SitePolymorphism.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_SITEPOLYMORPHISM_HPP
#define EGGLIB_SITEPOLYMORPHISM_HPP



namespace egglib {


    class SitePolymorphism {

        public:

            SitePolymorphism();


            SitePolymorphism(unsigned int npop);


            virtual ~SitePolymorphism();


            SitePolymorphism(const SitePolymorphism& source);


            SitePolymorphism& operator=(const SitePolymorphism& source);


            void numberOfPopulations(unsigned int npop);


            void load(unsigned int populationIndex, char character);


            void outgroup(char state);


            unsigned int numberOfAlleles() const;
            
            
            char allele(unsigned int index) const;


            unsigned int alleleFrequency(unsigned int alleleIndex) const;


            unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const;


            unsigned int derivedAlleleFrequency() const;


            unsigned int ns() const;


            unsigned int ns(unsigned int popIndex) const;


            bool isOrientable() const;

            bool isPolymorphic(unsigned int popIndex) const;
            bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const;
            bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const;
            bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const;
            bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const;




        protected:

            // helpers
            void init();
            void clear();
            void copy(const SitePolymorphism& site);


            // data
            unsigned int m_numberOfPopulations;
            unsigned int m_numberOfStates;
            char * m_states;
            unsigned int ** m_frequencies;
            unsigned int m_numberOfOutgroups;
            char * m_outgroups;
            unsigned int m_ns;
            unsigned int * m_pop_ns;
            
            bool m_cache_orientable;

    };
}

#endif