LogAverage.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/>.
 */


/*************************************************
 * sub is BLOSUM62 matrix standard log-odds form *
 *************************************************/

#ifndef __LogAverage_H__
#define __LogAverage_H__

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

namespace Victor { namespace Align2{

    class LogAverage : public ScoringFunction {
    public:

        // CONSTRUCTORS:

        LogAverage(SubMatrix *sub, Profile *pro1, Profile *pro2);

        LogAverage(const LogAverage &orig);

        virtual ~LogAverage();


        // OPERATORS:

        LogAverage& operator =(const LogAverage &orig);


        // PREDICATES:

        virtual double scoringSeq(int i, int j);


        // MODIFIERS:

        virtual void copy(const LogAverage &orig);

        virtual LogAverage* newCopy();


    protected:


    private:

        // ATTRIBUTES:

        SubMatrix *sub; 
        Profile *pro1; 
        Profile *pro2; 

    };

}} // namespace

#endif