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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: Dynamic-programming algorithm to compute Levenshtein alignment (edit)
*/
#include "utils/commons.h"
#include "system/mm_allocator.h"
#include "edit_dp.h"
/*
* Edit distance computation using dynamic-programming matrix
*/
void edit_dp_traceback(
score_matrix_t* const score_matrix,
cigar_t* const cigar) {
// Parameters
int** const dp = score_matrix->columns;
char* const operations = cigar->operations;
cigar->end_offset = cigar->max_operations;
int op_sentinel = cigar->end_offset - 1;
int h, v;
// Compute traceback
h = score_matrix->num_columns-1;
v = score_matrix->num_rows-1;
while (h>0 && v>0) {
if (dp[h][v]==dp[h][v-1]+1) {
operations[op_sentinel--] = 'D';
--v;
} else if (dp[h][v]==dp[h-1][v]+1) {
operations[op_sentinel--] = 'I';
--h;
} else if (dp[h][v]==dp[h-1][v-1]) {
operations[op_sentinel--] = 'M';
--h;
--v;
} else if (dp[h][v]==dp[h-1][v-1]+1) {
operations[op_sentinel--] = 'X';
--h;
--v;
} else {
fprintf(stderr,"Edit backtrace. No backtrace operation found");
exit(1);
}
}
while (h>0) {operations[op_sentinel--] = 'I'; --h;}
while (v>0) {operations[op_sentinel--] = 'D'; --v;}
cigar->begin_offset = op_sentinel + 1;
}
void edit_dp_align(
score_matrix_t* const score_matrix,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
cigar_t* const cigar) {
// Parameters
int** dp = score_matrix->columns;
int h, v;
// Init DP
for (v=0;v<=pattern_length;++v) dp[0][v] = v; // No ends-free
for (h=0;h<=text_length;++h) dp[h][0] = h; // No ends-free
// Compute DP
for (h=1;h<=text_length;++h) {
for (v=1;v<=pattern_length;++v) {
int min = dp[h-1][v-1] + (text[h-1]!=pattern[v-1]);
min = MIN(min,dp[h-1][v]+1); // Ins
min = MIN(min,dp[h][v-1]+1); // Del
dp[h][v] = min;
}
}
// Compute traceback
edit_dp_traceback(score_matrix,cigar);
// DEBUG
// score_matrix_print(stderr,score_matrix,pattern,text);
}
/*
* Edit distance computation using dynamic-programming matrix (banded)
*/
void edit_dp_align_banded(
score_matrix_t* const score_matrix,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
const int bandwidth,
cigar_t* const cigar) {
// Parameters
const int k_end = ABS(text_length-pattern_length)+1;
const int effective_bandwidth = MAX(k_end,bandwidth);
int** dp = score_matrix->columns;
int h, v;
// Initialize
dp[0][0] = 0;
for (v=1;v<=effective_bandwidth;++v) dp[0][v] = v;
// Compute DP
for (h=1;h<=text_length;++h) {
// Compute lo limit
const bool lo_band = (h <= effective_bandwidth);
const int lo = (lo_band) ? 1 : h - effective_bandwidth;
dp[h][lo-1] = (lo_band) ? h : INT16_MAX;
// Compute hi limit
const int hi = MIN(pattern_length,effective_bandwidth+h-1);
if (h > 1) dp[h-1][hi] = INT16_MAX;
// Compute column
for (v=lo;v<=hi;++v) {
const int sub = dp[h-1][v-1] + (text[h-1]!=pattern[v-1]); // Sub
const int ins = dp[h-1][v]; // Ins
const int del = dp[h][v-1]; // Del
dp[h][v] = MIN(MIN(ins,del)+1,sub);
}
}
// Compute traceback
edit_dp_traceback(score_matrix,cigar);
}
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