Checking in the name changes in selection procedures.

This impacts on many files, creating new entries in src (the old ones are moved
to obsolete dir), modifying t-eoSymreg.cpp and t-eobin.cpp in test,
as well as gprop.cc and mastermind.cc in app dir (not to mention almost all
files in tutorial:-(

eo/src/eo

@@ -92,21 +92,24 @@
 #include <eoEvalFuncPtr.h>
 
 // Continuators
-#include <eoContinue.h>
+// #include <eoContinue.h>    // already included in the following
 #include <eoCombinedContinue.h>
 #include <eoGenContinue.h>
 #include <eoSteadyFitContinue.h>
 #include <eoFitContinue.h>
 
 // Selection 
-#include <eoSelectOne.h>
-#include <eoSelectRandom.h>
-#include <eoDetTournament.h>
-#include <eoProportional.h>
-#include <eoStochTournament.h>
+// the eoSelectOne
+#include <eoRandomSelect.h>
+#include <eoDetTournamentSelect.h>
+#include <eoProportionalSelect.h>
+#include <eoStochTournamentSelect.h>
+// the batch selection - from an eoSelectOne
 #include <eoSelectPerc.h>
 #include <eoSelectNumber.h>
 #include <eoSelectMany.h>
+// other batch selections
+#include <eoDetSelect.h>
 
 
 // Replacement
@@ -129,6 +132,8 @@
 
 //#include <eoProportionalOpSel.h>
 
+#include <eoSGATransform.h>
+
 // Algorithms
 #include <eoEasyEA.h>
 #include <eoSGA.h>

eo/src/eoDetTournamentSelect.h

@@ -0,0 +1,69 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoDetTournament.h
+// (c) GeNeura Team, 1998 - EEAAX 1999
+/* 
+    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 eoDetTournament_h
+#define eoDetTournament_h
+
+//-----------------------------------------------------------------------------
+
+#include <functional>  // 
+#include <numeric>     // accumulate
+
+#include <eoFunctor.h>
+#include <eoPop.h>
+#include <utils/selectors.h>
+
+//-----------------------------------------------------------------------------
+/** eoDetTournamentSelect: a selection method that selects ONE individual by
+ deterministic tournament 
+ -MS- 24/10/99 */
+//-----------------------------------------------------------------------------
+
+template <class EOT> class eoDetTournamentSelect: public eoSelectOne<EOT>
+{
+ public:
+  /// (Default) Constructor.
+  eoDetTournamentSelect(unsigned _Tsize = 2 ):eoSelectOne<EOT>(), Tsize(_Tsize) {
+    // consistency check
+    if (Tsize < 2) {
+      cout << "Warning, Tournament size should be >= 2\nAdjusted\n";
+      Tsize = 2;
+    }
+  }
+  
+  /// Perform deterministic tournament
+  virtual const EOT& operator()(const eoPop<EOT>& pop) 
+  {
+    return deterministic_tournament(pop, Tsize);
+  }
+  
+ private:
+  unsigned Tsize;
+};
+
+//-----------------------------------------------------------------------------
+
+#endif eoDetTournamentSelect_h
+

eo/src/eoEvolutionStrategy.h

@@ -73,7 +73,7 @@ class eoEvolutionStrategy: public eoAlgo<EOT>
      eoPlus<EOT>    plus;
      eoNoElitism<EOT> noElitism;
      eoTruncate<EOT> truncate;
-     eoSelectRandom<EOT> randomSelect;
+     eoRandomSelect<EOT> randomSelect;
      eoSelectPerc<EOT> selectPerc;
      eoInplaceTransform2<EOT> transform;
 

eo/src/eoInplaceTransform.h

@@ -123,7 +123,7 @@ template<class Chrom> class eoInplaceTransform1 : public eoTransform<Chrom>
     
  private:
   eoOpSelector<Chrom>& opSel;
-  eoSelectRandom<Chrom> defaultSelect;
+  eoRandomSelect<Chrom> defaultSelect;
   eoSelectOne<Chrom>&  select;
   
 };
@@ -181,7 +181,7 @@ template<class Chrom> class eoInplaceTransform2 : public eoTransform<Chrom>
     
  private:
   eoGOpSelector<Chrom>& opSel;
-  eoSelectRandom<Chrom> defaultSelect;
+  eoRandomSelect<Chrom> defaultSelect;
   eoSelectOne<Chrom>&  select;
   
 };

eo/src/eoMergeReduce.h

@@ -94,5 +94,22 @@ class eoCommaReplacement : public eoMergeReduce<EOT>
         eoTruncate<EOT> truncate;
 };
 
+/**
+EP type of replacement strategy: first add parents to population, 
+   then truncate using EP tournament
+*/
+template <class EOT>
+class eoEPReplacement : public eoMergeReduce<EOT>
+{
+public :
+  eoEPReplacement(int _tSize) : eoMergeReduce<EOT>(plus, truncate), truncate(_tSize)
+    //  {truncate.setSize(_tSize);}
+  {}
+private :
+  eoPlus<EOT> plus;
+  eoEPReduce<EOT> truncate;
+};
+
+
 
 #endif

eo/src/eoProportionalSelect.h

@@ -0,0 +1,71 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoProportionalSelect.h
+// (c) GeNeura Team, 1998 - EEAAX 1999, Maarten Keijzer 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 eoProportionalSelect_h
+#define eoProportionalSelect_h
+
+//-----------------------------------------------------------------------------
+
+#include <utils/eoRNG.h>
+#include <utils/selectors.h>
+#include <eoSelectOne.h>
+
+//-----------------------------------------------------------------------------
+/** eoProportionalSelect: select an individual proportional to her stored fitness
+    value 
+
+*/
+//-----------------------------------------------------------------------------
+
+template <class EOT> class eoProportionalSelect: public eoSelectOne<EOT> 
+{
+public:
+  /// Sanity check
+  eoProportionalSelect(const eoPop<EOT>& pop = eoPop<EOT>()): 
+    total((pop.size() == 0) ? -1.0 : sum_fitness(pop))
+  {
+    if (minimizing_fitness<EOT>())
+      throw logic_error("eoProportionalSelect: minimizing fitness");
+  }
+
+  void setup(const eoPop<EOT>& _pop)
+  {
+    total = sum_fitness(_pop);
+  }
+    
+  /** do the selection, call roulette_wheel. 
+   */
+  const EOT& operator()(const eoPop<EOT>& _pop) 
+  {
+    return roulette_wheel(_pop, total) ;
+  }
+
+private :
+  typename EOT::Fitness total;
+};
+
+#endif 
+

eo/src/eoRandomSelect.h

@@ -0,0 +1,52 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoRandomSelect.h
+// (c) GeNeura Team, 1998 - EEAAX 1999, Maarten Keijzer 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 eoRandomSelect_h
+#define eoRandomSelect_h
+
+//-----------------------------------------------------------------------------
+
+#include <utils/eoRNG.h>
+#include <eoSelectOne.h>
+
+//-----------------------------------------------------------------------------
+/** eoRandomSelect: a selection method that selects ONE individual randomly
+ -MS- 22/10/99 */
+//-----------------------------------------------------------------------------
+
+template <class EOT> class eoRandomSelect: public eoSelectOne<EOT> 
+{
+ public:
+  
+  /// not a big deal!!!
+  virtual const EOT& operator()(const eoPop<EOT>& pop) 
+  {
+    return pop[rng.random(pop.size())] ;
+  }
+};
+
+#endif eoRandomSelect_h
+

eo/src/eoReduce.h

@@ -69,7 +69,7 @@ template <class EOT> class eoEPReduce : public eoReduce<EOT>
 public:
 typedef typename EOT::Fitness Fitness; 
 
-  eoEPReduce(unsigned _t_size):
+  eoEPReduce(unsigned _t_size  ):
     t_size(_t_size)
   {
     if (t_size < 2)
@@ -79,17 +79,24 @@ typedef typename EOT::Fitness Fitness;
   }
 
   /// helper struct for comparing on pairs
+  // compares the scores
+  // uses the fitness if scores are equals ????
   typedef pair<float, eoPop<EOT>::iterator>  EPpair;
-      struct Cmp {
-          bool operator()(const EPpair a, const EPpair b) const
-            { return b.first < a.first; }
-      };
-
-
-    void operator()(eoPop<EOT>& _newgen, unsigned _newsize)
-    {
-      unsigned int presentSize = _newgen.size();
-        if (presentSize == _newsize)
+  struct Cmp {
+    bool operator()(const EPpair a, const EPpair b) const
+    { 
+      if (b.first == a.first)
+	return  (*b.second < *a.second);
+      return b.first < a.first; 
+    }
+  };
+  
+  
+  void operator()(eoPop<EOT>& _newgen, unsigned _newsize)
+  {
+    unsigned int presentSize = _newgen.size();
+    
+    if (presentSize == _newsize)
             return;
 	if (presentSize < _newsize)
 	  throw std::logic_error("eoTruncate: Cannot truncate to a larger size!\n");
@@ -107,12 +114,30 @@ typedef typename EOT::Fitness Fitness;
 		  scores[i].first += 0.5;
 	      }
 	  }
+
 	// now we have the scores
 	typename vector<EPpair>::iterator it = scores.begin() + _newsize;
-	std::nth_element(scores.begin(), it, scores.end(), Cmp());
-	it = scores.begin() + _newsize;	// just in case ???
-	while (it < scores.end())
-	  _newgen.erase(it->second);
+        std::nth_element(scores.begin(), it, scores.end(), Cmp());
+	// sort(scores.begin(), scores.end(), Cmp());
+	unsigned j;
+// 	cout << "Les scores apres tri\n";
+// 	for (j=0; j<scores.size(); j++)
+// 	  {
+// 	    cout << scores[j].first << " " << *scores[j].second << endl;
+// 	  }
+	eoPop<EOT> tmPop;
+	for (j=0; j<_newsize; j++)
+	  {
+	    tmPop.push_back(*scores[j].second);
+	  }
+	_newgen.swap(tmPop);
+	// erase does not work, but I'm sure there is a way in STL to mark
+	// and later delete all inside a vector ??????
+	// this would avoid all copies here
+
+// 	it = scores.begin() + _newsize;
+// 	while (it < scores.end())
+// 	  _newgen.erase(it->second);
     }
 private:
   unsigned t_size;

eo/src/eoSGATransform.h

@@ -91,7 +91,7 @@ template<class EOT> class eoSGATransform : public eoTransform<EOT>
 };
 
 /*****************************************************************************
- * eoSDynGATransform: transforms a population using genetic operators.
+ * eoDynSGATransform: transforms a population using genetic operators.
  * It is the Dynamic version of the above eoSGATransform
  *    i.e. the operators probabilities can be passed as an eoValueParam, 
  *    and hence can be modified from outside
@@ -109,15 +109,15 @@ template<class EOT> class eoDynSGATransform : public eoTransform<EOT>
       mutate(_mutate), 
       mutationProbaHolder(_mProba), mutationProba(mutationProbaHolder) {}
 
-  /// This constructor receives references 
+  /// This constructor receives pointers
   //  these will usually be some eoValueParam<double>.value()
-  // the ...Holder will bever be used in this object
-  eoDynSGATransform(eoQuadraticOp<EOT>& _cross, double& _cProbaRef, 
-		 eoMonOp<EOT>& _mutate, double& _mProbaRef)
+  //  hence the ...Holder data will bever be used in this case
+  eoDynSGATransform(eoQuadraticOp<EOT>& _cross, double* _cProbaRef, 
+		 eoMonOp<EOT>& _mutate, double* _mProbaRef)
     : cross(_cross),
-      crossoverProbaHolder(0), crossoverProba(_cProbaRef),
+      crossoverProbaHolder(0), crossoverProba(*_cProbaRef),
       mutate(_mutate), 
-      mutationProbaHolder(0), mutationProba(_mProbaRef) {}
+      mutationProbaHolder(0), mutationProba(*_mProbaRef) {}
 
 
   /**
@@ -146,8 +146,11 @@ template<class EOT> class eoDynSGATransform : public eoTransform<EOT>
 	          
       }
   };
-    
- private:
+  // accessors - mainly for EASEA
+  double & PCrossHandle() { return crossoverProba;}    
+  double & PMutHandle() { return mutationProba;}    
+
+private:
   // difference with eoSGATransform: the operator probabilities 
   // they can be passed by reference or by value.
   // hence we need here to use a reference, and to eventually store a value

eo/src/eoStochTournamentSelect.h

@@ -0,0 +1,69 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoStochTournamentSelect.h
+// (c) GeNeura Team, 1998 - EEAAX 1999
+/* 
+    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 eoStochTournamentSelect_h
+#define eoStochTournamentSelect_h
+
+//-----------------------------------------------------------------------------
+
+#include <functional>
+#include <numeric>           // accumulate
+#include <eoSelectOne.h>     // eoSelectOne
+#include <utils/selectors.h> // stochastic_tournament
+
+//-----------------------------------------------------------------------------
+/** eoStochTournamentSelect: a selection method that selects ONE individual by
+ binary stochastic tournament 
+ -MS- 24/10/99 */
+//-----------------------------------------------------------------------------
+
+template <class EOT> class eoStochTournamentSelect: public eoSelectOne<EOT>
+{
+ public:
+
+  ///
+  eoStochTournamentSelect(float _Trate = 1.0 ) : eoSelectOne<EOT>(), Trate(_Trate) 
+  {
+    // consistency check
+    if (Trate < 0.5) {
+      cerr << "Warning, Tournament rate should be > 0.5\nAdjusted to 0.55\n";
+      Trate = 0.55;
+    }
+  }
+  
+  /** Perform the stochastic tournament  */
+  virtual const EOT& operator()(const eoPop<EOT>& pop) 
+  {
+      return stochastic_tournament(pop, Trate);
+  }
+  
+private:
+  float Trate;
+};
+
+//-----------------------------------------------------------------------------
+
+#endif eoStochTournamentSelect_h
+