Handle including from contrib/MGE nicely.
This commit is contained in:
kuepper
parent
c563e2c302
commit
7c3702f6a6
7 changed files with 145 additions and 124 deletions
|
|
@ -1,36 +1,36 @@
|
|||
/*
|
||||
eoVirus.h
|
||||
(c) GeNeura Team 2001, Marc Schoenauer 2000
|
||||
/* eoVirus.h
|
||||
|
||||
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.
|
||||
(c) GeNeura Team 2001, Marc Schoenauer 2000
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
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
|
||||
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.
|
||||
|
||||
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
|
||||
Marc.Schoenauer@polytechnique.fr
|
||||
CVS Info: $Date: 2004-12-23 15:29:07 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/contrib/MGE/eoVirus.h,v 1.3 2004-12-23 15:29:07 kuepper Exp $ $Author: kuepper $
|
||||
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
|
||||
*/
|
||||
|
||||
|
||||
#ifndef eoVirus_h
|
||||
#define eoVirus_h
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
#include <iostream>
|
||||
#include <functional>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
#include <iostream> // ostream, istream
|
||||
#include <functional> // bind2nd
|
||||
#include <string> // std::string
|
||||
|
||||
#include <ga/eoBit.h>
|
||||
#include "ga/eoBit.h"
|
||||
|
||||
/**
|
||||
\defgroup bitstring
|
||||
|
|
@ -38,13 +38,15 @@ CVS Info: $Date: 2004-12-23 15:29:07 $ $Header: /home/nojhan/dev/eodev/eodev_cvs
|
|||
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.
|
||||
/** 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>
|
||||
class eoVirus : public eoBit<FitT>
|
||||
{
|
||||
public:
|
||||
|
||||
|
|
@ -53,64 +55,67 @@ public:
|
|||
using eoBit<FitT>::size;
|
||||
|
||||
|
||||
/**
|
||||
* (Default) Constructor.
|
||||
* @param size Size of the binary std::string.
|
||||
*/
|
||||
eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
|
||||
eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
|
||||
/** (Default) Constructor
|
||||
|
||||
/// My class name.
|
||||
virtual std::string className() const {
|
||||
return "eoVirus";
|
||||
}
|
||||
@param size Size of the binary std::string.
|
||||
*/
|
||||
eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
|
||||
eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
|
||||
|
||||
/// 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(std::ostream& os) const {
|
||||
EO<FitT>::printOn(os);
|
||||
os << ' ';
|
||||
os << size() << ' ';
|
||||
std::copy(begin(), end(), std::ostream_iterator<bool>(os));
|
||||
std::cout << std::endl;
|
||||
std::copy(virus.begin(), virus.end(), std::ostream_iterator<bool>(os));
|
||||
}
|
||||
|
||||
/**
|
||||
* To read me from a stream.
|
||||
* @param is The istream.
|
||||
*/
|
||||
virtual void readFrom(std::istream& is){
|
||||
eoBit<FitT>::readFrom(is);
|
||||
unsigned s;
|
||||
is >> s;
|
||||
std::string bits;
|
||||
is >> bits;
|
||||
if (is) {
|
||||
virus.resize(bits.size());
|
||||
std::transform(bits.begin(), bits.end(), virus.begin(),
|
||||
std::bind2nd(std::equal_to<char>(), '1'));
|
||||
}
|
||||
/// My class name
|
||||
virtual std::string className() const {
|
||||
return "eoVirus";
|
||||
}
|
||||
private:
|
||||
std::vector<bool> virus;
|
||||
|
||||
/// 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(std::ostream& os) const {
|
||||
EO<FitT>::printOn(os);
|
||||
os << ' ';
|
||||
os << size() << ' ';
|
||||
std::copy(begin(), end(), std::ostream_iterator<bool>(os));
|
||||
std::cout << std::endl;
|
||||
std::copy(virus.begin(), virus.end(), std::ostream_iterator<bool>(os));
|
||||
}
|
||||
|
||||
/** To read me from a stream.
|
||||
|
||||
@param is The istream.
|
||||
*/
|
||||
virtual void readFrom(std::istream& is){
|
||||
eoBit<FitT>::readFrom(is);
|
||||
unsigned s;
|
||||
is >> s;
|
||||
std::string bits;
|
||||
is >> bits;
|
||||
if (is) {
|
||||
virus.resize(bits.size());
|
||||
std::transform(bits.begin(), bits.end(), virus.begin(),
|
||||
std::bind2nd(std::equal_to<char>(), '1'));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private:
|
||||
|
||||
std::vector<bool> virus;
|
||||
};
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
|
|
@ -119,6 +124,7 @@ public:
|
|||
|
||||
|
||||
// Local Variables:
|
||||
// coding: iso-8859-1
|
||||
// mode: C++
|
||||
// c-file-style: "Stroustrup"
|
||||
// End:
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@
|
|||
Marc.Schoenauer@polytechnique.fr
|
||||
mak@dhi.dk
|
||||
|
||||
CVS Info: $Date: 2004-12-23 15:29:06 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoVector.h,v 1.16 2004-12-23 15:29:06 kuepper Exp $ $Author: kuepper $
|
||||
CVS Info: $Date: 2005-10-06 17:22:40 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoVector.h,v 1.17 2005-10-06 17:22:40 kuepper Exp $ $Author: kuepper $
|
||||
|
||||
*/
|
||||
//-----------------------------------------------------------------------------
|
||||
|
|
@ -31,7 +31,7 @@
|
|||
#define _eoVector_h
|
||||
|
||||
#include <vector>
|
||||
#include <iterator> // needed for GCC 3.2
|
||||
#include <iterator>
|
||||
#include <EO.h>
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -39,18 +39,19 @@
|
|||
#include <functional> // bind2nd
|
||||
#include <string> // std::string
|
||||
|
||||
#include <eoVector.h>
|
||||
#include "eoVector.h"
|
||||
|
||||
/**
|
||||
\defgroup bitstring
|
||||
/** @defgroup bitstring
|
||||
|
||||
Various functions for a bitstring representation
|
||||
Various functions for a bitstring representation
|
||||
*/
|
||||
|
||||
/** eoBit: implementation of bitstring chromosome.
|
||||
\class eoBit eoBit.h ga/eoBit.h
|
||||
\ingroup bitstring
|
||||
* based on STL's std::vector<bool> specialization.
|
||||
/** Implementation of bitstring chromosome.
|
||||
|
||||
@class eoBit eoBit.h ga/eoBit.h
|
||||
@ingroup bitstring
|
||||
|
||||
Based on STL's std::vector<bool> specialization.
|
||||
*/
|
||||
template <class FitT> class eoBit: public eoVector<FitT, bool>
|
||||
{
|
||||
|
|
|
|||
|
|
@ -63,8 +63,11 @@ t_eofitness_SOURCES = t-eofitness.cpp
|
|||
t_eoFitnessAssembledEA_SOURCES = t-eoFitnessAssembledEA.cpp
|
||||
t_eobin_SOURCES = t-eobin.cpp
|
||||
t_eoVirus_SOURCES = t-eoVirus.cpp
|
||||
t_MGE1bit_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
|
||||
t_MGE1bit_SOURCES = t-MGE1bit.cpp
|
||||
t_MGE_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
|
||||
t_MGE_SOURCES = t-MGE.cpp
|
||||
t_MGE_control_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
|
||||
t_MGE_control_SOURCES = t-MGE-control.cpp
|
||||
t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp
|
||||
t_eoCheckpointing_SOURCES = t-eoCheckpointing.cpp
|
||||
|
|
|
|||
|
|
@ -2,20 +2,24 @@
|
|||
// t-eoMGE.cpp
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#ifndef __GNUG__
|
||||
// to avoid long name warnings
|
||||
#pragma warning(disable:4786)
|
||||
#endif // __GNUG__
|
||||
|
||||
#include <eo>
|
||||
#include <ga/eoBitOp.h>
|
||||
#include "eo"
|
||||
#include "ga/eoBitOp.h"
|
||||
|
||||
#include "RoyalRoad.h"
|
||||
|
||||
// Viri
|
||||
#include "../contrib/MGE/VirusOp.h"
|
||||
#include "../contrib/MGE/eoVirus.h"
|
||||
#include "../contrib/MGE/eoInitVirus.h"
|
||||
#include "VirusOp.h"
|
||||
#include "eoVirus.h"
|
||||
#include "eoInitVirus.h"
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
|
|
@ -29,25 +33,25 @@ int main()
|
|||
unsigned i;
|
||||
eoBooleanGenerator gen;
|
||||
|
||||
// the populations:
|
||||
eoPop<Chrom> pop;
|
||||
// the populations:
|
||||
eoPop<Chrom> pop;
|
||||
|
||||
// Evaluation
|
||||
RoyalRoad<Chrom> rr( 8 );
|
||||
RoyalRoad<Chrom> rr( 8 );
|
||||
eoEvalFuncCounter<Chrom> eval( rr );
|
||||
|
||||
eoInitVirus<float> random(CHROM_SIZE, gen);
|
||||
eoInitVirus<float> random(CHROM_SIZE, gen);
|
||||
for (i = 0; i < POP_SIZE; ++i) {
|
||||
Chrom chrom;
|
||||
random(chrom);
|
||||
eval(chrom);
|
||||
pop.push_back(chrom);
|
||||
}
|
||||
|
||||
|
||||
std::cout << "population:" << std::endl;
|
||||
for (i = 0; i < pop.size(); ++i)
|
||||
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
|
||||
|
||||
|
||||
// selection
|
||||
eoStochTournamentSelect<Chrom> lottery(0.9 );
|
||||
|
||||
|
|
@ -58,14 +62,14 @@ int main()
|
|||
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
|
||||
propSel.add(vm, 0.2);
|
||||
propSel.add(xover, 0.8);
|
||||
|
||||
|
||||
// Replace a single one
|
||||
eoCommaReplacement<Chrom> replace;
|
||||
|
||||
// Terminators
|
||||
eoGenContinue<Chrom> continuator1(10);
|
||||
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
|
||||
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
|
||||
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
|
||||
eoCheckPoint<Chrom> checkpoint(continuator);
|
||||
eoStdoutMonitor monitor;
|
||||
checkpoint.add(monitor);
|
||||
|
|
@ -88,7 +92,7 @@ int main()
|
|||
std::cout << "exception: " << e.what() << std::endl;;
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
|
||||
std::cout << "pop" << std::endl;
|
||||
for (i = 0; i < pop.size(); ++i)
|
||||
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
|
||||
|
|
|
|||
|
|
@ -2,6 +2,10 @@
|
|||
// t-eoMGE.cpp
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#ifndef __GNUG__
|
||||
// to avoid long name warnings
|
||||
#pragma warning(disable:4786)
|
||||
|
|
@ -13,9 +17,9 @@
|
|||
#include "RoyalRoad.h"
|
||||
|
||||
// Viri
|
||||
#include "../contrib/MGE/VirusOp.h"
|
||||
#include "../contrib/MGE/eoVirus.h"
|
||||
#include "../contrib/MGE/eoInitVirus.h"
|
||||
#include "VirusOp.h"
|
||||
#include "eoVirus.h"
|
||||
#include "eoInitVirus.h"
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
|
|
@ -29,25 +33,25 @@ int main()
|
|||
unsigned i;
|
||||
eoBooleanGenerator gen;
|
||||
|
||||
// the populations:
|
||||
eoPop<Chrom> pop;
|
||||
// the populations:
|
||||
eoPop<Chrom> pop;
|
||||
|
||||
// Evaluation
|
||||
RoyalRoad<Chrom> rr( 8 );
|
||||
RoyalRoad<Chrom> rr( 8 );
|
||||
eoEvalFuncCounter<Chrom> eval( rr );
|
||||
|
||||
eoInitVirus<float> random(CHROM_SIZE, gen);
|
||||
eoInitVirus<float> random(CHROM_SIZE, gen);
|
||||
for (i = 0; i < POP_SIZE; ++i) {
|
||||
Chrom chrom;
|
||||
random(chrom);
|
||||
eval(chrom);
|
||||
pop.push_back(chrom);
|
||||
}
|
||||
|
||||
|
||||
std::cout << "population:" << std::endl;
|
||||
for (i = 0; i < pop.size(); ++i)
|
||||
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
|
||||
|
||||
|
||||
// selection
|
||||
eoStochTournamentSelect<Chrom> lottery(0.9 );
|
||||
|
||||
|
|
@ -62,14 +66,14 @@ int main()
|
|||
propSel.add(vf, 0.05);
|
||||
propSel.add(vt, 0.05);
|
||||
propSel.add(xover, 0.8);
|
||||
|
||||
|
||||
// Replace a single one
|
||||
eoCommaReplacement<Chrom> replace;
|
||||
|
||||
// Terminators
|
||||
eoGenContinue<Chrom> continuator1(10);
|
||||
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
|
||||
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
|
||||
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
|
||||
eoCheckPoint<Chrom> checkpoint(continuator);
|
||||
eoStdoutMonitor monitor;
|
||||
checkpoint.add(monitor);
|
||||
|
|
@ -92,7 +96,7 @@ int main()
|
|||
std::cout << "exception: " << e.what() << std::endl;;
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
|
||||
std::cout << "pop" << std::endl;
|
||||
for (i = 0; i < pop.size(); ++i)
|
||||
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
|
||||
|
|
|
|||
|
|
@ -2,20 +2,23 @@
|
|||
// t-eoMGE.cpp
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#ifndef __GNUG__
|
||||
// to avoid long name warnings
|
||||
#pragma warning(disable:4786)
|
||||
#endif // __GNUG__
|
||||
|
||||
#include <eo>
|
||||
#include <ga/eoBitOp.h>
|
||||
|
||||
#include "eo"
|
||||
#include "ga/eoBitOp.h"
|
||||
#include "RoyalRoad.h"
|
||||
|
||||
// Viri
|
||||
#include "../contrib/MGE/VirusOp.h"
|
||||
#include "../contrib/MGE/eoVirus.h"
|
||||
#include "../contrib/MGE/eoInitVirus.h"
|
||||
#include "VirusOp.h"
|
||||
#include "eoVirus.h"
|
||||
#include "eoInitVirus.h"
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
|
|
|
|||
Reference in a new issue