Package org.biojava.bio.gui.sequence

Class BumpedRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.SequenceRendererWrapper

org.biojava.bio.gui.sequence.BumpedRenderer

All Implemented Interfaces:

Serializable, SequenceRenderer, Changeable

public class BumpedRenderer
extends SequenceRendererWrapper

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

SequenceRenderer.RendererForwarder

Field Summary

Fields inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

RENDERER

Constructor Summary

Constructors

Constructor	Description
BumpedRenderer()
BumpedRenderer(SequenceRenderer renderer)
BumpedRenderer(SequenceRenderer renderer, int leading, int trailing)

Method Summary

Modifier and Type	Method	Description
protected List	doLayer(SequenceRenderContext src, FeatureFilter filt)
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
double	getDepth(SequenceRenderContext src)	Retrieve the depth of this renderer when rendering src.
int	getLeadingPixles()
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.
int	getTrailingPixles()
protected boolean	hasListeners()	Discover if we have any listeners registered.
protected List	layer(SequenceRenderContext src)
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	setLeadingPixles(int leading)
void	setTrailingPixles(int trailing)

Methods inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getRenderer, setRenderer

Methods inherited from class org.biojava.utils.AbstractChangeable

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

Methods inherited from class java.lang.Object

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

Constructor Detail

BumpedRenderer

public BumpedRenderer()

BumpedRenderer

public BumpedRenderer(SequenceRenderer renderer)

BumpedRenderer

public BumpedRenderer(SequenceRenderer renderer,
                      int leading,
                      int trailing)

Method Detail

getLeadingPixles

public int getLeadingPixles()

setLeadingPixles

public void setLeadingPixles(int leading)

getTrailingPixles

public int getTrailingPixles()

setTrailingPixles

public void setTrailingPixles(int trailing)

hasListeners

protected boolean hasListeners()

Description copied from class: AbstractChangeable

Discover if we have any listeners registered.

Overrides:

hasListeners in class AbstractChangeable

Returns:

true if there is at least one listener

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class SequenceRendererWrapper

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

Overrides:

getDepth in class SequenceRendererWrapper

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

Overrides:

getMinimumLeader in class SequenceRendererWrapper

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

Overrides:

getMinimumTrailer in class SequenceRendererWrapper

Parameters:

src - the SequenceRenderContext to return info for

Returns:

the trailing distance of the renderer for that sequence panel

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

Overrides:

paint in class SequenceRendererWrapper

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

Overrides:

processMouseEvent in class SequenceRendererWrapper

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

layer

protected List layer(SequenceRenderContext src)

doLayer

protected List doLayer(SequenceRenderContext src,
                       FeatureFilter filt)