pars_align_gapp_seq.cpp

/*
 * Copyright (C) 2009-2012 Simon A. Berger
 * 
 * This file is part of papara.
 * 
 *  papara 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.
 *
 *  papara 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 papara.  If not, see <http://www.gnu.org/licenses/>.
 */


#include <climits>
#include <cmath>
#include <time.h>
#include <cstdlib>
#include <cstdio>
#include <ctype.h>
#include <cassert>
#include <cstring>
#include <stdint.h>
#include <algorithm>
#include <vector>
#include <limits>
#include <stdexcept>

#include "pars_align_gapp_seq.h"

const pars_align_gapp_seq::score_t pars_align_gapp_seq::LARGE_VALUE = 32000;

pars_align_gapp_seq::pars_align_gapp_seq(const int* seqA, const unsigned char* seqB, size_t n_a, size_t n_b, size_t aStride, const double* gapp, size_t aAuxStride, pars_align_gapp_seq::arrays &arr, const unsigned int *bvtrans, pars_align_gapp_seq::score_t gapOpen, score_t gapExtend, pars_align_gapp_seq::score_t mismatch, pars_align_gapp_seq::score_t matchCGap) : GAP_OPEN(gapOpen),
        GAP_EXTEND(gapExtend),
        GAP_OPEN_EXTEND( GAP_OPEN + GAP_EXTEND ),
        MISMATCH_PENALTY(mismatch),
        MATCH_CGAP(matchCGap),
        g_dump(false),
        m_ncups(0),
        m_arr(arr),
        m_tbStartA(-1),
        m_tbStartB(-1),
        m_bvtrans(bvtrans)
        

{
    if( n_a <= n_b ) {
        throw std::runtime_error( "n_a <= n_b\n" );
    }
    
    m_na = n_a;
    m_nb = n_b;

    m_ma = n_a + 1;
    m_mb = n_b + 1;


    m_a = seqA;
    m_b = seqB;

    m_gapp = gapp;
    m_aStride = aStride;



    m_msize = m_ma * m_mb;

    
    m_arr.size( m_msize );

}
pars_align_gapp_seq::~pars_align_gapp_seq() {

}
void pars_align_gapp_seq::alignFreeshiftS11() {
    
    if( m_na > m_nb ) {
        for ( size_t ia = 0; ia <= m_na - m_nb - 1; ia++ ) {
            //  std::cout << "init: " << ia << " " << m_na << " " << m_nb << "\n";
            
            //size_t xxx = saddr ( ia, -1 );
            //         if( xxx >= m_arr.size() ) {
                //             std::cout << "meeeep: " << xxx << " " << ia << "\n";
                //         }
                m_arr.scoreL[saddr ( ia, -1 ) ] = 0;
                m_arr.score[saddr ( ia, -1 ) ] = 0;
        }
    }

    m_arr.score[saddr ( -1, -1 ) ] = 0;
    m_arr.scoreL[saddr ( -1, -1 ) ] = 0;

    for ( size_t i = 0; i < m_nb; i++ ) {
        m_arr.score[saddr ( i-1, i )] = LARGE_VALUE;
        m_arr.scoreL[saddr ( i-1, i )] = LARGE_VALUE;
        m_arr.scoreL[saddr ( i, i )] = LARGE_VALUE;
        m_arr.score[saddr ( (m_na - m_nb) + i, i - 1 )] = LARGE_VALUE;
    }

    for( size_t i = 0; i < m_na; i++ ) {
        m_arr.score[saddr ( i, -1 )] = 0;
    }

    if ( m_arr.m_haveDir ) {
        
        if( m_na > m_nb ) {
            for ( size_t ia = 0; ia <= m_na - m_nb - 1; ia++ ) {
                m_arr.dir[saddr ( ia, -1 ) ] = BT_STAY_L;
            }
        }
    }
}


void pars_align_gapp_seq::tracebackCompressed(std::vector< uint8_t >& bvec) {
//     int idx_b = m_na-1;
    ptrdiff_t ba = m_tbStartA;
    ptrdiff_t bb = m_tbStartB;
    bool inL = false;

    
    
    
    if ( m_tbStartA < ptrdiff_t(m_na) - 1 ) {
        for ( ptrdiff_t ba = m_na - 1; ba > m_tbStartA; ba-- ) {
            bvec.push_back(1);
            
        }
    }

    // traceback

    while ( ( ba >= 0 || bb >= 0 ) ) {
        if ( !inL ) {

            // we are currently not in a gap. see if we should match ('go diagonal') or open a gap ('jump to gap-matrix')
            if ( ( m_arr.dir[saddr ( ba, bb ) ] & BT_STAY ) != 0 ) {
                bvec.push_back(0);
//                 idx_b--;
                ba--;
                bb--;
            } else if( ( m_arr.dir[saddr ( ba, bb ) ] & BT_UP ) != 0 ) {
            	bb--;
            	bvec.push_back(2);
        
        } else {
                // open gap. keep position and switch to gap-matrix
                inL = true;
            }
        } else {
            // we are in a gap

            // output gap
            bvec.push_back(1);

//             idx_b--;
            // check if we should stay in the gap-matrix
            inL = ( m_arr.dir[saddr ( ba, bb ) ] & BT_STAY_L ) != 0;
            ba--;
        }
    }
    
//     for( int i = 0; i <  bvec.size(); i++ ) {
//         printf( "tb %d: %d\n", i, bvec[i] );
//     }

}