org.utgenome.gwt.utgb.client.track
Class TrackWindow

java.lang.Object
  org.utgenome.gwt.utgb.client.track.TrackWindow

All Implemented Interfaces:

Serializable, Comparable<TrackWindow>

public class TrackWindow
extends Object
implements Serializable, Comparable<TrackWindow>

TrackWindow manages a track-window size and a region on the genome displayed in the window. An instance of TrackWindow is immutable, so you can safely copy a reference of TrackWindow to preserve a current track window state.

Author:

leo

See Also:

Serialized Form

Constructor Summary

TrackWindow()

TrackWindow(int pixelWidth, int startIndexOnGenome, int endIndexOnGenome)

TrackWindow(TrackWindow other)

Method Summary

int	center()
int	compareTo(TrackWindow o)
boolean	contains(TrackWindow other)
int	convertToGenomePosition(int xOnWindow)
int	convertToPixelLength(int rangeOnGenome)
int	convertToPixelX(int indexOnGenome) calculate the X position (pixel address) in a track window of a given index on genome.
double	convertToPixelXDouble(int indexOnGenome)
boolean	equals(Object o)
int	getEndOnGenome()
double	getPixelLengthPerBase()
int	getPixelWidth()
int	getSequenceLength()
int	getStartOnGenome()
int	getViewEndOnGenome()
int	getViewStartOnGenome()
int	hashCode()
boolean	hasSameScaleWith(TrackWindow other)
boolean	isPositiveStrand()
boolean	isReverseStrand()
TrackWindow	mask(TrackWindow mask)
TrackWindow	newPixelWidthWindow(int pixelSize)
TrackWindow	newWindow(int newStartOnGenome, int newEndOnGenome)
boolean	overlapWith(GenomeRange g)
boolean	overlapWith(TrackWindow other)
boolean	sameRangeWith(TrackWindow window)
TrackWindow	scroll(int startDiff)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

TrackWindow

public TrackWindow()

TrackWindow

public TrackWindow(int pixelWidth,
                   int startIndexOnGenome,
                   int endIndexOnGenome)

TrackWindow

public TrackWindow(TrackWindow other)

Method Detail

convertToPixelX

public int convertToPixelX(int indexOnGenome)

calculate the X position (pixel address) in a track window of a given index on genome.

Parameters:

indexOnGenome -

Returns:

relative X position in a window (0 origin).

convertToPixelXDouble

public double convertToPixelXDouble(int indexOnGenome)

convertToGenomePosition

public int convertToGenomePosition(int xOnWindow)

Parameters:

xOnWindow - calculate the genome index of a given x position in the current window

Returns:

genome position

convertToPixelLength

public int convertToPixelLength(int rangeOnGenome)

getPixelLengthPerBase

public double getPixelLengthPerBase()

Returns:

pixel length / (genome end - genome start);

getPixelWidth

public int getPixelWidth()

Returns:

the window size

getSequenceLength

public int getSequenceLength()

Returns:

the sequence width

getViewStartOnGenome

public int getViewStartOnGenome()

getViewEndOnGenome

public int getViewEndOnGenome()

getStartOnGenome

public int getStartOnGenome()

Returns:

start position on the genome currently displayed in the window

getEndOnGenome

public int getEndOnGenome()

Returns:

end position on the genome currently displayed in the window

sameRangeWith

public boolean sameRangeWith(TrackWindow window)

isReverseStrand

public boolean isReverseStrand()

isPositiveStrand

public boolean isPositiveStrand()

newWindow

public TrackWindow newWindow(int newStartOnGenome,
                             int newEndOnGenome)

scroll

public TrackWindow scroll(int startDiff)

newPixelWidthWindow

public TrackWindow newPixelWidthWindow(int pixelSize)

contains

public boolean contains(TrackWindow other)

overlapWith

public boolean overlapWith(GenomeRange g)

overlapWith

public boolean overlapWith(TrackWindow other)

hasSameScaleWith

public boolean hasSameScaleWith(TrackWindow other)

mask

public TrackWindow mask(TrackWindow mask)

compareTo

public int compareTo(TrackWindow o)

Specified by:

compareTo in interface Comparable<TrackWindow>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

center

public int center()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object