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

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jmerelo 2001-05-17 10:08:25 +00:00
commit 17dc4f9d10
6 changed files with 81 additions and 14 deletions
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144
eo/contrib/MGE/VirusOp.h Normal file
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@ -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

86
eo/contrib/MGE/eoInitVirus.h Normal file
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@ -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

112
eo/contrib/MGE/eoVirus.h Normal file
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@ -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

11
eo/test/Makefile.am
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@ -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)

6
eo/test/t-MGE-control.cpp
View file

@ -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(xover, 0.1);
propSel.add(vm, 0.2);
propSel.add(xover, 0.8);
// Replace a single one
eoCommaReplacement<Chrom> replace;

6
eo/test/t-MGE.cpp
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@ -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;