Convert.hpp

/*
    Copyright 2009,2013 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_CONVERT_HPP
#define EGGLIB_CONVERT_HPP

#include "DataMatrix.hpp"
#include "Align.hpp"
#include "EggException.hpp"
#include "Random.hpp"
#include <string>

#include "config.h"

#ifdef HAVE_LIBBPP_SEQ
#include <Bpp/Seq/Alphabet/DNA.h>
#include <Bpp/Seq/Alphabet/RNA.h>
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/Sequence.h>
#include <Bpp/Seq/Container/AlignedSequenceContainer.h>
#endif

namespace egglib {


    class Convert {

        public:
        
            static Align align(
                DataMatrix& dataMatrix,
                unsigned int length=0,
                Random* random=NULL,
                bool randomizePositions=false,
                bool randomizeNonVaryingStates=false,
                bool randomizeAlleles=false,
                bool enforceLength=false,
                std::string mapping="ACGT",
                char unknown='?',
                char nonVaryingState='A'
            );


#ifdef HAVE_LIBBPP_SEQ

            static bpp::AlignedSequenceContainer egglib2bpp(Align& align, unsigned int alphabetID, unsigned int outgroupFlag, unsigned int offset=0);

#endif

        protected:

            Convert() { }


            Convert(const Convert& source) { }


            Convert& operator=(const Convert& source) { return *this; }


            virtual ~Convert() { }

#ifdef HAVE_LIBBPP_SEQ
            static bpp::DNA dnaAlphabet;
            static bpp::RNA rnaAlphabet;
            static bpp::ProteicAlphabet proteicAlphabet;
            static bpp::CodonAlphabet CodonAlphabet;
#endif

    };
}

#endif