Controller.hpp

/*
    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol

    This file is part of the EggLib library.

    EggLib is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    EggLib 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 General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef EGGLIB_CONTROLLER_HPP
#define EGGLIB_CONTROLLER_HPP

#include "Current.hpp"
#include "Arg.hpp"
#include "ParamSet.hpp"

namespace egglib {
    
    class Random;

    class Controller {

        public:
    
            Controller();

            ~Controller();
            
            Controller(const ParamSet* paramSet, Random* random);
            
           void reset();
            
            unsigned int step();
            
            Arg* getArg();

            void bottleneck(unsigned int populationIndex, double strength);

            void moveAllLineages(unsigned int source, unsigned int dest);
            
            void moveSomeLineages(unsigned int source, unsigned int dest, double probability);

            void addPopulation();

        private:
        
            Controller(const Controller& source) {}
            
            Controller& operator=(const Controller& source) {return *this;}

            void diploids();
            double getMigrationTime(double& migrationParameterDestination);
            void getCoalescenceTime(double& destTime, unsigned int& destPopIndex);
            double getCoalescenceTimeForPopulation(unsigned int populationIndex);
            double getRecombinationTime() const;
            void migrate(double migrationParameter);

            const ParamSet* initialParamSet;
            ParamSet paramSet;
            Current current;
            Arg arg;
            
            Random* random;

    };

}

#endif