SecSequenceData.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 __SecSequenceData_H__
#define __SecSequenceData_H__

#include <AlignmentData.h>

namespace Victor { namespace Align2{

    class SecSequenceData : public AlignmentData {
    public:

        // CONSTRUCTORS:

        SecSequenceData(int n, const string &seq1, const string &seq2,
                const string &sec1, const string &sec2, const string &name1 = "Seq1",
                const string &name2 = "Seq2");

        SecSequenceData(const SecSequenceData &orig);

        virtual ~SecSequenceData();


        // OPERATORS:

        SecSequenceData& operator =(const SecSequenceData &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 SecSequenceData &orig);

        virtual SecSequenceData* newCopy();

        virtual void setSequence(string s, int n);


    protected:


    private:

        // ATTRIBUTES:

        string seq1; 
        string seq2; 
        string sec1; 
        string sec2; 

    };

}} // namespace

#endif