ScoringP2S.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 __ScoringP2S_H__
#define __ScoringP2S_H__

#include <Profile.h>
#include <ScoringScheme.h>

namespace Victor { namespace Align2{

    class ScoringP2S : public ScoringScheme {
    public:

        // CONSTRUCTORS:

        ScoringP2S(SubMatrix *sub, AlignmentData *ad, Structure *str, Profile *pro,
                double cSeq);

        ScoringP2S(const ScoringP2S &orig);

        virtual ~ScoringP2S();


        // OPERATORS:

        ScoringP2S& operator =(const ScoringP2S &orig);


        // PREDICATES:

        virtual double scoring(int i, int j);


        // MODIFIERS:

        virtual void copy(const ScoringP2S &orig);

        virtual ScoringP2S* newCopy();

        virtual void reverse();


    protected:


    private:

        // ATTRIBUTES:

        string seq1; 
        string seq2; 
        Profile *pro; 
        double cSeq; 

    };

}} // namespace

#endif