89 lines
2.6 KiB
C++
89 lines
2.6 KiB
C++
/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <string.h>
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#include "aligner_sw_common.h"
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#include "aligner_swsse.h"
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/**
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* Given a number of rows (nrow), a number of columns (ncol), and the
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* number of words to fit inside a single __m128i vector, initialize the
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* matrix buffer to accomodate the needed configuration of vectors.
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*/
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void SSEMatrix::init(
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size_t nrow,
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size_t ncol,
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size_t wperv)
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{
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nrow_ = nrow;
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ncol_ = ncol;
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wperv_ = wperv;
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nvecPerCol_ = (nrow + (wperv-1)) / wperv;
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// The +1 is so that we don't have to special-case the final column;
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// instead, we just write off the end of the useful part of the table
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// with pvEStore.
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try {
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matbuf_.resizeNoCopy((ncol+1) * nvecPerCell_ * nvecPerCol_);
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} catch(exception& e) {
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cerr << "Tried to allocate DP matrix with " << (ncol+1)
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<< " columns, " << nvecPerCol_
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<< " vectors per column, and and " << nvecPerCell_
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<< " vectors per cell" << endl;
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throw e;
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}
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assert(wperv_ == 8 || wperv_ == 16);
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vecshift_ = (wperv_ == 8) ? 3 : 4;
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nvecrow_ = (nrow + (wperv_-1)) >> vecshift_;
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nveccol_ = ncol;
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colstride_ = nvecPerCol_ * nvecPerCell_;
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rowstride_ = nvecPerCell_;
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inited_ = true;
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}
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/**
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* Initialize the matrix of masks and backtracking flags.
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*/
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void SSEMatrix::initMasks() {
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assert_gt(nrow_, 0);
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assert_gt(ncol_, 0);
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masks_.resize(nrow_);
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reset_.resizeNoCopy(nrow_);
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reset_.fill(false);
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}
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/**
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* Given a row, col and matrix (i.e. E, F or H), return the corresponding
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* element.
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*/
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int SSEMatrix::eltSlow(size_t row, size_t col, size_t mat) const {
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assert_lt(row, nrow_);
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assert_lt(col, ncol_);
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assert_leq(mat, 3);
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// Move to beginning of column/row
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size_t rowelt = row / nvecrow_;
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size_t rowvec = row % nvecrow_;
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size_t eltvec = (col * colstride_) + (rowvec * rowstride_) + mat;
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if(wperv_ == 16) {
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return (int)((uint8_t*)(matbuf_.ptr() + eltvec))[rowelt];
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} else {
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assert_eq(8, wperv_);
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return (int)((int16_t*)(matbuf_.ptr() + eltvec))[rowelt];
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}
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}
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