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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 components module
*/
#ifndef WAVEFRONT_WAVEFRONT_COMPONENTS_H_
#define WAVEFRONT_WAVEFRONT_COMPONENTS_H_
#include "wavefront/wavefront.h"
#include "wavefront/wavefront_backtrace_buffer.h"
#include "wavefront/wavefront_penalties.h"
/*
* Wavefront Components
*/
typedef struct {
// Configuration
bool memory_modular; // Memory strategy (modular wavefronts)
bool bt_piggyback; // Backtrace Piggyback
// Wavefronts dimensions
int num_wavefronts; // Total number of allocated wavefronts
int max_score_scope; // Maximum score-difference between dependent wavefronts
int historic_max_hi; // Maximum WF hi-limit seen during current alignment
int historic_min_lo; // Minimum WF lo-limit seen during current alignment
// Wavefronts
wavefront_t** mwavefronts; // M-wavefronts
wavefront_t** i1wavefronts; // I1-wavefronts
wavefront_t** i2wavefronts; // I2-wavefronts
wavefront_t** d1wavefronts; // D1-wavefronts
wavefront_t** d2wavefronts; // D2-wavefronts
wavefront_t* wavefront_null; // Null wavefront (orthogonal reading)
wavefront_t* wavefront_victim; // Dummy wavefront (orthogonal writing)
// BT-Buffer
wf_backtrace_buffer_t* bt_buffer; // Backtrace Buffer
// MM
mm_allocator_t* mm_allocator; // MM-Allocator
} wavefront_components_t;
/*
* Setup
*/
void wavefront_components_allocate(
wavefront_components_t* const wf_components,
const int max_pattern_length,
const int max_text_length,
wavefront_penalties_t* const penalties,
const bool memory_modular,
const bool bt_piggyback,
mm_allocator_t* const mm_allocator);
void wavefront_components_reap(
wavefront_components_t* const wf_components);
void wavefront_components_clear(
wavefront_components_t* const wf_components);
void wavefront_components_free(
wavefront_components_t* const wf_components);
/*
* Resize
*/
void wavefront_components_resize(
wavefront_components_t* const wf_components,
const int max_pattern_length,
const int max_text_length,
wavefront_penalties_t* const penalties);
void wavefront_components_resize_null__victim(
wavefront_components_t* const wf_components,
const int lo,
const int hi);
/*
* Compact
*/
void wavefront_components_compact_bt_buffer(
wavefront_components_t* const wf_components,
const int score,
const int verbose);
#endif /* WAVEFRONT_WAVEFRONT_COMPONENTS_H_ */
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