ParamSet.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_PARAMSET_HPP
#define EGGLIB_PARAMSET_HPP


#include "DataMatrix.hpp"


namespace egglib {

    class Change;
    class Controller;


    class ParamSet {

        public:
    
            ParamSet();

            ~ParamSet();
            
            ParamSet(const ParamSet&);
            
            ParamSet& operator=(const ParamSet&);

            void reset();

            unsigned int numberOfPopulations() const;
            
            double pairwiseMigrationRate(unsigned int source, unsigned int dest) const;
            
            void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value);
            
            void migrationRate(double value);
            
            double populationSize(unsigned int populationIndex) const;
            
            void populationSize(unsigned int populationIndex, double value);
            
            double growthRate(unsigned int populationIndex) const;
            
            void growthRate(unsigned int populationIndex, double value);
            
            double recombinationRate() const;
            
            void recombinationRate(double value);

            unsigned int numberOfSegments() const;
            
            void numberOfSegments(unsigned int value);

            double selfingRate() const;
            
            void selfingRate(double value);
            
            void addPopulation(double migr);
            
            void addChange(const Change* change);

            double nextChangeDate() const;
            
            void nextChangeDo(Controller* controller);
            
            unsigned int singles(unsigned int populationIndex) const;

            void singles(unsigned int populationIndex, unsigned int value);

            unsigned int doubles(unsigned int populationIndex) const;

            void doubles(unsigned int populationIndex, unsigned int value);
            
            unsigned int numberOfSamples() const;
            
            double dateOfLastChange(unsigned int populationIndex) const;


            void dateOfLastChange(unsigned int populationIndex, double date) const;

            
            void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false);

        private:

            void clear();
            void init();
            void copy(const ParamSet&);
        
            double _selfingRate;
            double _recombinationRate;
            unsigned int _numberOfSegments;
            unsigned int _numberOfPopulations;
            unsigned int* _singles;
            unsigned int* _doubles;
            double* _growthRates;
            double* _populationSize;
            double* _dateOfLastChange;
            double** migrationMatrix;
            unsigned int _numberOfChanges;
            unsigned int nextChangeIndex;
            Change const** changes;
    };

}

#endif