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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: Padded string module to avoid handling corner conditions
*/
#include "utils/commons.h"
#include "system/mm_allocator.h"
#include "utils/string_padded.h"
/*
* Strings (text/pattern) padded
*/
void strings_padded_add_padding(
const char* const buffer,
const int buffer_length,
const int begin_padding_length,
const int end_padding_length,
const char padding_value,
char** const buffer_padded,
char** const buffer_padded_begin,
const bool reverse_sequence,
mm_allocator_t* const mm_allocator) {
// Allocate
const int buffer_padded_length = begin_padding_length + buffer_length + end_padding_length;
*buffer_padded = mm_allocator_malloc(mm_allocator,buffer_padded_length);
// Add begin padding
memset(*buffer_padded,padding_value,begin_padding_length);
// Copy buffer
*buffer_padded_begin = *buffer_padded + begin_padding_length;
if (reverse_sequence) {
int i;
for (i=0;i<buffer_length;i++) {
(*buffer_padded_begin)[i] = buffer[buffer_length-1-i];
}
} else {
memcpy(*buffer_padded_begin,buffer,buffer_length);
}
// Add end padding
memset(*buffer_padded_begin+buffer_length,padding_value,end_padding_length);
}
strings_padded_t* strings_padded_new(
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
const int padding_length,
const bool reverse_sequences,
mm_allocator_t* const mm_allocator) {
// Allocate
strings_padded_t* const strings_padded =
mm_allocator_alloc(mm_allocator,strings_padded_t);
strings_padded->mm_allocator = mm_allocator;
// Compute padding dimensions
const int pattern_begin_padding_length = 0;
const int pattern_end_padding_length = padding_length;
const int text_begin_padding_length = 0;
const int text_end_padding_length = padding_length;
// Add padding
strings_padded_add_padding(
pattern,pattern_length,
pattern_begin_padding_length,pattern_end_padding_length,'?',
&(strings_padded->pattern_padded_buffer),
&(strings_padded->pattern_padded),
reverse_sequences,mm_allocator);
strings_padded_add_padding(
text,text_length,
text_begin_padding_length,text_end_padding_length,'!',
&(strings_padded->text_padded_buffer),
&(strings_padded->text_padded),
reverse_sequences,mm_allocator);
// Return
return strings_padded;
}
strings_padded_t* strings_padded_new_rhomb(
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
const int padding_length,
const bool reverse_sequences,
mm_allocator_t* const mm_allocator) {
// Allocate
strings_padded_t* const strings_padded =
mm_allocator_alloc(mm_allocator,strings_padded_t);
strings_padded->mm_allocator = mm_allocator;
// Compute padding dimensions
const int pattern_begin_padding_length = text_length + padding_length;
const int pattern_end_padding_length = pattern_length + text_length + padding_length;
const int text_begin_padding_length = padding_length;
const int text_end_padding_length = text_length + padding_length;
// Add padding
strings_padded_add_padding(
pattern,pattern_length,
pattern_begin_padding_length,pattern_end_padding_length,'?',
&(strings_padded->pattern_padded_buffer),
&(strings_padded->pattern_padded),
reverse_sequences,mm_allocator);
strings_padded_add_padding(
text,text_length,
text_begin_padding_length,text_end_padding_length,'!',
&(strings_padded->text_padded_buffer),
&(strings_padded->text_padded),
reverse_sequences,mm_allocator);
// Set lengths
strings_padded->pattern_length = pattern_length;
strings_padded->text_length = text_length;
// Return
return strings_padded;
}
void strings_padded_delete(strings_padded_t* const strings_padded) {
mm_allocator_free(strings_padded->mm_allocator,strings_padded->pattern_padded_buffer);
mm_allocator_free(strings_padded->mm_allocator,strings_padded->text_padded_buffer);
mm_allocator_free(strings_padded->mm_allocator,strings_padded);
}
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