move paradiseo/eo to deprecated/ before merge with eodev

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