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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: Simple linear vector for generic type elements
*/
#include "utils/commons.h"
#include "utils/sequence_buffer.h"
/*
* Setup
*/
sequence_buffer_t* sequence_buffer_new(
const uint64_t num_sequences_hint,
const uint64_t sequence_length_hint) {
// Alloc
sequence_buffer_t* const sequence_buffer = malloc(sizeof(sequence_buffer_t));
// ID
sequence_buffer->sequence_id = 1;
// Initialize sequences
sequence_buffer->offsets = malloc(num_sequences_hint*sizeof(sequence_offset_t));
sequence_buffer->offsets_used = 0;
sequence_buffer->offsets_allocated = num_sequences_hint;
// Initialize buffer
const uint64_t buffer_size = num_sequences_hint*sequence_length_hint;
sequence_buffer->buffer = malloc(buffer_size);
sequence_buffer->buffer_used = 0;
sequence_buffer->buffer_allocated = buffer_size;
// Stats
sequence_buffer->max_pattern_length = 0;
sequence_buffer->max_text_length = 0;
// Return
return sequence_buffer;
}
void sequence_buffer_clear(
sequence_buffer_t* const sequence_buffer) {
sequence_buffer->sequence_id = 1;
sequence_buffer->offsets_used = 0;
sequence_buffer->buffer_used = 0;
sequence_buffer->max_pattern_length = 0;
sequence_buffer->max_text_length = 0;
}
void sequence_buffer_delete(
sequence_buffer_t* const sequence_buffer) {
free(sequence_buffer->buffer);
free(sequence_buffer->offsets);
free(sequence_buffer);
}
/*
* Accessors
*/
void sequence_buffer_add_offsets(
sequence_buffer_t* const sequence_buffer,
const uint64_t pattern_offset,
const uint64_t pattern_length,
const uint64_t text_offset,
const uint64_t text_length) {
// Check allocated memory
if (sequence_buffer->offsets_used == sequence_buffer->offsets_allocated) {
const uint64_t num_offsets = (float)(sequence_buffer->offsets_used+1) * (3.0/2.0);
sequence_buffer->offsets = realloc(sequence_buffer->offsets,num_offsets*sizeof(sequence_offset_t));
sequence_buffer->offsets_allocated = num_offsets;
}
// Add sequence pair
sequence_offset_t* const current_offsets = sequence_buffer->offsets + sequence_buffer->offsets_used;
current_offsets->pattern_offset = pattern_offset;
current_offsets->pattern_length = pattern_length;
current_offsets->text_offset = text_offset;
current_offsets->text_length = text_length;
sequence_buffer->offsets_used += 1;
}
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) {
// Allocate memory
const uint64_t bytes_required = pattern_length + text_length + 4; // Padding
if (sequence_buffer->buffer_used+bytes_required > sequence_buffer->buffer_allocated) {
const uint64_t proposed_buffer_size = (3*(sequence_buffer->buffer_used+bytes_required))/2;
sequence_buffer->buffer_allocated = proposed_buffer_size;
sequence_buffer->buffer = realloc(sequence_buffer->buffer,proposed_buffer_size);
}
// Copy pattern sequence
char* mem_ptr = sequence_buffer->buffer + sequence_buffer->buffer_used;
memcpy(mem_ptr,pattern,pattern_length);
mem_ptr += pattern_length;
mem_ptr[0] = '\0';
mem_ptr[1] = '!';
mem_ptr += 2; // Padding sentinels
// Copy text sequence
memcpy(mem_ptr,text,text_length);
mem_ptr += text_length;
mem_ptr[0] = '\0';
mem_ptr[1] = '?';
mem_ptr += 2; // Padding sentinels
// Add sequence pair
const uint64_t pattern_offset = sequence_buffer->buffer_used;
const uint64_t text_offset = pattern_offset + pattern_length + 2;
sequence_buffer_add_offsets(
sequence_buffer,pattern_offset,
pattern_length,text_offset,text_length);
// Update used
sequence_buffer->buffer_used += bytes_required;
// Update stats
sequence_buffer->max_pattern_length = MAX(sequence_buffer->max_pattern_length,pattern_length);
sequence_buffer->max_text_length = MAX(sequence_buffer->max_text_length,text_length);
}
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