HaplotypeDiversity.hpp

/*
    Copyright 2008-2009 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_HAPLOTYPEDIVERSITY_HPP
#define EGGLIB_HAPLOTYPEDIVERSITY_HPP

#include "BaseDiversity.hpp"

namespace egglib {


    class HaplotypeDiversity : public BaseDiversity {

        public:

            HaplotypeDiversity();
            
            virtual ~HaplotypeDiversity();

            void load(CharMatrix& data,
                bool allowMultipleMutations=false,
                unsigned int ignoreFrequency=0,
                std::string characterMapping=dnaMapping
            );
            
            unsigned int K() const;
            
            double He() const;
            
            unsigned int haplotypeIndex(unsigned int) const;
            
            double Kst() const;

            double Fst() const;

            double Gst() const;

            double Hst() const;
            
            double Snn() const;


        protected:
        
            void init();
            void clear();
                        
            inline unsigned int diff(CharMatrix& data, unsigned int ind1, unsigned int ind2) const;

            bool m_loaded;
            unsigned int m_K;
            double m_He;
            double m_Kst;
            double m_Fst;
            double m_Gst;
            double m_Hst;
            double m_Snn;
            unsigned int *m_haplotypeIndex;


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

    };
}

#endif