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
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@ -1,36 +1,36 @@
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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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/* eoVirus.h
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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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(c) GeNeura Team 2001, Marc Schoenauer 2000
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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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This library is free software; you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as
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published by the Free Software Foundation; either version 2 of the
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License, or (at your option) any later version.
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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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This library is distributed in the hope that it will be useful, but
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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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Contact: todos@geneura.ugr.es, http://geneura.ugr.es
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Marc.Schoenauer@polytechnique.fr
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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 $
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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
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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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*/
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#ifndef eoVirus_h
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#define eoVirus_h
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//-----------------------------------------------------------------------------
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#include <iostream>
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#include <functional>
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#include <string>
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#include <vector>
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#include <iostream> // ostream, istream
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#include <functional> // bind2nd
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#include <string> // std::string
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#include <ga/eoBit.h>
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#include "ga/eoBit.h"
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/**
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\defgroup bitstring
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@ -38,13 +38,15 @@ CVS Info: $Date: 2004-12-23 15:29:07 $ $Header: /home/nojhan/dev/eodev/eodev_cvs
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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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/** 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>
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class eoVirus: public eoBit<FitT>
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class eoVirus : public eoBit<FitT>
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{
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public:
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@ -53,64 +55,67 @@ public:
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using eoBit<FitT>::size;
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/**
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* (Default) Constructor.
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* @param size Size of the binary std::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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/** (Default) Constructor
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/// My class name.
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virtual std::string className() const {
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return "eoVirus";
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}
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@param size Size of the binary std::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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/// 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(std::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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std::copy(begin(), end(), std::ostream_iterator<bool>(os));
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std::cout << std::endl;
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std::copy(virus.begin(), virus.end(), std::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(std::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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std::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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std::transform(bits.begin(), bits.end(), virus.begin(),
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std::bind2nd(std::equal_to<char>(), '1'));
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}
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/// My class name
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virtual std::string className() const {
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return "eoVirus";
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}
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private:
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std::vector<bool> virus;
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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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/** 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(std::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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std::copy(begin(), end(), std::ostream_iterator<bool>(os));
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std::cout << std::endl;
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std::copy(virus.begin(), virus.end(), std::ostream_iterator<bool>(os));
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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(std::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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std::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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std::transform(bits.begin(), bits.end(), virus.begin(),
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std::bind2nd(std::equal_to<char>(), '1'));
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}
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}
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private:
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std::vector<bool> virus;
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};
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//-----------------------------------------------------------------------------
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@ -119,6 +124,7 @@ public:
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// Local Variables:
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// coding: iso-8859-1
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// mode: C++
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// c-file-style: "Stroustrup"
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// End:
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@ -22,7 +22,7 @@
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Marc.Schoenauer@polytechnique.fr
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mak@dhi.dk
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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 $
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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 $
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*/
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//-----------------------------------------------------------------------------
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#define _eoVector_h
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#include <vector>
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#include <iterator> // needed for GCC 3.2
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#include <iterator>
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#include <EO.h>
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/**
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@ -39,18 +39,19 @@
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#include <functional> // bind2nd
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#include <string> // std::string
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#include <eoVector.h>
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#include "eoVector.h"
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/**
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\defgroup bitstring
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/** @defgroup bitstring
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Various functions for a bitstring representation
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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 std::vector<bool> specialization.
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/** 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 std::vector<bool> specialization.
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*/
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template <class FitT> class eoBit: public eoVector<FitT, bool>
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{
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@ -63,8 +63,11 @@ t_eofitness_SOURCES = t-eofitness.cpp
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t_eoFitnessAssembledEA_SOURCES = t-eoFitnessAssembledEA.cpp
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t_eobin_SOURCES = t-eobin.cpp
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t_eoVirus_SOURCES = t-eoVirus.cpp
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t_MGE1bit_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
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t_MGE1bit_SOURCES = t-MGE1bit.cpp
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t_MGE_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
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t_MGE_SOURCES = t-MGE.cpp
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t_MGE_control_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
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t_MGE_control_SOURCES = t-MGE-control.cpp
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t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp
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t_eoCheckpointing_SOURCES = t-eoCheckpointing.cpp
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// t-eoMGE.cpp
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//-----------------------------------------------------------------------------
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif
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#ifndef __GNUG__
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// to avoid long name warnings
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#pragma warning(disable:4786)
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#endif // __GNUG__
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#include <eo>
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#include <ga/eoBitOp.h>
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#include "eo"
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#include "ga/eoBitOp.h"
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#include "RoyalRoad.h"
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// Viri
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#include "../contrib/MGE/VirusOp.h"
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#include "../contrib/MGE/eoVirus.h"
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#include "../contrib/MGE/eoInitVirus.h"
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#include "VirusOp.h"
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#include "eoVirus.h"
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#include "eoInitVirus.h"
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//-----------------------------------------------------------------------------
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@ -29,25 +33,25 @@ int main()
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unsigned i;
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eoBooleanGenerator gen;
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// the populations:
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eoPop<Chrom> pop;
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// the populations:
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eoPop<Chrom> pop;
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// Evaluation
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RoyalRoad<Chrom> rr( 8 );
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RoyalRoad<Chrom> rr( 8 );
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eoEvalFuncCounter<Chrom> eval( rr );
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eoInitVirus<float> random(CHROM_SIZE, gen);
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eoInitVirus<float> random(CHROM_SIZE, gen);
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for (i = 0; i < POP_SIZE; ++i) {
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Chrom chrom;
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random(chrom);
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eval(chrom);
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pop.push_back(chrom);
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}
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std::cout << "population:" << std::endl;
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for (i = 0; i < pop.size(); ++i)
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std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
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// selection
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eoStochTournamentSelect<Chrom> lottery(0.9 );
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eoGeneralBreeder<Chrom> breeder( lottery, propSel );
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propSel.add(vm, 0.2);
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propSel.add(xover, 0.8);
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// Replace a single one
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eoCommaReplacement<Chrom> replace;
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// Terminators
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eoGenContinue<Chrom> continuator1(10);
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eoFitContinue<Chrom> continuator2(CHROM_SIZE);
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eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
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eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
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eoCheckPoint<Chrom> checkpoint(continuator);
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eoStdoutMonitor monitor;
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checkpoint.add(monitor);
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@ -88,7 +92,7 @@ int main()
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std::cout << "exception: " << e.what() << std::endl;;
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exit(EXIT_FAILURE);
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}
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std::cout << "pop" << std::endl;
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for (i = 0; i < pop.size(); ++i)
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std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
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@ -2,6 +2,10 @@
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// t-eoMGE.cpp
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//-----------------------------------------------------------------------------
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif
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#ifndef __GNUG__
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// to avoid long name warnings
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#pragma warning(disable:4786)
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@ -13,9 +17,9 @@
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#include "RoyalRoad.h"
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// Viri
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#include "../contrib/MGE/VirusOp.h"
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#include "../contrib/MGE/eoVirus.h"
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#include "../contrib/MGE/eoInitVirus.h"
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#include "VirusOp.h"
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#include "eoVirus.h"
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#include "eoInitVirus.h"
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//-----------------------------------------------------------------------------
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@ -29,25 +33,25 @@ int main()
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unsigned i;
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eoBooleanGenerator gen;
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// the populations:
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eoPop<Chrom> pop;
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// the populations:
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eoPop<Chrom> pop;
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// Evaluation
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RoyalRoad<Chrom> rr( 8 );
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RoyalRoad<Chrom> rr( 8 );
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eoEvalFuncCounter<Chrom> eval( rr );
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eoInitVirus<float> random(CHROM_SIZE, gen);
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eoInitVirus<float> random(CHROM_SIZE, gen);
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for (i = 0; i < POP_SIZE; ++i) {
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Chrom chrom;
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random(chrom);
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eval(chrom);
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pop.push_back(chrom);
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}
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std::cout << "population:" << std::endl;
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for (i = 0; i < pop.size(); ++i)
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std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
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// selection
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eoStochTournamentSelect<Chrom> lottery(0.9 );
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@ -62,14 +66,14 @@ int main()
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propSel.add(vf, 0.05);
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propSel.add(vt, 0.05);
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propSel.add(xover, 0.8);
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// Replace a single one
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eoCommaReplacement<Chrom> replace;
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// Terminators
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eoGenContinue<Chrom> continuator1(10);
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eoFitContinue<Chrom> continuator2(CHROM_SIZE);
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eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
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eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
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eoCheckPoint<Chrom> checkpoint(continuator);
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eoStdoutMonitor monitor;
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checkpoint.add(monitor);
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@ -92,7 +96,7 @@ int main()
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std::cout << "exception: " << e.what() << std::endl;;
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exit(EXIT_FAILURE);
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}
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std::cout << "pop" << std::endl;
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for (i = 0; i < pop.size(); ++i)
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std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
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@ -2,20 +2,23 @@
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// t-eoMGE.cpp
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//-----------------------------------------------------------------------------
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif
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#ifndef __GNUG__
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// to avoid long name warnings
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#pragma warning(disable:4786)
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#endif // __GNUG__
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#include <eo>
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#include <ga/eoBitOp.h>
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#include "eo"
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#include "ga/eoBitOp.h"
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#include "RoyalRoad.h"
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// Viri
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#include "../contrib/MGE/VirusOp.h"
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#include "../contrib/MGE/eoVirus.h"
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#include "../contrib/MGE/eoInitVirus.h"
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#include "VirusOp.h"
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#include "eoVirus.h"
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#include "eoInitVirus.h"
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//-----------------------------------------------------------------------------
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