SEXP debug_match_pattern_indels()
{
#ifdef DEBUG_BIOSTRINGS
const char *p = "ABCDE", *s = "BCDExAxBCDDxDABCxExxABDCExExAABCDEE";
debug = !debug;
Rprintf("Debug mode turned %s in file %s\n",
debug ? "on" : "off", __FILE__);
if (debug == 1) {
_init_match_reporting("MATCHES_AS_NULL", 1);
test_match_pattern_indels(p, s, 0, "30:34");
test_match_pattern_indels(p, s, 1, "1:4, 14:18, 30:34");
test_match_pattern_indels(p, s, 2, "1:4, 8:10, 14:18, 21:23, 30:34");
}
#else
Rprintf("Debug mode not available in file %s\n", __FILE__);
#endif
return R_NilValue;
}
/* --- .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();
}
static SEXP vwhich_XStringSet_XStringSet(SEXP pattern,
SEXP subject,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
SEXP algorithm)
{
XStringSet_holder P, S;
int P_length, S_length, i, j;
Chars_holder P_elt, S_elt;
const char *algo;
IntAEAE *ans_buf;
P = _hold_XStringSet(pattern);
P_length = _get_length_from_XStringSet_holder(&P);
S = _hold_XStringSet(subject);
S_length = _get_length_from_XStringSet_holder(&S);
algo = CHAR(STRING_ELT(algorithm, 0));
ans_buf = new_IntAEAE(S_length, S_length);
for (j = 0; j < S_length; j++)
IntAE_set_nelt(ans_buf->elts[j], 0);
_init_match_reporting("MATCHES_AS_COUNTS", 1);
for (i = 0; i < P_length; i++) {
P_elt = _get_elt_from_XStringSet_holder(&P, i);
for (j = 0; j < S_length; j++) {
S_elt = _get_elt_from_XStringSet_holder(&S, j);
_match_pattern_XString(&P_elt, &S_elt,
max_mismatch, min_mismatch, with_indels, fixed,
algo);
if (_get_match_count() != 0)
IntAE_insert_at(ans_buf->elts[j],
IntAE_get_nelt(ans_buf->elts[j]),
i + 1);
_drop_reported_matches();
}
}
return new_LIST_from_IntAEAE(ans_buf, 0);
}
/* --- .Call ENTRY POINT ---
* Arguments are the same as for XString_match_pattern() except for:
* subject: XStringSet object.
*/
SEXP XStringSet_vmatch_pattern(SEXP pattern, SEXP subject,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
SEXP algorithm, SEXP ms_mode)
{
Chars_holder P, S_elt;
XStringSet_holder S;
int S_length, j;
const char *algo;
P = hold_XRaw(pattern);
S = _hold_XStringSet(subject);
S_length = _get_XStringSet_length(subject);
algo = CHAR(STRING_ELT(algorithm, 0));
_init_match_reporting(CHAR(STRING_ELT(ms_mode, 0)), S_length);
for (j = 0; j < S_length; j++) {
S_elt = _get_elt_from_XStringSet_holder(&S, j);
_set_active_PSpair(j);
_match_pattern_XString(&P, &S_elt,
max_mismatch, min_mismatch, with_indels, fixed,
algo);
}
return _MatchBuf_as_SEXP(_get_internal_match_buf(), R_NilValue);
}
