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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 SEQUENCE_BUFFER_H_
#define SEQUENCE_BUFFER_H_
#include "system/mm_allocator.h"
typedef struct {
uint64_t pattern_offset;
uint64_t pattern_length;
uint64_t text_offset;
uint64_t text_length;
} sequence_offset_t;
typedef struct {
// ID
uint64_t sequence_id;
// Sequences
sequence_offset_t* offsets;
uint64_t offsets_used;
uint64_t offsets_allocated;
// Buffer
char* buffer;
uint64_t buffer_used;
uint64_t buffer_allocated;
// Stats
int max_pattern_length;
int max_text_length;
} sequence_buffer_t;
/*
* Setup
*/
sequence_buffer_t* sequence_buffer_new(
const uint64_t num_sequences_hint,
const uint64_t sequence_length_hint);
void sequence_buffer_clear(
sequence_buffer_t* const sequence_buffer);
void sequence_buffer_delete(
sequence_buffer_t* const sequence_buffer);
/*
* Accessors
*/
void sequence_buffer_add_pair(
sequence_buffer_t* const sequence_buffer,
char* const pattern,
const uint64_t pattern_length,
char* const text,
const uint64_t text_length);
#endif /* SEQUENCE_BUFFER_H_ */
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