Handle including from contrib/MGE nicely.

eo/contrib/MGE/eoVirus.h

@@ -1,36 +1,36 @@
-/*
+/* eoVirus.h
-   eoVirus.h
-   (c) GeNeura Team 2001, Marc Schoenauer 2000
 
-    This library is free software; you can redistribute it and/or
+(c) GeNeura Team 2001, Marc Schoenauer 2000
-    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,
+This library is free software; you can redistribute it and/or modify
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
+it under the terms of the GNU Lesser General Public License as
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+published by the Free Software Foundation; either version 2 of the
-    Lesser General Public License for more details.
+License, or (at your option) any later version.
 
-    You should have received a copy of the GNU Lesser General Public
+This library is distributed in the hope that it will be useful, but
-    License along with this library; if not, write to the Free Software
+WITHOUT ANY WARRANTY; without even the implied warranty of
-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
 
-    Contact: todos@geneura.ugr.es, http://geneura.ugr.es
+You should have received a copy of the GNU Lesser General Public
-             Marc.Schoenauer@polytechnique.fr
+License along with this library; if not, write to the Free Software
-CVS Info: $Date: 2004-12-23 15:29:07 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/contrib/MGE/eoVirus.h,v 1.3 2004-12-23 15:29:07 kuepper Exp $ $Author: kuepper $
+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 <iostream>    // ostream, istream
+#include "ga/eoBit.h"
-#include <functional>  // bind2nd
-#include <string>      // std::string
-
-#include <ga/eoBit.h>
 
 /**
 \defgroup bitstring
@@ -38,13 +38,15 @@ CVS Info: $Date: 2004-12-23 15:29:07 $ $Header: /home/nojhan/dev/eodev/eodev_cvs
   Various functions for a bitstring representation
 */
 
-/** eoBit: implementation of bitstring chromosome.
+/** Implementation of bitstring chromosome.
-\class eoBit eoBit.h ga/eoBit.h
+
-\ingroup bitstring
+@class eoBit eoBit.h ga/eoBit.h
-  * based on STL's vector<bool> specialization.
+@ingroup bitstring
+
+Based on STL's vector<bool> specialization.
 */
 template <class FitT>
-class eoVirus: public eoBit<FitT>
+class eoVirus : public eoBit<FitT>
 {
 public:
 
@@ -53,64 +55,67 @@ public:
     using eoBit<FitT>::size;
 
 
-  /**
+    /** (Default) Constructor
-   * (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.
+    @param size Size of the binary std::string.
-  virtual std::string className() const {
+    */
-      return "eoVirus";
+    eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
-  }
+        eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
 
-  /// Access to virus features
+    /// My class name
-  void virResize( unsigned _i ) {
+    virtual std::string className() const {
-	virus.resize(_i );
+        return "eoVirus";
-  }
-
-  /// 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;
+    /// 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;
 };
 
 //-----------------------------------------------------------------------------
@@ -119,6 +124,7 @@ public:
 
 
 // Local Variables:
+// coding: iso-8859-1
 // mode: C++
 // c-file-style: "Stroustrup"
 // End:

eo/src/eoVector.h

@@ -22,7 +22,7 @@
              Marc.Schoenauer@polytechnique.fr
 	     mak@dhi.dk
 
-    CVS Info: $Date: 2004-12-23 15:29:06 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoVector.h,v 1.16 2004-12-23 15:29:06 kuepper Exp $ $Author: kuepper $
+    CVS Info: $Date: 2005-10-06 17:22:40 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoVector.h,v 1.17 2005-10-06 17:22:40 kuepper Exp $ $Author: kuepper $
 
  */
 //-----------------------------------------------------------------------------
@@ -31,7 +31,7 @@
 #define _eoVector_h
 
 #include <vector>
-#include <iterator> // needed for GCC 3.2
+#include <iterator>
 #include <EO.h>
 
 /**

eo/src/ga/eoBit.h

@@ -39,18 +39,19 @@
 #include <functional>  // bind2nd
 #include <string>      // std::string
 
-#include <eoVector.h>
+#include "eoVector.h"
 
-/**
+/** @defgroup bitstring
-\defgroup bitstring
 
-  Various functions for a bitstring representation
+Various functions for a bitstring representation
 */
 
-/** eoBit: implementation of bitstring chromosome.
+/** Implementation of bitstring chromosome.
-\class eoBit eoBit.h ga/eoBit.h
+
-\ingroup bitstring
+@class eoBit eoBit.h ga/eoBit.h
-  * based on STL's std::vector<bool> specialization.
+@ingroup bitstring
+
+Based on STL's std::vector<bool> specialization.
 */
 template <class FitT> class eoBit: public eoVector<FitT, bool>
 {

eo/test/Makefile.am

@@ -63,8 +63,11 @@ t_eofitness_SOURCES 		= t-eofitness.cpp
 t_eoFitnessAssembledEA_SOURCES 	= t-eoFitnessAssembledEA.cpp
 t_eobin_SOURCES 		= t-eobin.cpp
 t_eoVirus_SOURCES 		= t-eoVirus.cpp
+t_MGE1bit_CXXFLAGS 		= -I$(top_srcdir)/contrib/MGE
 t_MGE1bit_SOURCES 		= t-MGE1bit.cpp
+t_MGE_CXXFLAGS 			= -I$(top_srcdir)/contrib/MGE
 t_MGE_SOURCES 			= t-MGE.cpp
+t_MGE_control_CXXFLAGS 		= -I$(top_srcdir)/contrib/MGE
 t_MGE_control_SOURCES 		= t-MGE-control.cpp
 t_eoStateAndParser_SOURCES 	= t-eoStateAndParser.cpp
 t_eoCheckpointing_SOURCES 	= t-eoCheckpointing.cpp

eo/test/t-MGE-control.cpp

@@ -2,20 +2,24 @@
 // t-eoMGE.cpp
 //-----------------------------------------------------------------------------
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #ifndef __GNUG__
 // to avoid long name warnings
 #pragma warning(disable:4786)
 #endif // __GNUG__
 
-#include <eo>
+#include "eo"
-#include <ga/eoBitOp.h>
+#include "ga/eoBitOp.h"
 
 #include "RoyalRoad.h"
 
 // Viri
-#include "../contrib/MGE/VirusOp.h"
+#include "VirusOp.h"
-#include "../contrib/MGE/eoVirus.h"
+#include "eoVirus.h"
-#include "../contrib/MGE/eoInitVirus.h"
+#include "eoInitVirus.h"
 
 //-----------------------------------------------------------------------------
 

eo/test/t-MGE.cpp

@@ -2,6 +2,10 @@
 // t-eoMGE.cpp
 //-----------------------------------------------------------------------------
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #ifndef __GNUG__
 // to avoid long name warnings
 #pragma warning(disable:4786)
@@ -13,9 +17,9 @@
 #include "RoyalRoad.h"
 
 // Viri
-#include "../contrib/MGE/VirusOp.h"
+#include "VirusOp.h"
-#include "../contrib/MGE/eoVirus.h"
+#include "eoVirus.h"
-#include "../contrib/MGE/eoInitVirus.h"
+#include "eoInitVirus.h"
 
 //-----------------------------------------------------------------------------
 

eo/test/t-MGE1bit.cpp

@@ -2,20 +2,23 @@
 // t-eoMGE.cpp
 //-----------------------------------------------------------------------------
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #ifndef __GNUG__
 // to avoid long name warnings
 #pragma warning(disable:4786)
 #endif // __GNUG__
 
-#include <eo>
+#include "eo"
-#include <ga/eoBitOp.h>
+#include "ga/eoBitOp.h"
-
 #include "RoyalRoad.h"
 
 // Viri
-#include "../contrib/MGE/VirusOp.h"
+#include "VirusOp.h"
-#include "../contrib/MGE/eoVirus.h"
+#include "eoVirus.h"
-#include "../contrib/MGE/eoInitVirus.h"
+#include "eoInitVirus.h"
 
 //-----------------------------------------------------------------------------