/* --- .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 match_XStringSet_XStringViews(SEXP pattern,
SEXP subject, SEXP views_start, SEXP views_width,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
SEXP algorithm, SEXP matches_as, SEXP envir)
{
XStringSet_holder P;
int P_length, i;
Chars_holder S, P_elt;
const char *algo, *ms_mode;
P = _hold_XStringSet(pattern);
P_length = _get_length_from_XStringSet_holder(&P);
S = hold_XRaw(subject);
algo = CHAR(STRING_ELT(algorithm, 0));
ms_mode = CHAR(STRING_ELT(matches_as, 0));
_init_match_reporting(ms_mode, P_length);
for (i = 0; i < P_length; i++) {
P_elt = _get_elt_from_XStringSet_holder(&P, i);
_set_active_PSpair(i);
_match_pattern_XStringViews(&P_elt,
&S, views_start, views_width,
max_mismatch, min_mismatch, with_indels, fixed,
algo);
}
return _MatchBuf_as_SEXP(_get_internal_match_buf(), envir);
}
/* --- .Call ENTRY POINT ---
* Args:
* x: An XStringSetList object.
* sep: An XString object of the same seqtype as 'x'.
* Returns an XStringSet object parallel to and of the same seqtype as 'x'.
*/
SEXP XStringSetList_unstrsplit(SEXP x, SEXP sep, SEXP seqtype)
{
XStringSetList_holder x_holder;
XStringSet_holder x_elt_holder, ans_holder;
Chars_holder sep_holder, ans_elt_holder;
int x_len, sep_len, i;
const char *seqtype0;
char ans_elt_type[37]; /* longest string should be "DNAString" */
char ans_classname[40]; /* longest string should be "DNAStringSet" */
SEXP ans, ans_width, ans_names;
x_holder = _hold_XStringSetList(x);
x_len = _get_length_from_XStringSetList_holder(&x_holder);
sep_holder = hold_XRaw(sep);
sep_len = sep_holder.length;
seqtype0 = CHAR(STRING_ELT(seqtype, 0));
if (snprintf(ans_elt_type, sizeof(ans_elt_type),
"%sString", seqtype0) >= sizeof(ans_elt_type))
error("Biostrings internal error in "
"XStringSetList_unstrsplit(): "
"'ans_elt_type' buffer too small");
if (snprintf(ans_classname, sizeof(ans_classname),
"%sSet", ans_elt_type) >= sizeof(ans_classname))
error("Biostrings internal error in "
"XStringSetList_unstrsplit(): "
"'ans_classname' buffer too small");
/* 1st pass: compute 'ans_width' */
PROTECT(ans_width = NEW_INTEGER(x_len));
for (i = 0; i < x_len; i++) {
x_elt_holder = _get_elt_from_XStringSetList_holder(
&x_holder, i);
INTEGER(ans_width)[i] = compute_joined_strings_length(
&x_elt_holder, sep_len);
}
/* Allocate 'ans' */
PROTECT(ans = alloc_XRawList(ans_classname, ans_elt_type, ans_width));
/* 2nd pass: fill 'ans' */
ans_holder = _hold_XStringSet(ans);
for (i = 0; i < x_len; i++) {
x_elt_holder = _get_elt_from_XStringSetList_holder(
&x_holder, i);
ans_elt_holder = _get_elt_from_XStringSet_holder(
&ans_holder, i);
join_strings_in_buf((char *) ans_elt_holder.ptr, &x_elt_holder,
sep_holder.ptr, sep_holder.length);
}
PROTECT(ans_names = duplicate(get_CompressedList_names(x)));
_set_XStringSet_names(ans, ans_names);
UNPROTECT(3);
return ans;
}
/* --- .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();
}
/* --- .Call ENTRY POINT --- */
SEXP match_PDict3Parts_XString(SEXP pptb, SEXP pdict_head, SEXP pdict_tail,
SEXP subject,
SEXP max_mismatch, SEXP min_mismatch, SEXP fixed,
SEXP matches_as, SEXP envir)
{
HeadTail headtail;
Chars_holder S;
MatchPDictBuf matchpdict_buf;
headtail = _new_HeadTail(pdict_head, pdict_tail, pptb,
max_mismatch, fixed, 1);
S = hold_XRaw(subject);
matchpdict_buf = new_MatchPDictBuf_from_PDict3Parts(matches_as,
pptb, pdict_head, pdict_tail);
match_pdict(pptb, &headtail,
&S, max_mismatch, min_mismatch, fixed,
&matchpdict_buf);
return _MatchBuf_as_SEXP(&(matchpdict_buf.matches), envir);
}
/* --- .Call ENTRY POINT --- */
SEXP palindrome_arm_length(SEXP x, SEXP max_mismatch, SEXP L2R_lkup)
{
Chars_holder x_holder;
int x_len, max_nmis, lkup_len, arm_len;
const int *lkup;
x_holder = hold_XRaw(x);
x_len = x_holder.length;
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);
}
arm_len = get_palindrome_arm_length(x_holder.ptr, x_len, max_nmis,
lkup, lkup_len);
return ScalarInteger(arm_len);
}
/* --- .Call ENTRY POINT --- */
SEXP match_PDict3Parts_XStringViews(SEXP pptb, SEXP pdict_head, SEXP pdict_tail,
SEXP subject, SEXP views_start, SEXP views_width,
SEXP max_mismatch, SEXP min_mismatch, SEXP fixed,
SEXP matches_as, SEXP envir)
{
HeadTail headtail;
int tb_length;
Chars_holder S, S_view;
int nviews, v, *view_start, *view_width, view_offset;
MatchPDictBuf matchpdict_buf;
MatchBuf global_match_buf;
tb_length = _get_PreprocessedTB_length(pptb);
headtail = _new_HeadTail(pdict_head, pdict_tail, pptb,
max_mismatch, fixed, 1);
S = hold_XRaw(subject);
matchpdict_buf = new_MatchPDictBuf_from_PDict3Parts(matches_as,
pptb, pdict_head, pdict_tail);
global_match_buf = _new_MatchBuf(matchpdict_buf.matches.ms_code,
tb_length);
nviews = LENGTH(views_start);
for (v = 0,
view_start = INTEGER(views_start),
view_width = INTEGER(views_width);
v < nviews;
v++, view_start++, view_width++)
{
view_offset = *view_start - 1;
if (view_offset < 0 || view_offset + *view_width > S.length)
error("'subject' has \"out of limits\" views");
S_view.ptr = S.ptr + view_offset;
S_view.length = *view_width;
match_pdict(pptb, &headtail, &S_view,
max_mismatch, min_mismatch, fixed,
&matchpdict_buf);
_MatchPDictBuf_append_and_flush(&global_match_buf,
&matchpdict_buf, view_offset);
}
return _MatchBuf_as_SEXP(&global_match_buf, envir);
}
/* --- .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);
}
