Panchenko.h

/*  This file is part of Victor.

    Victor 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.

    Victor 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 Victor.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef __Panchenko_H__
#define __Panchenko_H__

#include <Profile.h>
#include <PssmInput.h>
#include <ScoringFunction.h>

namespace Victor { namespace Align2{

    class Panchenko : public ScoringFunction {
    public:

        // CONSTRUCTORS:

        Panchenko(Profile *pro1, Profile *pro2, PssmInput *pssm1, PssmInput *pssm2);

        Panchenko(const Panchenko &orig);

        virtual ~Panchenko();


        // OPERATORS:

        Panchenko& operator =(const Panchenko &orig);


        // PREDICATES:

        virtual double scoringSeq(int i, int j);

        int returnAaColumnTarget(int i);

        int returnAaColumnTemplate(int i);


        // MODIFIERS:

        virtual void copy(const Panchenko &orig);

        virtual Panchenko* newCopy();


    protected:


    private:

        // ATTRIBUTES:

        Profile *pro1; 
        Profile *pro2; 
        PssmInput *pssm1; 
        PssmInput *pssm2; 

    };

}} // namespace

#endif