void
BlastSeqLocCombine(BlastSeqLoc** mask_loc, Int4 link_value)
{
BlastSeqLoc** ptrs = NULL;
Int4 i = 0, num_elems = 0;
/* Break up the list into an array of pointers and sort it */
ptrs = s_BlastSeqLocListToArrayOfPointers(*mask_loc, &num_elems);
if (num_elems == 0) {
return;
}
ASSERT(ptrs);
qsort(ptrs, (size_t)num_elems, sizeof(*ptrs),
s_SeqRangeSortByStartPosition);
/* Merge the overlapping elements */
{
BlastSeqLoc* curr_tail = *mask_loc = ptrs[0];
for (i = 0; i < num_elems - 1; i++) {
const SSeqRange* next_ssr = ptrs[i+1]->ssr;
const Int4 stop = curr_tail->ssr->right;
if ((stop + link_value) > next_ssr->left) {
curr_tail->ssr->right = MAX(stop, next_ssr->right);
ptrs[i+1] = BlastSeqLocNodeFree(ptrs[i+1]);
} else {
curr_tail = ptrs[i+1];
}
}
}
/* Rebuild the linked list */
{
BlastSeqLoc* tail = *mask_loc;
for (i = 1; i < num_elems; i++) {
if (ptrs[i]) {
tail->next = ptrs[i];
tail = ptrs[i];
}
}
tail->next = NULL;
}
sfree(ptrs);
}
/** Reverse elements in the list
* @param head pointer to pointer to the head of the list. [in|out]
* (this is not declared static so that it can be tested in the unit tests
*/
void BlastSeqLocListReverse(BlastSeqLoc** head)
{
BlastSeqLoc** ptrs = NULL; /* array of pointers to BlastSeqLoc elements */
int32_t num_elems = 0, i = 0;
if ( !head ) {
return;
}
ptrs = s_BlastSeqLocListToArrayOfPointers(*head, &num_elems);
if (num_elems == 0) {
return;
}
assert(ptrs);
*head = ptrs[num_elems-1];
for (i = num_elems-1; i > 0; i--) {
ptrs[i]->next = ptrs[i-1];
}
ptrs[0]->next = NULL;
sfree(ptrs);
}
