// ----------------------------------------------------------------------------
// CNATFWUNSAFHostResolver::RunL
// ----------------------------------------------------------------------------
//
void CNATFWUNSAFHostResolver::RunL()
{
NATFWUNSAF_INTLOG("CNATFWUNSAFHostResolver::RunL: status", iStatus.Int())
NATFWUNSAF_INTLOG("CNATFWUNSAFHostResolver::RunL: observerCancel",
iObserverCancel)
iFailed = EFalse;
TBool subquery = EFalse;
TInt status = iStatus.Int();
MNATFWUNSAFServerResolverObserver* observer =
iQuery->ServerResolverObserver();
if ( !iObserverCancel )
{
subquery = iQuery->HandleQueryResultL( iStatus.Int() );
}
NATFWUNSAF_INTLOG("CNATFWUNSAFHostResolver::RunL: subquery", subquery);
if ( subquery )
{
iQuery->Query( *this );
SetActive();
}
else
{
if ( iObserverCancel )
{
iObserverCancel = EFalse;
NextQuery();
}
else
{
if ( status == KErrNone )
{
NextQuery();
observer->CompletedL();
}
else
{//status _ne_ KErrNone || iFailed
NextQuery();
observer->ErrorOccured( status );
}
}
}
}
/*
Constructor with filenames
*/
ChromSweep::ChromSweep(string &queryFile, string &dbFile)
{
_hits.reserve(100000);
_query = new BedFile(queryFile);
_db = new BedFile(dbFile);
_query->Open();
_db->Open();
NextQuery();
NextDatabase();
}
/*
// constructor using existing BedFile pointers
*/
ChromSweep::ChromSweep(BedFile *query, BedFile *db,
bool sameStrand, bool diffStrand,
float overlapFraction, bool reciprocal,
bool useMergedIntervals, bool printHeader)
: _query(query)
, _db(db)
, _overlapFraction(overlapFraction)
, _sameStrand(sameStrand)
, _diffStrand(diffStrand)
, _reciprocal(reciprocal)
, _useMergedIntervals(useMergedIntervals)
{
_hits.reserve(100000);
_query->Open();
if (printHeader) _query->PrintHeader();
_db->Open();
NextQuery();
NextDatabase();
}
bool ChromSweep::ChromChange()
{
// the files are on the same chrom
if (_curr_qy.chrom == _curr_db.chrom) {
return false;
}
// the query is ahead of the database.
// fast-forward the database to catch-up.
else if ((_curr_qy.chrom > _curr_db.chrom) && (!_db->Empty())) {
while (NextDatabase() &&
_curr_db.chrom < _curr_qy.chrom)
{
}
_cache.clear();
return false;
}
// the database is ahead of the query.
else {
// 1. scan the cache for remaining hits on the query's current chrom.
if (_curr_qy.chrom == _curr_chrom)
{
ScanCache();
_results.push(make_pair(_curr_qy, _hits));
_hits.clear();
}
// 2. fast-forward until we catch up and report 0 hits until we do.
else if (_curr_qy.chrom < _curr_db.chrom)
{
_results.push(make_pair(_curr_qy, _no_hits));
_cache.clear();
}
NextQuery();
_curr_chrom = _curr_qy.chrom;
return true;
}
}
bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
if (!_query->Empty()) {
// have we changed chromosomes?
if (ChromChange() == false) {
// scan the database cache for hits
ScanCache();
// advance the db until we are ahead of the query.
// update hits and cache as necessary
while (!_db->Empty() &&
_curr_qy.chrom == _curr_db.chrom &&
!(after(_curr_db, _curr_qy)))
{
if (IsValidHit(_curr_qy, _curr_db)) {
_hits.push_back(_curr_db);
}
_cache.push_back(_curr_db);
NextDatabase();
}
// add the hits for this query to the pump
_results.push(make_pair(_curr_qy, _hits));
// reset for the next query
_hits.clear();
NextQuery();
_curr_chrom = _curr_qy.chrom;
}
}
// report the next set if hits if there are still overlaps in the pump
if (!_results.empty()) {
next = _results.front();
_results.pop();
return true;
}
else {
return false;
}
}
