Skip to content

Commit

Permalink
Changed the BWT interface
Browse files Browse the repository at this point in the history 
I simplified the interface to the BWT code by putting references to the suffix array and the remap table in the bwt_table structure.
  • Loading branch information
@mailund
mailund committed Feb 20, 2019
1 parent 9843c03 commit 8a4697f
Show file tree
Hide file tree
Showing 4 changed files with 20 additions and 38 deletions.
46 changes: 17 additions & 29 deletions stralg/bwt.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ void dealloc_bwt_exact_match_iter(struct bwt_exact_match_iter *iter)
struct bwt_approx_internal_match {
const char *cigar;
size_t match_length;
struct suffix_array *sa;
const struct suffix_array *sa;
size_t L;
size_t R;
};
Expand All @@ -125,24 +125,18 @@ struct bwt_approx_frame {
size_t R;
};
struct bwt_approx_match_internal_iter {
struct suffix_array *sa;
struct bwt_table *bwt_table;
struct remap_table *remap_table;

struct bwt_table *bwt_table;
struct bwt_approx_frame sentinel;

const char *remapped_pattern;
char *full_cigar_buf;
char *cigar_buf;
};


void init_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_iter *iter,
struct bwt_table *bwt_table,
struct suffix_array *sa,
struct remap_table *remap_table,
const char *remapped_pattern,
int edits);
struct bwt_table *bwt_table,
const char *remapped_pattern,
int edits);

bool next_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_iter *iter,
struct bwt_approx_internal_match *match);
Expand Down Expand Up @@ -210,14 +204,15 @@ static void push_edits(struct bwt_approx_match_internal_iter *iter,
struct bwt_table *bwt_table = iter->bwt_table;
uint32_t *c_table = bwt_table->c_table;
uint32_t *o_table = bwt_table->o_table;
const struct remap_table *remap_table = iter->bwt_table->remap_table;

size_t new_L;
size_t new_R;

// M-operations
unsigned char match_a = iter->remapped_pattern[i];
// Iterating alphabet from 1 so I don't include the sentinel.
for (unsigned char a = 1; a < iter->remap_table->alphabet_size; ++a) {
for (unsigned char a = 1; a < remap_table->alphabet_size; ++a) {
size_t o_contrib = (L == 0) ? 0 : o_table[o_index(a, L - 1, bwt_table)];
new_L = c_table[a] + o_contrib + 1;
new_R = c_table[a] + o_table[o_index(a, R, bwt_table)];
Expand All @@ -242,7 +237,7 @@ static void push_edits(struct bwt_approx_match_internal_iter *iter,
// D-operation
if (!first) { // never start with a deletion
// Iterating alphabet from 1 so I don't include the sentinel.
for (unsigned char a = 1; a < iter->remap_table->alphabet_size; ++a) {
for (unsigned char a = 1; a < remap_table->alphabet_size; ++a) {
size_t o_contrib = (L == 0) ? 0 : o_table[o_index(a, L - 1, bwt_table)];
new_L = c_table[a] + o_contrib + 1;
new_R = c_table[a] + o_table[o_index(a, R, bwt_table)];
Expand Down Expand Up @@ -283,16 +278,11 @@ static void pop_edits(struct bwt_approx_match_internal_iter *iter,
}


void init_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_iter *iter,
struct bwt_table *bwt_table,
struct suffix_array *sa,
struct remap_table *remap_table,
const char *p,
int edits)
void init_bwt_approx_match_internal_iter
(struct bwt_approx_match_internal_iter *iter,
struct bwt_table *bwt_table, const char *p, int edits)
{
iter->sa = sa;
iter->bwt_table = bwt_table;
iter->remap_table = remap_table;
iter->remapped_pattern = p;

// one edit can max cost four characters
Expand All @@ -308,7 +298,7 @@ void init_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_ite
printf("\n");
#endif

size_t n = iter->sa->length;
size_t n = iter->bwt_table->sa->length;
size_t m = strlen(p);

size_t L = 0;
Expand All @@ -320,8 +310,9 @@ void init_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_ite
iter->full_cigar_buf, 0, edits, L, R, i);
}

bool next_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_iter *iter,
struct bwt_approx_internal_match *res)
bool next_bwt_approx_match_internal_iter
(struct bwt_approx_match_internal_iter *iter,
struct bwt_approx_internal_match *res)
{
char edit_op;
int edits;
Expand Down Expand Up @@ -355,7 +346,7 @@ bool next_bwt_approx_match_internal_iter (struct bwt_approx_match_internal_ite

res->cigar = iter->cigar_buf;
res->match_length = match_length;
res->sa = iter->sa;
res->sa = iter->bwt_table->sa;
res->L = L;
res->R = R;

Expand Down Expand Up @@ -389,14 +380,11 @@ void init_bwt_exact_match_from_approx_match(const struct bwt_approx_internal_mat
// it for all exact matches.
void init_bwt_approx_iter(struct bwt_approx_iter *iter,
struct bwt_table *bwt_table,
struct suffix_array *sa,
struct remap_table *remap_table,
const char *remapped_pattern,
int edits)
{
iter->internal_approx_iter = malloc(sizeof(struct bwt_approx_match_internal_iter));
init_bwt_approx_match_internal_iter(iter->internal_approx_iter, bwt_table, sa,
remap_table, remapped_pattern, edits);
init_bwt_approx_match_internal_iter(iter->internal_approx_iter, bwt_table, remapped_pattern, edits);
iter->internal_exact_iter = malloc(sizeof(struct bwt_exact_match_iter));
init_bwt_exact_match_iter(iter->internal_exact_iter, bwt_table, remapped_pattern);
iter->outer = true;
Expand Down
2 changes: 0 additions & 2 deletions stralg/bwt.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,6 @@ struct bwt_approx_match {
};
void init_bwt_approx_iter(struct bwt_approx_iter *iter,
struct bwt_table *bwt_table,
struct suffix_array *sa,
struct remap_table *remap_table,
const char *remapped_pattern,
int edits);
bool next_bwt_approx_match(struct bwt_approx_iter *iter,
Expand Down
2 changes: 1 addition & 1 deletion tests/approx_match_test.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,7 @@ static void bwt_match(struct suffix_array *sa,

struct bwt_approx_iter iter;
struct bwt_approx_match match;
init_bwt_approx_iter(&iter, bwt_table, sa, remap_table, pattern, edits);
init_bwt_approx_iter(&iter, bwt_table, pattern, edits);
while (next_bwt_approx_match(&iter, &match)) {
rev_remap_between0(rev_mapped_match,
string + match.position,
Expand Down
8 changes: 2 additions & 6 deletions tests/match_test.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -157,9 +157,6 @@ static void general_match_test(const char *pattern,
}

static void bwt_match(index_vector *naive,
// the original pattern and string parameters
// are here for debugging.
const char *pattern, const char *string,
struct remap_table *remap_table,
char *remapped_pattern, char *remapped_string)
{
Expand All @@ -174,7 +171,7 @@ static void bwt_match(index_vector *naive,
struct bwt_exact_match_iter bwt_iter;
struct bwt_exact_match bwt_match;

init_bwt_exact_match_iter(&bwt_iter, &bwt_table, sa, remapped_pattern);
init_bwt_exact_match_iter(&bwt_iter, &bwt_table, remapped_pattern);
while (next_bwt_exact_match_iter(&bwt_iter, &bwt_match)) {
index_vector_append(&bwt, bwt_match.pos);
}
Expand Down Expand Up @@ -226,8 +223,7 @@ static void remap_match_test(const char *pattern,
simple_exact_matchers(&naive, remapped_pattern, remapped_string);
general_suffix_test(&naive, remapped_pattern, remapped_string);

bwt_match(&naive, pattern, string, &remap_table,
remapped_pattern, remapped_string);
bwt_match(&naive, &remap_table, remapped_pattern, remapped_string);

dealloc_remap_table(&remap_table);
dealloc_index_vector(&naive);
Expand Down

0 comments on commit 8a4697f

Please sign in to comment.