IntAE *_new_IntAE_from_INTEGER(SEXP x)
{
IntAE *ae;
ae = _new_IntAE(LENGTH(x), 0, 0);
copy_INTEGER_to_IntAE(x, ae);
return ae;
}
IntAE *_new_IntAE_from_CHARACTER(SEXP x, int keyshift)
{
IntAE *ae;
int i, *elt;
ae = _new_IntAE(LENGTH(x), 0, 0);
_IntAE_set_nelt(ae, ae->_buflength);
for (i = 0, elt = ae->elts; i < ae->_buflength; i++, elt++) {
sscanf(CHAR(STRING_ELT(x, i)), "%d", elt);
*elt += keyshift;
}
return ae;
}
/* --- .Call ENTRY POINT --- */
SEXP CompressedIRangesList_gaps(SEXP x, SEXP start, SEXP end)
{
SEXP ans, ans_names, ans_unlistData,
ans_partitioning, ans_partitioning_end;
cachedCompressedIRangesList cached_x;
cachedIRanges cached_ir;
int max_in_length, x_length, start_length, *start_elt, *end_elt, i;
RangeAE in_ranges, out_ranges;
IntAE tmpbuf;
cached_x = _cache_CompressedIRangesList(x);
max_in_length = get_cachedCompressedIRangesList_max_eltLengths(
&cached_x);
in_ranges = _new_RangeAE(0, 0);
out_ranges = _new_RangeAE(0, 0);
tmpbuf = _new_IntAE(max_in_length, 0, 0);
x_length = _get_cachedCompressedIRangesList_length(&cached_x);
start_length = LENGTH(start);
if ((start_length != 1 && start_length != x_length) ||
start_length != LENGTH(end))
error("'start' and 'end' should both be integer vectors of length 1 or length(x)");
PROTECT(ans_partitioning_end = NEW_INTEGER(x_length));
start_elt = INTEGER(start);
end_elt = INTEGER(end);
for (i = 0; i < x_length; i++) {
cached_ir = _get_cachedCompressedIRangesList_elt(&cached_x, i);
_RangeAE_set_nelt(&in_ranges, 0);
append_cachedIRanges_to_RangeAE(&in_ranges, &cached_ir);
_gaps_ranges(in_ranges.start.elts, in_ranges.width.elts,
_RangeAE_get_nelt(&in_ranges),
*start_elt, *end_elt,
tmpbuf.elts, &out_ranges);
INTEGER(ans_partitioning_end)[i] = _RangeAE_get_nelt(&out_ranges);
if (start_length != 1) {
start_elt++;
end_elt++;
}
}
PROTECT(ans_unlistData = _new_IRanges_from_RangeAE("IRanges",
&out_ranges));
PROTECT(ans_names = duplicate(_get_CompressedList_names(x)));
PROTECT(ans_partitioning = _new_PartitioningByEnd(
"PartitioningByEnd",
ans_partitioning_end, ans_names));
PROTECT(ans = _new_CompressedList(_get_classname(x),
ans_unlistData, ans_partitioning));
UNPROTECT(5);
return ans;
}
/* --- .Call ENTRY POINT --- */
SEXP CompressedIRangesList_reduce(SEXP x, SEXP drop_empty_ranges,
SEXP min_gapwidth)
{
SEXP ans, ans_names, ans_unlistData,
ans_partitioning, ans_partitioning_end;
cachedCompressedIRangesList cached_x;
cachedIRanges cached_ir;
int max_in_length, x_length, i;
RangeAE in_ranges, out_ranges;
IntAE tmpbuf;
cached_x = _cache_CompressedIRangesList(x);
max_in_length = get_cachedCompressedIRangesList_max_eltLengths(
&cached_x);
in_ranges = _new_RangeAE(0, 0);
out_ranges = _new_RangeAE(0, 0);
tmpbuf = _new_IntAE(max_in_length, 0, 0);
x_length = _get_cachedCompressedIRangesList_length(&cached_x);
PROTECT(ans_partitioning_end = NEW_INTEGER(x_length));
for (i = 0; i < x_length; i++) {
cached_ir = _get_cachedCompressedIRangesList_elt(&cached_x, i);
_RangeAE_set_nelt(&in_ranges, 0);
append_cachedIRanges_to_RangeAE(&in_ranges, &cached_ir);
_reduce_ranges(in_ranges.start.elts, in_ranges.width.elts,
_RangeAE_get_nelt(&in_ranges),
LOGICAL(drop_empty_ranges)[0], INTEGER(min_gapwidth)[0],
tmpbuf.elts, &out_ranges, NULL);
INTEGER(ans_partitioning_end)[i] = _RangeAE_get_nelt(&out_ranges);
}
PROTECT(ans_unlistData = _new_IRanges_from_RangeAE("IRanges",
&out_ranges));
PROTECT(ans_names = duplicate(_get_CompressedList_names(x)));
PROTECT(ans_partitioning = _new_PartitioningByEnd(
"PartitioningByEnd",
ans_partitioning_end, ans_names));
PROTECT(ans = _new_CompressedList(_get_classname(x),
ans_unlistData, ans_partitioning));
UNPROTECT(5);
return ans;
}
