Alignment.hpp

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/*******************************************************************************
 *
 * Copyright (c) 2010-2015   Edans Sandes
 *
 * This file is part of MASA-Core.
 * 
 * MASA-Core 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.
 * 
 * MASA-Core 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 MASA-Core.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/

class Alignment;

#ifndef _ALIGNMENT_HPP
#define _ALIGNMENT_HPP

#include <string>
using namespace std;

#include "AlignmentParams.hpp"

#define TYPE_MATCH      (0)
#define TYPE_GAP_1      (1) //HORIZONTAL (gap on sequence 0) // TODO alterar constantes
#define TYPE_GAP_2      (2) //VERTICAL (gap on sequence 1) // TODO alterar constantes

struct gap_sequence_t {
        int i0;
        int j0;
        int i1;
        int j1;
        int type() {
                if (i0==i1) return 1;
                if (j0==j1) return 2;
                return 0; //TODO ERROR
        }
        
        int len() {
                return (i1-i0)+(j1-j0);
        }
};      

struct gap_t {
        int pos;
        int len;

        gap_t() {

        }

        gap_t(int pos, int len) {
                this->pos = pos;
                this->len = len;
        }
};

class Alignment {
public:
        
    Alignment(AlignmentParams* params);
    Alignment(const Alignment& orig);
    virtual ~Alignment();

    void addGapInSeq0(int i);
    void addGapInSeq1(int j);
    void finalize /*int i0, int j0, int i1, int j1*/
        ();
        bool isFinalized();
        //void printBinary(string filename);
        //void loadBinary(string filename);
        vector<gap_sequence_t>* getGapSequences();
        AlignmentParams* getAlignmentParams() const;
        int getRawScore() const;
        void setRawScore(int rawScore);

        vector<gap_t>* getGaps(int seq) {
                return &gaps[seq];
        }

        void setStart(int seq, int pos);
        void setEnd(int seq, int pos);
        int getStart(int seq);
        int getEnd(int seq);
        string getPruningFile() const;
        void setPruningFile(string pruningFile);
        int getGapExtensions() const;
        void setGapExtensions(int gapExtensions);
        int getGapOpen() const;
        void setGapOpen(int gapOpen);
        int getMatches() const;
        void setMatches(int matches);
        int getMismatches() const;
        void setMismatches(int mismatches);

private:
        int start[2];
        int end[2];

        int rawScore;
        int matches;
        int mismatches;
        int gapOpen;
        int gapExtensions;
        
        bool alignmentFinalized;
        AlignmentParams* params;

    vector<gap_t> gaps[2];
        vector<gap_sequence_t> gap_sequences;
        string pruningFile;

    void addGap(int seq, int i);

};

#endif  /* _ALIGNMENT_HPP */