Moved epAtom* out of the obsolete dir; added some CVS headers to some files, and made everything work with my elipse classes

eo/src/eoAtomMutation.h

@@ -0,0 +1,98 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoAtomMutation.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
+
+    CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/Attic/eoAtomMutation.h,v 1.7 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $ 
+*/
+//-----------------------------------------------------------------------------
+#ifndef _EOATOMMUTATION_H
+#define _EOATOMMUTATION_H
+
+// STL includes
+#include <iterator>
+
+// EO includes
+#include <eoOp.h>
+#include <utils/eoRNG.h>
+#include <eoAtomMutator.h>
+
+/** Atomic mutation of an EO. Acts on containers, and applies a mutation
+    operator to each element of the container with some probability. EOT must
+    be a container of any type
+*/
+template <class EOT>
+class eoAtomMutation: public eoMonOp<EOT> {
+public:
+
+#ifdef _MSC_VER
+  typedef EOT::AtomType Type;
+#else
+  typedef typename EOT::AtomType Type;
+#endif
+
+  /// 
+  eoAtomMutation(eoAtomMutator<Type>& _atomMut, const double _rate=0.0) 
+    : eoMonOp< EOT >(), rate(_rate), atomMutator( _atomMut ) {};
+  
+  ///
+  virtual ~eoAtomMutation() {};
+  
+  ///
+  virtual bool operator()( EOT& _eo ) {
+    typename EOT::iterator i;
+    for ( i = _eo.begin(); i != _eo.end(); i ++ )
+      if ( rng.flip( rate ) ) {
+	atomMutator( *i );
+      }
+    return true;
+  }
+  
+  /** To print me on a stream.
+      @param os The ostream.
+  */
+  void printOn(ostream& os) const {
+    os << rate ;
+  }
+  
+  /** To read me from a stream.
+      @param is The istream */
+  void readFrom(istream& is) {
+    is >> rate ;
+  }
+      
+  /** @name Methods from eoObject
+  */  
+  //@{
+  /** Inherited from eoObject 
+      @see eoObject
+  */
+  string className() const {return "eoMutation";};
+  //@}
+
+private:  
+
+  double rate;  
+  eoAtomMutator<Type>& atomMutator;
+};
+
+
+#endif
+

eo/src/eoAtomMutator.h

@@ -0,0 +1,41 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+//-----------------------------------------------------------------------------
+// eoAtomMutator.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
+    CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/Attic/eoAtomMutator.h,v 1.4 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $ 
+ */
+//-----------------------------------------------------------------------------
+#ifndef _EOATOMMUTATOR_H
+#define _EOATOMMUTATOR_H
+
+#include <eoFunctor.h>
+
+/** Abstract base class for functors that modify a single element in an EO 
+    that is composed of several atomic components. An atom would, for instance, flip
+    a bit, or change a real number, or things like that. The header is completely
+    empty and thus just provides a name rather than functionality.
+*/
+
+template <class T>
+class eoAtomMutator: public eoUF<T&, bool> {};
+
+
+#endif
+

eo/src/eoFunctor.h

@@ -20,6 +20,7 @@
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
              mak@dhi.dk
+    CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoFunctor.h,v 1.5 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $ 
  */
 //-----------------------------------------------------------------------------
 

eo/src/eoOp.h

@@ -18,6 +18,7 @@
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
+    CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoOp.h,v 1.27 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $ 
  */
 //-----------------------------------------------------------------------------
 
@@ -63,7 +64,6 @@ how to build them from a description in a file.
 
 */
 template<class EOType>
-
 class eoOp
 {
 public:

eo/src/eoVector.h

@@ -20,7 +20,10 @@
 
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
              Marc.Schoenauer@polytechnique.fr
-             mak@dhi.dk
+	     mak@dhi.dk
+
+    CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoVector.h,v 1.9 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $ 
+
  */
 //-----------------------------------------------------------------------------
 
@@ -32,9 +35,11 @@
 /**
 
   Base class for fixed length chromosomes, just derives from EO and vector and
-  redirects the smaller than operator to EO (fitness based comparison)
+  redirects the smaller than operator to EO (fitness based comparison). GeneType
-*/
+  must have the following methods: void ctor (needed for the vector<>), copy ctor,
   
+  
+*/
 template <class FitT, class GeneType>
 class eoVector : public EO<FitT>, public std::vector<GeneType>
 {