Changes to eo1d interface and bug fixes

eo/src/EO.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // EO.h
 // (c) GeNeura Team 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef EO_H

eo/src/eo

@@ -1,6 +1,23 @@
 //-----------------------------------------------------------------------------
 // eo
 // (c) GeNeura Team 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _eo_
@@ -12,6 +29,7 @@
 #include <eoObject.h>
 #include <eoPrintable.h>
 #include <eoPersistent.h>
+#include <eoFitness.h>
 #include <EO.h>
 
 #include <eoID.h>

eo/src/eo1d.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eo1d.h 
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EO1D_H
@@ -16,7 +33,7 @@
 
 using namespace std;
 
-/** @name EO1d class 
+/** @name eo1d class 
 * Randomly accesible  evolvable object with one dimension, with
 variable length.  
 * Use this if you want to evolve "linear" things, like bitstrings, or
@@ -52,8 +69,9 @@ public:
   */
   eo1d( unsigned _size, eoRnd<T>& _rndGen, const string& _ID = "");
 
- /** Ctor from a istream. It just passes the stream to EO.
+ /** Ctor from a istream. It just passes the stream to EO, subclasses should
-     @param _is the input stream; eo1d just cares about the fitness
+     have to implement this.
+     @param _is the input stream
  */ 
   eo1d( istream& _is): EO<fitnessT>( _is ){};
 
@@ -77,7 +95,7 @@ public:
       @return what's inside the gene, with the correct type
 	  @exception out_of_range if _i > size()
     */
-  virtual T gene( unsigned _i ) const = 0;
+  virtual T getGene( unsigned _i ) const = 0;
 
   /** Overwrites the gene placed in position _i with a
    * new value. This means that the assignment operator
@@ -86,7 +104,7 @@ public:
    @return what's inside the gene, with the correct type
    @exception out_of_range if _i > size()
   */
-  virtual T& gene( unsigned _i ) = 0;
+  virtual void setGene( unsigned _i, const T& _value ) = 0;
 
   /** Inserts a gene, moving the rest to the right. If
    * _i = length(), it should insert it at the end.
@@ -116,19 +134,21 @@ public:
   virtual void readFrom(istream& _s) {
 
     for ( unsigned i = 0; i < length(); i ++ ) {
-      _s >> gene( i );
+      T tmp;
+      _s >> tmp;
+      setGene( i, tmp );
     }
     // there is no way of distinguishing fitness from the object, so
     // it's skipped
   }
 
-  /** Print itself: inherited from eoObject implementation. Declared virtual so that 
+  /** Print itself: inherited from eoObject implementation. 
-      it can be reimplemented anywhere. Instance from base classes are processed in
+      Instance from base classes are processed in
-	  base classes, so you don´t have to worry about, for instance, fitness.
+      base classes, so you don´t have to worry about, for instance, fitness.
   @param _s the ostream in which things are written*/
   virtual void printOn( ostream& _s ) const{
     for ( unsigned i = 0; i < length(); i ++ ) {
-      _s << gene( i ) << " ";
+      _s << getGene( i ) << " ";
     }
   }
 

eo/src/eoAged.h

@@ -1,8 +1,26 @@
+// eoAged.h
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
 
 //-----------------------------------------------------------------------------
 // eoAge.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef EOAGED_H

eo/src/eoBin.h

@@ -25,20 +25,20 @@ template <class F> class eoBin: public eoVector<bool, F>
    * (Default) Constructor.
    * @param size Size of the binary string.
    */
-  eoBin(const unsigned& size = 0, const bool& value = false): 
+  eoBin(unsigned size = 0, bool value = false): 
     eoVector<bool,F>(size, value) {}
   
   /**
    * Constructor.
    * @param size Size of the binary string.
    */
-  eoBin(const unsigned& size, const eoRnd<bool>& rnd): eoVector<bool,F>(size) 
+  eoBin(unsigned size, const eoRnd<bool>& rnd): eoVector<bool,F>(size) 
     {
       generate(begin(), end(), rnd);
     }
   
-  /// Constructor from istream.
+  /** Constructor from istream.
-  /// @param is The istream to read from.
+      @param is The istream to read from.*/
   eoBin(istream& _is):eoVector<bool,F>(_is){};
   
   /// My class name.

eo/src/eoBitOpFactory.h

@@ -1,8 +1,26 @@
+// eoBitOpFactory.h
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
 
 //-----------------------------------------------------------------------------
 // eoOpFactory.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EOBITOPFACTORY_H

eo/src/eoDrawable.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoDrawable.h
 // (c) GeNeura Team, 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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef EODRAWABLE_H

eo/src/eoDup.h

@@ -1,8 +1,26 @@
+// eoDup.h
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
 
 //-----------------------------------------------------------------------------
 // eoKill.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EODUP_h

eo/src/eoESChrom.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoESChrom.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 

eo/src/eoEvalFunc.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoEvalFunc.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef eoEvalFunc_H

eo/src/eoEvaluator.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoEvaluator.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EOEVALUATOR_H

eo/src/eoFactory.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoFactory.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EOFACTORY_H

eo/src/eoFitness.h

@@ -1,6 +1,24 @@
+// eoFitness.h
 //-----------------------------------------------------------------------------
 // eoFitness.cpp
 // (c) GeNeura Team 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef EOFITNESS_H

eo/src/eoID.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoID.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef EOID_H

eo/src/eoInsertion.h

@@ -19,7 +19,7 @@ template<class Chrom> class eoInsertion: public eoMerge<Chrom>
 {
  public:
   /// (Default) Constructor.
-  eoInsertion(const float& _rate = 1.0): eoMerge(_rate) {}
+  eoInsertion(const float& _rate = 1.0): eoMerge<Chrom>(_rate) {}
 
   /**
    * Creates a new population based on breeders and original populations.

eo/src/eoKill.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoKill.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EOKILL_h

eo/src/eoMultiMonOp.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoMultiMonOp.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EOMULTIMONOP_h

eo/src/eoMutation.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoMutation.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 #ifndef _EOMUTATION_H
 #define _EOMUTATION_H

eo/src/eoNegExp.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoNegExp.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EONEGEXP_H

eo/src/eoNormal.h

@@ -3,6 +3,23 @@
 //-----------------------------------------------------------------------------
 // eoNormal.h
 // (c) GeNeura Team, 1998
+/* 
+    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
+ */
 //-----------------------------------------------------------------------------
 
 #ifndef _EONORMAL_H