HFStatistics.hpp

/*
    Copyright 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_HFSTATISTICS_HPP
#define EGGLIB_HFSTATISTICS_HPP



namespace egglib {


    class HFStatistics {
    
        public:
    
            HFStatistics();

            
            virtual ~HFStatistics();

            
            void reserve(unsigned int numberOfIndividuals);


            void loadIndividual(unsigned int genotype, unsigned int populationLabel);


            unsigned int populationLabel(unsigned int populationIndex);


            unsigned int alleleValue(unsigned int alleleIndex);


            unsigned int allele(unsigned int individualIndex) const;

            unsigned int individualLabel(unsigned int individualIndex) const;


            unsigned int numberOfAlleles();


            unsigned int numberOfPopulations();


            unsigned int numberOfGenotypes() const;


            unsigned int alleleFrequencyTotal(unsigned int alleleIndex);
            

            unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex);


            unsigned int populationFrequency(unsigned int populationIndex);


            double theta();


            double T1();


            double T2();
            

        protected:
    
            bool d_flag;
            void d_init();
            void d_clear();
            unsigned int  d_reserved;
            unsigned int  d_numberOfGenotypes;
            unsigned int *d_genotypes;
            unsigned int *d_populationLabels;

            bool s_flag;
            void s_init();
            void s_clear();
            void s_compute();
            void processPopulations();
            void processAlleles();
            unsigned int getPopulationIndex(unsigned int) const;
            unsigned int getAlleleIndex(unsigned int) const;
            unsigned int    s_numberOfAlleles;
            unsigned int   *s_alleleValueMapping;
            unsigned int    s_numberOfPopulations;
            unsigned int   *s_populationLabelMapping;
            unsigned int   *s_populationFrequencies;
            unsigned int   *s_alleleFrequenciesTotal;
            unsigned int  **s_alleleFrequenciesPerPopulation;

            bool w_flag;
            void w_init();
            void w_clear();
            void w_compute();
            double  w_T;
            double *w_T1;
            double *w_T2;
            double  w_nbar;
            double  w_nc;
            double *w_pbar;
            double *w_ssquare;
            double  w_sum_T1;
            double  w_sum_T2;

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

    };
}

#endif