void NewChromSweep::masterScan(RecordKeyVector &retList) {
for (int i=0; i < _numDBs; i++) {
if (dbFinished(i) || chromChange(i, retList, true)) {
continue;
} else {
// scan the database cache for hits
scanCache(i, retList);
//skip if we hit the end of the DB
// advance the db until we are ahead of the query. update hits and cache as necessary
while (_currDbRecs[i] != NULL &&
_currQueryRec->sameChrom(_currDbRecs[i]) &&
!(_currDbRecs[i]->after(_currQueryRec))) {
if (intersects(_currQueryRec, _currDbRecs[i])) {
retList.push_back(_currDbRecs[i]);
}
if (_currQueryRec->after(_currDbRecs[i])) {
_dbFRMs[i]->deleteRecord(_currDbRecs[i]);
_currDbRecs[i] = NULL;
} else {
_caches[i].push_back(_currDbRecs[i]);
_currDbRecs[i] = NULL;
}
nextRecord(false, i);
}
}
}
}
void CloseSweep::masterScan(RecordKeyVector &retList) {
//first clear out everything from the previous scan
if (_context->reportDistance()) {
_finalDistances.clear();
}
//initialize distances
for (int i=0; i < _numDBs; i++) {
_minUpstreamDist[i] = INT_MAX;
_minDownstreamDist[i] = INT_MAX;
}
for (int i=0; i < _numDBs; i++) {
_minUpstreamRecs[i]->clear();
_minDownstreamRecs[i]->clear();
_overlapRecs[i]->clear();
if (dbFinished(i) || chromChange(i, retList)) {
continue;
} else {
// scan the database cache for hits
scanCache(i, retList);
// skip if we hit the end of the DB
// advance the db until we are ahead of the query. update hits and cache as necessary
bool stopScanning = false;
while (_currDbRecs[i] != NULL &&
_currQueryRec->sameChrom(_currDbRecs[i]) &&
!stopScanning) {
if (considerRecord(_currDbRecs[i], i, stopScanning) == DELETE) {
_dbFRMs[i]->deleteRecord(_currDbRecs[i]);
_currDbRecs[i] = NULL;
} else {
_caches[i].push_back(_currDbRecs[i]);
_currDbRecs[i] = NULL;
}
nextRecord(false, i);
}
}
finalizeSelections(i, retList);
}
checkMultiDbs(retList);
}
