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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: Score matrix for alignment using dynamic programming
*/
#include "utils/commons.h"
#include "score_matrix.h"
/*
* Setup
*/
void score_matrix_allocate(
score_matrix_t* const score_matrix,
const int num_rows,
const int num_columns,
mm_allocator_t* const mm_allocator) {
// Allocate DP matrix
int h;
score_matrix->num_rows = num_rows;
score_matrix->num_columns = num_columns;
score_matrix->columns = mm_allocator_malloc(mm_allocator,num_columns*sizeof(int*)); // Columns
for (h=0;h<num_columns;++h) {
score_matrix->columns[h] = mm_allocator_calloc(mm_allocator,num_rows,int,false); // Rows
}
// MM
score_matrix->mm_allocator = mm_allocator;
}
void score_matrix_free(
score_matrix_t* const score_matrix) {
// Parameters
mm_allocator_t* const mm_allocator = score_matrix->mm_allocator;
// DP matrix
const int num_columns = score_matrix->num_columns;
int h;
for (h=0;h<num_columns;++h) {
mm_allocator_free(mm_allocator,score_matrix->columns[h]);
}
mm_allocator_free(mm_allocator,score_matrix->columns);
}
/*
* Display
*/
void score_matrix_print_score(
FILE* const stream,
const int score) {
if (-1 < score && score < 10000) {
fprintf(stream," %3d ",score);
} else {
fprintf(stream," * ");
}
}
void score_matrix_print_char(
FILE* const stream,
const char c) {
fprintf(stream," %c ",c);
}
void score_matrix_print(
FILE* const stream,
const score_matrix_t* const score_matrix,
const char* const pattern,
const char* const text) {
// Parameters
int** const matrix = score_matrix->columns;
const int num_columns = score_matrix->num_columns;
const int num_rows = score_matrix->num_rows;
int h;
// Print Header
fprintf(stream," ");
for (h=0;h<num_columns-1;++h) {
score_matrix_print_char(stream,text[h]);
}
fprintf(stream,"\n ");
for (h=0;h<num_columns;++h) {
score_matrix_print_score(stream,h);
}
fprintf(stream,"\n ");
for (h=0;h<num_columns;++h) {
score_matrix_print_score(stream,matrix[h][0]);
}
fprintf(stream,"\n");
// Print Rows
int v;
for (v=1;v<num_rows;++v) {
fprintf(stream,"%c",pattern[v-1]);
for (h=0;h<num_columns;++h) {
score_matrix_print_score(stream,matrix[h][v]);
}
fprintf(stream,"\n");
}
fprintf(stream,"\n");
}
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