Small modif in moIndexedSwapNeighbor

INSTALL

@@ -183,9 +183,9 @@ Easy, isn't it ?
 
 By performing tests, you can check your installation. 
 Testing is disable by default, except if you build with the full install type.
-To enable testing, define -DENABLE_TESTING when you launch cmake.
+To enable testing, define -DENABLE_CMAKE_TESTING=true when you launch cmake.
 
-To perform tests simply type ctest ou make test.
+To perform tests simply type ctest or make test.
 
 ------------------------------------------------------------------------------------------
 5.2 REPORTING

eo/src/CMakeLists.txt

@@ -47,7 +47,7 @@ install(DIRECTORY do es ga gp other utils
 add_subdirectory(es)
 add_subdirectory(ga)
 add_subdirectory(utils)
-add_subdirectory(serial)
+#add_subdirectory(serial)
 
 if(ENABLE_PYEO)
   add_subdirectory(pyeo)

eo/src/utils/eoDistance.h

@@ -62,13 +62,15 @@ public:
 };
 
 /**
+   SV: from eoHammingDistance, it is in fact the L1 distance
+   
     This is a generic class for L1 distance computation:
     assumes the 2 things are std::vectors of something
     that is double-castable
     For bitstrings, this is the Hamming distance
 */
 template< class EOT >
-class eoHammingDistance : public eoDistance<EOT>
+class eoL1Distance : public eoDistance<EOT>
 {
 public:
   double operator()(const EOT & _v1, const EOT & _v2)
@@ -83,6 +85,27 @@ public:
   }
 };
 
+/**
+   SV: change to have the Hamming (number of differences)
+
+   For bitstrings, this is the Hamming distance
+*/
+template< class EOT >
+class eoHammingDistance : public eoDistance<EOT>
+{
+public:
+  double operator()(const EOT & _v1, const EOT & _v2)
+  {
+    double sum=0.0;
+    for (unsigned i=0; i<_v1.size(); i++)
+      {
+	if (_v1[i] != _v2[i])
+	  sum++;
+      }
+    return sum;
+  }
+};
+
 /* this distance measures the difference in fitness
  * I am not sure it can be of any use, though ...
  * except for some testing

eo/test/CMakeLists.txt

@@ -69,6 +69,7 @@ set (TEST_LIST
   #t-openmp # does not work anymore since functions used in this test were removed from EO
   #t-eoDualFitness
   t-eoParser
+  t-eoPartiallyMappedXover
   )
 
 

mo/src/algo/moRandomWalk.h

@@ -60,7 +60,7 @@ public:
      */
     moRandomWalk(Neighborhood& _neighborhood, eoEvalFunc<EOT>& _fullEval, moEval<Neighbor>& _eval, unsigned _nbStepMax):
       moLocalSearch<Neighbor>(explorer, iterCont, _fullEval),
-      iterCont(_nbStepMax),
+      iterCont(_nbStepMax, false),
       explorer(_neighborhood, _eval)
     {}
 

mo/src/continuator/moVectorMonitor.h

@@ -53,7 +53,7 @@ public:
 	 * Constructor
 	 * @param _param the parameter of type double to save in the vector
 	 */
-	moVectorMonitor(eoValueParam<double> & _param) : doubleParam(&_param), intParam(NULL), eotParam(NULL)
+	moVectorMonitor(eoValueParam<double> & _param) : doubleParam(&_param), intParam(NULL), intLongParam(NULL), eotParam(NULL)
 	{ 
 		// precision of the output by default
 		precisionOutput = std::cout.precision();
@@ -63,7 +63,17 @@ public:
 	 * Default Constructor
 	 * @param _param the parameter of type unsigned int to save in the vector
 	 */
-	moVectorMonitor(eoValueParam<unsigned int> & _param) : doubleParam(NULL), intParam(&_param), eotParam(NULL)
+	moVectorMonitor(eoValueParam<unsigned int> & _param) : doubleParam(NULL), intParam(&_param), intLongParam(NULL), eotParam(NULL)
+	{ 
+		// precision of the output by default
+		precisionOutput = std::cout.precision();
+	}
+
+	/**
+	 * Default Constructor
+	 * @param _param the parameter of type unsigned int to save in the vector
+	 */
+	moVectorMonitor(eoValueParam<unsigned long> & _param) : doubleParam(NULL), intParam(NULL), intLongParam(&_param), eotParam(NULL)
 	{ 
 		// precision of the output by default
 		precisionOutput = std::cout.precision();
@@ -73,7 +83,7 @@ public:
 	 * Default Constructor
 	 * @param _param the parameter of type EOT to save in the vector
 	 */
-	moVectorMonitor(eoValueParam<EOT> & _param) : doubleParam(NULL), intParam(NULL), eotParam(&_param)
+	moVectorMonitor(eoValueParam<EOT> & _param) : doubleParam(NULL), intParam(NULL), intLongParam(NULL), eotParam(&_param)
 	{ 
 		// precision of the output by default
 		precisionOutput = std::cout.precision();
@@ -84,7 +94,7 @@ public:
 	 * @param _param the parameter of type eoScalarFitness to save in the vector
 	 */
 	template <class ScalarType, class Compare>
-	moVectorMonitor(eoValueParam<eoScalarFitness<ScalarType, Compare> > & _param) : doubleParam( & (eoValueParam<double>&)_param), intParam(NULL), eotParam(NULL)
+	moVectorMonitor(eoValueParam<eoScalarFitness<ScalarType, Compare> > & _param) : doubleParam( & (eoValueParam<double>&)_param), intParam(NULL), intLongParam(NULL), eotParam(NULL)
 	{ 
 		// precision of the output by default
 		precisionOutput = std::cout.precision();
@@ -95,7 +105,7 @@ public:
 	 * @param _param unvalid Parameter
 	 */
 	template <class T>
-	moVectorMonitor(eoValueParam<T> & _param) : doubleParam(NULL), intParam(NULL), eotParam(NULL)
+	moVectorMonitor(eoValueParam<T> & _param) : doubleParam(NULL), intParam(NULL), intLongParam(NULL), eotParam(NULL)
 	{
 		std::cerr << "Sorry the type can not be in a vector of moVectorMonitor" << std::endl;
 	}
@@ -121,7 +131,10 @@ public:
 	    if (intParam != NULL)
 	      valueVec.push_back((double) intParam->value());
 	    else
-	      eotVec.push_back(eotParam->value());
+	      if (intLongParam != NULL)
+		valueVec.push_back((double) intLongParam->value());
+	      else 
+		eotVec.push_back(eotParam->value());
 	  return *this ;
 	}
 
@@ -227,6 +240,7 @@ public:
 protected:
 	eoValueParam<double> * doubleParam ;
 	eoValueParam<unsigned int> * intParam ;
+	eoValueParam<unsigned long> * intLongParam ;
 	eoValueParam<EOT> * eotParam ;
 
 	std::vector<double> valueVec;

mo/src/mo.h

@@ -190,6 +190,7 @@
 //#include <problems/eval/moUBQPSimpleIncrEval.h>
 //#include <problems/eval/moUBQPdoubleIncrEvaluation.h>
 //#include <problems/eval/moUBQPBitsIncrEval.h>
+#include <problems/eval/moNKlandscapesIncrEval.h>
 
 
 #include <sampling/moAdaptiveWalkSampling.h>

mo/src/neighborhood/moIndexNeighbor.h

@@ -109,9 +109,9 @@ public:
 	 * @param _solution solution from which the neighborhood is visited
 	 * @param _key index of the IndexNeighbor
 	 */
-  virtual void index(EOT & _solution, unsigned int _key) {
+         virtual void index(EOT & _solution, unsigned int _key) {
-    key = _key;
+           key = _key;
-  }
+         }
 
 	/**
 	 * @param _neighbor a neighbor
@@ -121,6 +121,22 @@ public:
 		return (key == _neighbor.index());
 	}
 
+  /**
+   * Write object with its index
+   * @param _os A std::ostream.
+   */
+  virtual void printOn(std::ostream& _os) const {
+    if (this->invalid()) {
+        _os << "INVALID ";
+    }
+    else
+    {
+      _os << this->fitness() << ' ';
+    }
+
+    _os << key ;
+  }
+
 protected:
 	// key allowing to describe the neighbor
 	unsigned int key;

mo/src/neighborhood/moRndWithoutReplNeighborhood.h

@@ -130,7 +130,7 @@ public:
         return "moRndWithoutReplNeighborhood";
     }
 
-private:
+protected:
     unsigned int maxIndex;
     std::vector<unsigned int> indexVector;
 };

mo/src/problems/permutation/moIndexedSwapNeighbor.h

@@ -46,6 +46,33 @@ public:
   using moIndexNeighbor<EOT>::index;
   
   /**
+   * Default Constructor
+   */
+  moIndexedSwapNeighbor() : moIndexNeighbor<EOT, Fitness>() {
+  }
+
+  /**
+   * Copy Constructor
+   * @param _n the neighbor to copy
+   */
+  moIndexedSwapNeighbor(const moIndexedSwapNeighbor<EOT, Fitness> & _n) : moIndexNeighbor<EOT, Fitness>(_n)
+  {
+    indices.first = _n.first();
+    indices.second = _n.second();
+  }
+
+  /**
+   * Assignment operator
+   * @param _source the source neighbor
+   */
+  moIndexedSwapNeighbor<EOT, Fitness> & operator=(const moIndexedSwapNeighbor<EOT, Fitness> & _source) {
+    moIndexNeighbor<EOT, Fitness>::operator=(_source);
+    indices.first = _source.first();
+    indices.second = _source.second();
+    return *this;
+  }
+
+ /**
    * Apply the swap
    * @param _solution the solution to move
    */
@@ -111,7 +138,7 @@ public:
    * Getter of the firt location
    * @return first indice
    */
-  unsigned int first() {
+  unsigned int first() const {
     return indices.first;
   }
 
@@ -119,11 +146,11 @@ public:
    * Getter of the second location
    * @return second indice
    */
-  unsigned int second() {
+  unsigned int second() const {
     return indices.second;
   }
 
-private:
+protected:
   std::pair<unsigned int, unsigned int> indices;    
 
 };

mo/test/CMakeLists.txt

@@ -18,6 +18,7 @@ set (TEST_LIST
 		t-moOrderNeighborhood
 		t-moFullEvalByCopy
 		t-moFullEvalByModif
+		t-moNKlandscapesIncrEval
 		t-moNeighborComparator
 		t-moSolNeighborComparator
 		t-moTrueContinuator

mo/tutorial/Lesson6/adaptiveWalks.cpp

@@ -85,6 +85,7 @@ void main_function(int argc, char **argv)
     string str_out = "out.dat"; // default value
     eoValueParam<string> outParam(str_out.c_str(), "out", "Output file of the sampling", 'o');
     parser.processParam(outParam, "Persistence" );
+    str_out = outParam.value();
 
     // the name of the "status" file where all actual parameter values will be saved
     string str_status = parser.ProgramName() + ".status"; // default value

mo/tutorial/Lesson6/autocorrelation.cpp

@@ -89,6 +89,7 @@ void main_function(int argc, char **argv)
     string str_out = "out.dat"; // default value
     eoValueParam<string> outParam(str_out.c_str(), "out", "Output file of the sampling", 'o');
     parser.processParam(outParam, "Persistence" );
+    str_out = outParam.value();
 
     // the name of the "status" file where all actual parameter values will be saved
     string str_status = parser.ProgramName() + ".status"; // default value

mo/tutorial/Lesson6/densityOfStates.cpp

@@ -83,6 +83,7 @@ void main_function(int argc, char **argv)
     string str_out = "out.dat"; // default value
     eoValueParam<string> outParam(str_out.c_str(), "out", "Output file of the sampling", 'o');
     parser.processParam(outParam, "Persistence" );
+    str_out = outParam.value();
 
     // the name of the "status" file where all actual parameter values will be saved
     string str_status = parser.ProgramName() + ".status"; // default value

moeo/src/metric/moeoHyperVolumeMetric.h

@@ -83,7 +83,7 @@ class moeoHyperVolumeMetric : public moeoVectorUnaryMetric < ObjectiveVector , d
      * @param _ref_point the reference point
      * @param _bounds bounds value
      */
-    moeoHyperVolumeMetric(ObjectiveVector& _ref_point=NULL, std::vector < eoRealInterval >& _bounds=NULL): normalize(false), rho(0.0), ref_point(_ref_point), bounds(_bounds){}
+    moeoHyperVolumeMetric(ObjectiveVector& _ref_point, std::vector < eoRealInterval >& _bounds): normalize(false), rho(0.0), ref_point(_ref_point), bounds(_bounds){}
 
     /**
      * calculates and returns the HyperVolume value of a pareto front

moeo/src/selection/moeoRouletteSelect.h

@@ -80,7 +80,7 @@ class moeoRouletteSelect:public moeoSelectOne < MOEOT >
   protected:
 
     /** size */
-    double & tSize;
+    unsigned int & tSize;
 
   };
 

problems/eval/nkLandscapesEval.h

@@ -31,6 +31,7 @@ Contact: paradiseo-help@lists.gforge.inria.fr
 #define __nkLandscapesEval_H
 
 #include <eoEvalFunc.h>
+#include <fstream>
 
 template< class EOT >
 class nkLandscapesEval : public eoEvalFunc<EOT> {
@@ -79,7 +80,7 @@ public:
    */
   nkLandscapesEval(const char * _fileName)
   { 
-    string fname(_fileName);
+    std::string fname(_fileName);
     load(fname);
   };
 
@@ -132,16 +133,16 @@ public:
    *
    * @param _fileName file name of the instance
    */
-  virtual void load(const string _fileName)
+  virtual void load(const std::string _fileName)
   {
-    fstream file;
+    std::fstream file;
-    file.open(_fileName.c_str(), ios::in);
+    file.open(_fileName.c_str(), std::fstream::in);
 
     if (file.is_open()) {
-      string s;
+      std::string s;
 
       // Read the commentairies
-      string line;
+      std::string line;
       file >> s;
       while (s[0] == 'c') {
 	getline(file,line,'\n');
@@ -150,14 +151,14 @@ public:
 
       // Read the parameters
       if (s[0] != 'p') {
-	string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] at the begining." ;
+	std::string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] at the begining." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
       }
 
       file >> s;
       if (s != "NK") {
-	string str = "nkLandscapesEval.load: -- NK -- expected in [" + _fileName + "] at the begining." ;
+	std::string str = "nkLandscapesEval.load: -- NK -- expected in [" + _fileName + "] at the begining." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
       }
 
       // read parameters N and K
@@ -166,22 +167,22 @@ public:
 
       // read the links
       if (s[0] != 'p') {
-	string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the parameters N and K." ;
+	std::string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the parameters N and K." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
       }
 
       file >> s;
       if (s == "links") {
 	loadLinks(file);
       } else {
-	string str = "nkLandscapesEval.load: -- links -- expected in [" + _fileName + "] after the parameters N and K." ;
+	std::string str = "nkLandscapesEval.load: -- links -- expected in [" + _fileName + "] after the parameters N and K." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
       }
 
       // lecture des tables
       if (s[0] != 'p') {
-	string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the links." ;
+	std::string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the links." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
      }
 
       file >> s;
@@ -189,14 +190,14 @@ public:
       if (s == "tables") {
 	loadTables(file);
       } else {
-	string str = "nkLandscapesEval.load: -- tables -- expected in [" + _fileName + "] after the links." ;
+	std::string str = "nkLandscapesEval.load: -- tables -- expected in [" + _fileName + "] after the links." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
       }
 
       file.close();
     } else {
-	string str = "nkLandscapesEval.load: Could not open file [" + _fileName + "]." ;
+	std::string str = "nkLandscapesEval.load: Could not open file [" + _fileName + "]." ;
-	throw runtime_error(str);
+	throw std::runtime_error(str);
     }
 
   };
@@ -206,7 +207,7 @@ public:
    *
    * @param file the file to read 
    */
-  void loadLinks(fstream & file) {
+  void loadLinks(std::fstream & file) {
     for(int j = 0; j < K+1; j++)
       for(int i = 0; i < N; i++) {
 	file >> links[i][j];
@@ -218,7 +219,7 @@ public:
    *
    * @param file the file to read 
    */
-  void loadTables(fstream & file) {
+  void loadTables(std::fstream & file) {
     for(int j = 0; j < (1<<(K+1)); j++)
       for(int i = 0; i < N; i++)
 	file >> tables[i][j];
@@ -230,29 +231,29 @@ public:
    * @param _fileName the file name of instance
    */
   virtual void save(const char * _fileName) {
-    fstream file;
+    std::fstream file;
-    file.open(_fileName, ios::out);
+    file.open(_fileName, std::fstream::out);
 
     if (file.is_open()) {
-      file << "c name of the file : " << _fileName << endl;
+      file << "c name of the file : " << _fileName << std::endl;
-      file << "p NK " << N << " " << K <<endl;
+      file << "p NK " << N << " " << K <<std::endl;
 
-      file << "p links" << endl;
+      file << "p links" << std::endl;
       for(int j=0; j<K+1; j++)
 	for(int i=0; i<N; i++)
-	  file << links[i][j] << endl;
+	  file << links[i][j] << std::endl;
 
-      file << "p tables" << endl;
+      file << "p tables" << std::endl;
       for(int j=0; j<(1<<(K+1)); j++) {
 	for(int i=0; i<N; i++)
 	  file << tables[i][j] << " ";
-	file << endl;
+	file << std::endl;
       }
       file.close();
     } else {
-      string fname(_fileName);
+      std::string fname(_fileName);
-      string str = "nkLandscapesEval.save: Could not open file [" + fname + "]." ;
+      std::string str = "nkLandscapesEval.save: Could not open file [" + fname + "]." ;
-      throw runtime_error(str);
+      throw std::runtime_error(str);
     }
   };