HenikoffProfile.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 __HenikoffProfile_H__
#define __HenikoffProfile_H__

#include <Profile.h>

namespace Victor { namespace Align2{

    class HenikoffProfile : public Profile {
    public:

        // CONSTRUCTORS:

        HenikoffProfile();

        HenikoffProfile(const HenikoffProfile &orig);

        virtual ~HenikoffProfile();


        // OPERATORS:

        HenikoffProfile& operator =(const HenikoffProfile &orig);


        // MODIFIERS:

        virtual void copy(const HenikoffProfile &orig);

        virtual HenikoffProfile* newCopy();


        // HELPERS:

        //to save computational time we suggest cLen=25. Francesco Lovo 2012
        virtual void pCalculateWeight(Alignment &ali, unsigned int cLen = 50);

        virtual void pCalculateRawFrequency(vector<double> &freq, double &gapFreq,
                Alignment &ali, unsigned int i);

        virtual void pConstructData(Alignment &ali);


    protected:


    private:

        vector< vector<double> > aliWeight; 

    };

}} // namespace

#endif