org.biojava.bio.gui.sequence

Class SixFrameRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.SixFrameRenderer

All Implemented Interfaces:

SequenceRenderer, Changeable

public class SixFrameRenderer
extends AbstractChangeable
implements SequenceRenderer

Class that handles drawing in six frames for other classes. Suitable for use with CDS features particularly.

Partly based on Matthew Pocock's ZiggyFeatureRenderer.

Author:

David Huen

Nested Class Summary

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

SequenceRenderer.RendererForwarder

Constructor Summary

Constructors

Constructor and Description
SixFrameRenderer()

Method Summary

Methods

Modifier and Type	Method and Description
void	drawLine(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) draws required bar in correct translation frame.
double	getBlockWidth()
double	getDepth(SequenceRenderContext src) Retrieve the depth of this renderer when rendering src.
Paint	getFill()
double	getMinimumLeader(SequenceRenderContext src) Retrieve the minimum leading distance for this renderer when rendering src.
double	getMinimumTrailer(SequenceRenderContext src) Retrieve the minimum trailing distance for this renderer when rendering src.
Paint	getOutline()
void	paint(Graphics2D g, SequenceRenderContext src) Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
SequenceViewerEvent	processMouseEvent(SequenceRenderContext src, MouseEvent me, List path) Produce a SequenceViewerEvent in response to a mouse gesture.
void	renderLocation(Graphics2D g, SequenceRenderContext src, Location loc) Render another "exon" in the correct translation frame.
List	sequenceExtentOfPixels(SequenceRenderContext src)
void	setBlockWidth(double width)
void	setFill(Paint p)
void	setOutline(Paint p)
void	startZiggy(StrandedFeature.Strand strand) Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.
void	startZiggy(StrandedFeature.Strand strand, int phase) This method is called to initialise the renderer for a spliced transcript.

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

Constructor Detail

SixFrameRenderer

public SixFrameRenderer()

Method Detail

getDepth

public double getDepth(SequenceRenderContext src)

Description copied from interface: SequenceRenderer

Retrieve the depth of this renderer when rendering src.

The depth may vary between sequence panels - for example based upon sequence length. Each line of information in the SequenceRendererContext only renders a region of the sequence. The depth for one complete line may be different from that for another due to the sequence having more or less information in that region to show. For example, a feature renderer implementation may chose to collapse down to a depth of zero pixels if there are no features to render within a region.

Specified by:

getDepth in interface SequenceRenderer

Parameters:

src - the SequenceRenderContext to return info for

Returns:

the depth of the renderer for that sequence panel

getMinimumLeader

public double getMinimumLeader(SequenceRenderContext src)

Description copied from interface: SequenceRenderer

Retrieve the minimum leading distance for this renderer when rendering src.

The leading distance may vary between sequence panels - for example based upon sequence length.

Specified by:

getMinimumLeader in interface SequenceRenderer

Parameters:

src - the SequenceRenderContext to return info for

Returns:

the leading distance of the renderer for that sequence panel

getMinimumTrailer

public double getMinimumTrailer(SequenceRenderContext src)

Description copied from interface: SequenceRenderer

Retrieve the minimum trailing distance for this renderer when rendering src.

The trailing distance may vary between sequence panels - for example based upon sequence length.

Specified by:

getMinimumTrailer in interface SequenceRenderer

Parameters:

src - the SequenceRenderContext to return info for

Returns:

the trailing distance of the renderer for that sequence panel

setFill

public void setFill(Paint p)
             throws ChangeVetoException

Throws:

ChangeVetoException

getFill

public Paint getFill()

setOutline

public void setOutline(Paint p)
                throws ChangeVetoException

Throws:

ChangeVetoException

getOutline

public Paint getOutline()

setBlockWidth

public void setBlockWidth(double width)
                   throws ChangeVetoException

Throws:

ChangeVetoException

getBlockWidth

public double getBlockWidth()

startZiggy

public void startZiggy(StrandedFeature.Strand strand)

Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.

startZiggy

public void startZiggy(StrandedFeature.Strand strand,
              int phase)

This method is called to initialise the renderer for a spliced transcript.

Parameters:

strand - the strand that the transcipt is on.

phase - the initial translation phase of transcript coding region.

renderLocation

public void renderLocation(Graphics2D g,
                  SequenceRenderContext src,
                  Location loc)

Render another "exon" in the correct translation frame.

sequenceExtentOfPixels

public List sequenceExtentOfPixels(SequenceRenderContext src)

drawLine

public void drawLine(Graphics2D g,
            SequenceRenderContext src,
            int base,
            StrandedFeature.Strand strand)

draws required bar in correct translation frame.

Parameters:

base - the sequence coordinate of the bar.

strand - strand that the bar annotates.

paint

public void paint(Graphics2D g,
         SequenceRenderContext src)

Description copied from interface: SequenceRenderer

Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.

Specified by:

paint in interface SequenceRenderer

Parameters:

g - the Graphics2D to render to

src - the SequenceRenderContext that encapsulates the information to render

processMouseEvent

public SequenceViewerEvent processMouseEvent(SequenceRenderContext src,
                                    MouseEvent me,
                                    List path)

Description copied from interface: SequenceRenderer

Produce a SequenceViewerEvent in response to a mouse gesture.

A SequenceRenderer that performs any form of coordinate remapping should ensure that it appropriately transforms the mouse event. However, in the SequenceViewerEvent returned, the MouseEvent should be in untransformed coordinates.

The SequenceRenderer implementation should append itself to the path list before constructing the SequenceViewerEvent.

Specified by:

processMouseEvent in interface SequenceRenderer

Parameters:

src - the SequenceRenderContext currently in scope

me - a MouseEvent that caused this request

path - the List of SequenceRenderer instances passed through so far

Returns:

a SequenceViewerEvent encapsulating the mouse gesture