void gbUpdateCountAligns(struct gbUpdate* update, struct gbAligned* aligned,
unsigned numAligns)
/* increment the count of the number of alignments */
{
if (aligned->alignOrgCat == GB_NATIVE)
update->numNativeAligns[gbTypeIdx(aligned->entry->type)] += numAligns;
else
update->numXenoAligns[gbTypeIdx(aligned->entry->type)] += numAligns;
}
unsigned gbUpdateGetNumAligns(struct gbUpdate* update,
unsigned type, unsigned orgCat)
/* Get the number of alignments for a type and orgCat */
{
switch (orgCat) {
case GB_NATIVE:
return update->numNativeAligns[gbTypeIdx(type)];
case GB_XENO:
return update->numXenoAligns[gbTypeIdx(type)];
}
assert(FALSE);
return 0;
}
void oiDataProcessUpdate(struct gbSelect* select)
/* Get orientationInfo records for a partition and update. Partition
* processed and aligned indexes should be loaded and selected versions
* flaged. */
{
assert(select->orgCats & GB_NATIVE);
if (select->update->numNativeAligns[gbTypeIdx(select->type)] > 0)
processOrgCatOi(select, GB_NATIVE);
flagUnaligned(select, GB_NATIVE);
}
boolean updateSelected(struct gbUpdate* update, struct gbSelect* select)
/* check if an update is selected and has alignments based on selection
* criteria */
{
int typeIdx = gbTypeIdx(select->type);
if (!update->selectAlign)
return FALSE; /* not selected */
return ((select->orgCats & GB_NATIVE)
&& (update->numNativeAligns[typeIdx] > 0))
|| ((select->orgCats & GB_XENO)
&& (update->numXenoAligns[typeIdx] > 0));
}
