AtchleyDistance.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 __AtchleyDistance_H__
#define __AtchleyDistance_H__

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

namespace Victor { namespace Align2{

    class AtchleyDistance : public ScoringFunction {
    public:

        // CONSTRUCTORS:

        AtchleyDistance(Profile *pro1, Profile *pro2);

        AtchleyDistance(Profile *pro1, Profile *pro2, double offset);

        AtchleyDistance(const AtchleyDistance &orig);

        virtual ~AtchleyDistance();


        // OPERATORS:

        AtchleyDistance& operator =(const AtchleyDistance &orig);


        // PREDICATES:

        virtual double scoringSeq(int i, int j);

        virtual double getOffset();


        // MODIFIERS:

        virtual void copy(const AtchleyDistance &orig);

        virtual AtchleyDistance* newCopy();

        virtual void setOffset(double off);


        // HELPERS:

        virtual void pLoadFactor();


    protected:


    private:

        // ATTRIBUTES:

        Profile *pro1; 
        Profile *pro2; 
        double offset; 
        double factor[20][5]; 

    };

    // -----------------------------------------------------------------------------
    //                               AtchleyDistance
    // -----------------------------------------------------------------------------

    // PREDICATES:

    inline double AtchleyDistance::getOffset() {
        return offset;
    }


    // MODIFIERS:

    inline void AtchleyDistance::setOffset(double off) {
        offset = off;
    }

}} // namespace

#endif