org.biojava.bio.gui.sequence

Class PairwiseDiagonalRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

All Implemented Interfaces:

java.io.Serializable, PairwiseSequenceRenderer, Changeable

public class PairwiseDiagonalRenderer
extends AbstractChangeable
implements PairwiseSequenceRenderer, java.io.Serializable

PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line. The effect produced is similar to a dotplot. This implementation requires that these regions be represented by SimilarityPairFeatures.

Drawing outside the visible area using a range of valid doubles may cause Java to hang (Sun JDK 1.3.1 on Linux, Compaq JDK 1.3.1 on Tru64, but not Sun JDK 1.4.0-beta2-b77 on Linux). I got round this by manual clipping of the lines to the clip area. The code uses an implementation of the Cohen-Sutherland line-clipping algorithm which clips lines to within a rectangle.

The clipping code is taken from Computer Graphics for Java Programmers by Leen Ammeraal (1998, ISBN 0-471-98142-7) and cosmetically altered to support Java2D objects. Any bugs introduced are my responsibility.

Since:

1.2

Author:

Keith James, Leen Ammeraal

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer

PairwiseSequenceRenderer.PairwiseRendererForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected java.awt.geom.Line2D.Float	line line is the line to be drawn for each feature.
protected java.awt.Paint	outline outline is the line colour.
static ChangeType	OUTLINE Constant OUTLINE indicating a change to the fill of the features.

Constructor Summary

Constructors

Constructor and Description
PairwiseDiagonalRenderer() Creates a new PairwiseDiagonalRenderer which will draw black lines.
PairwiseDiagonalRenderer(java.awt.Paint outline) Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint.

Method Summary

Modifier and Type	Method and Description
java.awt.Paint	getOutline() getOutline returns the colour used to draw the lines.
void	paint(java.awt.Graphics2D g2, PairwiseRenderContext context) paint renders the feature as a simple line.
SequenceViewerEvent	processMouseEvent(PairwiseRenderContext context, java.awt.event.MouseEvent me, java.util.List path) processMouseEvent acts on a mouse gesture.
void	setOutline(java.awt.Paint outline) setOutline sets the the colour used to draw the lines.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Field Detail

OUTLINE

public static final ChangeType OUTLINE

Constant OUTLINE indicating a change to the fill of the features.

line

protected java.awt.geom.Line2D.Float line

line is the line to be drawn for each feature.

outline

protected java.awt.Paint outline

outline is the line colour.

Constructor Detail

PairwiseDiagonalRenderer

public PairwiseDiagonalRenderer()

Creates a new PairwiseDiagonalRenderer which will draw black lines.

PairwiseDiagonalRenderer

public PairwiseDiagonalRenderer(java.awt.Paint outline)

Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint.

Parameters:

outline - a Paint.

Method Detail

paint

public void paint(java.awt.Graphics2D g2,
                  PairwiseRenderContext context)

paint renders the feature as a simple line.

Specified by:

paint in interface PairwiseSequenceRenderer

Parameters:

g2 - a Graphics2D.

context - a PairwiseRenderContext.

getOutline

public java.awt.Paint getOutline()

getOutline returns the colour used to draw the lines.

Returns:

a Paint.

setOutline

public void setOutline(java.awt.Paint outline)
                throws ChangeVetoException

setOutline sets the the colour used to draw the lines.

Parameters:

outline - a Paint.

Throws:

ChangeVetoException - if an error occurs.

processMouseEvent

public SequenceViewerEvent processMouseEvent(PairwiseRenderContext context,
                                             java.awt.event.MouseEvent me,
                                             java.util.List path)

processMouseEvent acts on a mouse gesture. The target object is a FeatureHolder containing the features on the primary sequence which contain the mouse pointer.

Specified by:

processMouseEvent in interface PairwiseSequenceRenderer

Parameters:

context - a PairwiseRenderContext.

me - a MouseEvent.

path - a List.

Returns:

a SequenceViewerEvent.