Package org.broad.igv.bbfile
Class ZoomLevelIterator
- java.lang.Object
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- org.broad.igv.bbfile.ZoomLevelIterator
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- Direct Known Subclasses:
ZoomLevelIterator.EmptyIterator
public class ZoomLevelIterator extends java.lang.Object
Created by IntelliJ IDEA. User: martind Date: Apr 16, 2010 Time: 4:19:29 PM To change this template use File | Settings | File Templates.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
ZoomLevelIterator.EmptyIterator
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Constructor Summary
Constructors Constructor Description ZoomLevelIterator()
Default constructor.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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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SeekableStream
getBBFis()
BPTree
getChromosomeIDTree()
RPChromosomeRegion
getSelectionRegion()
RPTree
getZoomDataTree()
int
getZoomLevel()
boolean
hasNext()
boolean
isContained()
ZoomDataRecord
next()
Method returns the current bed feature and advances to the next bed record.void
remove()
int
setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)
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Constructor Detail
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ZoomLevelIterator
public ZoomLevelIterator()
Default constructor. This is provided to support return of a subclassed "empty" iterator
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ZoomLevelIterator
public ZoomLevelIterator(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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Method Detail
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hasNext
public boolean hasNext()
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next
public ZoomDataRecord next()
Method returns the current bed feature and advances to the next bed record. Returns: Bed feature for current BigBed data record. Note: If "next" method is called when a "next item" does not exist, an UnsupportedOperationException will be thrown.
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remove
public void remove()
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getZoomLevel
public int getZoomLevel()
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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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getZoomDataTree
public RPTree getZoomDataTree()
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