paradiseo/problems/eval/nkqLandscapesEval.h

/*
<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
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ParadisEO WebSite : http://paradiseo.gforge.inria.fr
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*/

#ifndef __nkqLandscapesEval_H
#define __nkqLandscapesEval_H

#include <eval/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;
  using nkLandscapesEval<EOT>::generateTables;

  // 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();

    generateTables();
  }

  /**
   * 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 eoException(str);
      }

      file >> s;
      if (s != "NKq") {
	string str = "nkqLandscapesEval.load: -- NKq -- expected in [" + _fileName + "] at the begining." ;
	throw eoException(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 eoException(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 eoException(str);
      }

      // lecture des tables
      if (s[0] != 'p') {
	string str = "nkqLandscapesEval.load: -- p -- expected in [" + _fileName + "] after the links." ;
	throw eoException(str);
     }

      file >> s;

      if (s == "tables") {
	loadTables(file);
      } else {
	string str = "nkqLandscapesEval.load: -- tables -- expected in [" + _fileName + "] after the links." ;
	throw eoException(str);
      }

      file.close();
    } else {
	// string str = "nkqLandscapesEval.load: Could not open file [" + _fileName + "]." ;
	throw eoFileError(_fileName);
    }

  };

  /**
   * 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 eoFileError(fname);
    }
  };

protected:

  /**
   * To generate a contribution in the table f_i 
   *
   */
  virtual double contribution() {
    return ((double) rng.random(q)) / (double) (q-1);
  }
  
 
};

#endif