MultipleSequentialModel.hpp

/*
 *       MultipleSequentialModel.hpp
 *
 *       Copyright 2011 Andre Yoshiaki Kashiwabara <akashiwabara@usp.br>
 *                      Ígor Bonádio <ibonadio@ime.usp.br>
 *                      Vitor Onuchic <vitoronuchic@gmail.com>
 *                      Alan Mitchell Durham <aland@usp.br>
 *
 *       This program 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.
 *
 *       This program 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 this program; if not, write to the Free Software
 *       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 *       MA 02110-1301, USA.
 */

#ifndef MULTIPLE_SEQUENTIAL_MODEL
#define MULTIPLE_SEQUENTIAL_MODEL

#include "crossplatform.hpp"

#include "Sequence.hpp"
#include "Alphabet.hpp"

#include "ProbabilisticModel.hpp"
#include "FactorableModel.hpp"
#include "MultipleSequentialModelCreator.hpp"
#include "ProbabilisticModelParameter.hpp"
#include "util.hpp"
#include <cstdarg>
#include <vector>

namespace tops {


    class DLLEXPORT MultipleSequentialModel : public ProbabilisticModel
    {
    public:

        MultipleSequentialModel()  {
        };
        virtual double prefix_sum_array_compute(int begin, int end, int phase);

        virtual double prefix_sum_array_compute(int begin, int end) ;

        virtual bool initialize_prefix_sum_array(const Sequence & s);

        virtual bool initialize_prefix_sum_array(const Sequence & s, int phase);

        virtual ~MultipleSequentialModel() {}
        virtual void initialize (const ProbabilisticModelParameters & p ) ;
        virtual ProbabilisticModelParameters parameters() const;
        virtual std::string model_name() const {
            return "MultipleSequentialModel";
        }

        virtual double evaluate(const Sequence & s, unsigned int begin, unsigned int end) const;

        virtual double evaluate(const Sequence & s, unsigned int begin, unsigned int end, int phase) const ;
        virtual std::string str() const;
        virtual Sequence &  choose(Sequence & h, int size) const;
    private:
        std::vector<ProbabilisticModelPtr> _sub_models;
        std::vector<int> _max_size;
        int _idx_not_limited;
        std::map<std::string, ProbabilisticModelPtr> _models;
        ProbabilisticModelParameters _parameters;
        int _seqsize;
    };

    typedef boost::shared_ptr<MultipleSequentialModel> MultipleSequentialModelPtr;
}



#endif