/* --- .Call ENTRY POINT ---
* 'query_start', 'query_width', 'query_space': integer vectors of the same
* length M (or NULL for 'query_space').
* 'query_break': single integer.
* 'subject_start', 'subject_width', 'subject_space': integer vectors of the
* same length N (or NULL for 'subject_space').
* Integer vectors 'query_start', 'query_width', 'subject_start' and
* 'subject_width' are assumed to be NA free. 'query_width' and 'subject_width'
* are assumed to contain non-negative values. For efficiency reasons, those
* assumptions are not checked.
* Return the matrix of 1-letter codes (if 'as_matrix' is TRUE), otherwise a
* named list with the 3 following components:
* 1. Loffset: single integer;
* 2. Roffset: single integer;
* 3. encoding: the compact encoding as a single string (if 'as_raw' is
* FALSE) or a raw vector (if 'as_raw' is TRUE).
*/
SEXP encode_overlaps1(SEXP query_start, SEXP query_width, SEXP query_space,
SEXP query_break, SEXP flip_query,
SEXP subject_start, SEXP subject_width, SEXP subject_space,
SEXP as_matrix, SEXP as_raw)
{
int query_break0, flip_query0, as_matrix0, as_raw0, Loffset, Roffset;
CharAE buf;
SEXP encoding, ans_Loffset, ans_Roffset, ans;
query_break0 = INTEGER(query_break)[0];
flip_query0 = LOGICAL(flip_query)[0];
as_matrix0 = as_matrix != R_NilValue && LOGICAL(as_matrix)[0];
as_raw0 = as_raw != R_NilValue && LOGICAL(as_raw)[0];
buf = _new_CharAE(0);
overlap_encoding(
query_start, query_width, query_space,
query_break0, flip_query0,
subject_start, subject_width, subject_space,
as_matrix0, &Loffset, &Roffset, &buf);
PROTECT(encoding = make_encoding_from_CharAE(&buf,
as_raw0 ? 2 : 1, as_matrix0,
LENGTH(query_start),
query_break0,
LENGTH(subject_start)));
if (as_matrix0) {
UNPROTECT(1);
return encoding;
}
PROTECT(ans_Loffset = ScalarInteger(Loffset));
PROTECT(ans_Roffset = ScalarInteger(Roffset));
PROTECT(ans = make_LIST_from_ovenc_parts(ans_Loffset, ans_Roffset,
encoding));
UNPROTECT(4);
return ans;
}
CharAE *_new_CharAE_from_string(const char *string)
{
CharAE *ae;
ae = _new_CharAE(strlen(string));
_CharAE_set_nelt(ae, ae->_buflength);
memcpy(ae->elts, string, ae->_buflength);
return ae;
}
/* --- .Call ENTRY POINT ---/
* Same arguments as RangesList_encode_overlaps() plus:
* 'query_hits', 'subject_hits': integer vectors of the same length.
* 'flip_query': logical vector of the same length as 'query_hits'.
*/
SEXP Hits_encode_overlaps(SEXP query_starts, SEXP query_widths,
SEXP query_spaces, SEXP query_breaks,
SEXP subject_starts, SEXP subject_widths,
SEXP subject_spaces,
SEXP query_hits, SEXP subject_hits, SEXP flip_query)
{
int q_len, s_len, ans_len, i, j, k;
const int *q_hits, *s_hits;
SEXP ans_Loffset, ans_Roffset, ans_encoding, ans_encoding_elt, ans;
CharAE buf;
/* TODO: Add some basic checking of the input values. */
q_len = LENGTH(query_starts);
s_len = LENGTH(subject_starts);
ans_len = _check_integer_pairs(query_hits, subject_hits,
&q_hits, &s_hits,
"queryHits(hits)", "subjectHits(hits)");
PROTECT(ans_Loffset = NEW_INTEGER(ans_len));
PROTECT(ans_Roffset = NEW_INTEGER(ans_len));
PROTECT(ans_encoding = NEW_CHARACTER(ans_len));
buf = _new_CharAE(0);
for (k = 0; k < ans_len; k++) {
i = q_hits[k];
j = s_hits[k];
if (i == NA_INTEGER || i < 1 || i > q_len ||
j == NA_INTEGER || j < 1 || j > s_len) {
UNPROTECT(3);
error("'queryHits(hits)' or 'subjectHits(hits)' "
"contain invalid indices");
}
i--;
j--;
PROTECT(ans_encoding_elt = RangesList_encode_overlaps_ij(
query_starts, query_widths,
query_spaces, query_breaks,
subject_starts, subject_widths, subject_spaces,
i, j, LOGICAL(flip_query)[k],
INTEGER(ans_Loffset) + k,
INTEGER(ans_Roffset) + k,
&buf));
SET_STRING_ELT(ans_encoding, k, ans_encoding_elt);
UNPROTECT(1);
_CharAE_set_nelt(&buf, 0);
}
PROTECT(ans = make_LIST_from_ovenc_parts(ans_Loffset, ans_Roffset,
ans_encoding));
UNPROTECT(4);
return ans;
}
/* --- .Call ENTRY POINT ---/
* 'query_starts', 'query_widths', 'query_spaces': lists of integer vectors.
* The 3 lists are assumed to have the same length (M) and shape.
* 'query_breaks': NULL or integer vector of length M.
* 'subject_starts', 'subject_widths', 'subject_spaces': lists of integer
* vectors. The 3 lists are assumed to have the same length (N) and shape.
* Return a named list with the 3 following components (all of the same
* length):
* 1. Loffset: integer vector;
* 2. Roffset: integer vector;
* 3. encoding: character vector containing the compact encodings (type
* II).
*/
SEXP RangesList_encode_overlaps(SEXP query_starts, SEXP query_widths,
SEXP query_spaces, SEXP query_breaks,
SEXP subject_starts, SEXP subject_widths,
SEXP subject_spaces)
{
int q_len, s_len, ans_len, i, j, k;
SEXP ans_Loffset, ans_Roffset, ans_encoding, ans_encoding_elt, ans;
CharAE buf;
/* TODO: Add some basic checking of the input values. */
q_len = LENGTH(query_starts);
s_len = LENGTH(subject_starts);
if (q_len == 0 || s_len == 0)
ans_len = 0;
else
ans_len = q_len >= s_len ? q_len : s_len;
PROTECT(ans_Loffset = NEW_INTEGER(ans_len));
PROTECT(ans_Roffset = NEW_INTEGER(ans_len));
PROTECT(ans_encoding = NEW_CHARACTER(ans_len));
buf = _new_CharAE(0);
for (i = j = k = 0; k < ans_len; i++, j++, k++) {
if (i >= q_len)
i = 0; /* recycle i */
if (j >= s_len)
j = 0; /* recycle j */
PROTECT(ans_encoding_elt = RangesList_encode_overlaps_ij(
query_starts, query_widths,
query_spaces, query_breaks,
subject_starts, subject_widths, subject_spaces,
i, j, 0,
INTEGER(ans_Loffset) + k,
INTEGER(ans_Roffset) + k,
&buf));
SET_STRING_ELT(ans_encoding, k, ans_encoding_elt);
UNPROTECT(1);
_CharAE_set_nelt(&buf, 0);
}
if (ans_len != 0 && (i != q_len || j != s_len))
warning("longer object length is not a multiple "
"of shorter object length");
PROTECT(ans = make_LIST_from_ovenc_parts(ans_Loffset, ans_Roffset,
ans_encoding));
UNPROTECT(4);
return ans;
}