Uses of Class
org.broad.igv.bbfile.RPChromosomeRegion
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Packages that use RPChromosomeRegion Package Description org.broad.igv.bbfile -
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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 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 featuresBigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)
Constructor for a BigWig iterator over the specified chromosome regionRPChromosomeRegion(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
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