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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>
*/
#ifndef WAVEFRONT_BIALIGNER_H_
#define WAVEFRONT_BIALIGNER_H_
#include "wavefront_penalties.h"
#include "wavefront_attributes.h"
#include "wavefront_heuristic.h"
#include "wavefront_offset.h"
#include "wavefront_sequences.h"
// Wavefront ahead definition
typedef struct _wavefront_aligner_t wavefront_aligner_t;
typedef struct {
// Scores
int score; // Score total
int score_forward; // Score (forward)
int score_reverse; // Score (reverse)
// Location
int k_forward; // Breakpoint diagonal (forward)
int k_reverse; // Breakpoint diagonal (reverse)
wf_offset_t offset_forward; // Offset (forward)
wf_offset_t offset_reverse; // Offset (reverse)
affine2p_matrix_type component; // Component (M/I/D)
} wf_bialign_breakpoint_t;
typedef struct {
// Wavefronts
wavefront_aligner_t* wf_forward; // Breakpoint Forward aligner
wavefront_aligner_t* wf_reverse; // Breakpoint Reverse aligner
wavefront_aligner_t* wf_base; // Base/Subsidiary aligner
// Operators
void (*wf_align_compute)(wavefront_aligner_t* const,const int);
} wavefront_bialigner_t;
/*
* Setup
*/
wavefront_bialigner_t* wavefront_bialigner_new(
wavefront_aligner_attr_t* const attributes,
wavefront_plot_t* const plot);
void wavefront_bialigner_reap(
wavefront_bialigner_t* const wf_bialigner);
void wavefront_bialigner_delete(
wavefront_bialigner_t* const wf_bialigner);
/*
* Sequences
*/
void wavefront_bialigner_set_sequences_ascii(
wavefront_bialigner_t* const wf_bialigner,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length);
void wavefront_bialigner_set_sequences_lambda(
wavefront_bialigner_t* const wf_bialigner,
alignment_match_funct_t match_funct,
void* match_funct_arguments,
const int pattern_length,
const int text_length);
void wavefront_bialigner_set_sequences_packed2bits(
wavefront_bialigner_t* const wf_bialigner,
const uint8_t* const pattern,
const int pattern_length,
const uint8_t* const text,
const int text_length);
void wavefront_bialigner_set_sequences_bounds(
wavefront_bialigner_t* const wf_bialigner,
const int pattern_begin,
const int pattern_end,
const int text_begin,
const int text_end);
/*
* Accessors
*/
uint64_t wavefront_bialigner_get_size(
wavefront_bialigner_t* const wf_bialigner);
void wavefront_bialigner_set_heuristic(
wavefront_bialigner_t* const wf_bialigner,
wavefront_heuristic_t* const heuristic);
void wavefront_bialigner_set_max_alignment_steps(
wavefront_bialigner_t* const wf_bialigner,
const int max_alignment_steps);
void wavefront_bialigner_set_max_memory(
wavefront_bialigner_t* const wf_bialigner,
const uint64_t max_memory_resident,
const uint64_t max_memory_abort);
void wavefront_bialigner_set_max_num_threads(
wavefront_bialigner_t* const wf_bialigner,
const int max_num_threads);
void wavefront_bialigner_set_min_offsets_per_thread(
wavefront_bialigner_t* const wf_bialigner,
const int min_offsets_per_thread);
#endif /* WAVEFRONT_BIALIGNER_H_ */