move paradiseo/eo to deprecated/ before merge with eodev

deprecated/eo/contrib/MGE/ChangeLog

@@ -0,0 +1,11 @@
+2006-12-02  Jochen Küpper  <jochen@fhi-berlin.mpg.de>
+
+	* contrib/MGE/VirusOp.h (VirusShiftMutation::operator()): Fix test for
+	i>1. This makes t-MGE1bit pass on x86_64 using GCC.
+
+
+	* Local Variables:
+	* coding: iso-8859-1
+	* mode: flyspell
+	* fill-column: 80
+	* End:

deprecated/eo/contrib/MGE/VirusOp.h

@@ -0,0 +1,145 @@
+/*
+   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:     eodev-main@lists.sourceforge.net
+    old contact: todos@geneura.ugr.es, http://geneura.ugr.es
+                 Marc.Schoenauer@polytechnique.fr
+*/
+
+#ifndef VirusOp_h
+#define VirusOp_h
+
+//-----------------------------------------------------------------------------
+
+#include <iostream>    // ostream, istream
+#include <functional>  // bind2nd
+#include <string>      // std::string
+
+#include <utils/eoRNG.h>
+#include "eoVirus.h"
+
+/** VirusBitFlip --> changes 1 bit
+*/
+
+template<class FitT>
+class VirusBitFlip: public eoMonOp<eoVirus<FitT> > {
+ public:
+  /// The class name.
+  virtual std::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 std::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
+        std::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 std::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 ) {
+                        _chrom.virusBitSet(i-1,true);
+                        _chrom.virusBitSet(i, false);
+                    }
+                }
+            }
+        }
+        return true;
+    }
+};
+
+
+template<class FitT>
+class VirusTransmission: public eoBinOp<eoVirus<FitT> > {
+ public:
+  /// The class name.
+  virtual std::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

deprecated/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

deprecated/eo/contrib/MGE/eoVirus.h

@@ -0,0 +1,130 @@
+/* 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
+*/
+
+
+#ifndef eoVirus_h
+#define eoVirus_h
+
+#include <iostream>
+#include <functional>
+#include <string>
+#include <vector>
+
+#include "ga/eoBit.h"
+
+/**
+\defgroup bitstring
+
+  Various functions for a bitstring representation
+*/
+
+/** 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:
+
+    using eoBit<FitT>::begin;
+    using eoBit<FitT>::end;
+    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) {}
+
+    /// My class name
+    virtual std::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(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;
+};
+
+//-----------------------------------------------------------------------------
+
+#endif //eoBit_h
+
+
+// Local Variables:
+// coding: iso-8859-1
+// mode: C++
+// c-file-style: "Stroustrup"
+// End: