SequenceData.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 __SequenceData_H__
#define __SequenceData_H__

#include <AlignmentData.h>

namespace Victor { namespace Align2{

    class SequenceData : public AlignmentData {
    public:

        // CONSTRUCTORS:

        SequenceData(int n, const string &seq1, const string &seq2,
                const string &name1 = "Seq1", const string &name2 = "Seq2");

        SequenceData(const SequenceData &orig);

        virtual ~SequenceData();


        // OPERATORS:

        SequenceData& operator =(const SequenceData &orig);


        // PREDICATES:

        virtual string getSequence(int n);

        virtual void calculateMatch(int i, int tbi, int j, int tbj);

        virtual void getMatch();

        virtual void outputMatch(ostream &os, bool fasta = false);

        virtual Alignment& generateMatch(double score = 0.00);


        // MODIFIERS:

        virtual void copy(const SequenceData &orig);

        virtual SequenceData* newCopy();

        virtual void setSequence(string s, int n);


    protected:


    private:

        // ATTRIBUTES:

        string seq1; 
        string seq2; 

    };

}} // namespace

#endif