Added 'Viral' operators with test. Implements the Mobile Genetic Elements Technique
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jmerelo
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7 changed files with 500 additions and 26 deletions
106
eo/src/MGE/VirusOp.h
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106
eo/src/MGE/VirusOp.h
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/*
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ViruOp.h
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(c) GeNeura Team 2001, Marc Schoenauer 2000
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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version 2 of the License, or (at your option) any later version.
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public
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License along with this library; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Contact: todos@geneura.ugr.es, http://geneura.ugr.es
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Marc.Schoenauer@polytechnique.fr
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CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/MGE/Attic/VirusOp.h,v 1.1 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
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*/
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#ifndef VirusOp_h
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#define VirusOp_h
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//-----------------------------------------------------------------------------
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#include <iostream> // ostream, istream
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#include <functional> // bind2nd
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#include <string> // string
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#include <utils/eoRNG.h>
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#include <MGE/eoVirus.h>
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/** eoBitFlip --> changes 1 bit
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\class eoBitBitFlip eoBitOp.h ga/eoBitOp.h
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\ingroup bitstring
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*/
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template<class FitT>
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class VirusBitFlip: public eoMonOp<eoVirus<FitT> > {
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public:
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/// The class name.
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virtual string className() const { return "VirusBitFlip"; };
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/**
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* Change one bit.
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* @param chrom The cromosome which one bit is going to be changed.
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*/
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bool operator()(eoVirus<FitT>& _chrom) {
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unsigned i = eo::rng.random(_chrom.size());
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_chrom.virusBitSet(i, _chrom.virusBit(i) ? false : true );
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return true;
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}
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};
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template<class FitT>
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class VirusMutation: public eoMonOp<eoVirus<FitT> > {
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public:
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/// The class name.
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virtual string className() const { return "VirusMutation"; };
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/**
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* Change one bit.
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* @param chrom The cromosome which one bit is going to be changed.
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*/
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bool operator()(eoVirus<FitT>& _chrom) {
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// Search for virus bits
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vector<unsigned> bitsSet;
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for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
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if ( _chrom.virusBit(i) ) {
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bitsSet.push_back( i );
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}
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}
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if ( !bitsSet.size() ) {
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return false;
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}
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unsigned flipSite = eo::rng.random(bitsSet.size());
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unsigned flipValue = bitsSet[ flipSite ];
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_chrom[flipValue] = _chrom[flipValue] ? false : true;
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return true;
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}
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};
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template<class FitT>
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class VirusTransmission: public eoBinOp<eoVirus<FitT> > {
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public:
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/// The class name.
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virtual string className() const { return "VirusTransmission"; };
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/**
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* Change one bit.
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* @param _chrom The "receptor" chromosome
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* @param _chrom2 The "donor" chromosome
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*/
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bool operator()(eoVirus<FitT>& _chrom,const eoVirus<FitT>& _chrom2) {
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// Search for virus bits
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for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
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_chrom.virusBitSet(i, _chrom2.virusBit(i) );
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}
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return true;
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}
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};
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#endif //VirusOp_h
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64
eo/src/MGE/eoInitVirus.h
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64
eo/src/MGE/eoInitVirus.h
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@ -0,0 +1,64 @@
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
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//-----------------------------------------------------------------------------
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// eoInit.h
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// (c) Maarten Keijzer 2000, GeNeura Team, 2000
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/*
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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version 2 of the License, or (at your option) any later version.
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public
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License along with this library; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Contact: todos@geneura.ugr.es, http://geneura.ugr.es
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Marc.Schoenauer@polytechnique.fr
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mak@dhi.dk
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*/
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//-----------------------------------------------------------------------------
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#ifndef _eoInitVirus_H
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#define _eoInitVirus_H
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#include <algorithm>
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#include <eoOp.h>
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#include <eoSTLFunctor.h>
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#include <utils/eoRndGenerators.h>
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#include <eoInit.h>
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/**
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Initializer for binary chromosome with MGE
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*/
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template <class FitT>
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class eoInitVirus: public eoInit< eoVirus<FitT> > {
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public:
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eoInitVirus(unsigned _combien, eoRndGenerator<bool>& _generator)
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: combien(_combien), generator(_generator) {}
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virtual void operator()( eoVirus<FitT>& chrom)
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{
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chrom.resize(combien);
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chrom.virResize(combien);
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std::generate(chrom.begin(), chrom.end(), generator);
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for ( unsigned i = 0; i < combien; i ++ ) {
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chrom.virusBitSet(i, generator() );
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}
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chrom.invalidate();
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}
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private :
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unsigned combien;
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/// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics
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eoSTLF<bool> generator;
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};
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#endif
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112
eo/src/MGE/eoVirus.h
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112
eo/src/MGE/eoVirus.h
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@ -0,0 +1,112 @@
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/*
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eoVirus.h
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(c) GeNeura Team 2001, Marc Schoenauer 2000
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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version 2 of the License, or (at your option) any later version.
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public
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License along with this library; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Contact: todos@geneura.ugr.es, http://geneura.ugr.es
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Marc.Schoenauer@polytechnique.fr
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CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/MGE/Attic/eoVirus.h,v 1.1 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
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*/
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#ifndef eoVirus_h
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#define eoVirus_h
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//-----------------------------------------------------------------------------
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#include <iostream> // ostream, istream
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#include <functional> // bind2nd
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#include <string> // string
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#include <ga/eoBit.h>
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/**
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\defgroup bitstring
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Various functions for a bitstring representation
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*/
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/** eoBit: implementation of bitstring chromosome.
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\class eoBit eoBit.h ga/eoBit.h
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\ingroup bitstring
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* based on STL's vector<bool> specialization.
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*/
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template <class FitT> class eoVirus: public eoBit<FitT>
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{
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public:
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/**
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* (Default) Constructor.
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* @param size Size of the binary string.
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*/
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eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
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eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
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/// My class name.
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virtual string className() const {
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return "eoVirus";
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}
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/// Access to virus features
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void virResize( unsigned _i ) {
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virus.resize(_i );
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}
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/// Access to virus features
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bool virusBit( unsigned _i ) const {
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return virus[_i];
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}
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/// Change virus features
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void virusBitSet( unsigned _i, bool _bit ) {
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virus[_i ] = _bit;
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}
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/**
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* To print me on a stream.
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* @param os The ostream.
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*/
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virtual void printOn(ostream& os) const {
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EO<FitT>::printOn(os);
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os << ' ';
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os << size() << ' ';
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copy(begin(), end(), ostream_iterator<bool>(os));
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cout << endl;
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copy(virus.begin(), virus.end(), ostream_iterator<bool>(os));
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}
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/**
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* To read me from a stream.
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* @param is The istream.
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*/
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virtual void readFrom(istream& is){
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eoBit<FitT>::readFrom(is);
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unsigned s;
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is >> s;
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string bits;
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is >> bits;
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if (is) {
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virus.resize(bits.size());
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transform(bits.begin(), bits.end(), virus.begin(),
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bind2nd(equal_to<char>(), '1'));
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}
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}
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private:
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vector<bool> virus;
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};
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//-----------------------------------------------------------------------------
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#endif //eoBit_h
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@ -21,33 +21,9 @@
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Contact: todos@geneura.ugr.es, http://geneura.ugr.es
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Marc.Schoenauer@polytechnique.fr
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mak@dhi.dk
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CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/ga/eoBitOp.h,v 1.13 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
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*/
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//-----------------------------------------------------------------------------
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// MS 17/10/2000
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// Added the uniform crossover - which, for some reasons, had dissapeared!
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// Added the eoDetBitFlip, which flips exactly num_bit bits
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// Aslo added the above standard header
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// I also want to start the discussion about the "gene" crossover.
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// I think the word "gene" is not appropriate: if real numbers are coded in
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// binary format, then a "gene" is a bit, and that's it
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// if you want to exchange real number per se, then use real coding
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//
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// Because all crossover operators here except that Gene crossover
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// ARE generic, i.e. appky to any vertor of something.
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// Note that for mutations, if instead of
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// chrom[i] = (chrom[i]) ? false : true;
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// we were calling something like
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// specific_mutate(chrom[i])
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// all mutation would also be generic ... except those eoBitNext and eoBitPrev
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// If anybody reads this and want to change that (I'm also testing to see
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// if someone ever reads the headers :-), drop me a mail
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// Marc (Marc.Schoenauer@polytechnique.fr)
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//-----------------------------------------------------------------------------
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// eoBitOp.h
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//-----------------------------------------------------------------------------
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#ifndef eoBitOp_h
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#define eoBitOp_h
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