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);
}
bool NewChromSweep::next(RecordKeyList &next) {
if (_currQueryRec != NULL) {
_queryFRM->deleteRecord(_currQueryRec);
}
nextRecord(true);
if (_currQueryRec == NULL) { //eof hit!
return false;
}
if (_currDatabaseRec == NULL && _cache.empty() && !_runToQueryEnd) {
return false;
}
_hits.clear();
_currChromName = _currQueryRec->getChrName();
// have we changed chromosomes?
if (!chromChange()) {
// scan the database cache for hits
scanCache();
//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 (_currDatabaseRec != NULL &&
_currQueryRec->sameChrom(_currDatabaseRec) &&
!(_currDatabaseRec->after(_currQueryRec))) {
if (intersects(_currQueryRec, _currDatabaseRec)) {
_hits.push_back(_currDatabaseRec);
}
if (_currQueryRec->after(_currDatabaseRec)) {
_databaseFRM->deleteRecord(_currDatabaseRec);
_currDatabaseRec = NULL;
} else {
_cache.push_back(_currDatabaseRec);
_currDatabaseRec = NULL;
}
nextRecord(false);
}
}
next.setKey(_currQueryRec);
next.setListNoCopy(_hits);
return true;
}
