/* --- .Call ENTRY POINT --- */
SEXP find_palindromes(SEXP x, SEXP min_armlength, SEXP max_looplength,
SEXP max_mismatch, SEXP L2R_lkup)
{
Chars_holder x_holder;
int x_len, min_arm_len, max_loop_len1, max_nmis, lkup_len, n;
const int *lkup;
x_holder = hold_XRaw(x);
x_len = x_holder.length;
min_arm_len = INTEGER(min_armlength)[0];
max_loop_len1 = INTEGER(max_looplength)[0] + 1;
max_nmis = INTEGER(max_mismatch)[0];
if (L2R_lkup == R_NilValue) {
lkup = NULL;
lkup_len = 0;
} else {
lkup = INTEGER(L2R_lkup);
lkup_len = LENGTH(L2R_lkup);
}
_init_match_reporting("MATCHES_AS_RANGES", 1);
for (n = 0; n < x_len; n++) {
/* Find palindromes centered on n. */
get_find_palindromes_at(x_holder.ptr, x_len, n - 1, n + 1,
max_loop_len1, min_arm_len, max_nmis,
lkup, lkup_len);
/* Find palindromes centered on n + 0.5. */
get_find_palindromes_at(x_holder.ptr, x_len, n, n + 1,
max_loop_len1, min_arm_len, max_nmis,
lkup, lkup_len);
}
return _reported_matches_asSEXP();
}
/* --- .Call ENTRY POINT --- */
SEXP XString_match_pattern(SEXP pattern, SEXP subject,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
SEXP algorithm, SEXP count_only)
{
Chars_holder P, S;
const char *algo;
int is_count_only;
P = hold_XRaw(pattern);
S = hold_XRaw(subject);
algo = CHAR(STRING_ELT(algorithm, 0));
is_count_only = LOGICAL(count_only)[0];
_init_match_reporting(is_count_only ?
"MATCHES_AS_COUNTS" : "MATCHES_AS_RANGES", 1);
_match_pattern_XString(&P, &S,
max_mismatch, min_mismatch, with_indels, fixed,
algo);
return _reported_matches_asSEXP();
}
SEXP match_BOC2_exact(SEXP p_xp, SEXP p_offset, SEXP p_length,
SEXP s_xp, SEXP s_offset, SEXP s_length,
SEXP code1, SEXP code2, SEXP code3, SEXP code4,
SEXP buf_xp,
SEXP stats, SEXP count_only)
{
int pat_offset, pat_length, subj_offset, subj_length,
c1, c2, c3, c4, is_count_only;
const Rbyte *pat, *subj;
SEXP buf;
pat_offset = INTEGER(p_offset)[0];
pat_length = INTEGER(p_length)[0];
pat = RAW(R_ExternalPtrTag(p_xp)) + pat_offset;
subj_offset = INTEGER(s_offset)[0];
subj_length = INTEGER(s_length)[0];
subj = RAW(R_ExternalPtrTag(s_xp)) + subj_offset;
c1 = INTEGER(code1)[0];
c2 = INTEGER(code2)[0];
c3 = INTEGER(code3)[0];
c4 = INTEGER(code4)[0];
buf = R_ExternalPtrTag(buf_xp);
is_count_only = LOGICAL(count_only)[0];
_init_match_reporting(is_count_only ?
"MATCHES_AS_COUNTS" : "MATCHES_AS_RANGES", 1);
BOC2_exact_search(
(char *) pat, pat_length,
(char *) subj, subj_length,
(char) c1, (char) c2, (char) c3, (char) c4,
INTEGER(buf),
REAL(VECTOR_ELT(stats, 0)),
INTEGER(VECTOR_ELT(stats, 1)),
INTEGER(VECTOR_ELT(stats, 2)),
INTEGER(VECTOR_ELT(stats, 3)),
INTEGER(VECTOR_ELT(stats, 4)));
return _reported_matches_asSEXP();
}
