FSAlign.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 __FSAlign_H__
#define __FSAlign_H__

#include <Align.h>

namespace Victor { namespace Align2{

    class FSAlign : public Align {
    public:

        // CONSTRUCTORS:

        FSAlign(AlignmentData *ad, GapFunction *gf, ScoringScheme *ss);

        FSAlign(AlignmentData *ad, GapFunction *gf, ScoringScheme *ss,
                const vector<unsigned int> &v1, const vector<unsigned int> &v2);

        FSAlign(const FSAlign &orig);

        virtual ~FSAlign();


        // OPERATORS:

        FSAlign& operator =(const FSAlign &orig);


        // PREDICATES:

        virtual void getMultiMatch();


        // MODIFIERS:

        virtual void copy(const FSAlign &orig);

        virtual FSAlign* newCopy();


        // HELPERS:

        virtual void pCalculateMatrix(bool update = true);

        virtual void pCalculateMatrix(const vector<unsigned int> &v1,
                const vector<unsigned int> &v2, bool update = true);


    protected:


    private:

    };

}} // namespace

#endif