AlignmentData.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 __AlignmentData_H__
#define __AlignmentData_H__

#include <Alignment.h>
#include <AlignmentBase.h>
#include <IoTools.h>
#include <algorithm>
#include <iostream>
#include <string>

namespace Victor { namespace Align2{

    class AlignmentData {
    public:

        // CONSTRUCTORS:

        AlignmentData(int n, const string &name1 = "Seq1",
                const string &name2 = "Seq2");

        AlignmentData(const AlignmentData &orig);

        virtual ~AlignmentData();


        // OPERATORS:

        AlignmentData& operator =(const AlignmentData &orig);


        // PREDICATES:

        virtual bool similar(char a, char b);

        virtual string getSequence(int n) = 0;

        virtual void calculateMatch(int i, int tbi, int j, int tbj) = 0;

        virtual void getMatch() = 0;

        virtual void outputMatch(ostream &os, bool fasta = false) = 0;

        virtual Alignment& generateMatch(double score = 0.00) = 0;


        // MODIFIERS:

        virtual void copy(const AlignmentData &orig);

        virtual AlignmentData* newCopy() = 0;

        virtual void add(string s, int n);

        virtual void clear();


        // ATTRIBUTES:

        vector<string> match; 
        int n; 
        string name1; 
        string name2; 


    protected:


    private:

    };

    // -----------------------------------------------------------------------------
    //                                AlignmentData
    // -----------------------------------------------------------------------------

    // MODIFIERS:

    inline void
    AlignmentData::add(string s, int n) {
        match[n] += s;
    }

    inline void
    AlignmentData::clear() {
        for (int i = 0; i < n; i++)
            match[i] = "";
    }

}} // namespace

#endif