SubMatrix.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 __SubMatrix_H__
#define __SubMatrix_H__

#include <Substitution.h>

namespace Victor { namespace Align2{

    class SubMatrix : public Substitution {
    public:

        // CONSTRUCTORS:

        SubMatrix();

        SubMatrix(istream &is);

        SubMatrix(const SubMatrix &orig);

        virtual ~SubMatrix();


        // OPERATORS:

        SubMatrix& operator =(const SubMatrix &orig);

        friend ostream& operator <<(ostream &os, const SubMatrix &object);

        friend istream& operator >>(istream &is, SubMatrix &object);


        // PREDICATES:

        virtual string getResidues() const;

        virtual unsigned int size() const;


        // MODIFIERS:

        virtual void copy(const SubMatrix &orig);

        virtual SubMatrix* newCopy();


    protected:


    private:

        // ATTRIBUTES:

        vector< vector<int> > residuescores; 
        string residues; 

    };

    // -----------------------------------------------------------------------------
    //                                 SubMatrix
    // -----------------------------------------------------------------------------

    // PREDICATES:

    inline string
    SubMatrix::getResidues() const {
        return residues;
    }

    inline unsigned int
    SubMatrix::size() const {
        return residuescores.size();
    }

}} // namespace

#endif