/**
* seek forward on the iterator
*
* @param interval the interval to seek to
* @return a RODRecordList at that location, null otherwise
*/
@Override
public RODRecordList seekForward(GenomeLoc interval) {
RODRecordList lt = iterator.seekForward(interval);
createPastRecord(lt);
return lt;
}
/**
* get the next record, either from the queue or from the iterator
*
* @return a RODRecordList
*/
private RODRecordList getNext() {
if (aheadQueue.size() > 0) {
RODRecordList ret = aheadQueue.getFirst().getList();
aheadQueue.removeFirst();
return ret;
} else {
RODRecordList ret = iterator.next();
createPastRecord(ret);
return ret;
}
}
/**
* get the position of this iterator
*
* @return
*/
@Override
public GenomeLoc position() {
return (aheadQueue.size() > 0) ? aheadQueue.getFirst().getLocation() : iterator.position();
}
/**
* Gets the sequence dictionary associated with the backing input stream.
*
* @return sequence dictionary from the ROD header.
*/
@Override
public SAMSequenceDictionary getSequenceDictionary() {
return iterator.getSequenceDictionary();
}
/**
* Gets the header associated with the backing input stream.
*
* @return the ROD header.
*/
@Override
public Object getHeader() {
return iterator.getHeader();
}
/**
* can we flash back to the specified location?
*
* @param location the location to try and flash back to
* @return true if we can, false otherwise
*/
public boolean canFlashBackTo(GenomeLoc location) {
GenomeLoc farthestBack =
(pastQueue.size() > 0) ? pastQueue.getFirst().getLocation() : iterator.peekNextLocation();
return (!farthestBack.isPast(location));
}
/**
* do we have a next record
*
* @return true if we have another record
*/
@Override
public boolean hasNext() {
return (aheadQueue.size() > 0 || iterator.hasNext());
}