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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: Edit-distance alignment algorithms wrapper
*/
#include "benchmark/benchmark_utils.h"
#include "benchmark/benchmark_check.h"
#include "edit/edit_dp.h"
#include "edit/edit_bpm.h"
#include "wavefront/wavefront_align.h"
/*
* Benchmark Edit
*/
void benchmark_edit_bpm(
align_input_t* const align_input) {
// Allocate
bpm_pattern_t bpm_pattern;
edit_bpm_pattern_compile(
&bpm_pattern,align_input->pattern,
align_input->pattern_length,align_input->mm_allocator);
bpm_matrix_t bpm_matrix;
edit_bpm_matrix_allocate(
&bpm_matrix,align_input->pattern_length,
align_input->text_length,align_input->mm_allocator);
// Align
timer_start(&align_input->timer);
edit_bpm_compute(
&bpm_matrix,&bpm_pattern,align_input->text,
align_input->text_length,align_input->pattern_length);
timer_stop(&align_input->timer);
// DEBUG
if (align_input->debug_flags) {
benchmark_check_alignment(align_input,bpm_matrix.cigar);
}
// Output
if (align_input->output_file) {
benchmark_print_output(align_input,edit,false,bpm_matrix.cigar);
}
// Free
edit_bpm_pattern_free(&bpm_pattern,align_input->mm_allocator);
edit_bpm_matrix_free(&bpm_matrix,align_input->mm_allocator);
}
void benchmark_edit_dp(
align_input_t* const align_input) {
// Parameters
const int pattern_length = align_input->pattern_length;
const int text_length = align_input->text_length;
// Allocate
score_matrix_t score_matrix;
score_matrix_allocate(
&score_matrix,pattern_length+1,
text_length+1,align_input->mm_allocator);
cigar_t* const cigar = cigar_new(
pattern_length+text_length,
align_input->mm_allocator);
// Align
timer_start(&align_input->timer);
edit_dp_align(&score_matrix,
align_input->pattern,pattern_length,
align_input->text,text_length,cigar);
timer_stop(&align_input->timer);
// DEBUG
if (align_input->debug_flags) {
benchmark_check_alignment(align_input,cigar);
}
// Output
if (align_input->output_file) {
benchmark_print_output(align_input,edit,false,cigar);
}
// Free
score_matrix_free(&score_matrix);
cigar_free(cigar);
}
void benchmark_edit_dp_banded(
align_input_t* const align_input,
const int bandwidth) {
// Parameters
const int pattern_length = align_input->pattern_length;
const int text_length = align_input->text_length;
// Allocate
score_matrix_t score_matrix;
score_matrix_allocate(
&score_matrix,pattern_length+1,
text_length+1,align_input->mm_allocator);
cigar_t* const cigar = cigar_new(
pattern_length+text_length,
align_input->mm_allocator);
// Align
timer_start(&align_input->timer);
edit_dp_align_banded(&score_matrix,
align_input->pattern,pattern_length,
align_input->text,text_length,
bandwidth,cigar);
timer_stop(&align_input->timer);
// DEBUG
if (align_input->debug_flags) {
benchmark_check_alignment(align_input,cigar);
}
// Output
if (align_input->output_file) {
benchmark_print_output(align_input,edit,false,cigar);
}
// Free
score_matrix_free(&score_matrix);
cigar_free(cigar);
}
void benchmark_edit_wavefront(
align_input_t* const align_input) {
// Parameters
wavefront_aligner_t* const wf_aligner = align_input->wf_aligner;
// Align
timer_start(&align_input->timer);
wavefront_align(wf_aligner,
align_input->pattern,align_input->pattern_length,
align_input->text,align_input->text_length);
timer_stop(&align_input->timer);
// DEBUG
if (align_input->debug_flags) {
benchmark_check_alignment(align_input,wf_aligner->cigar);
}
// Output
if (align_input->output_file) {
const int score_only = (wf_aligner->alignment_scope == compute_score);
benchmark_print_output(align_input,edit,score_only,wf_aligner->cigar);
}
}
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