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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: WaveFront alignment module for sequence pairwise alignment
*/
#include "utils/commons.h"
#include "wavefront_align.h"
#include "wavefront_unialign.h"
#include "wavefront_bialign.h"
#include "wavefront_compute.h"
#include "wavefront_compute_edit.h"
#include "wavefront_compute_linear.h"
#include "wavefront_compute_affine.h"
#include "wavefront_compute_affine2p.h"
#include "wavefront_extend.h"
#include "wavefront_backtrace.h"
#include "wavefront_debug.h"
/*
* Checks
*/
void wavefront_align_checks(
wavefront_aligner_t* const wf_aligner,
const int pattern_length,
const int text_length) {
alignment_form_t* const form = &wf_aligner->alignment_form;
if (wf_aligner->bialigner != NULL) {
const bool ends_free =
form->pattern_begin_free > 0 ||
form->pattern_end_free > 0 ||
form->text_begin_free > 0 ||
form->text_end_free > 0;
if (ends_free) {
fprintf(stderr,"[WFA] BiWFA and ends-free is not supported yet\n");
exit(1);
}
}
const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric;
const bool is_heuristic_drop =
(wf_aligner->heuristic.strategy & wf_heuristic_xdrop) ||
(wf_aligner->heuristic.strategy & wf_heuristic_zdrop);
if (is_heuristic_drop && (distance_metric==edit || distance_metric==indel)) {
fprintf(stderr,"[WFA] Heuristics drops are not compatible with 'edit'/'indel' distance metrics\n");
exit(1);
}
if (form->span == alignment_endsfree) {
if (form->pattern_begin_free > pattern_length ||
form->pattern_end_free > pattern_length ||
form->text_begin_free > text_length ||
form->text_end_free > text_length) {
fprintf(stderr,"[WFA] Ends-free parameters must be not larger than the sequences "
"(P0=%d,Pf=%d,T0=%d,Tf=%d). Must be (P0<=|P|,Pf<=|P|,T0<=|T|,Tf<=|T|) where (|P|,|T|)=(%d,%d)\n",
form->pattern_begin_free,form->pattern_end_free,
form->text_begin_free,form->text_end_free,
pattern_length,text_length);
exit(1);
}
}
}
/*
* Wavefront Alignment Unidirectional
*/
void wavefront_align_unidirectional_cleanup(
wavefront_aligner_t* const wf_aligner) {
// Compute memory used
uint64_t memory_used = wavefront_aligner_get_size(wf_aligner);
wf_aligner->align_status.memory_used = memory_used;
// Reap memory (controlled reaping)
if (memory_used > wf_aligner->system.max_memory_resident) {
// Wavefront components
wavefront_components_reap(&wf_aligner->wf_components);
// Check memory
memory_used = wavefront_aligner_get_size(wf_aligner);
wf_aligner->align_status.memory_used = memory_used;
// Slab
if (memory_used > wf_aligner->system.max_memory_resident) {
wavefront_slab_reap(wf_aligner->wavefront_slab);
if (wf_aligner->bialigner != NULL) {
wavefront_bialigner_reap(wf_aligner->bialigner);
}
}
}
}
void wavefront_align_unidirectional(
wavefront_aligner_t* const wf_aligner,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length) {
// Prepare alignment
wavefront_unialign_init(
wf_aligner,pattern,pattern_length,text,text_length,
affine2p_matrix_M,affine2p_matrix_M);
// DEBUG
wavefront_debug_prologue(wf_aligner,pattern,pattern_length,text,text_length);
// Wavefront align sequences
wavefront_unialign(wf_aligner);
// Finish
if (wf_aligner->align_status.status == WF_STATUS_MAX_SCORE_REACHED) return; // Alignment paused
wavefront_align_unidirectional_cleanup(wf_aligner);
// DEBUG
wavefront_debug_epilogue(wf_aligner);
wavefront_debug_check_correct(wf_aligner);
}
/*
* Wavefront Alignment Bidirectional
*/
void wavefront_align_bidirectional(
wavefront_aligner_t* const wf_aligner,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length) {
// DEBUG
wavefront_debug_prologue(wf_aligner,pattern,pattern_length,text,text_length);
// Bidirectional alignment
wavefront_bialign(wf_aligner,pattern,pattern_length,text,text_length);
// Finish
const uint64_t memory_used = wavefront_aligner_get_size(wf_aligner);
wf_aligner->align_status.memory_used = memory_used;
// DEBUG
wavefront_debug_epilogue(wf_aligner);
wavefront_debug_check_correct(wf_aligner);
}
/*
* Wavefront Alignment Dispatcher
*/
int wavefront_align(
wavefront_aligner_t* const wf_aligner,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length) {
// Checks
wavefront_align_checks(wf_aligner,pattern_length,text_length);
// Plot
if (wf_aligner->plot != NULL) {
wavefront_plot_resize(wf_aligner->plot,pattern_length,text_length);
}
// Dispatcher
if (wf_aligner->bialigner != NULL) {
wavefront_align_bidirectional(wf_aligner,pattern,pattern_length,text,text_length);
} else {
wavefront_align_unidirectional(wf_aligner,pattern,pattern_length,text,text_length);
}
// Return
return wf_aligner->align_status.status;
}
int wavefront_align_resume(
wavefront_aligner_t* const wf_aligner) {
// Parameters
wavefront_align_status_t* const align_status = &wf_aligner->align_status;
// Check current alignment status
if (align_status->status != WF_STATUS_MAX_SCORE_REACHED ||
wf_aligner->bialigner != NULL) {
fprintf(stderr,"[WFA] Alignment cannot be resumed\n");
exit(1);
}
// Resume aligning sequences
wavefront_unialign(wf_aligner);
// Finish alignment
if (align_status->status == WF_STATUS_MAX_SCORE_REACHED) {
return WF_STATUS_MAX_SCORE_REACHED; // Alignment paused
}
wavefront_align_unidirectional_cleanup(wf_aligner);
// DEBUG
wavefront_debug_epilogue(wf_aligner);
wavefront_debug_check_correct(wf_aligner);
// Return
return align_status->status;
}
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