/LICENSE_1_0.txt).
@@ -19,5 +19,3 @@
 #ifdef BOOST_HAS_ABI_HEADERS
 #  include BOOST_ABI_SUFFIX
 #endif
-
-

eo/contrib/boost/config/auto_link.hpp

@@ -18,13 +18,13 @@ USAGE:
 Before including this header you must define one or more of define the following macros:
 
 BOOST_LIB_NAME:           Required: A string containing the basename of the library,
-                          for example boost_regex.
+			  for example boost_regex.
 BOOST_LIB_TOOLSET:        Optional: the base name of the toolset.
 BOOST_DYN_LINK:           Optional: when set link to dll rather than static library.
 BOOST_LIB_DIAGNOSTIC:     Optional: when set the header will print out the name
-                          of the library selected (useful for debugging).
+			  of the library selected (useful for debugging).
 BOOST_AUTO_LINK_NOMANGLE: Specifies that we should link to BOOST_LIB_NAME.lib,
-                          rather than a mangled-name version.
+			  rather than a mangled-name version.
 
 These macros will be undef'ed at the end of the header, further this header
 has no include guards - so be sure to include it only once from your library!
@@ -56,13 +56,13 @@ BOOST_LIB_TOOLSET:    The compiler toolset name (vc6, vc7, bcb5 etc).
 BOOST_LIB_THREAD_OPT: "-mt" for multithread builds, otherwise nothing.
 
 BOOST_LIB_RT_OPT:     A suffix that indicates the runtime library used,
-                      contains one or more of the following letters after
+		      contains one or more of the following letters after
-                      a hiphen:
+		      a hiphen:
 
-                      s      static runtime (dynamic if not present).
+		      s      static runtime (dynamic if not present).
-                      d      debug build (release if not present).
+		      d      debug build (release if not present).
-                      g      debug/diagnostic runtime (release if not present).
+		      g      debug/diagnostic runtime (release if not present).
-                      p      STLPort Build.
+		      p      STLPort Build.
 
 BOOST_LIB_VERSION:    The Boost version, in the form x_y, for Boost version x.y.
 
@@ -342,13 +342,3 @@ BOOST_LIB_VERSION:    The Boost version, in the form x_y, for Boost version x.y.
 #if defined(BOOST_AUTO_LINK_NOMANGLE)
 #  undef BOOST_AUTO_LINK_NOMANGLE
 #endif
-
-
-
-
-
-
-
-
-
-

eo/contrib/boost/limits.hpp

@@ -1,5 +1,4 @@
-
+//  (C) Copyright John maddock 1999.
-//  (C) Copyright John maddock 1999. 
 //  (C) David Abrahams 2002.  Distributed under the Boost
 //  Software License, Version 1.0. (See accompanying file
 //  LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
@@ -33,7 +32,7 @@
 namespace std
 {
   template<>
-  class numeric_limits<BOOST_LLT> 
+  class numeric_limits<BOOST_LLT>
   {
    public:
 
@@ -82,11 +81,11 @@ namespace std
       BOOST_STATIC_CONSTANT(bool, traps = false);
       BOOST_STATIC_CONSTANT(bool, tinyness_before = false);
       BOOST_STATIC_CONSTANT(float_round_style, round_style = round_toward_zero);
-      
+
   };
 
   template<>
-  class numeric_limits<BOOST_ULLT> 
+  class numeric_limits<BOOST_ULLT>
   {
    public:
 
@@ -135,9 +134,9 @@ namespace std
       BOOST_STATIC_CONSTANT(bool, traps = false);
       BOOST_STATIC_CONSTANT(bool, tinyness_before = false);
       BOOST_STATIC_CONSTANT(float_round_style, round_style = round_toward_zero);
-      
+
   };
 }
-#endif 
+#endif
 
 #endif

eo/contrib/eoAged.h

@@ -4,7 +4,7 @@
 //-----------------------------------------------------------------------------
 // eoAge.h
 // (c) GeNeura Team, 1998
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either
@@ -38,7 +38,7 @@ using namespace std;
 //-----------------------------------------------------------------------------
 
 /** eoAge is a template class that adds an age to an object.\\
-Requisites for template instantiation are that the object must admit a default ctor 
+Requisites for template instantiation are that the object must admit a default ctor
 and a copy ctor. The Object must be an eoObject, thus, it must have its methods: className,
 printOn, readFrom.
 @see eoObject
@@ -55,7 +55,7 @@ class eoAged: public Object
 
   /// Virtual dtor. They are needed in virtual class hierarchies
   virtual ~eoAged() {};
-  
+
 
   ///returns the age of the object
   unsigned long Age() const {return age;}
@@ -67,7 +67,7 @@ class eoAged: public Object
 	readFrom and printOn are directly inherited from eo1d
 	*/
 //@{
-  /** Return the class id. This should be redefined in each class; but 
+  /** Return the class id. This should be redefined in each class; but
   it's got code as an example of implementation. Only "leaf" classes
   can be non-virtual.
   */
@@ -83,7 +83,7 @@ class eoAged: public Object
 	  _is >> age;
   }
 
-  
+
   /**
    * Write object. It's called printOn since it prints the object _on_ a stream.
    * @param _os A ostream.
@@ -93,7 +93,7 @@ class eoAged: public Object
 	  _os << age;
   }
 //@}
-  
+
  private:
 
 	 /** Default Constructor. \\
@@ -106,4 +106,3 @@ class eoAged: public Object
 };
 
 #endif EOAGE_H
-

eo/contrib/eoDrawable.h

@@ -1,9 +1,9 @@
-// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-
+
 //-----------------------------------------------------------------------------
-// eoDrawable.h
+// eoDrawable.h
 // (c) GeNeura Team, 1999
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either
@@ -27,38 +27,38 @@
 
 //-----------------------------------------------------------------------------
 
-using namespace std;
+using namespace std;
 
 //-----------------------------------------------------------------------------
 // eoDrawable
 //-----------------------------------------------------------------------------
-
+
-/** eoDrawable is a template class that adds a drawing interface to an object.\\
+/** eoDrawable is a template class that adds a drawing interface to an object.
-Requisites for template instantiation are that the object must admit a default ctor 
+Requisites for template instantiation are that the object must admit a default ctor
-and a copy ctor. The Object must be an eoObject, thus, it must have its methods: className,
+and a copy ctor. The Object must be an eoObject, thus, it must have its methods: className,
-eoDrawables can be drawn on any two-dimensional surface; it can be added to any
+eoDrawables can be drawn on any two-dimensional surface; it can be added to any
-object with above characteristics.
+object with above characteristics.
-@see eoObject
+@see eoObject
-*/
+*/
 template <class Object>
 class eoDrawable
 {
  public:
-	/// Main ctor from an already built Object.
+	/// Main ctor from an already built Object.
-	eoDrawable( const Object& _o): Object( _o ){};
+	eoDrawable( const Object& _o): Object( _o ){};
 
 	/// Copy constructor.
-	eoDrawable( const eoDrawable& _d): Object( _d ){};
+	eoDrawable( const eoDrawable& _d): Object( _d ){};
-
-  /// Virtual dtor. They are needed in virtual class hierarchies
-  virtual ~eoDrawable() {};
-  
-
-  /**Draws the object. It must be redefined in any subclass, it´s impossible
-  to have a general drawing method
-  @param _x, _y coorinates */
-  virtual void draw( unsigned _x, unsigned _y) = 0;
-  	
-};
 
-#endif EODRAWABLE_H
+  /// Virtual dtor. They are needed in virtual class hierarchies
+  virtual ~eoDrawable() {};
+
+
+  /**Draws the object. It must be redefined in any subclass, it´s impossible
+  to have a general drawing method
+  @param _x, _y coorinates */
+  virtual void draw( unsigned _x, unsigned _y) = 0;
+
+};
+
+#endif //! EODRAWABLE_H

eo/install_symlink.py.cmake

@@ -9,9 +9,9 @@ PREFIX  = "/usr"
 DATA = {
     'dirs': [ "%s/share/%s" % (PREFIX, NAME) ],
     'links': [ ("%s/src" % SOURCE, "%s/include/%s" % (PREFIX, NAME)),
-               ("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
+	       ("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
-               ("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
+	       ("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
-               ]
+	       ]
     }
 
 LIBRARIES = ["libcma.a", "libeo.a", "libeoutils.a", "libes.a", "libga.a"]
@@ -21,8 +21,8 @@ import os, sys
 
 def isroot():
     if os.getuid() != 0:
-        print '[WARNING] you have to be root'
+	print '[WARNING] you have to be root'
-        return False
+	return False
     return True
 
 def uninstall():
@@ -41,11 +41,11 @@ def data():
 
 if __name__ == '__main__':
     if not isroot():
-        sys.exit()
+	sys.exit()
 
     if len(sys.argv) < 2:
-        print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
+	print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
-        sys.exit()
+	sys.exit()
 
     if sys.argv[1] == 'install': install()
     elif sys.argv[1] == 'uninstall': uninstall()

eo/src/CMakeLists.txt

@@ -11,14 +11,15 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
 SET(EO_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib)
 SET(LIBRARY_OUTPUT_PATH ${EO_LIB_OUTPUT_PATH})
 
-SET (EO_SOURCES     eoFunctorStore.cpp 
+SET(EO_SOURCES
-					eoPersistent.cpp 
+  eoFunctorStore.cpp
-					eoPrintable.cpp 
+  eoPersistent.cpp
-					eoCtrlCContinue.cpp 
+  eoPrintable.cpp
-					eoScalarFitnessAssembled.cpp
+  eoCtrlCContinue.cpp
-					eoSIGContinue.cpp)
+  eoScalarFitnessAssembled.cpp
+  eoSIGContinue.cpp
+  )
 
- 
 ADD_LIBRARY(eo STATIC ${EO_SOURCES})
 INSTALL(TARGETS eo ARCHIVE DESTINATION lib COMPONENT libraries)
 
@@ -42,6 +43,6 @@ ADD_SUBDIRECTORY(ga)
 ADD_SUBDIRECTORY(gp)
 ADD_SUBDIRECTORY(other)
 ADD_SUBDIRECTORY(utils)
+ADD_SUBDIRECTORY(pyeo)
 
 ######################################################################################
-

eo/src/EO.h

@@ -40,17 +40,17 @@
  */
 
 /** EO is the base class for objects with a fitness.
- 
+
     Those evolvable objects are the subjects of
     evolution. EOs have only got a fitness, which at the same time needs to be
     only an object with the operation less than (<) defined. Fitness says how
     good is the object; evolution or change of these objects is left to the
-    genetic operators. 
+    genetic operators.
-    
+
     A fitness less than another means a worse fitness, in
     whatever the context; thus, fitness is always maximized; although it can
-    be minimized with a proper definition of the < operator. 
+    be minimized with a proper definition of the < operator.
-    
+
     A fitness can be invalid if undefined, trying to read an invalid fitness will raise an error.
     @ref Operators that effectively modify EO objects must invalidate them.
 
@@ -123,23 +123,23 @@ public:
    * @throw runtime_std::exception If a valid object can't be read.
    */
   virtual void readFrom(std::istream& _is) {
-     
+
         // the new version of the reafFrom function.
-        // It can distinguish between valid and invalid fitness values. 
+        // It can distinguish between valid and invalid fitness values.
         std::string fitness_str;
         int pos = _is.tellg();
-	_is >> fitness_str;
+        _is >> fitness_str;
 
-	if (fitness_str == "INVALID")
+        if (fitness_str == "INVALID")
-	{
+        {
-		invalidFitness = true;
+                invalidFitness = true;
-	}
+        }
-	else
+        else
-	{
+        {
-		invalidFitness = false;
+                invalidFitness = false;
-		_is.seekg(pos); // rewind
+                _is.seekg(pos); // rewind
-		_is >> repFitness;
+                _is >> repFitness;
-	}
+        }
   }
 
   /**
@@ -151,13 +151,13 @@ public:
 
     // the latest version of the code. Very similar to the old code
     if (invalid()) {
-  	_os << "INVALID ";
+        _os << "INVALID ";
     }
     else
     {
- 	_os << repFitness << ' ';
+        _os << repFitness << ' ';
     }
-	      
+
   }
 
   //@}
@@ -171,4 +171,3 @@ private:
 #endif
 
 /** @} */
-

eo/src/PO.h

@@ -1,5 +1,5 @@
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
- 
+
 //-----------------------------------------------------------------------------
 // PO.h
 // (c) OPAC 2007
@@ -43,11 +43,11 @@ template < class F > class PO:public EO < F >
 
 public:
 
-	#if defined(__CUDACC__)
+        #if defined(__CUDACC__)
-		typedef typename EO < F >::Fitness Fitness;
+                typedef typename EO < F >::Fitness Fitness;
-	#else
+        #else
-		typedef typename PO<F>::Fitness Fitness;
+                typedef typename PO<F>::Fitness Fitness;
-	#endif
+        #endif
 
     /** Default constructor.
         Fitness must have a ctor which takes 0 as a value. Best fitness mush also have the same constructor.

eo/src/apply.h

@@ -26,8 +26,12 @@
 #ifndef _apply_h
 #define _apply_h
 
+#include <utils/eoParallel.h>
+#include <utils/eoParser.h>
+#include <utils/eoLogger.h>
 #include <eoFunctor.h>
 #include <vector>
+#include <omp.h>
 
 /**
   Applies a unary function to a std::vector of things.
@@ -37,7 +41,76 @@
 template <class EOT>
 void apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
 {
-    for (unsigned i = 0; i < _pop.size(); ++i)
+    size_t size = _pop.size();
+
+#ifdef _OPENMP
+
+    double t1 = 0;
+
+    if ( eo::parallel.enableResults() )
+	{
+	    t1 = omp_get_wtime();
+	}
+
+    if (!eo::parallel.isDynamic())
+	{
+#pragma omp parallel for if(eo::parallel.isEnabled()) //default(none) shared(_proc, _pop, size)
+	    for (size_t i = 0; i < size; ++i) { _proc(_pop[i]); }
+	}
+    else
+	{
+#pragma omp parallel for schedule(dynamic) if(eo::parallel.isEnabled())
+	    //doesnot work with gcc 4.1.2
+	    //default(none) shared(_proc, _pop, size)
+	    for (size_t i = 0; i < size; ++i) { _proc(_pop[i]); }
+	}
+
+    if ( eo::parallel.enableResults() )
+	{
+	    double t2 = omp_get_wtime();
+	    eoLogger log;
+	    log << eo::file(eo::parallel.prefix()) << t2 - t1 << ' ';
+	}
+
+#else // _OPENMP
+
+    for (size_t i = 0; i < size; ++i) { _proc(_pop[i]); }
+
+#endif // !_OPENMP
+}
+
+/**
+  This is a variant of apply<EOT> which is called in parallel
+  thanks to OpenMP.
+
+  @ingroup Utilities
+*/
+template <class EOT>
+void omp_apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
+{
+    size_t size = _pop.size();
+#pragma omp parallel for if(eo::parallel.isEnabled())
+    //doesnot work with gcc 4.1.2
+    //default(none) shared(_proc, _pop, size)
+    for (size_t i = 0; i < size; ++i)
+    {
+        _proc(_pop[i]);
+    }
+}
+
+/**
+  And now we are using the dynamic scheduling.
+
+  @ingroup Utilities
+*/
+template <class EOT>
+void omp_dynamic_apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
+{
+    size_t size = _pop.size();
+#pragma omp parallel for if(eo::parallel.isEnabled()) schedule(dynamic)
+    //doesnot work with gcc 4.1.2
+    //default(none) shared(_proc, _pop, size)
+    for (size_t i = 0; i < size; ++i)
     {
         _proc(_pop[i]);
     }

eo/src/do/Readme

@@ -9,11 +9,11 @@ the functions here for eoBit<double> AND eoBit<eoMinimizingFitness>
 and in EO test dir the t-eoGA.cpp file that is a sample program that uses
 the whole facility.
 
-All make_XXX.h file define some parser-based constructions of basic 
+All make_XXX.h file define some parser-based constructions of basic
 Evolutionary Algorithms components, using state-based memory management
 (see in src/utils dir, or read the tutorial).
 
-In this src/do dir, the following ***representation indedendent*** code 
+In this src/do dir, the following ***representation indedendent*** code
 is defined
 
 make_algo_scalar.h     The selection/replacement for scalar fitnesses
@@ -23,7 +23,7 @@ make_pop.h             Init of the population (from an EOT initializer)
 make_run.h             Run the algorithm
 
 See also (NOW MOVED TO util DIR, as it was useful everywhere)
-make_help.cpp          Help on demand (+ status file) 
+make_help.cpp          Help on demand (+ status file)
 
 Note:
 -----

eo/src/do/make_algo_easea.h

@@ -3,7 +3,7 @@
 //-----------------------------------------------------------------------------
 // make_algo_easea.h
 // (c) Marc Schoenauer and Pierre Collet, 2002
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either
@@ -81,18 +81,18 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   eoParamParamType & ppSelect = selectionParam.value(); // std::pair<std::string,std::vector<std::string> >
 
   eoSelectOne<EOT>* select ;
-  if (ppSelect.first == std::string("DetTour")) 
+  if (ppSelect.first == std::string("DetTour"))
   {
     unsigned detSize;
 
     if (!ppSelect.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
+        std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
-	detSize = 2;
+        detSize = 2;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	ppSelect.second.push_back(std::string("2"));
+        ppSelect.second.push_back(std::string("2"));
       }
-    else	  // parameter passed by user as DetTour(T)
+    else          // parameter passed by user as DetTour(T)
       detSize = atoi(ppSelect.second[0].c_str());
     select = new eoDetTournamentSelect<EOT>(detSize);
   }
@@ -100,57 +100,57 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
     {
       double p;
       if (!ppSelect.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
+          std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
-	  p = 1;
+          p = 1;
-	  // put back p in parameter for consistency (and status file)
+          // put back p in parameter for consistency (and status file)
-	  ppSelect.second.push_back(std::string("1"));
+          ppSelect.second.push_back(std::string("1"));
-	}
+        }
-      else	  // parameter passed by user as DetTour(T)
+      else        // parameter passed by user as DetTour(T)
-	p = atof(ppSelect.second[0].c_str());
+        p = atof(ppSelect.second[0].c_str());
-      
+
       select = new eoStochTournamentSelect<EOT>(p);
     }
   else if (ppSelect.first == std::string("Ranking"))
     {
       double p,e;
       if (ppSelect.second.size()==2)   // 2 parameters: pressure and exponent
-	{
+        {
-	  p = atof(ppSelect.second[0].c_str());
+          p = atof(ppSelect.second[0].c_str());
-	  e = atof(ppSelect.second[1].c_str());
+          e = atof(ppSelect.second[1].c_str());
-	}
+        }
-      else if (ppSelect.second.size()==1)   // 1 parameter: pressure 
+      else if (ppSelect.second.size()==1)   // 1 parameter: pressure
-	{
+        {
-	  std::cerr << "WARNING, no exponent to Ranking, using 1" << std::endl;
+          std::cerr << "WARNING, no exponent to Ranking, using 1" << std::endl;
-	  e = 1;
+          e = 1;
-	  ppSelect.second.push_back(std::string("1"));
+          ppSelect.second.push_back(std::string("1"));
-	  p = atof(ppSelect.second[0].c_str());
+          p = atof(ppSelect.second[0].c_str());
-	}
+        }
       else // no parameters ... or garbage
-	{
+        {
-	  std::cerr << "WARNING, no parameter to Ranking, using (2,1)" << std::endl;
+          std::cerr << "WARNING, no parameter to Ranking, using (2,1)" << std::endl;
-	  p=2;
+          p=2;
-	  e=1;
+          e=1;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppSelect.second.resize(2); // just in case
+          ppSelect.second.resize(2); // just in case
-	  ppSelect.second[0] = (std::string("2"));
+          ppSelect.second[0] = (std::string("2"));
-	  ppSelect.second[1] = (std::string("1"));
+          ppSelect.second[1] = (std::string("1"));
-	}
+        }
       // check for authorized values
       // pressure in (0,1]
       if ( (p<=1) || (p>2) )
-	{
+        {
-	  std::cerr << "WARNING, selective pressure must be in (1,2] in Ranking, using 2\n";
+          std::cerr << "WARNING, selective pressure must be in (1,2] in Ranking, using 2\n";
-	  p=2;
+          p=2;
-	  ppSelect.second[0] = (std::string("2"));
+          ppSelect.second[0] = (std::string("2"));
-	}
+        }
       // exponent >0
       if (e<=0)
-	{
+        {
-	  std::cerr << "WARNING, exponent must be positive in Ranking, using 1\n";
+          std::cerr << "WARNING, exponent must be positive in Ranking, using 1\n";
-	  e=1;
+          e=1;
-	  ppSelect.second[1] = (std::string("1"));
+          ppSelect.second[1] = (std::string("1"));
-	}
+        }
       // now we're OK
       eoPerf2Worth<EOT> & p2w = _state.storeFunctor( new eoRanking<EOT>(p,e) );
       select = new eoRouletteWorthSelect<EOT>(p2w);
@@ -159,13 +159,13 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
     {
       bool b;
       if (ppSelect.second.size() == 0)   // no argument -> default = ordered
-	{
+        {
-	  b=true;
+          b=true;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppSelect.second.push_back(std::string("ordered"));
+          ppSelect.second.push_back(std::string("ordered"));
-	}
+        }
       else
-	b = !(ppSelect.second[0] == std::string("unordered"));
+        b = !(ppSelect.second[0] == std::string("unordered"));
       select = new eoSequentialSelect<EOT>(b);
     }
   else if (ppSelect.first == std::string("EliteSequential")) // Best first, one after the other in random order afterwards
@@ -188,7 +188,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
 
   _state.storeFunctor(select);
 
-  // the number of offspring 
+  // the number of offspring
     eoValueParam<eoHowMany>& offspringRateParam =  _parser.createParam(eoHowMany(1.0), "nbOffspring", "Nb of offspring (percentage or absolute)", 'O', "Evolution Engine");
 
   /////////////////////////////////////////////////////
@@ -196,7 +196,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   /////////////////////////////////////////////////////
 
   /** Replacement type - high level: predefined replacements
-   * ESComma : 
+   * ESComma :
    *          elite = 0
    *          surviveParents=0 (no reduce)
    *          surviveOffspring=100% (no reduce)
@@ -208,8 +208,8 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
    * GGA : generational GA - idem ESComma except for
    *          offspringRate = 100%
    *          all reducers are unused
-   * 
+   *
-   * SSGA(T/t) : Steady-State GA  
+   * SSGA(T/t) : Steady-State GA
    *               surviveParents = 1.0 - offspringRate
    *               reduceFinal = DetTour(T>1) ou StochTour(0.5<t<1)
    *
@@ -246,28 +246,28 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
     // the tournament size
     if (!replacementParam.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to MGG replacement, using 2" << std::endl;
+        std::cerr << "WARNING, no parameter passed to MGG replacement, using 2" << std::endl;
-	tSize = 2;
+        tSize = 2;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	replacementParam.second.push_back(std::string("2"));
+        replacementParam.second.push_back(std::string("2"));
       }
     else
       {
-	t = atof(replacementParam.second[0].c_str());
+        t = atof(replacementParam.second[0].c_str());
-	if (t>=2)
+        if (t>=2)
-	  {			   // build the appropriate deafult value
+          {                        // build the appropriate deafult value
-	    tSize = unsigned(t);
+            tSize = unsigned(t);
-	  }
+          }
-	else
+        else
-	  {
+          {
-	    throw std::runtime_error("Sorry, only deterministic tournament available at the moment");
+            throw std::runtime_error("Sorry, only deterministic tournament available at the moment");
-	  }
+          }
       }
-    ptReplace = new eoMGGReplacement<EOT>(-surviveParents, tSize);    
+    ptReplace = new eoMGGReplacement<EOT>(-surviveParents, tSize);
     _state.storeFunctor(ptReplace);
     }
   else {   // until the end of what was the only loop/switch
-    
+
   // the default deafult values
   eoHowMany elite (0.0);
   bool strongElitism (false);
@@ -283,12 +283,12 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   // ---------- General
   if (replacementParam.first == std::string("General"))
   {
-    ;				   // defaults OK
+    ;                              // defaults OK
   }
   // ---------- ESComma
   else if (replacementParam.first == std::string("ESComma"))
   {
-    ;				   // OK too
+    ;                              // OK too
   }
   // ---------- ESPlus
   else if (replacementParam.first == std::string("ESPlus"))
@@ -298,16 +298,16 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   // ---------- Generational
   else if (replacementParam.first == std::string("Generational"))
   {
-    ;			     // OK too (we should check nb of offspring)
+    ;                        // OK too (we should check nb of offspring)
   }
   // ---------- EP
   else if (replacementParam.first == std::string("EP"))
   {
     if (!replacementParam.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to EP replacement, using 6" << std::endl;
+        std::cerr << "WARNING, no parameter passed to EP replacement, using 6" << std::endl;
-	// put back 6 in parameter for consistency (and status file)
+        // put back 6 in parameter for consistency (and status file)
-	replacementParam.second.push_back(std::string("6"));
+        replacementParam.second.push_back(std::string("6"));
       }
     // by coincidence, the syntax for the EP reducer is the same than here:
     reduceFinalType = replacementParam;
@@ -318,28 +318,28 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   {
     if (!replacementParam.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to SSGA replacement, using 2" << std::endl;
+        std::cerr << "WARNING, no parameter passed to SSGA replacement, using 2" << std::endl;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	replacementParam.second.push_back(std::string("2"));
+        replacementParam.second.push_back(std::string("2"));
-	reduceParentType = eoParamParamType(std::string("DetTour(2)"));
+        reduceParentType = eoParamParamType(std::string("DetTour(2)"));
       }
     else
       {
-	t = atof(replacementParam.second[0].c_str());
+        t = atof(replacementParam.second[0].c_str());
-	if (t>=2)
+        if (t>=2)
-	  {			   // build the appropriate deafult value
+          {                        // build the appropriate deafult value
-	    reduceParentType = eoParamParamType(std::string("DetTour(") + replacementParam.second[0].c_str() + ")");
+            reduceParentType = eoParamParamType(std::string("DetTour(") + replacementParam.second[0].c_str() + ")");
-	  }
+          }
-	else   // check for [0.5,1] will be made in make_general_replacement
+        else   // check for [0.5,1] will be made in make_general_replacement
-	  {			   // build the appropriate deafult value
+          {                        // build the appropriate deafult value
-	    reduceParentType = eoParamParamType(std::string("StochTour(") + replacementParam.second[0].c_str() + ")");
+            reduceParentType = eoParamParamType(std::string("StochTour(") + replacementParam.second[0].c_str() + ")");
-	  }
+          }
       }
-    // 
+    //
     surviveParents = eoHowMany(-1);
     surviveOffspring = eoHowMany(1);
   }
-  else		       // no replacement recognized
+  else                 // no replacement recognized
     {
       throw std::runtime_error("Invalid replacement type " + replacementParam.first);
     }
@@ -353,7 +353,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
   ///////////////////////////////
   // the general breeder
   ///////////////////////////////
-  eoGeneralBreeder<EOT> *breed = 
+  eoGeneralBreeder<EOT> *breed =
     new eoGeneralBreeder<EOT>(*select, _op, offspringRateParam.value());
   _state.storeFunctor(breed);
 
@@ -381,7 +381,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalF
 template <class EOT>
 eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc<EOT>& _eval, eoContinue<EOT>& _continue, eoGenOp<EOT>& _op)
 {
-	 do_make_algo_scalar( _parser, _state, *(new eoPopLoopEval<EOT>(_eval)), _continue, _op); 
+         do_make_algo_scalar( _parser, _state, *(new eoPopLoopEval<EOT>(_eval)), _continue, _op);
 }
 
 

eo/src/do/make_algo_scalar.h

@@ -3,7 +3,7 @@
 //-----------------------------------------------------------------------------
 // make_algo_scalar.h
 // (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either
@@ -84,42 +84,42 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
   if (_dist == NULL)
     comment = "Selection: DetTour(T), StochTour(t), Roulette, Ranking(p,e) or Sequential(ordered/unordered)";
       else
-	comment = "Selection: DetTour(T), StochTour(t), Roulette, Ranking(p,e), Sharing(sigma_share) or Sequential(ordered/unordered)";
+        comment = "Selection: DetTour(T), StochTour(t), Roulette, Ranking(p,e), Sharing(sigma_share) or Sequential(ordered/unordered)";
 
   eoValueParam<eoParamParamType>& selectionParam = _parser.createParam(eoParamParamType("DetTour(2)"), "selection", comment, 'S', "Evolution Engine");
 
   eoParamParamType & ppSelect = selectionParam.value(); // std::pair<std::string,std::vector<std::string> >
 
   eoSelectOne<EOT>* select ;
-  if (ppSelect.first == std::string("DetTour")) 
+  if (ppSelect.first == std::string("DetTour"))
   {
     unsigned detSize;
 
     if (!ppSelect.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
+        std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
-	detSize = 2;
+        detSize = 2;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	ppSelect.second.push_back(std::string("2"));
+        ppSelect.second.push_back(std::string("2"));
       }
-    else	  // parameter passed by user as DetTour(T)
+    else          // parameter passed by user as DetTour(T)
       detSize = atoi(ppSelect.second[0].c_str());
     select = new eoDetTournamentSelect<EOT>(detSize);
   }
-  else if (ppSelect.first == std::string("Sharing")) 
+  else if (ppSelect.first == std::string("Sharing"))
   {
     double nicheSize;
 
     if (!ppSelect.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to Sharing, using 0.5" << std::endl;
+        std::cerr << "WARNING, no parameter passed to Sharing, using 0.5" << std::endl;
-	nicheSize = 0.5;
+        nicheSize = 0.5;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	ppSelect.second.push_back(std::string("0.5"));
+        ppSelect.second.push_back(std::string("0.5"));
       }
-    else	  // parameter passed by user as DetTour(T)
+    else          // parameter passed by user as DetTour(T)
       nicheSize = atof(ppSelect.second[0].c_str());
-    if (_dist == NULL)		   // no distance
+    if (_dist == NULL)             // no distance
           throw std::runtime_error("You didn't specify a distance when calling make_algo_scalar and using sharing");
     select = new eoSharingSelect<EOT>(nicheSize, *_dist);
   }
@@ -127,57 +127,57 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
     {
       double p;
       if (!ppSelect.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
+          std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
-	  p = 1;
+          p = 1;
-	  // put back p in parameter for consistency (and status file)
+          // put back p in parameter for consistency (and status file)
-	  ppSelect.second.push_back(std::string("1"));
+          ppSelect.second.push_back(std::string("1"));
-	}
+        }
-      else	  // parameter passed by user as DetTour(T)
+      else        // parameter passed by user as DetTour(T)
-	p = atof(ppSelect.second[0].c_str());
+        p = atof(ppSelect.second[0].c_str());
-      
+
       select = new eoStochTournamentSelect<EOT>(p);
     }
   else if (ppSelect.first == std::string("Ranking"))
     {
       double p,e;
       if (ppSelect.second.size()==2)   // 2 parameters: pressure and exponent
-	{
+        {
-	  p = atof(ppSelect.second[0].c_str());
+          p = atof(ppSelect.second[0].c_str());
-	  e = atof(ppSelect.second[1].c_str());
+          e = atof(ppSelect.second[1].c_str());
-	}
+        }
-      else if (ppSelect.second.size()==1)   // 1 parameter: pressure 
+      else if (ppSelect.second.size()==1)   // 1 parameter: pressure
-	{
+        {
-	  std::cerr << "WARNING, no exponent to Ranking, using 1" << std::endl;
+          std::cerr << "WARNING, no exponent to Ranking, using 1" << std::endl;
-	  e = 1;
+          e = 1;
-	  ppSelect.second.push_back(std::string("1"));
+          ppSelect.second.push_back(std::string("1"));
-	  p = atof(ppSelect.second[0].c_str());
+          p = atof(ppSelect.second[0].c_str());
-	}
+        }
       else // no parameters ... or garbage
-	{
+        {
-	  std::cerr << "WARNING, no parameter to Ranking, using (2,1)" << std::endl;
+          std::cerr << "WARNING, no parameter to Ranking, using (2,1)" << std::endl;
-	  p=2;
+          p=2;
-	  e=1;
+          e=1;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppSelect.second.resize(2); // just in case
+          ppSelect.second.resize(2); // just in case
-	  ppSelect.second[0] = (std::string("2"));
+          ppSelect.second[0] = (std::string("2"));
-	  ppSelect.second[1] = (std::string("1"));
+          ppSelect.second[1] = (std::string("1"));
-	}
+        }
       // check for authorized values
       // pressure in (0,1]
       if ( (p<=1) || (p>2) )
-	{
+        {
-	  std::cerr << "WARNING, selective pressure must be in (0,1] in Ranking, using 2\n";
+          std::cerr << "WARNING, selective pressure must be in (0,1] in Ranking, using 2\n";
-	  p=2;
+          p=2;
-	  ppSelect.second[0] = (std::string("2"));
+          ppSelect.second[0] = (std::string("2"));
-	}
+        }
       // exponent >0
       if (e<=0)
-	{
+        {
-	  std::cerr << "WARNING, exponent must be positive in Ranking, using 1\n";
+          std::cerr << "WARNING, exponent must be positive in Ranking, using 1\n";
-	  e=1;
+          e=1;
-	  ppSelect.second[1] = (std::string("1"));
+          ppSelect.second[1] = (std::string("1"));
-	}
+        }
       // now we're OK
       eoPerf2Worth<EOT> & p2w = _state.storeFunctor( new eoRanking<EOT>(p,e) );
       select = new eoRouletteWorthSelect<EOT>(p2w);
@@ -186,13 +186,13 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
     {
       bool b;
       if (ppSelect.second.size() == 0)   // no argument -> default = ordered
-	{
+        {
-	  b=true;
+          b=true;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppSelect.second.push_back(std::string("ordered"));
+          ppSelect.second.push_back(std::string("ordered"));
-	}
+        }
       else
-	b = !(ppSelect.second[0] == std::string("unordered"));
+        b = !(ppSelect.second[0] == std::string("unordered"));
       select = new eoSequentialSelect<EOT>(b);
     }
   else if (ppSelect.first == std::string("Roulette")) // no argument (yet)
@@ -211,7 +211,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
 
   _state.storeFunctor(select);
 
-  // the number of offspring 
+  // the number of offspring
     eoValueParam<eoHowMany>& offspringRateParam =  _parser.createParam(eoHowMany(1.0), "nbOffspring", "Nb of offspring (percentage or absolute)", 'O', "Evolution Engine");
 
   // the replacement
@@ -231,16 +231,16 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
   else if (ppReplace.first == std::string("EPTour"))
     {
       unsigned detSize;
-      
+
       if (!ppReplace.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to EPTour, using 6" << std::endl;
+          std::cerr << "WARNING, no parameter passed to EPTour, using 6" << std::endl;
-	  detSize = 6;
+          detSize = 6;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppReplace.second.push_back(std::string("6"));
+          ppReplace.second.push_back(std::string("6"));
-	}
+        }
-      else	  // parameter passed by user as EPTour(T)
+      else        // parameter passed by user as EPTour(T)
-	detSize = atoi(ppSelect.second[0].c_str());
+        detSize = atoi(ppSelect.second[0].c_str());
 
       replace = new eoEPReplacement<EOT>(detSize);
     }
@@ -251,32 +251,32 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
   else if (ppReplace.first == std::string("SSGADet"))
     {
       unsigned detSize;
-      
+
       if (!ppReplace.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to SSGADet, using 2" << std::endl;
+          std::cerr << "WARNING, no parameter passed to SSGADet, using 2" << std::endl;
-	  detSize = 2;
+          detSize = 2;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppReplace.second.push_back(std::string("2"));
+          ppReplace.second.push_back(std::string("2"));
-	}
+        }
-      else	  // parameter passed by user as SSGADet(T)
+      else        // parameter passed by user as SSGADet(T)
-	detSize = atoi(ppSelect.second[0].c_str());
+        detSize = atoi(ppSelect.second[0].c_str());
-      
+
       replace = new eoSSGADetTournamentReplacement<EOT>(detSize);
     }
   else if (ppReplace.first == std::string("SSGAStoch"))
     {
       double p;
       if (!ppReplace.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to SSGAStoch, using 1" << std::endl;
+          std::cerr << "WARNING, no parameter passed to SSGAStoch, using 1" << std::endl;
-	  p = 1;
+          p = 1;
-	  // put back in parameter for consistency (and status file)
+          // put back in parameter for consistency (and status file)
-	  ppReplace.second.push_back(std::string("1"));
+          ppReplace.second.push_back(std::string("1"));
-	}
+        }
-      else	  // parameter passed by user as SSGADet(T)
+      else        // parameter passed by user as SSGADet(T)
-	p = atof(ppSelect.second[0].c_str());
+        p = atof(ppSelect.second[0].c_str());
-      
+
       replace = new eoSSGAStochTournamentReplacement<EOT>(p);
     }
   else
@@ -294,10 +294,10 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
       eoReplacement<EOT> *replaceTmp = replace;
       replace = new eoWeakElitistReplacement<EOT>(*replaceTmp);
       _state.storeFunctor(replace);
-    }      
+    }
 
   // the general breeder
-  eoGeneralBreeder<EOT> *breed = 
+  eoGeneralBreeder<EOT> *breed =
     new eoGeneralBreeder<EOT>(*select, _op, offspringRateParam.value());
   _state.storeFunctor(breed);
 

eo/src/do/make_checkpoint.h

@@ -129,7 +129,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
     eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
 
-    bool dirOK = false;		   // not tested yet
+    bool dirOK = false;            // not tested yet
 
 
 
@@ -179,15 +179,15 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	bestStat = new eoBestFitnessStat<EOT>;
+        bestStat = new eoBestFitnessStat<EOT>;
 
-	// store it
+        // store it
 
-	_state.storeFunctor(bestStat);
+        _state.storeFunctor(bestStat);
 
-	// add it to the checkpoint
+        // add it to the checkpoint
 
-	checkpoint->add(*bestStat);
+        checkpoint->add(*bestStat);
 
       }
 
@@ -203,15 +203,15 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	averageStat = new eoAverageStat<EOT>;
+        averageStat = new eoAverageStat<EOT>;
 
-	// store it
+        // store it
 
-	_state.storeFunctor(averageStat);
+        _state.storeFunctor(averageStat);
 
-	// add it to the checkpoint
+        // add it to the checkpoint
 
-	checkpoint->add(*averageStat);
+        checkpoint->add(*averageStat);
 
       }
 
@@ -223,19 +223,19 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
     eoSecondMomentStats<EOT> *secondStat = NULL;
 
-	if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
+        if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
 
       {
 
-	secondStat = new eoSecondMomentStats<EOT>;
+        secondStat = new eoSecondMomentStats<EOT>;
 
-	// store it
+        // store it
 
-	_state.storeFunctor(secondStat);
+        _state.storeFunctor(secondStat);
 
-	// add it to the checkpoint
+        // add it to the checkpoint
 
-	checkpoint->add(*secondStat);
+        checkpoint->add(*secondStat);
 
       }
 
@@ -255,15 +255,15 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	  popStat = new eoSortedPopStat<EOT>;
+          popStat = new eoSortedPopStat<EOT>;
 
-	// store it
+        // store it
 
-	_state.storeFunctor(popStat);
+        _state.storeFunctor(popStat);
 
-	// add it to the checkpoint
+        // add it to the checkpoint
 
-	checkpoint->add(*popStat);
+        checkpoint->add(*popStat);
 
       }
 
@@ -287,7 +287,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
     bool needStdoutMonitor = printBestParam.value()
 
-	|| printPopParam.value() ;
+        || printPopParam.value() ;
 
 
 
@@ -297,53 +297,53 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
+        eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
 
-	_state.storeFunctor(monitor);
+        _state.storeFunctor(monitor);
 
 
 
-	// when called by the checkpoint (i.e. at every generation)
+        // when called by the checkpoint (i.e. at every generation)
 
-	checkpoint->add(*monitor);
+        checkpoint->add(*monitor);
 
 
 
-	// the monitor will output a series of parameters: add them
+        // the monitor will output a series of parameters: add them
 
-	monitor->add(*generationCounter);
+        monitor->add(*generationCounter);
 
-	if (useEvalParam.value()) // we want nb of evaluations
+        if (useEvalParam.value()) // we want nb of evaluations
 
-	      monitor->add(_eval);
+              monitor->add(_eval);
 
-	if (useTimeParam.value()) // we want time
+        if (useTimeParam.value()) // we want time
 
-	  {
+          {
 
-	    tCounter = new eoTimeCounter;
+            tCounter = new eoTimeCounter;
 
-	    _state.storeFunctor(tCounter);
+            _state.storeFunctor(tCounter);
 
-	    checkpoint->add(*tCounter);
+            checkpoint->add(*tCounter);
 
-	    monitor->add(*tCounter);
+            monitor->add(*tCounter);
 
-	  }
+          }
 
-	if (printBestParam.value())
+        if (printBestParam.value())
 
-	    {
+            {
 
-		monitor->add(*bestStat);
+                monitor->add(*bestStat);
 
-		monitor->add(*secondStat);
+                monitor->add(*secondStat);
 
-	    }
+            }
 
-	if ( printPopParam.value())
+        if ( printPopParam.value())
 
-	  monitor->add(*popStat);
+          monitor->add(*popStat);
 
       }
 
@@ -353,9 +353,9 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
     if ( ( fileBestParam.value() || plotBestParam.value() ||
 
-	   plotHistogramParam.value() )
+           plotHistogramParam.value() )
 
-	 && !dirOK )		   // just in case we add something before
+         && !dirOK )               // just in case we add something before
 
       dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
@@ -367,41 +367,41 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
 #ifdef _MSVC
 
-	std::string stmp = dirNameParam.value() + "\best.xg";
+        std::string stmp = dirNameParam.value() + "\best.xg";
 
 #else
 
-	std::string stmp = dirNameParam.value() + "/best.xg";
+        std::string stmp = dirNameParam.value() + "/best.xg";
 
 #endif
 
-	eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
+        eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
 
-	// save and give to checkpoint
+        // save and give to checkpoint
 
-	_state.storeFunctor(fileMonitor);
+        _state.storeFunctor(fileMonitor);
 
-	checkpoint->add(*fileMonitor);
+        checkpoint->add(*fileMonitor);
 
-	// and feed with some statistics
+        // and feed with some statistics
 
-	fileMonitor->add(*generationCounter);
+        fileMonitor->add(*generationCounter);
 
-	fileMonitor->add(_eval);
+        fileMonitor->add(_eval);
 
-	if (tCounter)		   // we want the time as well
+        if (tCounter)              // we want the time as well
 
-	  {
+          {
 
-	    //	    std::cout << "On met timecounter\n";
+            //      std::cout << "On met timecounter\n";
 
-	    fileMonitor->add(*tCounter);
+            fileMonitor->add(*tCounter);
 
-	  }
+          }
 
-	fileMonitor->add(*bestStat);
+        fileMonitor->add(*bestStat);
 
-	fileMonitor->add(*secondStat);
+        fileMonitor->add(*secondStat);
 
       }
 
@@ -413,33 +413,33 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	std::string stmp = dirNameParam.value() + "/gnu_best.xg";
+        std::string stmp = dirNameParam.value() + "/gnu_best.xg";
 
-	eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
+        eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
 
-	// save and give to checkpoint
+        // save and give to checkpoint
 
-	_state.storeFunctor(gnuMonitor);
+        _state.storeFunctor(gnuMonitor);
 
-	checkpoint->add(*gnuMonitor);
+        checkpoint->add(*gnuMonitor);
 
-	// and feed with some statistics
+        // and feed with some statistics
 
-	if (useEvalParam.value())  // do we want eval as X coordinate
+        if (useEvalParam.value())  // do we want eval as X coordinate
 
-	  gnuMonitor->add(_eval);
+          gnuMonitor->add(_eval);
 
-	else if (tCounter)	   // or time?
+        else if (tCounter)         // or time?
 
-	  gnuMonitor->add(*tCounter);
+          gnuMonitor->add(*tCounter);
 
-	else			   // default: generation
+        else                       // default: generation
 
-	  gnuMonitor->add(*generationCounter);
+          gnuMonitor->add(*generationCounter);
 
-	gnuMonitor->add(*bestStat);
+        gnuMonitor->add(*bestStat);
 
-	gnuMonitor->add(*averageStat);
+        gnuMonitor->add(*averageStat);
 
       }
 
@@ -451,25 +451,25 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       {
 
-	eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
+        eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
 
-	_state.storeFunctor(fitStat);
+        _state.storeFunctor(fitStat);
 
-	checkpoint->add(*fitStat);
+        checkpoint->add(*fitStat);
 
-	// a gnuplot-based monitor for snapshots: needs a dir name
+        // a gnuplot-based monitor for snapshots: needs a dir name
 
-	eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
+        eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
 
-	_state.storeFunctor(fitSnapshot);
+        _state.storeFunctor(fitSnapshot);
 
-	// add any stat that is a std::vector<double> to it
+        // add any stat that is a std::vector<double> to it
 
-	fitSnapshot->add(*fitStat);
+        fitSnapshot->add(*fitStat);
 
-	// and of course add it to the checkpoint
+        // and of course add it to the checkpoint
 
-	checkpoint->add(*fitSnapshot);
+        checkpoint->add(*fitSnapshot);
 
       }
 
@@ -499,7 +499,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       if (! dirOK )
 
-	dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
+        dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
 
 
@@ -537,7 +537,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
       if (! dirOK )
 
-	dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
+        dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
 
 
@@ -570,4 +570,3 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
 
 #endif
-

eo/src/do/make_checkpoint_FDC.h

@@ -70,7 +70,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     eoValueParam<std::string>& dirNameParam =  _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
     // shoudl we empty it if exists
     eoValueParam<bool>& eraseParam = _parser.createParam(false, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
-    bool dirOK = false;		   // not tested yet
+    bool dirOK = false;            // not tested yet
 
     /////////////////////////////////////////
     // now some statistics on the population:
@@ -98,11 +98,11 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() )
       // we need the bestStat for at least one of the 3 above
       {
-	bestStat = new eoBestFitnessStat<EOT>;
+        bestStat = new eoBestFitnessStat<EOT>;
-	// store it
+        // store it
-	_state.storeFunctor(bestStat);
+        _state.storeFunctor(bestStat);
-	// add it to the checkpoint
+        // add it to the checkpoint
-	checkpoint->add(*bestStat);
+        checkpoint->add(*bestStat);
       }
 
     // Average fitness alone
@@ -110,11 +110,11 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat?
     if ( plotBestParam.value() ) // we need it for gnuplot output
       {
-	averageStat = new eoAverageStat<EOT>;
+        averageStat = new eoAverageStat<EOT>;
-	// store it
+        // store it
-	_state.storeFunctor(averageStat);
+        _state.storeFunctor(averageStat);
-	// add it to the checkpoint
+        // add it to the checkpoint
-	checkpoint->add(*averageStat);
+        checkpoint->add(*averageStat);
       }
 
     // Second moment stats: average and stdev
@@ -122,11 +122,11 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     eoSecondMomentStats<EOT> *secondStat = NULL;
     if ( printBestParam.value() ) // we need it for sreen output
       {
-	secondStat = new eoSecondMomentStats<EOT>;
+        secondStat = new eoSecondMomentStats<EOT>;
-	// store it
+        // store it
-	_state.storeFunctor(secondStat);
+        _state.storeFunctor(secondStat);
-	// add it to the checkpoint
+        // add it to the checkpoint
-	checkpoint->add(*secondStat);
+        checkpoint->add(*secondStat);
       }
 
 
@@ -136,11 +136,11 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output");
     if ( printPopParam.value() ) // we do want pop dump
       {
-	  popStat = new eoSortedPopStat<EOT>("Dump of whole population");
+          popStat = new eoSortedPopStat<EOT>("Dump of whole population");
-	// store it
+        // store it
-	_state.storeFunctor(popStat);
+        _state.storeFunctor(popStat);
-	// add it to the checkpoint
+        // add it to the checkpoint
-	checkpoint->add(*popStat);
+        checkpoint->add(*popStat);
       }
 
 
@@ -152,14 +152,14 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     eoFDCStat<EOT> *fdcStat = NULL;
     if ( printFDCParam.value() || plotFDCParam.value() ) // we need FDCStat
       {
-	// need first an object to compute the distances - here Hamming dist.
+        // need first an object to compute the distances - here Hamming dist.
-	eoQuadDistance<EOT> *dist = new eoQuadDistance<EOT>;
+        eoQuadDistance<EOT> *dist = new eoQuadDistance<EOT>;
-	_state.storeFunctor(dist);
+        _state.storeFunctor(dist);
-	fdcStat = new eoFDCStat<EOT>(*dist);
+        fdcStat = new eoFDCStat<EOT>(*dist);
-	// storeFunctor it
+        // storeFunctor it
-	_state.storeFunctor(fdcStat);
+        _state.storeFunctor(fdcStat);
-	// add it to the checkpoint
+        // add it to the checkpoint
-	checkpoint->add(*fdcStat);
+        checkpoint->add(*fdcStat);
       }
 
     // do we wnat some histogram of fitnesses snpashots?
@@ -170,95 +170,95 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     ///////////////
     // do we want an eoStdoutMonitor?
     bool needStdoutMonitor = printBestParam.value() || printFDCParam.value()
-	|| printPopParam.value() ;
+        || printPopParam.value() ;
 
     // The Stdout monitor will print parameters to the screen ...
     if ( needStdoutMonitor )
       {
-	eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
+        eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
-	_state.storeFunctor(monitor);
+        _state.storeFunctor(monitor);
 
-	// when called by the checkpoint (i.e. at every generation)
+        // when called by the checkpoint (i.e. at every generation)
-	checkpoint->add(*monitor);
+        checkpoint->add(*monitor);
 
-	// the monitor will output a series of parameters: add them
+        // the monitor will output a series of parameters: add them
-	monitor->add(*generationCounter);
+        monitor->add(*generationCounter);
-	if (useEvalParam.value()) // we want nb of evaluations
+        if (useEvalParam.value()) // we want nb of evaluations
-	      monitor->add(_eval);
+              monitor->add(_eval);
-	if (printBestParam.value())
+        if (printBestParam.value())
-	    {
+            {
-		monitor->add(*bestStat);
+                monitor->add(*bestStat);
-		monitor->add(*secondStat);
+                monitor->add(*secondStat);
-	    }
+            }
-	if (printFDCParam.value())
+        if (printFDCParam.value())
-	  monitor->add(*fdcStat);
+          monitor->add(*fdcStat);
-	if ( printPopParam.value())
+        if ( printPopParam.value())
-	  monitor->add(*popStat);
+          monitor->add(*popStat);
       }
 
     // first handle the dir test - if we need at least one file
     if ( ( fileBestParam.value() || plotBestParam.value() ||
-	   plotFDCParam.value() || plotHistogramParam.value() )
+           plotFDCParam.value() || plotHistogramParam.value() )
-	 && !dirOK )		   // just in case we add something before
+         && !dirOK )               // just in case we add something before
       dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
     if (fileBestParam.value())    // A file monitor for best & secondMoment
       {
-	std::string stmp = dirNameParam.value() + "/best.xg";
+        std::string stmp = dirNameParam.value() + "/best.xg";
-	eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
+        eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
-	// save and give to checkpoint
+        // save and give to checkpoint
-	_state.storeFunctor(fileMonitor);
+        _state.storeFunctor(fileMonitor);
-	checkpoint->add(*fileMonitor);
+        checkpoint->add(*fileMonitor);
-	// and feed with some statistics
+        // and feed with some statistics
-	fileMonitor->add(*generationCounter);
+        fileMonitor->add(*generationCounter);
-	fileMonitor->add(_eval);
+        fileMonitor->add(_eval);
-	fileMonitor->add(*bestStat);
+        fileMonitor->add(*bestStat);
-	fileMonitor->add(*secondStat);
+        fileMonitor->add(*secondStat);
       }
 
     if (plotBestParam.value())    // an eoGnuplot1DMonitor for best & average
       {
-	std::string stmp = dirNameParam.value() + "_gnu_best.xg";
+        std::string stmp = dirNameParam.value() + "_gnu_best.xg";
-	eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
+        eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
-	// save and give to checkpoint
+        // save and give to checkpoint
-	_state.storeFunctor(gnuMonitor);
+        _state.storeFunctor(gnuMonitor);
-	checkpoint->add(*gnuMonitor);
+        checkpoint->add(*gnuMonitor);
-	// and feed with some statistics
+        // and feed with some statistics
-	if (useEvalParam.value())
+        if (useEvalParam.value())
-	  gnuMonitor->add(_eval);
+          gnuMonitor->add(_eval);
-	else
+        else
-	  gnuMonitor->add(*generationCounter);
+          gnuMonitor->add(*generationCounter);
-	gnuMonitor->add(*bestStat);
+        gnuMonitor->add(*bestStat);
-	gnuMonitor->add(*averageStat);
+        gnuMonitor->add(*averageStat);
       }
 
     if (plotFDCParam.value())    // a specific plot monitor for FDC
       {
-	// first into a file (it adds everything ti itself
+        // first into a file (it adds everything ti itself
-	eoFDCFileSnapshot<EOT> *fdcFileSnapshot = new eoFDCFileSnapshot<EOT>(*fdcStat, dirNameParam.value());
+        eoFDCFileSnapshot<EOT> *fdcFileSnapshot = new eoFDCFileSnapshot<EOT>(*fdcStat, dirNameParam.value());
-	_state.storeFunctor(fdcFileSnapshot);
+        _state.storeFunctor(fdcFileSnapshot);
-	// then to a Gnuplot monitor
+        // then to a Gnuplot monitor
-	eoGnuplot1DSnapshot *fdcGnuplot = new eoGnuplot1DSnapshot(*fdcFileSnapshot);
+        eoGnuplot1DSnapshot *fdcGnuplot = new eoGnuplot1DSnapshot(*fdcFileSnapshot);
-	_state.storeFunctor(fdcGnuplot);
+        _state.storeFunctor(fdcGnuplot);
 
-	// and of course add them to the checkPoint
+        // and of course add them to the checkPoint
-	checkpoint->add(*fdcFileSnapshot);
+        checkpoint->add(*fdcFileSnapshot);
-	checkpoint->add(*fdcGnuplot);
+        checkpoint->add(*fdcGnuplot);
       }
 
     // historgram?
     if (plotHistogramParam.value()) // want to see how the fitness is spread?
       {
-	eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
+        eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
-	_state.storeFunctor(fitStat);
+        _state.storeFunctor(fitStat);
-	checkpoint->add(*fitStat);
+        checkpoint->add(*fitStat);
-	// a gnuplot-based monitor for snapshots: needs a dir name
+        // a gnuplot-based monitor for snapshots: needs a dir name
-	eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
+        eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
-	_state.storeFunctor(fitSnapshot);
+        _state.storeFunctor(fitSnapshot);
-	// add any stat that is a std::vector<double> to it
+        // add any stat that is a std::vector<double> to it
-	fitSnapshot->add(*fitStat);
+        fitSnapshot->add(*fitStat);
-	// and of course add it to the checkpoint
+        // and of course add it to the checkpoint
-	checkpoint->add(*fitSnapshot);
+        checkpoint->add(*fitSnapshot);
       }
 
     //////////////////////////////////
@@ -273,7 +273,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     {
       // first make sure dirName is OK
       if (! dirOK )
-	dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
+        dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
       unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
       std::string stmp = dirNameParam.value() + "/generations";
@@ -288,7 +288,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
     {
       // first make sure dirName is OK
       if (! dirOK )
-	dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
+        dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
       std::string stmp = dirNameParam.value() + "/time";
       eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);

eo/src/do/make_checkpoint_assembled.h

@@ -49,7 +49,7 @@
 bool testDirRes(std::string _dirName, bool _erase);
 /////////////////// The checkpoint and other I/O //////////////
 
-/** Of course, Fitness needs to be an eoScalarFitnessAssembled!!! 
+/** Of course, Fitness needs to be an eoScalarFitnessAssembled!!!
  *
  *
  * @ingroup Builders
@@ -153,7 +153,7 @@ eoCheckPoint<EOT>& do_make_checkpoint_assembled(eoParser& _parser, eoState& _sta
     _state.storeFunctor(fitStat);
     checkpoint->add(*fitStat);
 #ifdef HAVE_GNUPLOT
-	// a gnuplot-based monitor for snapshots: needs a dir name
+        // a gnuplot-based monitor for snapshots: needs a dir name
      eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirName);
      _state.storeFunctor(fitSnapshot);
     // add any stat that is a vector<double> to it

eo/src/do/make_continue.h

@@ -55,7 +55,7 @@ It can then be instantiated, and compiled on its own for a given EOType
 template <class Indi>
 eoCombinedContinue<Indi> * make_combinedContinue(eoCombinedContinue<Indi> *_combined, eoContinue<Indi> *_cont)
 {
-  if (_combined)		   // already exists
+  if (_combined)                   // already exists
     _combined->add(*_cont);
   else
     _combined = new eoCombinedContinue<Indi>(*_cont);
@@ -81,10 +81,10 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
 
     if (maxGenParam.value()) // positive: -> define and store
       {
-	eoGenContinue<Indi> *genCont = new eoGenContinue<Indi>(maxGenParam.value());
+        eoGenContinue<Indi> *genCont = new eoGenContinue<Indi>(maxGenParam.value());
-	_state.storeFunctor(genCont);
+        _state.storeFunctor(genCont);
-	// and "add" to combined
+        // and "add" to combined
-	continuator = make_combinedContinue<Indi>(continuator, genCont);
+        continuator = make_combinedContinue<Indi>(continuator, genCont);
       }
 
   // the steadyGen continue - only if user imput
@@ -92,12 +92,12 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
   eoValueParam<unsigned>& minGenParam = _parser.createParam(unsigned(0), "minGen", "Minimum number of generations",'g', "Stopping criterion");
     if (_parser.isItThere(steadyGenParam))
       {
-	eoSteadyFitContinue<Indi> *steadyCont = new eoSteadyFitContinue<Indi>
+        eoSteadyFitContinue<Indi> *steadyCont = new eoSteadyFitContinue<Indi>
-	  (minGenParam.value(), steadyGenParam.value());
+          (minGenParam.value(), steadyGenParam.value());
-	// store
+        // store
-	_state.storeFunctor(steadyCont);
+        _state.storeFunctor(steadyCont);
-	// add to combinedContinue
+        // add to combinedContinue
-	continuator = make_combinedContinue<Indi>(continuator, steadyCont);
+        continuator = make_combinedContinue<Indi>(continuator, steadyCont);
       }
 
   // Same thing with Eval - but here default value is 0
@@ -108,10 +108,10 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
 
     if (maxEvalParam.value()) // positive: -> define and store
       {
-	eoEvalContinue<Indi> *evalCont = new eoEvalContinue<Indi>(_eval, maxEvalParam.value());
+        eoEvalContinue<Indi> *evalCont = new eoEvalContinue<Indi>(_eval, maxEvalParam.value());
-	_state.storeFunctor(evalCont);
+        _state.storeFunctor(evalCont);
-	// and "add" to combined
+        // and "add" to combined
-	continuator = make_combinedContinue<Indi>(continuator, evalCont);
+        continuator = make_combinedContinue<Indi>(continuator, evalCont);
       }
     /*
   // the steadyEval continue - only if user imput
@@ -119,12 +119,12 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
   eoValueParam<unsigned>& minGenParam = _parser.createParam(unsigned(0), "minGen", "Minimum number of generations",'g', "Stopping criterion");
     if (_parser.isItThere(steadyGenParam))
       {
-	eoSteadyGenContinue<Indi> *steadyCont = new eoSteadyFitContinue<Indi>
+        eoSteadyGenContinue<Indi> *steadyCont = new eoSteadyFitContinue<Indi>
-	  (minGenParam.value(), steadyGenParam.value());
+          (minGenParam.value(), steadyGenParam.value());
-	// store
+        // store
-	_state.storeFunctor(steadyCont);
+        _state.storeFunctor(steadyCont);
-	// add to combinedContinue
+        // add to combinedContinue
-	continuator = make_combinedContinue<Indi>(continuator, steadyCont);
+        continuator = make_combinedContinue<Indi>(continuator, steadyCont);
       }
     */
     // the target fitness
@@ -132,12 +132,12 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
     eoValueParam<double>& targetFitnessParam = _parser.createParam(double(0.0), "targetFitness", "Stop when fitness reaches",'T', "Stopping criterion");
     if (_parser.isItThere(targetFitnessParam))
       {
-	fitCont = new eoFitContinue<Indi>
+        fitCont = new eoFitContinue<Indi>
-	  (targetFitnessParam.value());
+          (targetFitnessParam.value());
-	// store
+        // store
-	_state.storeFunctor(fitCont);
+        _state.storeFunctor(fitCont);
-	// add to combinedContinue
+        // add to combinedContinue
-	continuator = make_combinedContinue<Indi>(continuator, fitCont);
+        continuator = make_combinedContinue<Indi>(continuator, fitCont);
       }
 
 #ifndef _MSC_VER
@@ -146,11 +146,11 @@ eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFu
     eoValueParam<bool>& ctrlCParam = _parser.createParam(false, "CtrlC", "Terminate current generation upon Ctrl C",'C', "Stopping criterion");
     if (ctrlCParam.value())
       {
-	ctrlCCont = new eoCtrlCContinue<Indi>;
+        ctrlCCont = new eoCtrlCContinue<Indi>;
-	// store
+        // store
-	_state.storeFunctor(ctrlCCont);
+        _state.storeFunctor(ctrlCCont);
-	// add to combinedContinue
+        // add to combinedContinue
-	continuator = make_combinedContinue<Indi>(continuator, ctrlCCont);
+        continuator = make_combinedContinue<Indi>(continuator, ctrlCCont);
       }
 #endif
 

eo/src/do/make_general_replacement.h

@@ -3,7 +3,7 @@
 //-----------------------------------------------------------------------------
 // make_general_replacement.h
 // (c) Marc Schoenauer and Pierre Collet, 2002
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either
@@ -49,8 +49,8 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
   eoReduce<EOT> * ptReduce;
 
   // ---------- Deterministic
-  if ( (_ppReduce.first == std::string("Deterministic")) || 
+  if ( (_ppReduce.first == std::string("Deterministic")) ||
-       (_ppReduce.first == std::string("Sequential")) 
+       (_ppReduce.first == std::string("Sequential"))
        )
   {
     ptReduce = new eoTruncate<EOT>;
@@ -65,7 +65,7 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
       // put back 6 in parameter for consistency (and status file)
       _ppReduce.second.push_back(std::string("6"));
     }
-    else	  // parameter passed by user as EP(T)
+    else          // parameter passed by user as EP(T)
       detSize = atoi(_ppReduce.second[0].c_str());
     ptReduce = new eoEPReduce<EOT>(detSize);
   }
@@ -74,12 +74,12 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
   {
     if (!_ppReduce.second.size())   // no parameter added
       {
-	std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
+        std::cerr << "WARNING, no parameter passed to DetTour, using 2" << std::endl;
-	detSize = 2;
+        detSize = 2;
-	// put back 2 in parameter for consistency (and status file)
+        // put back 2 in parameter for consistency (and status file)
-	_ppReduce.second.push_back(std::string("2"));
+        _ppReduce.second.push_back(std::string("2"));
       }
-    else	  // parameter passed by user as DetTour(T)
+    else          // parameter passed by user as DetTour(T)
       detSize = atoi(_ppReduce.second[0].c_str());
     ptReduce = new eoDetTournamentTruncate<EOT>(detSize);
   }
@@ -87,24 +87,24 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
     {
       double p;
       if (!_ppReduce.second.size())   // no parameter added
-	{
+        {
-	  std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
+          std::cerr << "WARNING, no parameter passed to StochTour, using 1" << std::endl;
-	  p = 1;
+          p = 1;
-	  // put back p in parameter for consistency (and status file)
+          // put back p in parameter for consistency (and status file)
-	  _ppReduce.second.push_back(std::string("1"));
+          _ppReduce.second.push_back(std::string("1"));
-	}
+        }
-      else	  // parameter passed by user as DetTour(T)
+      else        // parameter passed by user as DetTour(T)
-	{
+        {
-	  p = atof(_ppReduce.second[0].c_str());
+          p = atof(_ppReduce.second[0].c_str());
-	  if ( (p<=0.5) || (p>1) )
+          if ( (p<=0.5) || (p>1) )
-	    throw std::runtime_error("Stochastic tournament size should be in [0.5,1]");
+            throw std::runtime_error("Stochastic tournament size should be in [0.5,1]");
-	}
+        }
-      
+
       ptReduce = new eoStochTournamentTruncate<EOT>(p);
     }
-  else if ( (_ppReduce.first == std::string("Uniform")) || 
+  else if ( (_ppReduce.first == std::string("Uniform")) ||
-	    (_ppReduce.first == std::string("Random"))
+            (_ppReduce.first == std::string("Random"))
-	    )
+            )
     {
       ptReduce = new eoRandomReduce<EOT>;
     }
@@ -117,10 +117,10 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
   return (*ptReduce);
 }
 
-/** Helper function that creates a replacement from the class 
+/** Helper function that creates a replacement from the class
- * eoReduceMergeReduce using 6 parameters 
+ * eoReduceMergeReduce using 6 parameters
  *      (after the usual eoState and eoParser)
- * 
+ *
  *  eoHowMany _elite              the number of elite parents (0 = no elitism)
  *       see below
  *  bool _strongElitism           if elite > 0, std::string elitism or weak elitism
@@ -136,15 +136,15 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
  */
 template <class EOT>
 eoReplacement<EOT> & make_general_replacement(
-    eoParser& _parser, eoState& _state, 
+    eoParser& _parser, eoState& _state,
-    eoHowMany _elite = eoHowMany(0), 
+    eoHowMany _elite = eoHowMany(0),
     bool _strongElitism = false,
     eoHowMany _surviveParents = eoHowMany(0.0),
     eoParamParamType & _reduceParentType = eoParamParamType("Deterministic"),
     eoHowMany _surviveOffspring = eoHowMany(1.0),
     eoParamParamType & _reduceOffspringType = eoParamParamType("Deterministic"),
     eoParamParamType & _reduceFinalType  = eoParamParamType("Deterministic")
-	)
+        )
 {
   /////////////////////////////////////////////////////
   // the replacement
@@ -157,14 +157,14 @@ eoReplacement<EOT> & make_general_replacement(
 
   // reduce the parents
     eoHowMany surviveParents =  _parser.createParam(_surviveParents, "surviveParents", "Nb of surviving parents (percentage or absolute)", '\0', "Evolution Engine / Replacement").value();
-  
+
   eoParamParamType & reduceParentType = _parser.createParam(_reduceParentType, "reduceParents", "Parents reducer: Deterministic, EP(T), DetTour(T), StochTour(t), Uniform", '\0', "Evolution Engine / Replacement").value();
 
   eoReduce<EOT> & reduceParent = decode_reduce<EOT>(reduceParentType, _state);
 
   // reduce the offspring
     eoHowMany surviveOffspring =  _parser.createParam(_surviveOffspring, "surviveOffspring", "Nb of surviving offspring (percentage or absolute)", '\0', "Evolution Engine / Replacement").value();
-  
+
   eoParamParamType & reduceOffspringType = _parser.createParam(_reduceOffspringType, "reduceOffspring", "Offspring reducer: Deterministic, EP(T), DetTour(T), StochTour(t), Uniform", '\0', "Evolution Engine / Replacement").value();
 
   eoReduce<EOT> & reduceOffspring = decode_reduce<EOT>(reduceOffspringType, _state);

eo/src/do/make_pop.h

@@ -59,7 +59,7 @@ eoPop<EOT>&  do_make_pop(eoParser & _parser, eoState& _state, eoInit<EOT> & _ini
   // random seed
     eoValueParam<uint32_t>& seedParam = _parser.getORcreateParam(uint32_t(0), "seed", "Random number seed", 'S');
     if (seedParam.value() == 0)
-	seedParam.value() = time(0);
+        seedParam.value() = time(0);
     eoValueParam<unsigned>& popSize = _parser.getORcreateParam(unsigned(20), "popSize", "Population Size", 'P', "Evolution Engine");
 
   // Either load or initialize
@@ -82,17 +82,17 @@ eoPop<EOT>&  do_make_pop(eoParser & _parser, eoState& _state, eoInit<EOT> & _ini
       // the fitness is read in the file:
       // do only evaluate the pop if the fitness has changed
       if (recomputeFitnessParam.value())
-	{
+        {
-	  for (unsigned i=0; i<pop.size(); i++)
+          for (unsigned i=0; i<pop.size(); i++)
-	    pop[i].invalidate();
+            pop[i].invalidate();
-	}
+        }
       if (pop.size() < popSize.value())
-	std::cerr << "WARNING, only " << pop.size() << " individuals read in file " << loadNameParam.value() << "\nThe remaining " << popSize.value() - pop.size() << " will be randomly drawn" << std::endl;
+        std::cerr << "WARNING, only " << pop.size() << " individuals read in file " << loadNameParam.value() << "\nThe remaining " << popSize.value() - pop.size() << " will be randomly drawn" << std::endl;
       if (pop.size() > popSize.value())
-	{
+        {
-	  std::cerr << "WARNING, Load file contained too many individuals. Only the best will be retained" << std::endl;
+          std::cerr << "WARNING, Load file contained too many individuals. Only the best will be retained" << std::endl;
-	  pop.resize(popSize.value());
+          pop.resize(popSize.value());
-	}
+        }
     }
   else				// nothing loaded from a file
     {

eo/src/do/make_run.h

@@ -3,7 +3,7 @@
 //-----------------------------------------------------------------------------
 // make_run.h
 // (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
-/* 
+/*
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
     License as published by the Free Software Foundation; either

eo/src/eo

@@ -201,7 +201,7 @@
 
 #include <utils/eoParserLogger.h>
 
-//-----------------------------------------------------------------------------
+#include <utils/eoParallel.h>
 
 #endif 
 

eo/src/eoCellularEasyEA.h

@@ -8,16 +8,16 @@
    modify it under the terms of the GNU Lesser General Public
    License as published by the Free Software Foundation; either
    version 2 of the License, or (at your option) any later version.
-   
+
    This library 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
    Lesser General Public License for more details.
-   
+
    You should have received a copy of the GNU Lesser General Public
    License along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
-   
+
    Contact: cahon@lifl.fr
 */
 
@@ -32,26 +32,26 @@
 #include <eoOp.h>
 
 /**
-   The abstract cellular easy algorithm. 
+   The abstract cellular easy algorithm.
 
    @ingroup Algorithms
  */
 template <class EOT> class eoCellularEasyEA : public eoAlgo <EOT> {
-  
+
 public :
-  
+
   /**
      Two constructors
    */
 
   eoCellularEasyEA (eoContinue <EOT> & _cont, // Stop. criterion
-		    eoEvalFunc <EOT> & _eval, // Evaluation function
+                    eoEvalFunc <EOT> & _eval, // Evaluation function
-		    eoSelectOne <EOT> & _sel_neigh, // To choose a partner
+                    eoSelectOne <EOT> & _sel_neigh, // To choose a partner
-		    eoBinOp <EOT> & _cross, // Cross-over operator
+                    eoBinOp <EOT> & _cross, // Cross-over operator
-		    eoMonOp <EOT> & _mut, // Mutation operator
+                    eoMonOp <EOT> & _mut, // Mutation operator
-		    eoSelectOne <EOT> & _sel_repl /* Which to keep between the new
+                    eoSelectOne <EOT> & _sel_repl /* Which to keep between the new
-						     child and the old individual ? */
+                                                     child and the old individual ? */
-		    ) :
+                    ) :
     cont (_cont),
     eval (_eval),
     popEval (_eval),
@@ -60,18 +60,18 @@ public :
     mut (_mut),
     sel_child (eoSelectFirstOne ()),
     sel_repl (_sel_repl) {
-    
+
   }
-  
+
   eoCellularEasyEA (eoContinue <EOT> & _cont,
-		    eoEvalFunc <EOT> & _eval,
+                    eoEvalFunc <EOT> & _eval,
-		    eoSelectOne <EOT> & _sel_neigh,
+                    eoSelectOne <EOT> & _sel_neigh,
-		    eoQuadOp <EOT> & _cross,
+                    eoQuadOp <EOT> & _cross,
-		    eoMonOp <EOT> & _mut,
+                    eoMonOp <EOT> & _mut,
-		    eoSelectOne <EOT> & _sel_child, /* To choose one from
+                    eoSelectOne <EOT> & _sel_child, /* To choose one from
-						       the both children */
+                                                       the both children */
-		    eoSelectOne <EOT> & _sel_repl
+                    eoSelectOne <EOT> & _sel_repl
-		    ) :
+                    ) :
     cont (_cont),
     eval (_eval),
     popEval (_eval),
@@ -80,7 +80,7 @@ public :
     mut (_mut),
     sel_child (_sel_child),
     sel_repl (_sel_repl) {
-    
+
   }
 
   /**
@@ -88,55 +88,55 @@ public :
    */
 
   void operator () (eoPop <EOT> & pop) {
-    
+
     do {
-      
+
       for (unsigned i = 0 ; i < pop.size () ; i ++) {
-	
-	// Who are neighbouring to the current individual ?
-	eoPop <EOT> neigh = neighbours (pop, i) ;
-	
-	// To select a partner
-	EOT part, old_sol = pop [i] ;
-	part = sel_neigh (neigh) ;
 
-	// To perform cross-over
+        // Who are neighbouring to the current individual ?
-	cross (pop [i], part) ;
+        eoPop <EOT> neigh = neighbours (pop, i) ;
 
-	// To perform mutation
+        // To select a partner
-	mut (pop [i]) ;
+        EOT part, old_sol = pop [i] ;
-	mut (part) ;
+        part = sel_neigh (neigh) ;
-	
-	pop [i].invalidate () ;
-	part.invalidate () ;
-	eval (pop [i]) ;
-	eval (part) ;
 
-	// To choose one of the two children ...
+        // To perform cross-over
-	eoPop <EOT> pop_loc ;
+        cross (pop [i], part) ;
-	pop_loc.push_back (pop [i]) ;
-	pop_loc.push_back (part) ;
 
-	pop [i] = sel_child (pop_loc) ;
+        // To perform mutation
+        mut (pop [i]) ;
+        mut (part) ;
 
-	// To choose only one between the new made child and the old individual
+        pop [i].invalidate () ;
-	pop_loc.clear () ;
+        part.invalidate () ;
-	pop_loc.push_back (pop [i]) ;
+        eval (pop [i]) ;
-	
+        eval (part) ;
-	pop_loc.push_back (old_sol) ;
+
-	
+        // To choose one of the two children ...
-	pop [i] = sel_repl (pop_loc) ;	
+        eoPop <EOT> pop_loc ;
+        pop_loc.push_back (pop [i]) ;
+        pop_loc.push_back (part) ;
+
+        pop [i] = sel_child (pop_loc) ;
+
+        // To choose only one between the new made child and the old individual
+        pop_loc.clear () ;
+        pop_loc.push_back (pop [i]) ;
+
+        pop_loc.push_back (old_sol) ;
+
+        pop [i] = sel_repl (pop_loc) ;
       }
-      
+
     } while (cont (pop)) ;
   }
 
 protected :
-  
+
   virtual eoPop <EOT> neighbours (const eoPop <EOT> & pop, int rank) = 0 ;
 
 private :
-  
+
   eoContinue <EOT> & cont ;
   eoEvalFunc <EOT> & eval ;
   eoPopLoopEval <EOT> popEval ;
@@ -145,18 +145,18 @@ private :
   eoMonOp <EOT> & mut ;
   eoSelectOne <EOT> & sel_child ;
   eoSelectOne <EOT> & sel_repl ;
-  
+
   class eoSelectFirstOne : public eoSelectOne <EOT> {
-    
+
   public :
-    
+
     const EOT & operator () (const eoPop <EOT> & pop) {
-      
+
-      return pop [0] ; 
+      return pop [0] ;
     }
-    
+
-  } ; 
+  } ;
-  
+
 } ;
 
 #endif