| Constructors in org.broad.igv.bbfile with parameters of type RPTree |
BigBedIterator(net.sf.samtools.util.SeekableStream fis,
BPTree chromIDTree,
RPTree chromDataTree,
RPChromosomeRegion selectionRegion,
boolean contained)
Constructor for a BigBed iterator over the specified chromosome region
Parameters:
fis - file input stream handle
chromIDTree - B+ index tree returns chromomosme ID's for chromosome names
chromDataTree - R+ chromosome data locations tree
selectionRegion - chromosome region for selection of Bed feature extraction
consists of:
startChromID - ID of start chromosome
startBase - starting base position for features
endChromID - ID of end chromosome
endBase - starting base position for features
contained - specifies bed features must be contained by region, if true;
else return any intersecting region features |
BigWigIterator(net.sf.samtools.util.SeekableStream fis,
BPTree chromIDTree,
RPTree chromDataTree,
RPChromosomeRegion selectionRegion,
boolean contained)
Constructor for a BigWig iterator over the specified chromosome region
Parameters:
fis - file input stream handle
chromIDTree - B+ chromosome index tree provides chromosome ID's for chromosome names
chromDataTree - R+ chromosome data locations tree
selectionRegion - chromosome region for selection of Wig feature extraction
consists of:
startChromID - ID of start chromosome
startBase - starting base position for values
endChromID - ID of end chromosome
endBase - ending base position for values
contained - specifies wig values must be contained by region, if true;
else return any intersecting region values |
ZoomLevelIterator(net.sf.samtools.util.SeekableStream fis,
BPTree chromIDTree,
RPTree zoomDataTree,
int zoomLevel,
RPChromosomeRegion selectionRegion,
boolean contained)
Constructs a zoom level iterator over the specified chromosome region
Parameters:
fis - file input stream handle
chromIDTree - B+ index tree returns chromId for chromosome name key
zoomLevelTree - zoom level R+ chromosome index tree
zoomLevel - zoom level represented by the R+ tree
selectionRegion - chromosome region for selection of Bed feature extraction
consists of:
startChromID - ID of start chromosome
startBase - starting base position for features
endChromID - ID of end chromosome
endBase - starting base position for features
contained - specifies bed features must be contained by region, if true;
else return any intersecting region features |