Changed MGE to the contrib dir. No need to change the prefix, I guess

eo/contrib/MGE/VirusOp.h

@@ -0,0 +1,144 @@
+/*
+   ViruOp.h
+   (c) GeNeura Team 2001, Marc Schoenauer 2000
+
+    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
+CVS Info: $Date: 2001-05-17 10:08:25 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/contrib/MGE/VirusOp.h,v 1.1 2001-05-17 10:08:25 jmerelo Exp $ $Author: jmerelo $
+*/
+
+#ifndef VirusOp_h
+#define VirusOp_h
+
+//-----------------------------------------------------------------------------
+
+#include <iostream>    // ostream, istream
+#include <functional>  // bind2nd
+#include <string>      // string
+
+#include <utils/eoRNG.h>
+#include <MGE/eoVirus.h>
+
+/** VirusBitFlip --> changes 1 bit
+*/
+
+template<class FitT>
+class VirusBitFlip: public eoMonOp<eoVirus<FitT> > {
+ public:
+  /// The class name.
+  virtual string className() const { return "VirusBitFlip"; };
+
+  /**
+   * Change one bit.
+   * @param chrom The cromosome which one bit is going to be changed.
+   */
+  bool operator()(eoVirus<FitT>& _chrom) {
+      unsigned i = eo::rng.random(_chrom.size());
+      _chrom.virusBitSet(i, _chrom.virusBit(i) ? false : true );
+      return true;
+  }
+};
+
+template<class FitT>
+class VirusMutation: public eoMonOp<eoVirus<FitT> > {
+ public:
+  /// The class name.
+  virtual string className() const { return "VirusMutation"; };
+
+  /**
+   * Change one bit.
+   * @param chrom The cromosome which one bit is going to be changed.
+   */
+  bool operator()(eoVirus<FitT>& _chrom) {
+	// Search for virus bits
+	vector<unsigned> bitsSet;
+	for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
+	  if ( _chrom.virusBit(i) ) {
+		bitsSet.push_back( i );
+	  }
+	}
+	if ( !bitsSet.size() ) {
+	  return false;
+	}
+    unsigned flipSite = eo::rng.random(bitsSet.size());
+	unsigned flipValue = bitsSet[ flipSite ];
+	_chrom[flipValue] = _chrom[flipValue] ? false : true;
+	return true;
+  }
+};
+
+/// Works for 1-bit virus; shifts the one to the right or left
+template<class FitT>
+class VirusShiftMutation: public eoMonOp<eoVirus<FitT> > {
+ public:
+
+  /// Ctor
+  VirusShiftMutation( ) {};
+
+  /// The class name.
+  virtual string className() const { return "VirusShiftMutation"; };
+
+  /**
+   * Change one bit.
+   * @param chrom The cromosome which one bit is going to be changed.
+   */
+  bool operator()(eoVirus<FitT>& _chrom) {
+	// Search for virus bits
+	eoBooleanGenerator gen;
+	for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
+	  if ( _chrom.virusBit(i) ) {
+		if ( gen() ) {
+		  if ( i + 1 < _chrom.size() ) {
+			_chrom.virusBitSet(i+1,true);
+			_chrom.virusBitSet(i, false);
+		  }
+		} else {
+		  if ( i - 1 > 0 ) {
+			_chrom.virusBitSet(i-1,true);
+			_chrom.virusBitSet(i, false);
+		  }
+		}
+	  }
+	}
+	return true;
+  }
+
+ private:
+};
+
+
+template<class FitT>
+class VirusTransmission: public eoBinOp<eoVirus<FitT> > {
+ public:
+  /// The class name.
+  virtual string className() const { return "VirusTransmission"; };
+
+  /**
+   * Change one bit.
+   * @param _chrom The "receptor" chromosome
+   * @param _chrom2 The "donor" chromosome
+   */
+  bool operator()(eoVirus<FitT>& _chrom,const eoVirus<FitT>& _chrom2) {
+	// Search for virus bits
+	for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
+	  _chrom.virusBitSet(i, _chrom2.virusBit(i) );
+	}
+	return true;
+  }
+};
+
+#endif //VirusOp_h

eo/contrib/MGE/eoInitVirus.h

@@ -0,0 +1,86 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoInit.h
+// (c) Maarten Keijzer 2000, GeNeura Team, 2000
+/*
+    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
+             mak@dhi.dk
+ */
+//-----------------------------------------------------------------------------
+
+#ifndef _eoInitVirus_H
+#define _eoInitVirus_H
+
+#include <algorithm>
+
+#include <eoOp.h>
+#include <eoSTLFunctor.h>
+#include <utils/eoRndGenerators.h>
+#include <eoInit.h>
+
+/**
+    Initializer for binary chromosome with MGE
+*/
+template <class FitT>
+class eoInitVirus: public eoInit< eoVirus<FitT> > {
+public:
+
+  eoInitVirus(unsigned _combien, eoRndGenerator<bool>& _generator )
+	: combien(_combien), generator(_generator) {}
+  
+  virtual void operator()( eoVirus<FitT>& chrom)
+  {
+	chrom.resize(combien);
+	chrom.virResize(combien);
+	std::generate(chrom.begin(), chrom.end(), generator);
+	for ( unsigned i = 0; i < combien; i ++ ) {
+	  chrom.virusBitSet(i, generator() );
+	}
+	chrom.invalidate();
+  }
+  
+private :
+  unsigned combien;
+  /// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics
+  eoSTLF<bool> generator;
+};
+
+/// Inits the virus with one bit to the left set to one
+template <class FitT>
+class eoInitVirus1bit: public eoInit< eoVirus<FitT> > {
+public:
+
+  eoInitVirus1bit(unsigned _combien, eoRndGenerator<bool>& _generator )
+	: combien(_combien), generator(_generator) {}
+  
+  virtual void operator()( eoVirus<FitT>& chrom)
+  {
+	chrom.resize(combien);
+	chrom.virResize(combien);
+	std::generate(chrom.begin(), chrom.end(), generator);
+	chrom.virusBitSet(0, true );
+	chrom.invalidate();
+  }
+  
+private :
+  unsigned combien;
+  /// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics
+  eoSTLF<bool> generator;
+};
+#endif

eo/contrib/MGE/eoVirus.h

@@ -0,0 +1,112 @@
+/*
+   eoVirus.h
+   (c) GeNeura Team 2001, Marc Schoenauer 2000
+
+    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
+CVS Info: $Date: 2001-05-17 10:08:25 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/contrib/MGE/eoVirus.h,v 1.1 2001-05-17 10:08:25 jmerelo Exp $ $Author: jmerelo $
+*/
+
+#ifndef eoVirus_h
+#define eoVirus_h
+
+//-----------------------------------------------------------------------------
+
+#include <iostream>    // ostream, istream
+#include <functional>  // bind2nd
+#include <string>      // string
+
+#include <ga/eoBit.h>
+
+/**
+\defgroup bitstring
+
+  Various functions for a bitstring representation
+*/
+
+/** eoBit: implementation of bitstring chromosome.
+\class eoBit eoBit.h ga/eoBit.h
+\ingroup bitstring
+  * based on STL's vector<bool> specialization.
+*/
+template <class FitT> class eoVirus: public eoBit<FitT>
+{
+ public:
+
+  /**
+   * (Default) Constructor.
+   * @param size Size of the binary string.
+   */
+  eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
+    eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
+
+  /// My class name.
+  virtual string className() const {
+      return "eoVirus";
+  }
+
+  /// Access to virus features
+  void virResize( unsigned _i ) {
+	virus.resize(_i );
+  }
+
+  /// Access to virus features
+  bool virusBit( unsigned _i ) const {
+	return virus[_i];
+  }
+
+  /// Change virus features
+  void virusBitSet( unsigned _i, bool _bit ) {
+	virus[_i ] = _bit;
+  }
+
+  /**
+   * To print me on a stream.
+   * @param os The ostream.
+   */
+  virtual void printOn(ostream& os) const {
+      EO<FitT>::printOn(os);
+      os << ' ';
+      os << size() << ' ';
+      copy(begin(), end(), ostream_iterator<bool>(os));
+	  cout << endl;
+	  copy(virus.begin(), virus.end(), ostream_iterator<bool>(os));
+  }
+
+  /**
+   * To read me from a stream.
+   * @param is The istream.
+   */
+  virtual void readFrom(istream& is){
+      eoBit<FitT>::readFrom(is);
+      unsigned s;
+      is >> s;
+      string bits;
+      is >> bits;
+      if (is) {
+		virus.resize(bits.size());
+		transform(bits.begin(), bits.end(), virus.begin(),
+				  bind2nd(equal_to<char>(), '1'));
+	  }
+    }
+ private:
+  vector<bool> virus;
+};
+
+//-----------------------------------------------------------------------------
+
+#endif //eoBit_h

eo/test/Makefile.am

@@ -8,12 +8,13 @@ DEPS = $(top_builddir)/src/utils/libeoutils.a $(top_builddir)/src/libeo.a
 
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src
+INCLUDES = -I$(top_builddir)/src -I$(top_builddir)/contrib
 LDADDS = $(top_builddir)/src/utils/libeoutils.a $(top_builddir)/src/libeo.a
 CXXFLAGS = -g -Wall 
 ###############################################################################
 
-check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoVirus t-MGE t-MGE-control t-eoStateAndParser t-eoCheckpointing t-eoSSGA  \
+check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoVirus\
+	 t-MGE t-MGE1bit t-MGE-control t-eoStateAndParser t-eoCheckpointing t-eoSSGA  \
 	t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA t-eoReal t-eoVector t-eoESAll
 TESTS=run_tests t-eoVector t-eoRandom t-eoSSGA t-eoPareto t-eoParetoFitness
 # removing temporarily t-eoESFull
@@ -45,6 +46,12 @@ t_eoVirus_LDADD = $(LDADDS)
 
 ###############################################################################
 
+t_MGE1bit_SOURCES = t-MGE1bit.cpp binary_value.h
+t_MGE1bit_DEPENDENCIES = $(DEPS)
+t_MGE1bit_LDADD = $(LDADDS)
+
+###############################################################################
+
 t_MGE_SOURCES = t-MGE.cpp binary_value.h
 t_MGE_DEPENDENCIES = $(DEPS)
 t_MGE_LDADD = $(LDADDS)

eo/test/t-MGE-control.cpp

@@ -33,7 +33,7 @@ int main()
   eoPop<Chrom> pop; 
 
   // Evaluation
-  RoyalRoad<Chrom> rr( 4 ); 
+  RoyalRoad<Chrom> rr( 8 ); 
   eoEvalFuncCounter<Chrom> eval( rr );
 
   eoInitVirus<float> random(CHROM_SIZE, gen); 
@@ -56,8 +56,8 @@ int main()
   eoUBitXover<Chrom> xover;
   eoProportionalOp<Chrom> propSel;
   eoGeneralBreeder<Chrom> breeder( lottery, propSel );
-  propSel.add(vm, 0.8);
+  propSel.add(vm, 0.2);
-  propSel.add(xover, 0.1);
+  propSel.add(xover, 0.8);
   
   // Replace a single one
   eoCommaReplacement<Chrom> replace;

eo/test/t-MGE.cpp

@@ -33,7 +33,7 @@ int main()
   eoPop<Chrom> pop; 
 
   // Evaluation
-  RoyalRoad<Chrom> rr( 4 ); 
+  RoyalRoad<Chrom> rr( 8 ); 
   eoEvalFuncCounter<Chrom> eval( rr );
 
   eoInitVirus<float> random(CHROM_SIZE, gen); 
@@ -58,10 +58,10 @@ int main()
   eoUBitXover<Chrom> xover;
   eoProportionalOp<Chrom> propSel;
   eoGeneralBreeder<Chrom> breeder( lottery, propSel );
-  propSel.add(vm, 0.8);
+  propSel.add(vm, 0.1);
   propSel.add(vf, 0.05);
   propSel.add(vt, 0.05);
-  propSel.add(xover, 0.1);
+  propSel.add(xover, 0.8);
   
   // Replace a single one
   eoCommaReplacement<Chrom> replace;