geneticAlgorithm.h

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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Jan Fuhrmann, Marcel Schumann $
// ----------------------------------------------------

#ifndef BALL_DOCKING_GENETICDOCK_GENETICALGORITHM_H
#define BALL_DOCKING_GENETICDOCK_GENETICALGORITHM_H

#include <vector>
#include <BALL/MATHS/randomNumberGenerator.h>
#include <utility>
#include "geneticIndividual.h"
#include <BALL/DOCKING/GENETICDOCK/parameter.h>

namespace BALL
{

  class DockProblem;
  class DockingAlgorithm;

  class BALL_EXPORT GeneticAlgorithm
    {

      friend class EvolutionaryDocking;

    public:
      //CREATE(GeneticAlgorithm)

      GeneticAlgorithm();

      GeneticAlgorithm(const GeneticAlgorithm& ga);

      GeneticAlgorithm(DockingAlgorithm* docker, DockProblem*,
           int pop_number,
           int iter,
           int init,
           int pop,
           int surv,
           double mrate,
           int save,
           int citer,
           double cvalue,
           int cstart );

      virtual ~GeneticAlgorithm();

      virtual GeneticAlgorithm& operator = (const GeneticAlgorithm& ga);

    //  virtual GeneticAlgorithm* clone();

      void setup(DockProblem*,
     int pop_number,
     int iter,
     int init,
     int pop,
     int surv,
     double mrate,
     int save,
     int citer,
     double cvalue,
     int cstart);

      virtual void start();

      virtual double getValue() { return 0.0;};

      GeneticIndividual* getIndividual(Index i);

      bool registerParameter(GenericParameter*);

    protected:

      double calculate(GeneticIndividual*);

      vector<GenericParameter*> parameters_;

      void select(Size);

      void mate();

      void mutate();

      void cleanUp();

      void cleanPool(vector<GeneticIndividual>& pool);

      bool multiDemeCheck();

      void updatePool();

      Size population_size_;

      std::vector<std::vector<GeneticIndividual> > pools_;

      std::vector<std::pair<GeneticIndividual*, GeneticIndividual*> > selected_;

      std::vector<double> probabilities_;

      DockProblem* gp_;

      Size max_iterations_;

      Size immune_;

      double mutation_rate_;

      Size iteration_;

      Size survivors_;

      int conv_start_;

      bool finished_;

      DockingAlgorithm* docking_algorithm_;

      RandomNumberGenerator rng_;

      GeneticIndividual template_individual_;

    };
}

#endif /* BALL_DOCKING_GENETICDOCK_GENETICALGORITHM_H */