Changes

eo/Makefile.am

@@ -4,9 +4,14 @@
 ##
 ###############################################################################
 
-SUBDIRS = src test
+SUBDIRS = src test win
+#Directory for documents
 DOCDIR = ~/public_html/eodocs
+#Directory for indices -- not useful for the user
+IDXDIR = ~/index
+
+EXTRA_DIST=LICENSE
 
 docs: 
 	doc++ -d $(DOCDIR) -B foot.html -f src/*.h src/*.cpp
-	/home/jmerelo/bin/index -e html -i /home/jmerelo/index/neweo.idx /home/jmerelo/public_html/eodocs/ -v 3 
+	/home/jmerelo/bin/index -e html -i $(IDXDIR)/neweo.idx $(DOCDIR)/ -v 3 

eo/configure.in

@@ -1,11 +1,13 @@
 AC_INIT(src/eo)
 
-AM_INIT_AUTOMAKE(eo, 0.0.5)
+AM_INIT_AUTOMAKE(eo, 0.0.8)
 
 AC_PROG_CXX
 
+CXXFLAGS=-g
+
 AM_PROG_LIBTOOL
 
 AM_MAINTAINER_MODE
 
-AC_OUTPUT(Makefile src/Makefile test/Makefile)
+AC_OUTPUT(Makefile src/Makefile test/Makefile win/Makefile)

eo/src/eoBin.h

@@ -12,11 +12,9 @@
 #include <string>      // string
 #include <eoVector.h>  // EO
 
-/*****************************************************************************
+/** eoBin: implementation of binary chromosome.                               
- * eoBin: implementation of binary chromosome.                               *
+ * based on STL's bit_vector (vector<bool>).                                 
- * based on STL's bit_vector (vector<bool>).                                 *
+*/
- *****************************************************************************/
-
 template <class F> class eoBin: public eoVector<bool, F>
 {
  public:

eo/src/eoGeneration.h

@@ -31,10 +31,12 @@
 #include <eoEvalFunc.h> 
 #include <eoPopOps.h>  // eoSelect, eoTranform, eoMerge
 
-//-----------------------------------------------------------------------------
-// eoGeneration
 //-----------------------------------------------------------------------------
 
+/** eoGeneration
+ * Single step of a evolutionary algorithm. Applies selection, then genetic
+ * operators, replaces using a replacement policy, and finally evaluates the
+ * new ones */
 template<class Chrom> class eoGeneration: public eoAlgo<Chrom>
 {
  public:

eo/test/Makefile.am

@@ -5,6 +5,7 @@
 ###############################################################################
 
 DEPS = $(top_builddir)/src/libeo.a
+EXTRA_DIST = LICENSE
 
 ###############################################################################
 
@@ -13,7 +14,17 @@ LDADDS = $(top_builddir)/src/libeo.a
 
 ###############################################################################
 
-noinst_PROGRAMS = t-eobreeder t-eoinclusion t-eoinsertion t-eo t-eofitness t-eoproblem t-eobin t-eolottery t-eo2dVector t-eogeneration t-eoEasyEA t-eoNonUniform t-eoUniform t-eoRandom t-parser t-eoESFull t-eoESOps t-eoAtomOps
+noinst_PROGRAMS = t-eobreeder t-eoinclusion t-eoinsertion t-eo t-eofitness \
+	t-eoproblem t-eobin t-eolottery t-eo2dVector t-eogeneration t-eoEasyEA\
+	t-eoNonUniform t-eoUniform t-eoRandom t-parser t-eoESFull t-eoESOps\
+	t-eoAtomOps t-selectOne
+
+###############################################################################
+
+t_selectOne_SOURCES = t-selectOne.cpp
+t_selectOne_DEPENDENCIES = $(DEPS)
+t_selectOne_LDFLAGS = -lm
+t_selectOne_LDADD = $(LDADDS)
 
 ###############################################################################
 
@@ -73,7 +84,7 @@ t_eoEasyEA_LDADD = $(LDADDS)
 
 ###############################################################################
 
-t_eobreeder_SOURCES = t-eobreeder.cpp
+t_eobreeder_SOURCES = t-eobreeder.cpp binary_value.h
 t_eobreeder_DEPENDENCIES = $(DEPS)
 t_eobreeder_LDFLAGS = -lm
 t_eobreeder_LDADD = $(LDADDS)

eo/test/Makefile.in

@@ -1,4 +1,4 @@
-# Makefile.in generated automatically by automake 1.4a from Makefile.am
+# Makefile.in generated automatically by automake 1.4 from Makefile.am
 
 # Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
 # This Makefile.in is free software; the Free Software Foundation
@@ -49,10 +49,9 @@ AUTOMAKE = @AUTOMAKE@
 AUTOHEADER = @AUTOHEADER@
 
 INSTALL = @INSTALL@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_FLAG =
 transform = @program_transform_name@
 
 NORMAL_INSTALL = :
@@ -79,6 +78,7 @@ RANLIB = @RANLIB@
 VERSION = @VERSION@
 
 DEPS = $(top_builddir)/src/libeo.a
+EXTRA_DIST = LICENSE
 
 ###############################################################################
 
@@ -87,7 +87,15 @@ LDADDS = $(top_builddir)/src/libeo.a
 
 ###############################################################################
 
-noinst_PROGRAMS = t-eobreeder t-eoinclusion t-eoinsertion t-eo t-eofitness t-eoproblem t-eobin t-eolottery t-eo2dVector t-eogeneration t-eoEasyEA t-eoNonUniform t-eoUniform t-eoRandom t-parser t-eoESFull t-eoESOps t-eoAtomOps
+noinst_PROGRAMS = t-eobreeder t-eoinclusion t-eoinsertion t-eo t-eofitness 	t-eoproblem t-eobin t-eolottery t-eo2dVector t-eogeneration t-eoEasyEA 	t-eoNonUniform t-eoUniform t-eoRandom t-parser t-eoESFull t-eoESOps 	t-eoAtomOps t-selectOne
+
+
+###############################################################################
+
+t_selectOne_SOURCES = t-selectOne.cpp
+t_selectOne_DEPENDENCIES = $(DEPS)
+t_selectOne_LDFLAGS = -lm
+t_selectOne_LDADD = $(LDADDS)
 
 ###############################################################################
 
@@ -147,7 +155,7 @@ t_eoEasyEA_LDADD = $(LDADDS)
 
 ###############################################################################
 
-t_eobreeder_SOURCES = t-eobreeder.cpp
+t_eobreeder_SOURCES = t-eobreeder.cpp binary_value.h
 t_eobreeder_DEPENDENCIES = $(DEPS)
 t_eobreeder_LDFLAGS = -lm
 t_eobreeder_LDADD = $(LDADDS)
@@ -241,6 +249,7 @@ t_parser_OBJECTS =  t-parser.o
 t_eoESFull_OBJECTS =  t-eoESFull.o
 t_eoESOps_OBJECTS =  t-eoESOps.o
 t_eoAtomOps_OBJECTS =  t-eoAtomOps.o
+t_selectOne_OBJECTS =  t-selectOne.o
 CXXFLAGS = @CXXFLAGS@
 CXXCOMPILE = $(CXX) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
 LTCXXCOMPILE = $(LIBTOOL) --mode=compile $(CXX) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
@@ -258,8 +267,8 @@ DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
 
 TAR = gtar
 GZIP_ENV = --best
-SOURCES = $(t_eobreeder_SOURCES) $(t_eoinclusion_SOURCES) $(t_eoinsertion_SOURCES) $(t_eo_SOURCES) $(t_eofitness_SOURCES) $(t_eoproblem_SOURCES) $(t_eobin_SOURCES) $(t_eolottery_SOURCES) $(t_eo2dVector_SOURCES) $(t_eogeneration_SOURCES) $(t_eoEasyEA_SOURCES) $(t_eoNonUniform_SOURCES) $(t_eoUniform_SOURCES) $(t_eoRandom_SOURCES) $(t_parser_SOURCES) $(t_eoESFull_SOURCES) $(t_eoESOps_SOURCES) $(t_eoAtomOps_SOURCES)
+SOURCES = $(t_eobreeder_SOURCES) $(t_eoinclusion_SOURCES) $(t_eoinsertion_SOURCES) $(t_eo_SOURCES) $(t_eofitness_SOURCES) $(t_eoproblem_SOURCES) $(t_eobin_SOURCES) $(t_eolottery_SOURCES) $(t_eo2dVector_SOURCES) $(t_eogeneration_SOURCES) $(t_eoEasyEA_SOURCES) $(t_eoNonUniform_SOURCES) $(t_eoUniform_SOURCES) $(t_eoRandom_SOURCES) $(t_parser_SOURCES) $(t_eoESFull_SOURCES) $(t_eoESOps_SOURCES) $(t_eoAtomOps_SOURCES) $(t_selectOne_SOURCES)
-OBJECTS = $(t_eobreeder_OBJECTS) $(t_eoinclusion_OBJECTS) $(t_eoinsertion_OBJECTS) $(t_eo_OBJECTS) $(t_eofitness_OBJECTS) $(t_eoproblem_OBJECTS) $(t_eobin_OBJECTS) $(t_eolottery_OBJECTS) $(t_eo2dVector_OBJECTS) $(t_eogeneration_OBJECTS) $(t_eoEasyEA_OBJECTS) $(t_eoNonUniform_OBJECTS) $(t_eoUniform_OBJECTS) $(t_eoRandom_OBJECTS) $(t_parser_OBJECTS) $(t_eoESFull_OBJECTS) $(t_eoESOps_OBJECTS) $(t_eoAtomOps_OBJECTS)
+OBJECTS = $(t_eobreeder_OBJECTS) $(t_eoinclusion_OBJECTS) $(t_eoinsertion_OBJECTS) $(t_eo_OBJECTS) $(t_eofitness_OBJECTS) $(t_eoproblem_OBJECTS) $(t_eobin_OBJECTS) $(t_eolottery_OBJECTS) $(t_eo2dVector_OBJECTS) $(t_eogeneration_OBJECTS) $(t_eoEasyEA_OBJECTS) $(t_eoNonUniform_OBJECTS) $(t_eoUniform_OBJECTS) $(t_eoRandom_OBJECTS) $(t_parser_OBJECTS) $(t_eoESFull_OBJECTS) $(t_eoESOps_OBJECTS) $(t_eoAtomOps_OBJECTS) $(t_selectOne_OBJECTS)
 
 all: all-redirect
 .SUFFIXES:
@@ -390,6 +399,10 @@ t-eoESOps: $(t_eoESOps_OBJECTS) $(t_eoESOps_DEPENDENCIES)
 t-eoAtomOps: $(t_eoAtomOps_OBJECTS) $(t_eoAtomOps_DEPENDENCIES)
 	@rm -f t-eoAtomOps
 	$(CXXLINK) $(t_eoAtomOps_LDFLAGS) $(t_eoAtomOps_OBJECTS) $(t_eoAtomOps_LDADD) $(LIBS)
+
+t-selectOne: $(t_selectOne_OBJECTS) $(t_selectOne_DEPENDENCIES)
+	@rm -f t-selectOne
+	$(CXXLINK) $(t_selectOne_LDFLAGS) $(t_selectOne_OBJECTS) $(t_selectOne_LDADD) $(LIBS)
 .cc.o:
 	$(CXXCOMPILE) -c $<
 .cc.lo:
@@ -436,7 +449,7 @@ distdir: $(DISTFILES)
 	@for file in $(DISTFILES); do \
 	  d=$(srcdir); \
 	  if test -d $$d/$$file; then \
-	    cp -pr $$d/$$file $(distdir)/$$file; \
+	    cp -pr $$/$$file $(distdir)/$$file; \
 	  else \
 	    test -f $(distdir)/$$file \
 	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
@@ -465,7 +478,7 @@ uninstall: uninstall-am
 all-am: Makefile $(PROGRAMS)
 all-redirect: all-am
 install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_STRIP_FLAG=-s install
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
 installdirs:
 
 

eo/test/t-eoRandom.cpp

@@ -1,6 +1,30 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+/*-----------------------------------------------------------------------------
+ * t-eoRandom
+ *    Testing program for the eoRNG class
+ * (c) GeNeura Team, 1999 
+
+    This library is free software; you can redistribute it and/or
+    modify 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 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
+            
+*/
+
 //-----------------------------------------------------------------------------
-// t-eouniform
+
-//-----------------------------------------------------------------------------
 
 #include <iostream>   // cout
 #include <strstream>  // ostrstream, istrstream

eo/test/t-eobin.cpp

@@ -1,5 +1,27 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
 //-----------------------------------------------------------------------------
 // t-eobin.cpp
+//   This program test the the binary cromosomes and several genetic operators
+// (c) GeNeura Team, 1999 
+/* 
+    This library is free software; you can redistribute it and/or
+    modify 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 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
+            
+*/
 //-----------------------------------------------------------------------------
 
 #include <iostream>   // cout
@@ -102,7 +124,7 @@ main()
   
   for (float r = 0.1; r < 1.0; r += 0.1)
     {
-      eoBinUxOver<Chrom> uxover(r);
+      eoUniformXOver<Chrom> uxover(r);
       fill(chrom.begin(), chrom.end(), false);
       fill(chrom2.begin(), chrom2.end(), true);
       uxover(chrom, chrom2);
@@ -110,6 +132,20 @@ main()
 	   << chrom << " " << chrom2 << endl; 
     }
 
+  // Check multiOps
+  eoMultiMonOp<Chrom> mOp( &next );
+  mOp.adOp( &bitflip );
+  cout << "before multiMonOp............  " << chrom << endl;
+  mOp( chrom );
+  cout << "after multiMonOp .............. " << chrom << endl;
+
+  eoBinGxOver<Chrom> gxover(2, 4);
+  eoMultiBinOp<Chrom> mbOp( &gxover );
+  mOp.adOp( &bitflip );
+  cout << "before multiBinOp............  " << chrom << " " << chrom2 << endl;
+  mbOp( chrom, chrom2 );
+  cout << "after multiBinOp .............. " << chrom << " " << chrom2 <<endl;
+
   return 0;
 }
 

eo/test/t-eobreeder.cpp

@@ -1,5 +1,27 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
 //-----------------------------------------------------------------------------
 // t-eobreeder.cpp
+//   This program test the breeder object
+// (c) GeNeura Team, 1998 
+/* 
+    This library is free software; you can redistribute it and/or
+    modify 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 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
+            
+*/
 //-----------------------------------------------------------------------------
 
 // to avoid long name warnings
@@ -15,16 +37,7 @@
 
 typedef eoBin<float> Chrom;
 
-//-----------------------------------------------------------------------------
+#include "binary_value.h"
-
-void binary_value(Chrom& chrom)
-{
-  float sum = 0;
-  for (unsigned i = 0; i < chrom.size(); i++)
-    if (chrom[i])
-      sum += pow(2, chrom.size() - i - 1);
-  chrom.fitness(sum);
-}
 
 //-----------------------------------------------------------------------------
 

eo/test/t-eoinclusion.cpp

@@ -2,22 +2,15 @@
 // t-eoinclusion.cpp
 //-----------------------------------------------------------------------------
 
-#include <eo>  // eoBin, eoPop, eoInclusion
+#include <eoBin.h>
+#include <eoPop.h>
+#include <eoInclusion.h>
 
 //-----------------------------------------------------------------------------
 
 typedef eoBin<float> Chrom;
 
-//-----------------------------------------------------------------------------
+#include "binary_value.h"
-
-void binary_value(Chrom& chrom)
-{
-  float sum = 0;
-  for (unsigned i = 0; i < chrom.size(); i++)
-    if (chrom[i])
-      sum += pow(2, chrom.size() - i - 1);
-  chrom.fitness(sum);
-}
 
 //-----------------------------------------------------------------------------
 

eo/test/t-selectOne.cpp

@@ -0,0 +1,87 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// t-selectOne.cpp
+//   This program test the breeder object
+// (c) GeNeura Team, 1998 
+/* 
+    This program is free software; you can redistribute it and/or modify
+    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 program 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 General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; 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
+            
+*/
+//-----------------------------------------------------------------------------
+
+// to avoid long name warnings
+#pragma warning(disable:4786)
+
+#include <eoBin.h>  // eoBin, eoPop, eoBreeder
+#include <eoPop.h>
+#include <eoBitOp.h>
+
+#include <eoUniformSelect.h>
+#include <eoStochTournament.h>
+#include <eoDetTournament.h>
+
+
+//-----------------------------------------------------------------------------
+
+typedef eoBin<float> Chrom;
+
+#include "binary_value.h"
+
+//-----------------------------------------------------------------------------
+
+main()
+{
+  const unsigned POP_SIZE = 8, CHROM_SIZE = 4;
+  unsigned i;
+
+  eoUniform<Chrom::Type> uniform(false, true);
+  eoBinRandom<Chrom> random;
+  eoPop<Chrom> pop; 
+
+  // Create the population
+  for (i = 0; i < POP_SIZE; ++i) {
+    Chrom chrom(CHROM_SIZE);
+    random(chrom);
+    binary_value(chrom);
+    pop.push_back(chrom);
+  }
+  
+  // print population
+  cout << "population:" << endl;
+  for (i = 0; i < pop.size(); ++i)
+    cout << pop[i] << " " << pop[i].fitness() << endl;
+
+  // Declare 1-selectors
+  eoUniformSelect<Chrom> uSelect;
+
+  Chrom aChrom;
+  aChrom = uSelect( pop );
+  cout << "Uniform Select " << aChrom << " " << aChrom.fitness() << endl;
+
+  eoStochTournament<Chrom> sSelect(0.7);
+  aChrom = sSelect( pop );
+  cout << "Stochastic Tournament " << aChrom << " " << aChrom.fitness() << endl;
+
+  eoDetTournament<Chrom> dSelect(3);
+  aChrom = dSelect( pop );
+  cout << "Deterministic Tournament " << aChrom << " " << aChrom.fitness() << endl;
+
+  return 0;
+}
+
+//-----------------------------------------------------------------------------

eo/win/Makefile.am

@@ -0,0 +1,6 @@
+EXTRA_DIST=EO.dsw random.dsp t_eoinsertion.dsp t_ops.dsp\
+	atomops.dsp  t_eoaged.dsp     t_eornd.dsp        t_opsel.dsp\
+	t_eobin.dsp      t_eostring.dsp     t_opselmason.dsp\
+	eo.dsp       t_eobitfact.dsp  t_eovector.dsp     t_pop.dsp\
+	t_eobreeder.dsp  t_es.dsp           t_popops.dsp\
+	eolib.dsp    t_eoid.dsp       t_lottery.dsp\