Package org.biojava.bio.gui.sequence

Class MultiLineRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.MultiLineRenderer

All Implemented Interfaces:

Serializable, SequenceRenderer, Changeable

Direct Known Subclasses:

AbstractPeptideDigestRenderer

public class MultiLineRenderer
extends AbstractChangeable
implements SequenceRenderer, Serializable

MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.

Author:

Matthew Pocock, Keith James

See Also:

Serialized Form

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
protected List	renderers
static ChangeType	RENDERERS

Constructor Summary

Constructors

Constructor	Description
MultiLineRenderer()

Method Summary

Modifier and Type	Method	Description
protected void	_addRenderer(SequenceRenderer renderer)
protected void	_removeRenderer(SequenceRenderer renderer)
void	addRenderer(SequenceRenderer renderer)	addRenderer adds a renderer as a new track.
void	clearRenderers()	clearRenderers removes all renderers from this renderer.
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.
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	removeRenderer(SequenceRenderer renderer)	removeRenderer removes a renderer.

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

RENDERERS

public static final ChangeType RENDERERS

renderers

protected List renderers

Constructor Detail

MultiLineRenderer

public MultiLineRenderer()

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

addRenderer

public void addRenderer(SequenceRenderer renderer)
                 throws ChangeVetoException

addRenderer adds a renderer as a new track.

Parameters:

renderer - a SequenceRenderer to add.

Throws:

ChangeVetoException - if the renderer cannot be added.

_addRenderer

protected void _addRenderer(SequenceRenderer renderer)

removeRenderer

public void removeRenderer(SequenceRenderer renderer)
                    throws ChangeVetoException

removeRenderer removes a renderer.

Parameters:

renderer - a SequenceRenderer to remove.

Throws:

ChangeVetoException - if the renderer can not be removed.

_removeRenderer

protected void _removeRenderer(SequenceRenderer renderer)

clearRenderers

public void clearRenderers()
                    throws ChangeVetoException

clearRenderers removes all renderers from this renderer.

Throws:

ChangeVetoException - if the renderers can not be cleared.

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