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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/>.
*/
#ifndef __align_vec_h
#define __align_vec_h
#include "vec_unit.h"
#include "ivymike/aligned_buffer.h"
#include "ivymike/fasta.h"
using ivy_mike::aligned_buffer;
using ivy_mike::scoring_matrix;
template <class score_t>
struct persistent_state {
aligned_buffer<score_t> out;
aligned_buffer<score_t> s;
aligned_buffer<score_t> si;
};
//#define LIKELY(x) __builtin_expect((x),1)
// #define LIKELY(x) (x)
template <class score_t, class sscore_t, size_t W>
void align_vec( persistent_state<score_t> &ps, size_t asize, const std::vector<uint8_t> &b, const scoring_matrix &m, aligned_buffer<sscore_t> &qprofile, const sscore_t gap_open, const sscore_t gap_extend, std::vector<int> &out ) {
typedef vector_unit<score_t,W> vu;
typedef typename vu::vec_t vec_t;
// assert( a.size() % W == 0 );
// const size_t asize = a.size() / W;
// std::vector<score_t> s( a.size());
// std::vector<score_t> si( a.size());
aligned_buffer<score_t> &s = ps.s;
aligned_buffer<score_t> &si = ps.si;
aligned_buffer<score_t> pb(W);
if( s.size() < asize * W ) {
s.resize( asize * W );
si.resize( asize * W );
}
const score_t bias = vu::BIAS;
std::fill( s.begin(), s.end(), bias );
std::fill( si.begin(), si.end(), bias );
const score_t SMALL = vu::SMALL_VALUE;
vec_t max_vec = vu::set1(SMALL);
const vec_t GAP_EXT_vec = vu::set1(score_t(-gap_extend)); // these values are _subtracted_ from the score. so use negative of user parameters!
const vec_t GAP_OPEN_vec = vu::set1(score_t(-gap_open));
const vec_t BIAS_vec = vu::set1( vu::BIAS );
// vec_t len_vec = vu::load( len.m_ptr );
#define LOCAL_ALIGN
for( size_t ib = 0; ib < b.size(); ib++ ) {
#ifndef LOCAL_ALIGN
const bool lastrow = ib == (b.size() - 1);
#endif
char bc = b[ib];
// std::cout << "bc: " << bc << std::endl;
assert( bc < char(qprofile.size() / (W * asize)));
vec_t last_sl = vu::set1(SMALL);
vec_t last_s = vu::set1(vu::BIAS);
vec_t last_sdiag = vu::set1(vu::BIAS);
// std::cout << "sbm: " << m.state_backmap(bc) << " " << (W * asize) << std::endl;
// sscore_t *qpp_iter = qprofile(m.state_backmap(bc) * W * asize);
sscore_t *qpp_iter = qprofile( bc * W * asize);
score_t * __restrict s_iter = s.base();
score_t * __restrict su_iter = si.base();
score_t * __restrict s_end = s_iter + (asize * W);
for( ; s_iter != s_end; s_iter += W, su_iter += W, qpp_iter += W ) {
const vec_t match = vu::load( (score_t*) qpp_iter );
// getchar();
const vec_t sm = vu::add( last_sdiag, match );
last_sdiag = vu::load( s_iter );
#ifdef LOCAL_ALIGN
const vec_t sm_zero = vu::max( sm, BIAS_vec);
#else
const vec_t sm_zero = sm_vec;
#endif
const vec_t sl_open = vu::sub( last_s, GAP_OPEN_vec );
const vec_t sl_ext = vu::sub( last_sl, GAP_EXT_vec );
const vec_t sl = vu::max( sl_ext, sl_open );
last_sl = sl;
const vec_t su_ext = vu::sub( vu::load(su_iter), GAP_EXT_vec );
const vec_t su_open = vu::sub( last_sdiag, GAP_OPEN_vec );
const vec_t su = vu::max( su_ext, su_open );
vu::store( su, su_iter );
const vec_t s = vu::max( sm_zero, vu::max( sl, su ));
// vu::println( max_vec, pb.m_ptr );
last_s = s;
vu::store( s, s_iter );
#ifdef LOCAL_ALIGN
max_vec = vu::max( s, max_vec );
#else
if( s_iter == s_end - W || lastrow ) {
max_vec = vu::max( sc_vec, max_vec );
}
#endif
}
}
ps.out.resize(W);
vu::store( max_vec, ps.out.base() );
out.resize(0);
out.reserve(W);
for( size_t i = 0; i < W; i++ ) {
out.push_back(int(ps.out[i]) - vu::BIAS );
// std::cout << "x: " << int(ps.out.m_ptr[i]) << "\n";
}
//return max;
}
template<typename score_t, typename sscore_t>
struct block_cont {
score_t * __restrict s_iter;
score_t * __restrict su_iter;
score_t * __restrict s_end;
sscore_t * __restrict qpp_iter;
};
template <class score_t, class sscore_t>
struct persistent_state_blocked {
aligned_buffer<score_t> out;
aligned_buffer<score_t> s;
aligned_buffer<score_t> si;
aligned_buffer<score_t> bcv_store;
std::vector<block_cont<score_t, sscore_t> > bc_array;
};
template <class score_t, class sscore_t, size_t W, size_t BW>
void align_vec_blocked( persistent_state_blocked<score_t,sscore_t> &ps, size_t asize, const std::vector<uint8_t> &b, const scoring_matrix &m, aligned_buffer<sscore_t> &qprofile, const sscore_t gap_open, const sscore_t gap_extend, std::vector<int> &out ) {
typedef vector_unit<score_t,W> vu;
typedef typename vu::vec_t vec_t;
// assert( a.size() % W == 0 );
// const size_t asize = a.size() / W;
// std::vector<score_t> s( a.size());
// std::vector<score_t> si( a.size());
aligned_buffer<score_t> &s = ps.s;
aligned_buffer<score_t> &si = ps.si;
// aligned_buffer<score_t> pb(W);
if( s.size() < asize * W ) {
s.resize( asize * W );
si.resize( asize * W );
}
const score_t bias = vu::BIAS;
std::fill( s.begin(), s.end(), bias );
std::fill( si.begin(), si.end(), bias );
const score_t SMALL = vu::SMALL_VALUE;
vec_t max_vec = vu::set1(SMALL);
const vec_t GAP_EXT_vec = vu::set1(score_t(-gap_extend)); // these values are _subtracted_ from the score. so use negative of user parameters!
const vec_t GAP_OPEN_vec = vu::set1(score_t(-gap_open));
const vec_t BIAS_vec = vu::set1( vu::BIAS );
struct block_cont_vec {
vec_t last_sl;
vec_t last_s;
vec_t last_sdiag;
void init() {
last_sl = vu::set1(vu::SMALL_VALUE);
last_s = vu::set1(vu::BIAS);
last_sdiag = vu::set1(vu::BIAS);
}
void load( score_t *ptr ) {
last_sl = vu::load( ptr );
last_s = vu::load( ptr + W );
last_sdiag = vu::load( ptr + W + W );
}
void store( score_t *ptr ) {
vu::store( last_sl, ptr );
vu::store( last_s, ptr + W );
vu::store( last_sdiag, ptr + W + W );
}
};
size_t num_blocks = asize / BW;
if( asize % BW != 0 ) {
num_blocks++;
}
//aligned_buffer<score_t> bcv_store( b.size() * W * 3 );
aligned_buffer<score_t> &bcv_store = ps.bcv_store;
std::vector<block_cont<score_t, sscore_t> > &bc_array = ps.bc_array;
if( bcv_store.size() < b.size() * W * 3 ) {
bcv_store.resize(b.size() * W * 3);
bc_array.resize( b.size() );
}
//std::vector<block_cont> bc_array(b.size());
// vec_t len_vec = vu::load( len.m_ptr );
for( size_t iblock = 0; iblock < num_blocks; ++iblock ) {
block_cont_vec bcv_;
#define LOCAL_ALIGN
for( size_t ib = 0; ib < b.size(); ib++ ) {
#ifndef LOCAL_ALIGN
const bool lastrow = ib == (b.size() - 1);
#endif
block_cont<score_t, sscore_t> &bc_ = bc_array[ib];
if( iblock == 0 ) {
const char bchar = b[ib];
assert( bchar < char(qprofile.size() / (W * asize)));
bcv_.init();
bc_.s_iter = s.base();
bc_.su_iter = si.base();
bc_.s_end = bc_.s_iter + (asize * W);
bc_.qpp_iter = qprofile( bchar * W * asize );
} else {
bcv_.load( bcv_store( ib * W * 3 ) );
}
// std::cout << "bc: " << bc << std::endl;
// vec_t last_sl = vu::set1(SMALL);
// vec_t last_s = vu::set1(vu::BIAS);
// vec_t last_sdiag = vu::set1(vu::BIAS);
// std::cout << "sbm: " << m.state_backmap(bc) << " " << (W * asize) << std::endl;
sscore_t *qpp_iter = bc_.qpp_iter;
_mm_prefetch( (const char *) qpp_iter,_MM_HINT_T0);
score_t * __restrict s_iter = bc_.s_iter;
score_t * __restrict su_iter = bc_.su_iter;
score_t * __restrict s_end = bc_.s_end;
vec_t last_sdiag = bcv_.last_sdiag;
vec_t last_sl = bcv_.last_sl;
vec_t last_s = bcv_.last_s;
score_t * __restrict s_block_end;// = std::min( bc.s_iter + BW * W, bc.s_end );
if( s_iter + BW * W < s_end ) {
s_block_end = s_iter + BW * W;
} else {
s_block_end = s_end;
}
assert( s_block_end != s_iter );
for( ; s_iter != s_block_end; s_iter += W, su_iter += W, qpp_iter += W ) {
const vec_t match = vu::load( (score_t*) qpp_iter );
// getchar();
const vec_t sm = vu::add( last_sdiag, match );
last_sdiag = vu::load( s_iter );
#ifdef LOCAL_ALIGN
const vec_t sm_zero = vu::max( sm, BIAS_vec);
#else
const vec_t sm_zero = sm_vec;
#endif
const vec_t sl_open = vu::sub( last_s, GAP_OPEN_vec );
const vec_t sl_ext = vu::sub( last_sl, GAP_EXT_vec );
const vec_t sl = vu::max( sl_ext, sl_open );
last_sl = sl;
const vec_t su_ext = vu::sub( vu::load(su_iter), GAP_EXT_vec );
const vec_t su_open = vu::sub( last_sdiag, GAP_OPEN_vec );
const vec_t su = vu::max( su_ext, su_open );
vu::store( su, su_iter );
const vec_t s = vu::max( sm_zero, vu::max( sl, su ));
// vu::println( max_vec, pb.m_ptr );
last_s = s;
vu::store( s, s_iter );
#ifdef LOCAL_ALIGN
max_vec = vu::max( s, max_vec );
#else
if( s_iter == s_end - W || lastrow ) {
max_vec = vu::max( sc_vec, max_vec );
}
#endif
}
bcv_.last_sdiag = last_sdiag;
bcv_.last_sl = last_sl;
bcv_.last_s = last_s;
bcv_.store( bcv_store( ib * W * 3 ) );
bc_.qpp_iter = qpp_iter;
bc_.s_iter = s_iter;
bc_.su_iter = su_iter;
}
}
ps.out.resize(W);
vu::store( max_vec, ps.out.base() );
out.resize(0);
out.reserve(W);
for( size_t i = 0; i < W; i++ ) {
out.push_back(int(ps.out[i]) - vu::BIAS );
// std::cout << "x: " << int(ps.out.m_ptr[i]) << "\n";
}
//return max;
}
#endif
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