Uses of Class
org.broad.tribble.util.SeekableStream
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Packages that use SeekableStream Package Description org.broad.igv.bbfile org.broad.tribble.util -
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Uses of SeekableStream in org.broad.igv.bbfile
Fields in org.broad.igv.bbfile declared as SeekableStream Modifier and Type Field Description SeekableStream
RPTreeNodeProxy. fis
Methods in org.broad.igv.bbfile that return SeekableStream Modifier and Type Method Description SeekableStream
BBFileReader. getBBFis()
SeekableStream
BBZoomLevelFormat. getBBFis()
SeekableStream
BigBedIterator. getBBFis()
SeekableStream
BigWigIterator. getBBFis()
SeekableStream
ZoomLevelIterator. getBBFis()
SeekableStream
BPTree. getFis()
SeekableStream
BBTotalSummaryBlock. getMBBFis()
Constructors in org.broad.igv.bbfile with parameters of type SeekableStream Constructor Description BBFileHeader(java.lang.String path, SeekableStream fis, long fileOffset)
BBFileReader(java.lang.String path, SeekableStream stream)
BBTotalSummaryBlock(SeekableStream fis, long fileOffset, boolean isLowToHigh)
BBZoomLevelFormat(int zoomLevel, SeekableStream fis, long fileOffset, long dataSize, boolean isLowToHigh, int uncompressBufSize)
BBZoomLevelHeader(SeekableStream fis, long fileOffset, int zoomLevel, boolean isLowToHigh)
BBZoomLevels(SeekableStream fis, long fileOffset, int zoomLevels, boolean isLowToHigh, int uncompressBufSize)
BigBedDataBlock(SeekableStream fis, RPTreeLeafNodeItem leafHitItem, java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap, boolean isLowToHigh, int uncompressBufSize)
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 featuresBigWigDataBlock(SeekableStream fis, RPTreeLeafNodeItem leafHitItem, java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap, boolean isLowToHigh, int uncompressBufSize)
BigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)
Constructor for a BigWig iterator over the specified chromosome regionBPTree(SeekableStream fis, long fileOffset, boolean isLowToHigh)
BPTreeHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh)
RPTree(SeekableStream fis, long fileOffset, boolean isLowToHigh, int uncompressBuffSize, boolean forceDescend)
RPTreeHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh)
RPTreeNodeProxy(SeekableStream fis, long fileOffset, boolean lowToHigh, int chromId)
ZoomDataBlock(int zoomLevel, SeekableStream fis, RPTreeLeafNodeItem leafHitItem, java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap, boolean isLowToHigh, int uncompressBufSize)
ZoomLevelIterator(SeekableStream fis, BPTree chromIDTree, RPTree zoomDataTree, int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)
Constructs a zoom level iterator over the specified chromosome region -
Uses of SeekableStream in org.broad.tribble.util
Subclasses of SeekableStream in org.broad.tribble.util Modifier and Type Class Description class
SeekableFileStream
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