void _match_pattern_XString(const Chars_holder *P, const Chars_holder *S,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
const char *algo)
{
int max_nmis, min_nmis, fixedP, fixedS;
max_nmis = INTEGER(max_mismatch)[0];
min_nmis = INTEGER(min_mismatch)[0];
if (max_nmis < P->length - S->length
|| min_nmis > P->length)
return;
fixedP = LOGICAL(fixed)[0];
fixedS = LOGICAL(fixed)[1];
if (P->length <= max_nmis || strcmp(algo, "naive-inexact") == 0)
match_naive_inexact(P, S, max_nmis, min_nmis, fixedP, fixedS);
else if (strcmp(algo, "naive-exact") == 0)
match_naive_exact(P, S);
else if (strcmp(algo, "boyer-moore") == 0)
_match_pattern_boyermoore(P, S, -1, 0);
else if (strcmp(algo, "shift-or") == 0)
_match_pattern_shiftor(P, S, max_nmis, fixedP, fixedS);
else if (strcmp(algo, "indels") == 0)
_match_pattern_indels(P, S, max_nmis, fixedP, fixedS);
else
error("\"%s\": unknown algorithm", algo);
return;
}
static void test_match_pattern_indels(const char *p, const char *s,
int max_nmis, const char *expected_matches)
{
cachedCharSeq P, S;
Rprintf("P=%s S=%s max_nmis=%d expected_matches=%s\n", p, s,
max_nmis, expected_matches);
P.seq = p;
P.length = strlen(P.seq);
S.seq = s;
S.length = strlen(S.seq);
_match_pattern_indels(&P, &S, max_nmis, 1, 1);
return;
}
static void test_match_pattern_indels(const char *p, const char *s,
int max_nmis, const char *expected_matches)
{
Chars_holder P, S;
Rprintf("P=%s S=%s max_nmis=%d expected_matches=%s\n", p, s,
max_nmis, expected_matches);
P.ptr = p;
P.length = strlen(P.ptr);
S.ptr = s;
S.length = strlen(S.ptr);
_match_pattern_indels(&P, &S, max_nmis, 1, 1);
return;
}
