JensenShannon.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 __JensenShannon_H__
#define __JensenShannon_H__

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

namespace Victor { namespace Align2{

    class JensenShannon : public ScoringFunction {
    public:

        // CONSTRUCTORS:

        JensenShannon(Profile *pro1, Profile *pro2);

        JensenShannon(const JensenShannon &orig);

        virtual ~JensenShannon();


        // OPERATORS:

        JensenShannon& operator =(const JensenShannon &orig);


        // PREDICATES:

        virtual double scoringSeq(int i, int j);


        // MODIFIERS:

        virtual void copy(const JensenShannon &orig);

        virtual JensenShannon* newCopy();


    protected:


    private:

        // ATTRIBUTES:

        Profile *pro1; 
        Profile *pro2; 
        double p1[20]; 
        double p2[20]; 

    };

}} // namespace

#endif