VGPFunction2.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 __VGPFunction2_H__
#define __VGPFunction2_H__

#include <Alignment.h>
#include <GapFunction.h>
#include <math.h>
#include <string>
#include <vector>

namespace Victor { namespace Align2{

    class VGPFunction2 : public GapFunction {
    public:

        // CONSTRUCTORS:

        VGPFunction2(string secFileName);

        VGPFunction2(string secFileName, double o, double e, unsigned int extType,
                double wH, double wS);

        VGPFunction2(const VGPFunction2 &orig);

        virtual ~VGPFunction2();


        // OPERATORS:

        VGPFunction2& operator =(const VGPFunction2 &orig);


        // PREDICATES:

        virtual double getOpenPenalty(int p);

        virtual double getExtensionPenalty(int p);


        // MODIFIERS:

        virtual void copy(const VGPFunction2 &orig);

        virtual VGPFunction2* newCopy();

        virtual void setOpenPenalty(double pen);

        virtual void setExtensionPenalty(double pen);


        // HELPERS:

        void pExtractSecInfo(string secFileName);


    protected:


    private:

        // ATTRIBUTES:

        double o; 
        double e; 
        unsigned int extType; 
        unsigned int extCounter; 
        vector<double> hContent; 
        vector<double> sContent; 
        double wH; 
        double wS; 

    };

    // -----------------------------------------------------------------------------
    //                                 VGPFunction
    // -----------------------------------------------------------------------------

    // MODIFIERS:

    inline void
    VGPFunction2::setOpenPenalty(double pen) {
        o = pen;
    }

    inline void
    VGPFunction2::setExtensionPenalty(double pen) {
        e = pen;
    }

}} // namespace

#endif