Changed some includes for the new dir structure

eo/src/eo

@@ -25,7 +25,7 @@
 
 //-----------------------------------------------------------------------------
 
-#include <eoData.h>
+#include <utils/eoData.h>
 #include <eoObject.h>
 #include <eoPrintable.h>
 #include <eoPersistent.h>
@@ -33,13 +33,11 @@
 #include <EO.h>
 
 #include <eoID.h>
-#include <eoAged.h>
 
 #include <eoVector.h>
 #include <eo1d.h>
-#include <eoString.h>
-#include <eoESChrom.h>
-#include <eoBin.h>
+#include <other/eoString.h>
+#include <ga/eoBin.h>
 
 #include <eoRnd.h>
 #include <eoUniform.h>
@@ -58,7 +56,7 @@
 #include <eoPop.h>
 #include <eoPopOps.h>
 #include <eoMerge.h>
-#include <eoBitOp.h>
+#include <ga/eoBitOp.h>
 
 // Evaluation functions
 #include <eoEvalFunc.h>

eo/src/eoDetTournament.h

@@ -31,7 +31,7 @@
 #include <functional>  // 
 #include <numeric>     // accumulate
 #include "eoPopOps.h"          // eoPop eoSelect MINFLOAT
-#include "selectors.h"
+#include "utils/selectors.h"
 
 //-----------------------------------------------------------------------------
 /** eoDetTournament: a selection method that selects ONE individual by

eo/src/eoLottery.h

@@ -30,7 +30,7 @@
 
 #include <functional>  // 
 #include <numeric>     // accumulate
-#include "selectors.h"
+#include "utils/selectors.h"
 #include <eo>          // eoPop eoSelect MINFLOAT
 
 //-----------------------------------------------------------------------------

eo/src/eoNegExp.h

@@ -30,7 +30,7 @@
 #include <math.h>
 
 #include <eoRnd.h> // for base class
-#include <eoRNG.h> // for base class
+#include <utils/eoRNG.h> // for base class
 
 //-----------------------------------------------------------------------------
 // Class eoNegExp

eo/src/eoNormal.h

@@ -29,7 +29,7 @@
 
 #include <math.h>
 #include <eoRnd.h> // for base class
-#include <eoRNG.h> // for random number generator
+#include <utils/eoRNG.h> // for random number generator
 
 //-----------------------------------------------------------------------------
 // Class eoNormal

eo/src/eoObject.h

@@ -27,11 +27,11 @@
 
 //-----------------------------------------------------------------------------
 
-#include <eoData.h>		// For limits definition
+#include <utils/eoData.h>		// For limits definition
 #include <iostream>		// istream, ostream
 #include <string>		// string
 
-#include "compatibility.h"
+#include "utils/compatibility.h"
 
 using namespace std;
 
@@ -57,11 +57,15 @@ class eoObject
   /// Virtual dtor. They are needed in virtual class hierarchies.
   virtual ~eoObject() {}
   
-  /** Return the class id. This should be redefined in each class; but 
-  it's got code as an example of implementation. Only "leaf" classes
-  can be non-virtual.
+  /** Return the class id. This should be redefined in each class. 
+  Only "leaf" classes can be non-virtual.
+
+  Maarten: removed the default implementation as this proved to 
+  be too error-prone: I found several classes that had a typo in 
+  className (like classname), which would print eoObject instead of
+  their own...
   */
-  virtual string className() const { return "eoObject"; }
+  virtual string className() const = 0; 
 
 };
 

eo/src/eoStochTournament.h

@@ -31,7 +31,7 @@
 #include <functional>  // 
 #include <numeric>     // accumulate
 #include <eoPopOps.h>          // eoPop eoSelect MINFLOAT
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 
 //-----------------------------------------------------------------------------
 /** eoStochTournament: a selection method that selects ONE individual by

eo/src/eoUniform.h

@@ -29,7 +29,7 @@
 //-----------------------------------------------------------------------------
 
 #include <eoRnd.h>
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 
 //-----------------------------------------------------------------------------
 // Class eoUniform

eo/src/eoUniformSelect.h

@@ -32,7 +32,7 @@
 #include <functional>  // 
 #include <numeric>     // accumulate
 #include <eoPopOps.h>          // eoPop eoSelect MINFLOAT
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 
 //-----------------------------------------------------------------------------
 /** eoUniformSelect: a selection method that selects ONE individual randomly

eo/src/ga/eoBitOp.h

@@ -9,7 +9,7 @@
 
 #include <algorithm>    // swap_ranges
 #include <eoUniform.h>  // eoUniform
-#include <eoBin.h>      // eoBin
+#include <ga/eoBin.h>      // eoBin
 #include <eoOp.h>       // eoMonOp
 
 

eo/src/other/eoExternalOpFunctions.cpp

@@ -33,7 +33,7 @@
 #include "eoRnd.h"
 
 template <class F, class External>
-class eoExternalInitFunc
+class eoExternalInitFunc 
 {
 
 public :

eo/src/utils/compatibility.h

@@ -38,6 +38,7 @@ nasty habit of #define min and max in stdlib.h (and windows.h)
 I'm trying to undo this horrible macro magic (microsoft yet macrohard)
 here. Sure hope it works
 */
+#pragma warning(disable:4786)
 
 #include <stdlib.h>
 

eo/src/utils/eoParser.cpp

@@ -1,3 +1,7 @@
+#ifdef _MSC_VER
+#pragma warning(disable:4786)
+#endif
+
 #include <algorithm>
 #include <fstream>
 #include <iomanip> 
@@ -6,6 +10,11 @@
 
 using namespace std;
 
+void eoWarning(std::string str)
+{
+    cout << str << '\n';
+}
+
 std::ostream& printSectionHeader(std::ostream& os, std::string section)
 {
   os << '\n' << setw(10) << "######    " << setw(20) << section << setw(10) << "    ######\n";

eo/src/utils/eoParser.h

@@ -56,11 +56,6 @@ public :
     virtual void processParam(eoParam& param, std::string section = "") = 0;
 };
 
-void eoWarning(std::string str)
-{
-    cout << str << '\n';
-}
-
 /**
     eoParser: command line parser and configuration file reader
     This class is persistent, so it can be stored and reloaded to restore

eo/src/utils/eoRNG.h

@@ -240,6 +240,7 @@ public :
      _is >> cacheValue;
    }
 
+ std::string className(void) const { return "Mersenne-Twister"; }
 
 private :
   uint32 restart(void);

eo/src/utils/selectors.h

@@ -0,0 +1,314 @@
+/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+  -----------------------------------------------------------------------------
+  selectors.h
+    A bunch of useful selector functions. They generally have three forms:
+
+    template <class It>
+    It select(It begin, It end, params, eoRng& gen = rng);
+
+    template <class EOT>
+    const EOT& select(const eoPop<EOT>& pop, params, eoRng& gen = rng);
+    
+    template <class EOT>
+    EOT& select(eoPop<EOT>& pop, params, eoRng& gen = rng);
+
+    where select is one of: roulette_wheel, deterministic_tournament
+    and stochastic_tournament (at the moment).
+
+ (c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 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
+ */
+
+#ifndef SELECT__H
+#define SELECT__H
+
+#include <stdexcept>
+
+#include "eoRNG.h"
+
+template <class EOT>
+bool minimizing_fitness()
+{
+    EOT eo1; // Assuming people don't do anything fancy in the default constructor!
+    EOT eo2; 
+
+    /* Dear user, when the two line below do not compile you are most 
+       likely not working with scalar fitness values. In that case we're sorry
+       but you cannot use lottery or roulette_wheel selection...
+    */
+    eo1.fitness(0.0); // tried to cast it to an EOT::Fitness, but for some reason GNU barfs on this 
+    eo2.fitness(1.0); 
+
+    return eo2 < eo1; // check whether we have a minimizing fitness
+};
+
+inline double scale_fitness(const std::pair<double, double>& _minmax, double _value) 
+{
+    if (_minmax.first == _minmax.second)
+    {
+        return 0.0; // no differences in fitness, population converged!
+    }
+    // else
+    
+    return (_value - _minmax.first) / (_minmax.second - _minmax.first);
+}
+
+template <class It>
+double sum_fitness(It begin, It end)
+{
+    double sum = 0.0;
+
+    for (; begin != end; ++begin)
+    {
+        double v = static_cast<double>(begin->fitness());
+        if (v < 0.0)
+            throw std::logical_error("Negative Fitness Encountered");
+        sum += v;
+    }
+
+    return sum;
+}
+
+template <class EOT>
+double sum_fitness(const eoPop<EOT>& _pop)
+{
+    return sum_fitness(_pop.begin(), _pop.end());
+}
+
+template <class EOT>
+double sum_fitness(const eoPop<EOT>& _pop, std::pair<double, double>& _minmax)
+{
+    eoPop<EOT>::const_iterator it = _pop.begin();
+
+    _minmax.first = it->fitness();
+    _minmax.second = it++->fitness();
+
+    for(; it != _pop.end(); ++it)
+    {
+        double v = static_cast<double>(it->fitness());
+        
+        _minmax.first = std::min(_minmax.first, v);
+        _minmax.second = std::max(_minmax.second, v);
+    
+        rawTotal += v;
+    }
+    
+    if (minimizing_fitness<EOT>())
+    {
+        std::swap(_minmax.first, _minmax.second);
+    }
+
+    scaledTotal = 0.0;
+
+    // unfortunately a second loop is neccessary to scale the fitness
+    for (it = _pop.begin(); it != _pop.end(); ++it)
+    {
+        double v = scale_fitness(static_cast<double>(it->fitness()));
+
+        scaledTotal += v;
+    }
+}
+
+template <class It>
+It roulette_wheel(It _begin, It _end, double total, eoRng& _gen = rng)
+{
+    float roulette = _gen.uniform(total);
+ 
+    It i = _begin;
+ 
+    while (roulette > 0.0)
+    {
+	    roulette -= static_cast<double>(*(i++));
+    }
+ 
+    return --i;
+}
+
+template <class EOT>
+const EOT& roulette_wheel(const eoPop<EOT>& _pop, double total, eoRng& _gen = rng)
+{
+    float roulette = _gen.uniform(total);
+ 
+    eoPop<EOT>::const_iterator i = _pop.begin();
+ 
+    while (roulette > 0.0)
+    {
+	    roulette -= static_cast<double>((i++)->fitness());
+    }
+ 
+    return *--i;
+} 
+
+template <class EOT>
+EOT& roulette_wheel(eoPop<EOT>& _pop, double total, eoRng& _gen = rng)
+{
+    float roulette = _gen.uniform(total);
+ 
+    eoPop<EOT>::iterator i = _pop.begin();
+ 
+    while (roulette > 0.0)
+    {
+	    roulette -= static_cast<double>((i++)->fitness());
+    }
+ 
+    return *--i;
+} 
+
+template <class It>
+It deterministic_tournament(It _begin, It _end, unsigned _t_size, eoRng& _gen = rng)
+{
+    It best = _begin + _gen.random(_end - _begin);		
+    
+    for (unsigned i = 0; i < _t_size - 1; ++i)
+    {
+        It competitor = _begin + _gen.random(_end - _begin);
+
+        if (*best < *competitor)
+        {
+            best = competitor;
+        }
+    }
+
+    return best;
+}
+
+template <class EOT>
+const EOT& deterministic_tournament(const eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
+{
+    return *deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
+}
+
+template <class EOT>
+EOT& deterministic_tournament(eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
+{
+    return *deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
+}
+
+template <class It>
+It inverse_deterministic_tournament(It _begin, It _end, unsigned _t_size, eoRng& _gen = rng)
+{
+    It worst = _begin + _gen.random(_end - _begin);		
+    
+    for (unsigned i = 0; i < _t_size - 1; ++i)
+    {
+        It competitor = _begin + _gen.random(_end - _begin);
+
+        if (competitor == worst)
+        {
+            --i;
+            continue; // try again
+        }
+
+        if (*competitor < *worst)
+        {
+            worst = competitor;
+        }
+    }
+
+    return worst;
+}
+
+template <class EOT>
+const EOT& inverse_deterministic_tournament(const eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
+{
+    return *inverse_deterministic_tournament<EOT>(_pop.begin(), _pop.end(), _t_size, _gen);
+}
+
+template <class EOT>
+EOT& inverse_deterministic_tournament(eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
+{
+    return *inverse_deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
+}
+
+template <class It>
+It stochastic_tournament(It _begin, It _end, double _t_rate, eoRng& _gen = rng) 
+{
+  It i1 = _begin + _gen.random(_end - _begin);
+  It i2 = _begin + _gen.random(_end - _begin);
+
+  bool return_better = _gen.flip(_t_rate);
+
+  if (*i1 < *i2) 
+  {
+      if (return_better) return i2;
+      // else
+
+      return i1;
+   }
+    else 
+    {
+      if (return_better) return i1;
+      // else
+    }
+    // else
+    
+    return i2;
+}
+
+template <class EOT>
+const EOT& stochastic_tournament(const eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
+{
+    return *stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
+}
+
+template <class EOT>
+EOT& stochastic_tournament(eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
+{
+    return *stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
+}
+
+template <class It>
+It inverse_stochastic_tournament(It _begin, It _end, double _t_rate, eoRng& _gen = rng) 
+{
+  It i1 = _begin + _gen.random(_end - _begin);
+  It i2 = _begin + _gen.random(_end - _begin);
+
+  bool return_worse = _gen.flip(_t_rate);
+
+  if (*i1 < *i2) 
+  {
+      if (return_worse) return i1;
+      // else
+
+      return i2;
+   }
+    else 
+    {
+      if (return_worse) return i2;
+      // else
+    }
+    // else
+    
+    return i1;
+}
+
+template <class EOT>
+const EOT& inverse_stochastic_tournament(const eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
+{
+    return *inverse_stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
+}
+
+template <class EOT>
+EOT& inverse_stochastic_tournament(eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
+{
+    return *inverse_stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
+}
+
+
+#endif