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/*
* 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] );
// }
}