Package org.biojava.bio.gui.sequence

Class FeatureBlockSequenceRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

All Implemented Interfaces:

SequenceRenderer, Changeable

public class FeatureBlockSequenceRenderer
extends AbstractChangeable
implements SequenceRenderer

FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering. It is a SequenceRenderer which iterates through a Sequence's Features and makes method calls on a FeatureRenderer.

Author:

Matthew Pocock, Keith James, Thomas Down

Nested Class Summary

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

SequenceRenderer.RendererForwarder

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	FEATURE_COLLAPSING
static ChangeType	FEATURE_RENDERER

Constructor Summary

Constructors

Constructor	Description
FeatureBlockSequenceRenderer()	Creates a new FeatureBlockSequenceRenderer which uses a BasicFeatureRenderer as its renderer.
FeatureBlockSequenceRenderer(FeatureRenderer fRend)	Creates a new FeatureBlockSequenceRenderer which uses the specified FeatureRenderer.

Method Summary

Modifier and Type	Method	Description
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
boolean	getCollapsing()	Returns true if this class collapses to zero depth when there are no visible features.
double	getDepth(SequenceRenderContext src)	Retrieve the depth of this renderer when rendering src.
FeatureRenderer	getFeatureRenderer()	getFeatureRenderer returns the currently active renderer.
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.
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	setCollapsing(boolean b)	Specifies if the renderer should collapse to zero depth when no features are visible (default true).
void	setFeatureRenderer(FeatureRenderer renderer)	setFeatureRenderer sets the renderer to be used.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

FEATURE_RENDERER

public static ChangeType FEATURE_RENDERER

FEATURE_COLLAPSING

public static ChangeType FEATURE_COLLAPSING

Constructor Detail

FeatureBlockSequenceRenderer

public FeatureBlockSequenceRenderer()

Creates a new FeatureBlockSequenceRenderer which uses a BasicFeatureRenderer as its renderer.

FeatureBlockSequenceRenderer

public FeatureBlockSequenceRenderer(FeatureRenderer fRend)

Creates a new FeatureBlockSequenceRenderer which uses the specified FeatureRenderer.

Parameters:

fRend - a FeatureRenderer.

Method Detail

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 AbstractChangeable

getFeatureRenderer

public FeatureRenderer getFeatureRenderer()

getFeatureRenderer returns the currently active renderer.

Returns:

a FeatureRenderer.

setFeatureRenderer

public void setFeatureRenderer(FeatureRenderer renderer)
                        throws ChangeVetoException

setFeatureRenderer sets the renderer to be used.

Parameters:

renderer - a FeatureRenderer.

Throws:

ChangeVetoException - if the renderer can not be changed.

setCollapsing

public void setCollapsing(boolean b)
                   throws ChangeVetoException

Specifies if the renderer should collapse to zero depth when no features are visible (default true).

Throws:

ChangeVetoException

Since:

1.3

getCollapsing

public boolean getCollapsing()

Returns true if this class collapses to zero depth when there are no visible features.

Since:

1.3

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

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