Uses of Class
org.broad.igv.bbfile.RPTree
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Packages that use RPTree Package Description org.broad.igv.bbfile -
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Uses of RPTree in org.broad.igv.bbfile
Methods in org.broad.igv.bbfile that return RPTree Modifier and Type Method Description RPTree
BBFileReader. getChromosomeDataTree()
RPTree
BigBedIterator. getChromosomeDataTree()
RPTree
BigWigIterator. getChromosomeDataTree()
RPTree
ZoomLevelIterator. getZoomDataTree()
RPTree
BBZoomLevels. getZoomLevelRPTree(int level)
Constructors in org.broad.igv.bbfile with parameters of type RPTree Constructor Description BigBedIterator(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 featuresBigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)
Constructor for a BigWig iterator over the specified chromosome regionZoomLevelIterator(SeekableStream fis, BPTree chromIDTree, RPTree zoomDataTree, int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)
Constructs a zoom level iterator over the specified chromosome region
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