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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>
*/
#include "utils/commons.h"
#include "wavefront_bialigner.h"
#include "wavefront_aligner.h"
#include "wavefront_attributes.h"
#include "wavefront_heuristic.h"
/*
* Setup
*/
wavefront_bialigner_t* wavefront_bialigner_new(
wavefront_aligner_attr_t* const attributes,
wavefront_plot_t* const plot) {
// Allocate
wavefront_bialigner_t* const wf_bialigner = malloc(sizeof(wavefront_bialigner_t));
// Configure subsidiary aligners
wavefront_aligner_attr_t subsidiary_attr = wavefront_aligner_attr_default;
// Inherit attributes from master aligner
subsidiary_attr.distance_metric = attributes->distance_metric;
subsidiary_attr.linear_penalties = attributes->linear_penalties;
subsidiary_attr.affine_penalties = attributes->affine_penalties;
subsidiary_attr.affine2p_penalties = attributes->affine2p_penalties;
subsidiary_attr.match_funct = attributes->match_funct;
subsidiary_attr.match_funct_arguments = attributes->match_funct_arguments;
// Set specifics for subsidiary aligners
subsidiary_attr.heuristic = attributes->heuristic; // Inherit same heuristic
subsidiary_attr.memory_mode = wavefront_memory_high; // Classic WFA
subsidiary_attr.alignment_scope = compute_score;
// Set other parameter for subsidiary aligners
subsidiary_attr.system = attributes->system;
// Allocate forward/reverse aligners
wf_bialigner->alg_forward = wavefront_aligner_new(&subsidiary_attr);
wf_bialigner->alg_forward->align_mode = wf_align_biwfa_breakpoint_forward;
wf_bialigner->alg_forward->plot = plot;
wf_bialigner->alg_reverse = wavefront_aligner_new(&subsidiary_attr);
wf_bialigner->alg_reverse->align_mode = wf_align_biwfa_breakpoint_reverse;
wf_bialigner->alg_reverse->plot = plot;
// Allocate subsidiary aligner
subsidiary_attr.alignment_scope = compute_alignment;
wf_bialigner->alg_subsidiary = wavefront_aligner_new(&subsidiary_attr);
wf_bialigner->alg_subsidiary->align_mode = wf_align_biwfa_subsidiary;
wf_bialigner->alg_subsidiary->plot = plot;
// Return
return wf_bialigner;
}
void wavefront_bialigner_reap(
wavefront_bialigner_t* const wf_bialigner) {
wavefront_aligner_reap(wf_bialigner->alg_forward);
wavefront_aligner_reap(wf_bialigner->alg_reverse);
wavefront_aligner_reap(wf_bialigner->alg_subsidiary);
}
void wavefront_bialigner_delete(
wavefront_bialigner_t* const wf_bialigner) {
wavefront_aligner_delete(wf_bialigner->alg_forward);
wavefront_aligner_delete(wf_bialigner->alg_reverse);
wavefront_aligner_delete(wf_bialigner->alg_subsidiary);
free(wf_bialigner);
}
/*
* Accessors
*/
uint64_t wavefront_bialigner_get_size(
wavefront_bialigner_t* const wf_bialigner) {
return wavefront_aligner_get_size(wf_bialigner->alg_forward) +
wavefront_aligner_get_size(wf_bialigner->alg_reverse) +
wavefront_aligner_get_size(wf_bialigner->alg_subsidiary);
}
void wavefront_bialigner_set_heuristic(
wavefront_bialigner_t* const wf_bialigner,
wavefront_heuristic_t* const heuristic) {
wf_bialigner->alg_forward->heuristic = *heuristic;
wf_bialigner->alg_reverse->heuristic = *heuristic;
wf_bialigner->alg_subsidiary->heuristic = *heuristic;
}
void wavefront_bialigner_set_match_funct(
wavefront_bialigner_t* const wf_bialigner,
int (*match_funct)(int,int,void*),
void* const match_funct_arguments) {
wf_bialigner->alg_forward->match_funct = match_funct;
wf_bialigner->alg_forward->match_funct_arguments = match_funct_arguments;
wf_bialigner->alg_reverse->match_funct = match_funct;
wf_bialigner->alg_reverse->match_funct_arguments = match_funct_arguments;
wf_bialigner->alg_subsidiary->match_funct = match_funct;
wf_bialigner->alg_subsidiary->match_funct_arguments = match_funct_arguments;
}
void wavefront_bialigner_set_max_alignment_score(
wavefront_bialigner_t* const wf_bialigner,
const int max_alignment_score) {
wf_bialigner->alg_forward->system.max_alignment_score = max_alignment_score;
wf_bialigner->alg_reverse->system.max_alignment_score = max_alignment_score;
wf_bialigner->alg_subsidiary->system.max_alignment_score = max_alignment_score;
}
void wavefront_bialigner_set_max_memory(
wavefront_bialigner_t* const wf_bialigner,
const uint64_t max_memory_resident,
const uint64_t max_memory_abort) {
wf_bialigner->alg_forward->system.max_memory_resident = max_memory_resident;
wf_bialigner->alg_forward->system.max_memory_abort = max_memory_abort;
wf_bialigner->alg_reverse->system.max_memory_resident = max_memory_resident;
wf_bialigner->alg_reverse->system.max_memory_abort = max_memory_abort;
wf_bialigner->alg_subsidiary->system.max_memory_resident = max_memory_resident;
wf_bialigner->alg_subsidiary->system.max_memory_abort = max_memory_abort;
}
void wavefront_bialigner_set_max_num_threads(
wavefront_bialigner_t* const wf_bialigner,
const int max_num_threads) {
wf_bialigner->alg_forward->system.max_num_threads = max_num_threads;
wf_bialigner->alg_reverse->system.max_num_threads = max_num_threads;
wf_bialigner->alg_subsidiary->system.max_num_threads = max_num_threads;
}
void wavefront_bialigner_set_min_offsets_per_thread(
wavefront_bialigner_t* const wf_bialigner,
const int min_offsets_per_thread) {
wf_bialigner->alg_forward->system.min_offsets_per_thread = min_offsets_per_thread;
wf_bialigner->alg_reverse->system.min_offsets_per_thread = min_offsets_per_thread;
wf_bialigner->alg_subsidiary->system.min_offsets_per_thread = min_offsets_per_thread;
}
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