com.hfg.graphics

Class Gene2D

java.lang.Object

java.awt.geom.RectangularShape

java.awt.geom.Rectangle2D

java.awt.Rectangle

com.hfg.graphics.Gene2D

All Implemented Interfaces:

Shape, Serializable, Cloneable, Comparable<Gene2D>

public class Gene2D
extends Rectangle
implements Comparable<Gene2D>

Simple 2D representation of a gene.

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
Gene2D()

Method Summary

Modifier and Type	Method and Description
void	addExon(Exon inValue)
void	addURL(Link inValue) Add a URL to the gene.
int	compareTo(Gene2D gene2)
void	draw(Graphics2D g2)
boolean	equals(Object o2)
Color	getColor()
String	getDescription()
int	getEndLocation()
List<Exon>	getExons()
int	getHeightInPixels()
String	getId()
int	getLabelWidthInPixels()
int	getLeft() The leftmost basepair of the gene (the start location if the gene is on the forward strand or the end location if the gene is on the reverse strand).
int	getRight() The rightmost basepair of the gene (the end location if the gene is on the forward strand or the start location if the gene is on the reverse strand).
int	getScaledWidthInPixels()
SeqMappingCoverage	getSeqMappingCoverage()
boolean	getShowId()
NCBITaxon	getSpecies()
int	getStartLocation() Basepair location of the start of the gene.
Strand	getStrand()
String	getTooltipContent()
List<Link>	getURLs()
boolean	inDisplayRegion()
void	setColor(Color inValue)
void	setDescription(String inValue)
void	setDisplayRegion(int inDisplayStart, int inDisplayEnd)
void	setEndLocation(int inValue)
void	setHeightInPixels(int inValue)
void	setId(String inValue)
void	setLabelFont(Font inValue)
void	setSeqMappingCoverage(SeqMappingCoverage inValue)
void	setShowId(boolean inValue)
void	setSpecies(NCBITaxon inValue)
void	setStartLocation(int inValue)
void	setStrand(Strand inValue)
void	setXScalingFactor(double inValue)
SvgNode	toSVG()

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

Gene2D

public Gene2D()

Method Detail

addExon

public void addExon(Exon inValue)

getExons

public List<Exon> getExons()

setId

public void setId(String inValue)

getId

public String getId()

setDescription

public void setDescription(String inValue)

getDescription

public String getDescription()

setSeqMappingCoverage

public void setSeqMappingCoverage(SeqMappingCoverage inValue)

getSeqMappingCoverage

public SeqMappingCoverage getSeqMappingCoverage()

setSpecies

public void setSpecies(NCBITaxon inValue)

getSpecies

public NCBITaxon getSpecies()

addURL

public void addURL(Link inValue)

Add a URL to the gene. If more than one URL is defined, a popup menu will be shown.

Parameters:

inValue - the link to associate with the gene

getURLs

public List<Link> getURLs()

getStartLocation

public int getStartLocation()

Basepair location of the start of the gene.

Returns:

the 1-based location

setStartLocation

public void setStartLocation(int inValue)

getEndLocation

public int getEndLocation()

setEndLocation

public void setEndLocation(int inValue)

getLeft

public int getLeft()

The leftmost basepair of the gene (the start location if the gene is on the forward strand or the end location if the gene is on the reverse strand).

Returns:

the 1-based left location

getRight

public int getRight()

The rightmost basepair of the gene (the end location if the gene is on the forward strand or the start location if the gene is on the reverse strand).

Returns:

the 1-based right location

getStrand

public Strand getStrand()

setStrand

public void setStrand(Strand inValue)

setColor

public void setColor(Color inValue)

getColor

public Color getColor()

setLabelFont

public void setLabelFont(Font inValue)

setXScalingFactor

public void setXScalingFactor(double inValue)

setShowId

public void setShowId(boolean inValue)

getShowId

public boolean getShowId()

setDisplayRegion

public void setDisplayRegion(int inDisplayStart,
                             int inDisplayEnd)

inDisplayRegion

public boolean inDisplayRegion()

toSVG

public SvgNode toSVG()

draw

public void draw(Graphics2D g2)

getScaledWidthInPixels

public int getScaledWidthInPixels()

setHeightInPixels

public void setHeightInPixels(int inValue)

getHeightInPixels

public int getHeightInPixels()

getLabelWidthInPixels

public int getLabelWidthInPixels()

getTooltipContent

public String getTooltipContent()

equals

public boolean equals(Object o2)

Overrides:

equals in class Rectangle

compareTo

public int compareTo(Gene2D gene2)

Specified by:

compareTo in interface Comparable<Gene2D>