Some changes in names, before too many users have to modify their code :-)

Changed es.h in src/es into make_es.h (was ambiguous with src/es.h)
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!).

eo/src/do/make_help.cpp

@@ -1,54 +0,0 @@
-// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-
-//-----------------------------------------------------------------------------
-// make_help.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
-    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: todos@geneura.ugr.es, http://geneura.ugr.es
-             Marc.Schoenauer@polytechnique.fr
-             mkeijzer@dhi.dk
- */
-//-----------------------------------------------------------------------------
-#include <utils/eoParser.h>
-#include <fstream.h>
-
-/** Generation of the status file, and output of the help message if needed
- *
- * MUST be called after ALL parameters have been read in order to list them
- *
- * Warning: this is a plain .cpp file and shoudl NOT be included anywhere, 
- * but compiled separately and stored in a library.
- */
-void make_help(eoParser & _parser)
-{
-    // name of the "status" file where all actual parameter values will be saved
-    string str_status = _parser.ProgramName() + ".status"; // default value
-    eoValueParam<string>& statusParam = _parser.createParam(str_status, "status","Status file",'\0', "Persistence" );
-
-   // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
-   // i.e. in case you need parameters somewhere else, postpone these
-    if (_parser.userNeedsHelp())
-      {
-        _parser.printHelp(cout);
-        exit(1);
-      }
-    if (statusParam.value() != "")
-      {
-	ofstream os(statusParam.value().c_str());
-	os << _parser;		// and you can use that file as parameter file
-      }
-}

eo/src/es/Makefile.am

@@ -7,7 +7,7 @@
 INCLUDES = -I$(top_builddir)/src
 lib_LIBRARIES = libes.a
 libes_a_SOURCES = make_algo_scalar_real.cpp make_checkpoint_real.cpp \
-  make_continue_real.cpp make_genotype_real.cpp make_help.cpp \
+  make_continue_real.cpp make_genotype_real.cpp \
   make_op_real.cpp make_pop_real.cpp make_run_real.cpp \
   make_algo_scalar_es.cpp make_checkpoint_es.cpp \
   make_continue_es.cpp make_pop_es.cpp make_run_es.cpp

eo/src/es/make_genotype_real.cpp

@@ -30,23 +30,33 @@
  * files that you just need to link with your own main and fitness code).
  *
  * The corresponding ***INSTANCIATED DECLARATIONS*** are contained 
- *       in src/es/es.h
+ *       in src/es/make_real.h
- * while the TEMPLATIZED code is define in make_genotype_real.h in the src/es dir
+ * while the TEMPLATIZED code is define in make_genotype_real.h
  *
- * Unlike most EO .h files, it does not (and should not) contain any code, 
+ * It is instanciated in src/es/make_genotype_real.cpp - 
- * just declarations
+ * and incorporated in the ga/libga.a
+ *
+ * It returns an eoInit<EOT> that can later be used to initialize 
+ * the population (see make_pop.h).
+ *
+ * It uses a parser (to get user parameters) and a state (to store the memory)
+ * the last argument is to disambiguate the call upon different instanciations.
+ *
+ * WARNING: that last argument will generally be the result of calling 
+ *          the default ctor of EOT, resulting in most cases in an EOT 
+ *          that is ***not properly initialized***
 */
 
 // the templatized code
-#include <es/make_genotype.h>
+#include <es/make_genotype_real.h>
 
 /// The following function merely call the templatized do_* functions 
 
-eoInit<eoReal<double> > & make_genotype(eoParameterLoader& _parser, eoState& _state, double _d)
+eoInit<eoReal<double> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoReal<double> _eo)
 {
-  return do_make_genotype(_parser, _state, _d);
+  return do_make_genotype(_parser, _state, _eo);
 }
-eoInit<eoReal<eoMinimizingFitness> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness _d)
+eoInit<eoReal<eoMinimizingFitness> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoReal<eoMinimizingFitness> _eo)
 {
-  return do_make_genotype(_parser, _state, _d);
+  return do_make_genotype(_parser, _state, _eo);
 }

eo/src/es/make_genotype_real.h

@@ -35,23 +35,34 @@
 
 
 /*
- * This function does the initialization of what's needed for a particular 
+ * This fuction does the initialization of what's needed for a particular 
- * genotype (here, eoReal).
+ * genotype (here, vector<double> == eoReal).
- * It is templatized ***only on the fitness*** so it can be used to evolve 
+ * It could be here tempatied only on the fitness, as it can be used to evolve 
- * eoReal with any fitness.
+ * bitstrings with any fitness.
- * It is instanciated in es/make_genotype_real.cpp - 
+ * However, for consistency reasons, it was finally chosen, as in 
- * and incorporated in the es/libes.a
+ * the rest of EO, to templatize by the full EOT, as this eventually 
+ * allows to choose the type of genotype at run time (see in es dir)
  *
- * It returns an eoInit<eoReal<FitT> > tha can later be used to initialize 
+ * It is instanciated in src/es/make_genotyupe_real.cpp 
+ * and incorporated in the src/es/libes.a
+ *
+ * It returns an eoInit<EOT> tha can later be used to initialize 
  * the population (see make_pop.h).
  *
  * It uses a parser (to get user parameters) and a state (to store the memory)
  * the last argument is to disambiguate the call upon different instanciations.
+ *
+ * WARNING: that last argument will generally be the result of calling 
+ *          the default ctor of EOT, resulting in most cases in an EOT 
+ *          that is ***not properly initialized***
 */
 
-template <class FitT>
+template <class EOT>
-eoInit<eoReal<FitT> > & do_make_genotype(eoParameterLoader& _parser, eoState& _state, FitT)
+eoInit<EOT> & do_make_genotype(eoParameterLoader& _parser, eoState& _state, EOT)
 {
+  // the fitness type
+  typedef typename EOT::Fitness FitT;
+  
   // for eoReal, only thing needed is the size
     eoValueParam<unsigned>& vecSize = _parser.createParam(unsigned(10), "vecSize", "The number of variables ", 'n',"initialization");
 

eo/src/es/make_help.cpp

@@ -1,54 +0,0 @@
-// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-
-//-----------------------------------------------------------------------------
-// make_help.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
-    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: todos@geneura.ugr.es, http://geneura.ugr.es
-             Marc.Schoenauer@polytechnique.fr
-             mkeijzer@dhi.dk
- */
-//-----------------------------------------------------------------------------
-#include <utils/eoParser.h>
-#include <fstream.h>
-
-/** Generation of the status file, and output of the help message if needed
- *
- * MUST be called after ALL parameters have been read in order to list them
- *
- * Warning: this is a plain .cpp file and shoudl NOT be included anywhere, 
- * but compiled separately and stored in a library.
- */
-void make_help(eoParser & _parser)
-{
-    // name of the "status" file where all actual parameter values will be saved
-    string str_status = _parser.ProgramName() + ".status"; // default value
-    eoValueParam<string>& statusParam = _parser.createParam(str_status, "status","Status file",'\0', "Persistence" );
-
-   // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
-   // i.e. in case you need parameters somewhere else, postpone these
-    if (_parser.userNeedsHelp())
-      {
-        _parser.printHelp(cout);
-        exit(1);
-      }
-    if (statusParam.value() != "")
-      {
-	ofstream os(statusParam.value().c_str());
-	os << _parser;		// and you can use that file as parameter file
-      }
-}

eo/src/es/make_real.h

@@ -59,8 +59,8 @@
 //////////////////////////
 
 // the genotypes 
-eoInit<eoReal<double> > & make_genotype(eoParameterLoader& _parser, eoState& _state, double _d);
+eoInit<eoReal<double> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoReal<double> _eo);
-  eoInit<eoReal<eoMinimizingFitness> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness _d);
+  eoInit<eoReal<eoMinimizingFitness> > & make_genotype(eoParameterLoader& _parser, eoState& _state, eoReal<eoMinimizingFitness> _eo);
 
 // the operators
 eoGenOp<eoReal<double> >&  make_op(eoParameterLoader& _parser, eoState& _state, eoInit<eoReal<double> >& _init);
@@ -93,7 +93,8 @@ void run_ea(eoAlgo<eoReal<double> >& _ga, eoPop<eoReal<double> >& _pop);
 void run_ea(eoAlgo<eoReal<eoMinimizingFitness> >& _ga, eoPop<eoReal<eoMinimizingFitness> >& _pop);
 
 // end of parameter input (+ .status + help)
-// that one is not templatized, but is here for completeness
+// that one is not templatized
+// Because of that, the source is in src/utils dir
 void make_help(eoParser & _parser);
 
 #endif

eo/src/ga/Makefile.am

@@ -10,7 +10,6 @@ libga_a_SOURCES = make_algo_scalar_ga.cpp \
                   make_checkpoint_ga.cpp \
                   make_continue_ga.cpp \
                   make_genotype_ga.cpp \
-                  make_help.cpp \
                   make_op_ga.cpp \
                   make_pop_ga.cpp \
                   make_run_ga.cpp

eo/src/ga/make_ga.h

@@ -86,7 +86,8 @@ void run_ea(eoAlgo<eoBit<double> >& _ga, eoPop<eoBit<double> >& _pop);
 void run_ea(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFitness> >& _pop);
 
 // end of parameter input (+ .status + help)
-// that one is not templatized, but is here for the sake of completeness
+// that one is not templatized
+// Because of that, the source is in src/utils dir
 void make_help(eoParser & _parser);
 
 #endif

eo/src/ga/make_genotype_ga.h

@@ -36,7 +36,7 @@
 
 /////////////////// the bitstring ////////////////
 /*
- * This fuciont does the initialization of what's needed for a particular 
+ * This fuction does the initialization of what's needed for a particular 
  * genotype (here, bitstrings).
  * It could be here tempatied only on the fitness, as it can be used to evolve 
  * bitstrings with any fitness.
@@ -55,7 +55,6 @@
  * WARNING: that last argument will generally be the result of calling 
  *          the default ctor of EOT, resulting in most cases in an EOT 
  *          that is ***not properly initialized***
-
 */
 
 template <class EOT>

eo/src/utils/Makefile.am

@@ -7,7 +7,7 @@
 INCLUDES = -I$(top_builddir)/src
 CPPFLAGS = -O2 -Wall
 lib_LIBRARIES = libeoutils.a
-libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp eoRealBounds.cpp
+libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp eoRealBounds.cpp make_help.cpp
 
 libeoincdir = $(includedir)/eo/utils
 libeoinc_HEADERS = checkpointing *.h

eo/test/t-eoGA.cpp

@@ -1,6 +1,6 @@
 #include <iostream>
 
-#include <ga/ga.h>
+#include <ga/make_ga.h>
 #include "binary_value.h"
 #include <apply.h>
 
@@ -25,7 +25,7 @@ int main(int argc, char* argv[])
   eoEvalFuncCounter<EOT> eval(mainEval);
 
   // the genotype - through a genotype initializer
-  eoInit<EOT>& init = make_genotype(parser, state, double());
+  eoInit<EOT>& init = make_genotype(parser, state, EOT());
 
   // Build the variation operator (any seq/prop construct)
   eoGenOp<EOT>& op = make_op(parser, state, init);

eo/test/t-eoReal.cpp

@@ -1,6 +1,6 @@
 #include <iostream>
 
-#include <es/real.h>
+#include <es/make_real.h>
 #include "real_value.h"
 #include <apply.h>
 
@@ -26,7 +26,7 @@ int main(int argc, char* argv[])
   eoEvalFuncCounter<EOT> eval(mainEval);
 
   // the genotype - through a genotype initializer
-  eoInit<EOT>& init = make_genotype(parser, state, eoMinimizingFitness());
+  eoInit<EOT>& init = make_genotype(parser, state, EOT());
 
   // Build the variation operator (any seq/prop construct)
   eoGenOp<EOT>& op = make_op(parser, state, init);