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[similarity] a *NEW* sequence alignment algorithm which builds on Smith-Waterman-Gotoh with affine gap penalties. Like Smith-Waterman, it performs a local alignment, and like the cost-only version of Gotoh's improvement, it needs O(mn) time and O(m) space (where m is the length of the longer string). However, this version of the algorithm stores and returns a breakdown of the number and specific types of edits it makes (matches, mismatches, gap opens, gap extensions, and transpositions) rather than rolling them up into a single cost, and without needing to return/compute the full alignment as in Needleman-Wunsch or Hirschberg's variant

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Al
2017-11-11 03:07:39 -05:00
parent 665b780422
commit 751873e56b
2 changed files with 304 additions and 2 deletions
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21
src/string_similarity.h
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@@ -6,13 +6,30 @@
#include "collections.h"
#define DEFAULT_JARO_WINKLER_PREFIX_SCALE 0.1
#define DEFAULT_JARO_WINKLER_BONUS_THRESHOLD 0.7
#define DEFAULT_AFFINE_GAP_OPEN_COST 3
#define DEFAULT_AFFINE_GAP_EXTEND_COST 2
#define DEFAULT_AFFINE_GAP_MATCH_COST 0
#define DEFAULT_AFFINE_GAP_MISMATCH_COST 6
#define DEFAULT_AFFINE_GAP_TRANSPOSE_COST 4
typedef struct affine_gap_edits {
size_t num_matches;
size_t num_mismatches;
size_t num_transpositions;
size_t num_gap_opens;
size_t num_gap_extensions;
} affine_gap_edits_t;
affine_gap_edits_t affine_gap_distance(char *s1, char *s2);
affine_gap_edits_t affine_gap_distance_unicode(uint32_array *u1_array, uint32_array *u2_array);
ssize_t damerau_levenshtein_distance(const char *s1, const char *s2);
ssize_t damerau_levenshtein_distance_unicode(uint32_array *u1_array, uint32_array *u2_array, size_t replace_cost);
ssize_t damerau_levenshtein_distance_replace_cost(const char *s1, const char *s2, size_t replace_cost);
#define DEFAULT_JARO_WINKLER_PREFIX_SCALE 0.1
#define DEFAULT_JARO_WINKLER_BONUS_THRESHOLD 0.7
double jaro_distance(const char *s1, const char *s2);
double jaro_distance_unicode(uint32_array *u1_array, uint32_array *u2_array);
double jaro_winkler_distance_prefix_threshold(const char *s1, const char *s2, double prefix_scale, double bonus_threshold);