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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 computing wavefronts
*/
#ifndef WAVEFRONT_COMPUTE_H_
#define WAVEFRONT_COMPUTE_H_
#include "wavefront_aligner.h"
/*
* Compute limits
*/
void wavefront_compute_limits_input(
wavefront_aligner_t* const wf_aligner,
const wavefront_set_t* const wavefront_set,
int* const lo,
int* const hi);
void wavefront_compute_limits_output(
wavefront_aligner_t* const wf_aligner,
const int lo,
const int hi,
int* const effective_lo,
int* const effective_hi);
/*
* Score translation
*/
int wavefront_compute_classic_score(
wavefront_aligner_t* const wf_aligner,
const int pattern_length,
const int text_length,
const int wf_score);
/*
* Input wavefronts (fetch)
*/
void wavefront_compute_fetch_input(
wavefront_aligner_t* const wf_aligner,
wavefront_set_t* const wavefront_set,
const int score);
/*
* Output wavefronts (allocate)
*/
void wavefront_compute_allocate_output_null(
wavefront_aligner_t* const wf_aligner,
const int score);
void wavefront_compute_allocate_output(
wavefront_aligner_t* const wf_aligner,
wavefront_set_t* const wavefront_set,
const int score,
const int lo,
const int hi);
/*
* Initialize wavefronts ends
*/
void wavefront_compute_init_ends(
wavefront_aligner_t* const wf_aligner,
wavefront_set_t* const wavefront_set,
const int lo,
const int hi);
/*
* Process wavefronts ends
*/
void wavefront_compute_trim_ends(
wavefront_aligner_t* const wf_aligner,
wavefront_t* const wavefront);
void wavefront_compute_process_ends(
wavefront_aligner_t* const wf_aligner,
wavefront_set_t* const wavefront_set,
const int score);
/*
* Multithread dispatcher
*/
#ifdef WFA_PARALLEL
int wavefront_compute_num_threads(
wavefront_aligner_t* const wf_aligner,
const int lo,
const int hi);
void wavefront_compute_thread_limits(
const int thread_id,
const int num_theads,
const int lo,
const int hi,
int* const thread_lo,
int* const thread_hi);
#else
#define wavefront_compute_num_threads(wf_aligner,lo,hi) 1
#endif
#endif /* WAVEFRONT_COMPUTE_H_ */
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