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/****************************************************************************
* Low-level manipulation of CompressedIRangesList objects *
****************************************************************************/
#include "IRanges.h"
#include "S4Vectors_interface.h"
#include <limits.h>
#define R_INT_MIN (1+INT_MIN)
/****************************************************************************
* C-level abstract getters.
*/
CompressedIRangesList_holder _hold_CompressedIRangesList(SEXP x)
{
CompressedIRangesList_holder x_holder;
SEXP x_end;
x_holder.classname = get_classname(x);
x_end = _get_PartitioningByEnd_end(
_get_CompressedList_partitioning(x));
x_holder.length = LENGTH(x_end);
x_holder.end = INTEGER(x_end);
x_holder.unlistData_holder = _hold_IRanges(
_get_CompressedList_unlistData(x));
return x_holder;
}
int _get_length_from_CompressedIRangesList_holder(
const CompressedIRangesList_holder *x_holder)
{
return x_holder->length;
}
IRanges_holder _get_elt_from_CompressedIRangesList_holder(
const CompressedIRangesList_holder *x_holder, int i)
{
int offset, length;
offset = i == 0 ? 0 : x_holder->end[i - 1];
length = x_holder->end[i] - offset;
return _get_linear_subset_from_IRanges_holder(
&(x_holder->unlistData_holder),
offset, length);
}
int _get_eltNROWS_from_CompressedIRangesList_holder(
const CompressedIRangesList_holder *x_holder, int i)
{
/*
IRanges_holder ir_holder;
ir_holder = _get_elt_from_CompressedIRangesList_holder(x_holder, i);
return _get_length_from_IRanges_holder(&ir_holder);
*/
int offset;
offset = i == 0 ? 0 : x_holder->end[i - 1];
return x_holder->end[i] - offset; /* faster than the above */
}
/****************************************************************************
* CompressedIRangesList methods.
*/
/* --- .Call ENTRY POINT --- */
SEXP CompressedIRangesList_isNormal(SEXP x, SEXP use_names)
{
SEXP ans, ans_names;
CompressedIRangesList_holder x_holder;
IRanges_holder ir_holder;
int x_len, i;
x_holder = _hold_CompressedIRangesList(x);
x_len = _get_length_from_CompressedIRangesList_holder(&x_holder);
PROTECT(ans = NEW_LOGICAL(x_len));
for (i = 0; i < x_len; i++) {
ir_holder = _get_elt_from_CompressedIRangesList_holder(
&x_holder, i);
LOGICAL(ans)[i] = _is_normal_IRanges_holder(&ir_holder);
}
if (LOGICAL(use_names)[0]) {
PROTECT(ans_names = duplicate(_get_CompressedList_names(x)));
SET_NAMES(ans, ans_names);
UNPROTECT(1);
}
UNPROTECT(1);
return ans;
}
/* --- .Call ENTRY POINT --- */
SEXP CompressedIRangesList_summary(SEXP object)
{
int ans_len;
SEXP part_end;
SEXP ans, ans_names, col_names;
part_end = _get_PartitioningByEnd_end(
_get_CompressedList_partitioning(object));
ans_len = LENGTH(part_end);
PROTECT(ans = allocMatrix(INTSXP, ans_len, 2));
memset(INTEGER(ans), 0, 2 * ans_len * sizeof(int));
if (ans_len > 0) {
int i, j, prev_end = 0;
int *ans1_elt, *ans2_elt;
const int *part_end_elt, *ranges_width;
SEXP unlistData = _get_CompressedList_unlistData(object);
ranges_width = INTEGER(_get_IRanges_width(unlistData));
for (i = 0, ans1_elt = INTEGER(ans), ans2_elt = (INTEGER(ans) + ans_len),
part_end_elt = INTEGER(part_end);
i < ans_len; i++, ans1_elt++, ans2_elt++, part_end_elt++)
{
*ans1_elt = *part_end_elt - prev_end;
for (j = 0; j < *ans1_elt; j++) {
*ans2_elt += *ranges_width;
ranges_width++;
}
prev_end = *part_end_elt;
}
}
PROTECT(ans_names = NEW_LIST(2));
PROTECT(col_names = NEW_CHARACTER(2));
SET_STRING_ELT(col_names, 0, mkChar("Length"));
SET_STRING_ELT(col_names, 1, mkChar("WidthSum"));
SET_VECTOR_ELT(ans_names, 0,
duplicate(_get_CompressedList_names(object)));
SET_VECTOR_ELT(ans_names, 1, col_names);
SET_DIMNAMES(ans, ans_names);
UNPROTECT(3);
return ans;
}
/****************************************************************************
* CompressedNormalIRangesList methods.
*/
/* --- .Call ENTRY POINT --- */
SEXP CompressedNormalIRangesList_min(SEXP x, SEXP use_names)
{
SEXP ans, ans_names;
CompressedIRangesList_holder x_holder;
IRanges_holder ir_holder;
int x_len, ir_len, i;
int *ans_elt;
x_holder = _hold_CompressedIRangesList(x);
x_len = _get_length_from_CompressedIRangesList_holder(&x_holder);
PROTECT(ans = NEW_INTEGER(x_len));
for (i = 0, ans_elt = INTEGER(ans); i < x_len; i++, ans_elt++) {
ir_holder = _get_elt_from_CompressedIRangesList_holder(&x_holder, i);
ir_len = _get_length_from_IRanges_holder(&ir_holder);
if (ir_len == 0) {
*ans_elt = INT_MAX;
} else {
*ans_elt = _get_start_elt_from_IRanges_holder(&ir_holder, 0);
}
}
if (LOGICAL(use_names)[0]) {
PROTECT(ans_names = duplicate(_get_CompressedList_names(x)));
SET_NAMES(ans, ans_names);
UNPROTECT(1);
}
UNPROTECT(1);
return ans;
}
/* --- .Call ENTRY POINT --- */
SEXP CompressedNormalIRangesList_max(SEXP x, SEXP use_names)
{
SEXP ans, ans_names;
CompressedIRangesList_holder x_holder;
IRanges_holder ir_holder;
int x_len, ir_len, i;
int *ans_elt;
x_holder = _hold_CompressedIRangesList(x);
x_len = _get_length_from_CompressedIRangesList_holder(&x_holder);
PROTECT(ans = NEW_INTEGER(x_len));
for (i = 0, ans_elt = INTEGER(ans); i < x_len; i++, ans_elt++) {
ir_holder = _get_elt_from_CompressedIRangesList_holder(&x_holder, i);
ir_len = _get_length_from_IRanges_holder(&ir_holder);
if (ir_len == 0) {
*ans_elt = R_INT_MIN;
} else {
*ans_elt = _get_end_elt_from_IRanges_holder(&ir_holder, ir_len - 1);
}
}
if (LOGICAL(use_names)[0]) {
PROTECT(ans_names = duplicate(_get_CompressedList_names(x)));
SET_NAMES(ans, ans_names);
UNPROTECT(1);
}
UNPROTECT(1);
return ans;
}
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