com.hfg.graphics

Class Track

java.lang.Object

java.awt.geom.RectangularShape

java.awt.geom.Rectangle2D

java.awt.Rectangle

com.hfg.graphics.Track

All Implemented Interfaces:

Shape, Serializable, Cloneable, Comparable<Track>

public class Track
extends Rectangle
implements Comparable<Track>

An evidence Track of data to display on genomic coordinates.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.geom.Rectangle2D

Rectangle2D.Double, Rectangle2D.Float

Field Summary

Fields inherited from class java.awt.Rectangle

height, width, x, y

Fields inherited from class java.awt.geom.Rectangle2D

OUT_BOTTOM, OUT_LEFT, OUT_RIGHT, OUT_TOP

Constructor Summary

Constructors

Constructor and Description
Track()
Track(String inName)

Method Summary

Modifier and Type	Method and Description
void	addGene(Gene2D inValue)
void	addHighlightRegion(int start, int end)
int	compareTo(Track inTrack2)
void	draw(Graphics2D g2, Strand inStrand)
void	drawXAxis(Graphics2D g2)
boolean	equals(Object o2)
Color	getAxisColor()
Color	getBackgroundColor()
BufferedImage	getBufferedImage(Strand inStrand)
String	getDescription()
int	getForwardStrandImageHeight()
Collection<Gene2D>	getGenes()
Color	getHighlightColor()
Image	getImage(Strand inStrand)
ImageMap	getImageMap(Strand inStrand)
int	getImageWidth()
Script	getJavascript()
Color	getLabelColor()
int	getLabelWidthInPixels(String inLabel)
String	getName()
int	getReverseStrandImageHeight()
BufferedImage	getXAxisBufferedImage()
boolean	hasGenesOnStrand(Strand inStrand)
void	setAxisColor(Color inValue)
void	setBackgroundColor(Color inValue)
void	setDescription(String inValue)
void	setGenes(Collection<Gene2D> inValues)
void	setHighlightColor(Color inValue)
void	setImageWidth(int inValue)
void	setLabelColor(Color inValue)
void	setLabelFont(Font inValue)
void	setName(String inValue)
void	setShowId(boolean inValue)
void	setURL(String inValue)
void	setXAxisEndValue(int inValue)
void	setXAxisStartValue(int inValue)
void	writeImageAsJpeg(OutputStream inStream, Strand inStrand)
void	writeImageAsPng(OutputStream inStream, Strand inStrand)
SVG	writeImageAsSvg(Strand inStrand)
void	writeXAxisImageAsJpeg(OutputStream inStream)

Methods inherited from class java.awt.Rectangle

add, add, add, contains, contains, contains, contains, createIntersection, createUnion, getBounds, getBounds2D, getHeight, getLocation, getSize, getWidth, getX, getY, grow, inside, intersection, intersects, isEmpty, move, outcode, reshape, resize, setBounds, setBounds, setLocation, setLocation, setRect, setSize, setSize, toString, translate, union

Methods inherited from class java.awt.geom.Rectangle2D

add, add, add, contains, contains, getPathIterator, getPathIterator, hashCode, intersect, intersects, intersectsLine, intersectsLine, outcode, setFrame, setRect, union

Methods inherited from class java.awt.geom.RectangularShape

clone, contains, contains, getCenterX, getCenterY, getFrame, getMaxX, getMaxY, getMinX, getMinY, intersects, setFrame, setFrame, setFrameFromCenter, setFrameFromCenter, setFrameFromDiagonal, setFrameFromDiagonal

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.Shape

contains, contains, contains, contains, getPathIterator, getPathIterator, intersects, intersects

Constructor Detail

Track

public Track()

Track

public Track(String inName)

Method Detail

equals

public boolean equals(Object o2)

Overrides:

equals in class Rectangle

compareTo

public int compareTo(Track inTrack2)

Specified by:

compareTo in interface Comparable<Track>

hasGenesOnStrand

public boolean hasGenesOnStrand(Strand inStrand)

addHighlightRegion

public void addHighlightRegion(int start,
                               int end)

setGenes

public void setGenes(Collection<Gene2D> inValues)

addGene

public void addGene(Gene2D inValue)

getGenes

public Collection<Gene2D> getGenes()

setName

public void setName(String inValue)

getName

public String getName()

setURL

public void setURL(String inValue)

setDescription

public void setDescription(String inValue)

getDescription

public String getDescription()

setBackgroundColor

public void setBackgroundColor(Color inValue)

getBackgroundColor

public Color getBackgroundColor()

setLabelColor

public void setLabelColor(Color inValue)

getLabelColor

public Color getLabelColor()

setAxisColor

public void setAxisColor(Color inValue)

getAxisColor

public Color getAxisColor()

setHighlightColor

public void setHighlightColor(Color inValue)

getHighlightColor

public Color getHighlightColor()

setLabelFont

public void setLabelFont(Font inValue)

setXAxisStartValue

public void setXAxisStartValue(int inValue)

setXAxisEndValue

public void setXAxisEndValue(int inValue)

getForwardStrandImageHeight

public int getForwardStrandImageHeight()

getReverseStrandImageHeight

public int getReverseStrandImageHeight()

setImageWidth

public void setImageWidth(int inValue)

getImageWidth

public int getImageWidth()

getJavascript

public Script getJavascript()

getImageMap

public ImageMap getImageMap(Strand inStrand)

setShowId

public void setShowId(boolean inValue)

draw

public void draw(Graphics2D g2,
                 Strand inStrand)

getImage

public Image getImage(Strand inStrand)

getBufferedImage

public BufferedImage getBufferedImage(Strand inStrand)

getXAxisBufferedImage

public BufferedImage getXAxisBufferedImage()

writeImageAsJpeg

public void writeImageAsJpeg(OutputStream inStream,
                             Strand inStrand)
                      throws IOException

Throws:

IOException

writeXAxisImageAsJpeg

public void writeXAxisImageAsJpeg(OutputStream inStream)
                           throws IOException

Throws:

IOException

writeImageAsPng

public void writeImageAsPng(OutputStream inStream,
                            Strand inStrand)
                     throws IOException

Throws:

IOException

writeImageAsSvg

public SVG writeImageAsSvg(Strand inStrand)

drawXAxis

public void drawXAxis(Graphics2D g2)

getLabelWidthInPixels

public int getLabelWidthInPixels(String inLabel)