Package org.broad.igv.bbfile
Class BigWigIterator
- java.lang.Object
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- org.broad.igv.bbfile.BigWigIterator
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Constructor Summary
Constructors Constructor Description BigWigIterator()
Constructor for an "empty" iteratorBigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)
Constructor for a BigWig iterator over the specified chromosome region
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SeekableStream
getBBFis()
RPTree
getChromosomeDataTree()
BPTree
getChromosomeIDTree()
RPChromosomeRegion
getSelectionRegion()
boolean
hasNext()
boolean
isContained()
WigItem
next()
Method returns the current Wig item and advances to the next Wig record.void
remove()
int
setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)
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Constructor Detail
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BigWigIterator
public BigWigIterator(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
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BigWigIterator
public BigWigIterator()
Constructor for an "empty" iterator
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Method Detail
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hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfacejava.util.Iterator<WigItem>
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next
public WigItem next()
Method returns the current Wig item and advances to the next Wig record. Returns: Wig item for current BigWig data record. Note: If "next" method is called when a "next item" does not exist, an NoSuchElementException will be thrown.- Specified by:
next
in interfacejava.util.Iterator<WigItem>
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remove
public void remove()
- Specified by:
remove
in interfacejava.util.Iterator<WigItem>
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getSelectionRegion
public RPChromosomeRegion getSelectionRegion()
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setSelectionRegion
public int setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)
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isContained
public boolean isContained()
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getBBFis
public SeekableStream getBBFis()
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getChromosomeIDTree
public BPTree getChromosomeIDTree()
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getChromosomeDataTree
public RPTree getChromosomeDataTree()
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