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| Packages that use RPChromosomeRegion | |
|---|---|
| org.broad.igv.bbfile | |
| Uses of RPChromosomeRegion in org.broad.igv.bbfile |
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| Subclasses of RPChromosomeRegion in org.broad.igv.bbfile | |
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class |
RPTreeLeafNodeItem
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats. |
| Methods in org.broad.igv.bbfile that return types with arguments of type RPChromosomeRegion | |
|---|---|
java.util.ArrayList<RPChromosomeRegion> |
RPTree.getAllChromosomeRegions()
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java.util.ArrayList<RPChromosomeRegion> |
BBFileReader.getChromosomeRegions()
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java.util.ArrayList<RPChromosomeRegion> |
BBFileReader.getZoomLevelRegions(int zoomLevel)
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| Methods in org.broad.igv.bbfile with parameters of type RPChromosomeRegion | |
|---|---|
int |
RPChromosomeRegion.compareRegions(RPChromosomeRegion testRegion)
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int |
RPTreeChildNode.compareRegions(RPChromosomeRegion chromosomeRegion)
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int |
RPTreeChildNodeItem.compareRegions(RPChromosomeRegion chromosomeRegion)
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int |
RPTreeLeafNode.compareRegions(RPChromosomeRegion chromosomeRegion)
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int |
RPTreeNode.compareRegions(RPChromosomeRegion chromosomeRegion)
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boolean |
RPChromosomeRegion.containedIn(RPChromosomeRegion testRegion)
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boolean |
RPChromosomeRegion.disjointAbove(RPChromosomeRegion testRegion)
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boolean |
RPChromosomeRegion.disjointBelow(RPChromosomeRegion testRegion)
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boolean |
RPChromosomeRegion.equals(RPChromosomeRegion testRegion)
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void |
RPChromosomeRegion.expand(RPChromosomeRegion testRegion)
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java.util.ArrayList<BedFeature> |
BigBedDataBlock.getBedData(RPChromosomeRegion selectionRegion,
boolean contained)
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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 | |
|---|---|
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 |
|
RPChromosomeRegion(RPChromosomeRegion region)
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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 |
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