Uses of Class
org.broad.igv.bbfile.RPChromosomeRegion

Packages that use RPChromosomeRegion

Package	Description
org.broad.igv.bbfile

Uses of RPChromosomeRegion in org.broad.igv.bbfile

Subclasses of RPChromosomeRegion in org.broad.igv.bbfile

Modifier and Type	Class	Description
class	RPTreeLeafNodeItem	Created by IntelliJ IDEA.

Methods in org.broad.igv.bbfile that return RPChromosomeRegion

Modifier and Type	Method	Description
RPChromosomeRegion	BBFileReader.getChromosomeBounds()
RPChromosomeRegion	BBFileReader.getChromosomeBounds(int startChromID, int endChromID)
RPChromosomeRegion	RPTree.getChromosomeBounds()
RPChromosomeRegion	RPTreeChildNode.getChromosomeBounds()
RPChromosomeRegion	RPTreeChildNodeItem.getChromosomeBounds()
RPChromosomeRegion	RPTreeLeafNode.getChromosomeBounds()
RPChromosomeRegion	RPTreeLeafNodeItem.getChromosomeBounds()
RPChromosomeRegion	RPTreeNode.getChromosomeBounds()
RPChromosomeRegion	RPTreeNodeProxy.getChromosomeBounds()
RPChromosomeRegion	RPTree.getChromosomeRegion(int startChromID, int endChromID)
RPChromosomeRegion	RPChromosomeRegion.getExtremes(RPChromosomeRegion testRegion)
RPChromosomeRegion	BigBedIterator.getSelectionRegion()
RPChromosomeRegion	BigWigIterator.getSelectionRegion()
RPChromosomeRegion	ZoomLevelIterator.getSelectionRegion()
RPChromosomeRegion	BBFileReader.getZoomLevelBounds(int zoomLevel)
RPChromosomeRegion	BBFileReader.getZoomLevelBounds(int zoomLevel, int startChromID, int endChromID)

Methods in org.broad.igv.bbfile that return types with arguments of type RPChromosomeRegion

Modifier and Type	Method	Description
java.util.ArrayList<RPChromosomeRegion>	RPTree.getAllChromosomeRegions()
java.util.ArrayList<RPChromosomeRegion>	BBFileReader.getChromosomeRegions()
java.util.ArrayList<RPChromosomeRegion>	BBFileReader.getZoomLevelRegions(int zoomLevel)

Methods in org.broad.igv.bbfile with parameters of type RPChromosomeRegion

Modifier and Type	Method	Description
int	RPChromosomeRegion.compareRegions(RPChromosomeRegion testRegion)
int	RPTreeChildNode.compareRegions(RPChromosomeRegion chromosomeRegion)
int	RPTreeChildNodeItem.compareRegions(RPChromosomeRegion chromosomeRegion)
int	RPTreeLeafNode.compareRegions(RPChromosomeRegion chromosomeRegion)
int	RPTreeNode.compareRegions(RPChromosomeRegion chromosomeRegion)
int	RPTreeNodeProxy.compareRegions(RPChromosomeRegion chromosomeRegion)
boolean	RPChromosomeRegion.containedIn(RPChromosomeRegion testRegion)
boolean	RPChromosomeRegion.disjointAbove(RPChromosomeRegion testRegion)
boolean	RPChromosomeRegion.disjointBelow(RPChromosomeRegion testRegion)
boolean	RPChromosomeRegion.equals(RPChromosomeRegion testRegion)
void	RPChromosomeRegion.expand(RPChromosomeRegion testRegion)
java.util.ArrayList<BedFeature>	BigBedDataBlock.getBedData(RPChromosomeRegion selectionRegion, boolean contained)
java.util.ArrayList<RPTreeLeafNodeItem>	RPTree.getChromosomeDataHits(RPChromosomeRegion selectionRegion, boolean contained)
RPChromosomeRegion	RPChromosomeRegion.getExtremes(RPChromosomeRegion testRegion)
int	BigWigSection.getSectionData(RPChromosomeRegion selectionRegion, boolean contained, java.util.ArrayList<WigItem> wigItemList)
java.util.ArrayList<WigItem>	BigWigDataBlock.getWigData(RPChromosomeRegion selectionRegion, boolean contained)
java.util.ArrayList<ZoomDataRecord>	ZoomDataBlock.getZoomData(RPChromosomeRegion selectionRegion, boolean contained)
ZoomLevelIterator	BBFileReader.getZoomLevelIterator(int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)	Returns an iterator for zoom level records for the chromosome selection region.
boolean	RPChromosomeRegion.intersectsAbove(RPChromosomeRegion testRegion)
boolean	RPChromosomeRegion.intersectsBelow(RPChromosomeRegion testRegion)
int	BigBedIterator.setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)
int	BigWigIterator.setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)
int	ZoomLevelIterator.setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)

Constructors in org.broad.igv.bbfile with parameters of type RPChromosomeRegion

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 features
BigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)	Constructor for a BigWig iterator over the specified chromosome region
RPChromosomeRegion(RPChromosomeRegion region)
ZoomLevelIterator(SeekableStream fis, BPTree chromIDTree, RPTree zoomDataTree, int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)	Constructs a zoom level iterator over the specified chromosome region