Add the nkq and nkp landscapes evaluations

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1922 331e1502-861f-0410-8da2-ba01fb791d7f

trunk/problems/eval/nkLandscapesEval.h

@@ -364,6 +364,14 @@ protected:
     }
   }
 
+  /**
+   * To generate a contribution in the table f_i 
+   *
+   */
+  virtual double contribution() {
+    return rng.uniform();
+  }
+
   /**
    * To generate instance with random (without replacement) links
    *
@@ -380,7 +388,7 @@ protected:
       
       // table of contribution with random numbers from [0,1)
       for(int j = 0; j < (1<<(K+1)); j++) 
-	tables[i][j] = rng.uniform();
+	tables[i][j] = contribution();
     }
   }
  
@@ -397,7 +405,7 @@ protected:
       
       // table of contribution with random numbers from [0,1)
       for(int j = 0; j < (1<<(K+1)); j++) 
-	tables[i][j] = rng.uniform();
+	tables[i][j] = contribution();
     }
   }
  

trunk/problems/eval/nkpLandscapesEval.h

@@ -0,0 +1,213 @@
+/*
+<nkpLandscapesEval.h>
+Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
+
+Sebastien Verel
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software.  You can  ue,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean  that it is complicated to manipulate,  and  that  also
+therefore means  that it is reserved for developers  and  experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and,  more generally, to use and operate it in the
+same conditions as regards security.
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+
+ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+Contact: paradiseo-help@lists.gforge.inria.fr
+*/
+
+#ifndef __nkpLandscapesEval_H
+#define __nkpLandscapesEval_H
+
+#include <nkLandscapesEval.h>
+
+/*
+ * Neutral version of NK landscapes: the 'probabilistic' NK
+ * see work of L. Barnett  "Ruggedness and Neutrality - The NKp family of Fitness Landscapes" (1998)
+ */
+template< class EOT >
+class nkpLandscapesEval : public nkLandscapesEval<EOT> {
+public:
+  // parameter N : size of the bit string
+  using nkLandscapesEval<EOT>::N;
+  // parameter K : number of epistatic links
+  using nkLandscapesEval<EOT>::K;
+  // Table of contributions 
+  using nkLandscapesEval<EOT>::tables;
+  // Links between each bit
+  using nkLandscapesEval<EOT>::links;
+
+  using nkLandscapesEval<EOT>::buildTables;
+  using nkLandscapesEval<EOT>::loadLinks;
+  using nkLandscapesEval<EOT>::loadTables;
+  using nkLandscapesEval<EOT>::consecutiveTables;
+  using nkLandscapesEval<EOT>::randomTables;
+
+  // parameter p : probability to have the contribution to zero, otherwise random number from [0,1)
+  double p;
+
+  /**
+   * Empty constructor
+   */
+  nkpLandscapesEval() : nkLandscapesEval<EOT>(), p(0.0) { }
+
+  /**
+   * Constructor of random instance
+   *
+   * @param _N size of the bit string
+   * @param _K number of the epistatic links
+   * @param _p probability to have a contribution equals to zero
+   * @param consecutive : if true then the links are consecutive (i, i+1, i+2, ..., i+K), else the links are randomly choose from (1..N) 
+   */
+  nkpLandscapesEval(int _N, int _K, double _p, bool consecutive = false) : nkLandscapesEval<EOT>() {
+    N = _N;
+    K = _K;
+    p = _p;
+
+    if (consecutive)
+      consecutiveTables();
+    else
+      randomTables();
+  }
+
+  /**
+   * Constructor from a file instance
+   *
+   * @param _fileName the name of the file of the instance
+   */
+  nkpLandscapesEval(const char * _fileName) : nkLandscapesEval<EOT>(_fileName) { }
+
+  /**
+   * Load the instance from a file
+   *
+   * @param _fileName file name of the instance
+   */
+  virtual void load(const string _fileName)
+  {
+    fstream file;
+    file.open(_fileName.c_str(), ios::in);
+
+    if (file.is_open()) {
+      string s;
+
+      // Read the commentairies
+      string line;
+      file >> s;
+      while (s[0] == 'c') {
+	getline(file,line,'\n');
+	file >> s;
+      }
+
+      // Read the parameters
+      if (s[0] != 'p') {
+	string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] at the begining." ;
+	throw runtime_error(str);
+      }
+
+      file >> s;
+      if (s != "NKp") {
+	string str = "nkpLandscapesEval.load: -- NKp -- expected in [" + _fileName + "] at the begining." ;
+	throw runtime_error(str);
+      }
+
+      // read parameters N, K and p
+      file >> N >> K >> p;
+      buildTables();
+
+      // read the links
+      if (s[0] != 'p') {
+	string str = "nkpLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the parameters N, K, and p." ;
+	throw runtime_error(str);
+      }
+
+      file >> s;
+      if (s == "links") {
+	loadLinks(file);
+      } else {
+	string str = "nkpLandscapesEval.load: -- links -- expected in [" + _fileName + "] after the parameters N, K, and q." ;
+	throw runtime_error(str);
+      }
+
+      // lecture des tables
+      if (s[0] != 'p') {
+	string str = "nkpLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the links." ;
+	throw runtime_error(str);
+     }
+
+      file >> s;
+
+      if (s == "tables") {
+	loadTables(file);
+      } else {
+	string str = "nkpLandscapesEval.load: -- tables -- expected in [" + _fileName + "] after the links." ;
+	throw runtime_error(str);
+      }
+
+      file.close();
+    } else {
+	string str = "nkpLandscapesEval.load: Could not open file [" + _fileName + "]." ;
+	throw runtime_error(str);
+    }
+
+  };
+
+  /**
+   * Save the current intance into a file
+   * 
+   * @param _fileName the file name of instance
+   */
+  virtual void save(const char * _fileName) {
+    fstream file;
+    file.open(_fileName, ios::out);
+
+    if (file.is_open()) {
+      file << "c name of the file : " << _fileName << endl;
+      file << "p NKp " << N << " " << K << " " << p << endl;
+
+      file << "p links" << endl;
+      for(int j=0; j<K+1; j++)
+	for(int i=0; i<N; i++)
+	  file << links[i][j] << endl;
+
+      file << "p tables" << endl;
+      for(int j=0; j<(1<<(K+1)); j++) {
+	for(int i=0; i<N; i++)
+	  file << tables[i][j] << " ";
+	file << endl;
+      }
+      file.close();
+    } else {
+      string fname(_fileName);
+      string str = "nkpLandscapesEval.save: Could not open file [" + fname + "]." ;
+      throw runtime_error(str);
+    }
+  };
+
+protected:
+
+  /**
+   * To generate a contribution in the table f_i 
+   *
+   */
+  virtual double contribution() {
+    if (rng.uniform() < p)
+      return 0.0;
+    else
+      return rng.uniform();
+  }
+  
+ 
+};
+
+#endif

trunk/problems/eval/nkqLandscapesEval.h

@@ -0,0 +1,209 @@
+/*
+<nkqLandscapesEval.h>
+Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
+
+Sebastien Verel
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software.  You can  ue,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean  that it is complicated to manipulate,  and  that  also
+therefore means  that it is reserved for developers  and  experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and,  more generally, to use and operate it in the
+same conditions as regards security.
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+
+ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+Contact: paradiseo-help@lists.gforge.inria.fr
+*/
+
+#ifndef __nkqLandscapesEval_H
+#define __nkqLandscapesEval_H
+
+#include <nkLandscapesEval.h>
+
+/*
+ * Neutral version of NK landscapes: the 'quantised' NK
+ * see work of E. J. Newman, and R. Engelhardt "Effects of Neutral Selection on the Evolution of Molecular Species" (1998)
+ */
+template< class EOT >
+class nkqLandscapesEval : public nkLandscapesEval<EOT> {
+public:
+  // parameter N : size of the bit string
+  using nkLandscapesEval<EOT>::N;
+  // parameter K : number of epistatic links
+  using nkLandscapesEval<EOT>::K;
+  // Table of contributions 
+  using nkLandscapesEval<EOT>::tables;
+  // Links between each bit
+  using nkLandscapesEval<EOT>::links;
+
+  using nkLandscapesEval<EOT>::buildTables;
+  using nkLandscapesEval<EOT>::loadLinks;
+  using nkLandscapesEval<EOT>::loadTables;
+  using nkLandscapesEval<EOT>::consecutiveTables;
+  using nkLandscapesEval<EOT>::randomTables;
+
+  // parameter q : number of different integer values in the table: [0..q[
+  unsigned q;
+
+  /**
+   * Empty constructor
+   */
+  nkqLandscapesEval() : nkLandscapesEval<EOT>(), q(0) { }
+
+  /**
+   * Constructor of random instance
+   *
+   * @param _N size of the bit string
+   * @param _K number of the epistatic links
+   * @param consecutive : if true then the links are consecutive (i, i+1, i+2, ..., i+K), else the links are randomly choose from (1..N) 
+   */
+  nkqLandscapesEval(unsigned _N, unsigned _K, unsigned _q, bool consecutive = false) : nkLandscapesEval<EOT>() {
+    N = _N;
+    K = _K;
+    q = _q;
+
+    if (consecutive)
+      consecutiveTables();
+    else
+      randomTables();
+  }
+
+  /**
+   * Constructor from a file instance
+   *
+   * @param _fileName the name of the file of the instance
+   */
+  nkqLandscapesEval(const char * _fileName) : nkLandscapesEval<EOT>(_fileName) { }
+
+  /**
+   * Load the instance from a file
+   *
+   * @param _fileName file name of the instance
+   */
+  virtual void load(const string _fileName)
+  {
+    fstream file;
+    file.open(_fileName.c_str(), ios::in);
+
+    if (file.is_open()) {
+      string s;
+
+      // Read the commentairies
+      string line;
+      file >> s;
+      while (s[0] == 'c') {
+	getline(file,line,'\n');
+	file >> s;
+      }
+
+      // Read the parameters
+      if (s[0] != 'p') {
+	string str = "nkLandscapesEval.load: -- p -- expected in [" + _fileName + "] at the begining." ;
+	throw runtime_error(str);
+      }
+
+      file >> s;
+      if (s != "NKq") {
+	string str = "nkqLandscapesEval.load: -- NKq -- expected in [" + _fileName + "] at the begining." ;
+	throw runtime_error(str);
+      }
+
+      // read parameters N, K and q
+      file >> N >> K >> q;
+      buildTables();
+
+      // read the links
+      if (s[0] != 'p') {
+	string str = "nkqLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the parameters N, K, and q." ;
+	throw runtime_error(str);
+      }
+
+      file >> s;
+      if (s == "links") {
+	loadLinks(file);
+      } else {
+	string str = "nkqLandscapesEval.load: -- links -- expected in [" + _fileName + "] after the parameters N, K, and q." ;
+	throw runtime_error(str);
+      }
+
+      // lecture des tables
+      if (s[0] != 'p') {
+	string str = "nkqLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the links." ;
+	throw runtime_error(str);
+     }
+
+      file >> s;
+
+      if (s == "tables") {
+	loadTables(file);
+      } else {
+	string str = "nkqLandscapesEval.load: -- tables -- expected in [" + _fileName + "] after the links." ;
+	throw runtime_error(str);
+      }
+
+      file.close();
+    } else {
+	string str = "nkqLandscapesEval.load: Could not open file [" + _fileName + "]." ;
+	throw runtime_error(str);
+    }
+
+  };
+
+  /**
+   * Save the current intance into a file
+   * 
+   * @param _fileName the file name of instance
+   */
+  virtual void save(const char * _fileName) {
+    fstream file;
+    file.open(_fileName, ios::out);
+
+    if (file.is_open()) {
+      file << "c name of the file : " << _fileName << endl;
+      file << "p NKq " << N << " " << K << " " << q << endl;
+
+      file << "p links" << endl;
+      for(int j=0; j<K+1; j++)
+	for(int i=0; i<N; i++)
+	  file << links[i][j] << endl;
+
+      file << "p tables" << endl;
+      for(int j=0; j<(1<<(K+1)); j++) {
+	for(int i=0; i<N; i++)
+	  file << tables[i][j] << " ";
+	file << endl;
+      }
+      file.close();
+    } else {
+      string fname(_fileName);
+      string str = "nkqLandscapesEval.save: Could not open file [" + fname + "]." ;
+      throw runtime_error(str);
+    }
+  };
+
+protected:
+
+  /**
+   * To generate a contribution in the table f_i 
+   *
+   */
+  virtual double contribution() {
+    return ((double) rng.random(q)) / (double) q;
+  }
+  
+ 
+};
+
+#endif