org.broad.igv.tdf
Class TDFReader

java.lang.Object
  org.broad.igv.tdf.TDFReader

public class TDFReader
extends java.lang.Object

Author:

jrobinso, Thomas Abeel

Field Summary

static int

GZIP_FLAG

Method Summary

void	close()
double	getDataMax()
double	getDataMin()
TDFDataset	getDataset(java.lang.String name)
TDFDataset	getDataset(java.lang.String chr, int zoom, WindowFunction windowFunction)
java.util.Collection<java.lang.String>	getDatasetNames()
TDFGroup	getGroup(java.lang.String name)
java.util.Collection<java.lang.String>	getGroupNames()
java.lang.String	getLocator()
double	getLowerLimit()
int	getMaxZoom()
static TDFReader	getReader(net.sf.samtools.util.SeekableStream locator)
java.lang.String	getTrackLine()
java.lang.String[]	getTrackNames()
double	getUpperLimit() Return the default upper value for the data range.
int	getVersion()
java.util.List<WindowFunction>	getWindowFunctions()
byte[]	readBytes(long position, int nBytes)
TDFTile	readTile(TDFDataset ds, int tileNumber)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GZIP_FLAG

public static final int GZIP_FLAG

See Also:

Constant Field Values

Method Detail

getReader

public static TDFReader getReader(net.sf.samtools.util.SeekableStream locator)
                           throws java.net.URISyntaxException

Throws:

java.net.URISyntaxException

close

public void close()

getDataset

public TDFDataset getDataset(java.lang.String chr,
                             int zoom,
                             WindowFunction windowFunction)

getDataset

public TDFDataset getDataset(java.lang.String name)

getDatasetNames

public java.util.Collection<java.lang.String> getDatasetNames()

getGroupNames

public java.util.Collection<java.lang.String> getGroupNames()

getGroup

public TDFGroup getGroup(java.lang.String name)

readTile

public TDFTile readTile(TDFDataset ds,
                        int tileNumber)

getVersion

public int getVersion()

Returns:

the version

getTrackLine

public java.lang.String getTrackLine()

Returns:

the trackLine

getTrackNames

public java.lang.String[] getTrackNames()

Returns:

the trackNames

getUpperLimit

public double getUpperLimit()

Return the default upper value for the data range. A check is made to see if both upper and lower limits are equal to zero, within a tolerance. If they are the upper limit is arbitrarily set to "100". This is protection against the pathological case that can occur with datasets consisting of largely zero values.

Returns:

getLowerLimit

public double getLowerLimit()

getDataMax

public double getDataMax()

getDataMin

public double getDataMin()

readBytes

public byte[] readBytes(long position,
                        int nBytes)
                 throws java.io.IOException

Throws:

java.io.IOException

getWindowFunctions

public java.util.List<WindowFunction> getWindowFunctions()

Returns:

the windowFunctions

getLocator

public java.lang.String getLocator()

Returns:

getMaxZoom

public int getMaxZoom()