Package org.biojava.bio.gui.sequence

Class PairwiseFilteringRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

All Implemented Interfaces:

Serializable, PairwiseSequenceRenderer, Changeable

public class PairwiseFilteringRenderer
extends AbstractChangeable
implements PairwiseSequenceRenderer, Serializable

PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it. The renderer receives a new PairwiseRenderContext which has had both of its FeatureHolders filtered with the FeatureFilter.

Instances of this class cache up to 5 of the derived PairwiseRenderContexts. Therefore cycling through up to 5 different FeatureFilters will only be hitting the cache rather than recalculating everthing. Should the FeatureHolders themselves change, the cache will be flushed. As only the features overlapping the context's range are filtered, changing the range will also result in re-filtering.

Since:

1.2

Author:

Keith James, Matthew Pocock

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	Description
protected FeatureFilter	filter	filter is the filter applied to both FeatureHolders.
static ChangeType	FILTER	Constant FILTER indicating a change to the renderer's filter.
protected boolean	recurse	recurse indicates whether the filter should recurse through any subfeatures.
static ChangeType	RECURSE	Constant RECURSE indicating a change to the renderer's filter recursion flag.
static ChangeType	RENDERER	Constant RENDERER indicating a change to the renderer.

Constructor Summary

Constructors

Constructor	Description
PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer)	Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features.
PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer, FeatureFilter filter, boolean recurse)	Creates a new PairwiseFilteringRenderer.

Method Summary

Modifier and Type	Method	Description
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
FeatureFilter	getFilter()	getFilter returns the current filter.
boolean	getRecurse()	getRecurse returns the recursion flag of the filter.
PairwiseSequenceRenderer	getRenderer()	getRenderer return the current renderer.
protected PairwiseRenderContext	getSubContext(PairwiseRenderContext context)	getSubContext creates a new context which has FeatureHolders filtered using the current filter.
void	paint(Graphics2D g2, PairwiseRenderContext context)	paints some or all of the information about the sequence pair.
SequenceViewerEvent	processMouseEvent(PairwiseRenderContext context, MouseEvent me, List path)	processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.
void	setFilter(FeatureFilter filter)	setFilter sets the filter.
void	setRecurse(boolean recurse)	setRecurse sets the recursion flag on the filter.
void	setRenderer(PairwiseSequenceRenderer renderer)	setRenderer sets the 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

FILTER

public static final ChangeType FILTER

Constant FILTER indicating a change to the renderer's filter.

RECURSE

public static final ChangeType RECURSE

Constant RECURSE indicating a change to the renderer's filter recursion flag.

RENDERER

public static final ChangeType RENDERER

Constant RENDERER indicating a change to the renderer.

filter

protected FeatureFilter filter

filter is the filter applied to both FeatureHolders.

recurse

protected boolean recurse

recurse indicates whether the filter should recurse through any subfeatures.

Constructor Detail

PairwiseFilteringRenderer

public PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer)

Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features.

Parameters:

renderer - a PairwiseSequenceRenderer.

PairwiseFilteringRenderer

public PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer,
                                 FeatureFilter filter,
                                 boolean recurse)

Creates a new PairwiseFilteringRenderer.

Parameters:

renderer - a PairwiseSequenceRenderer.

filter - a FeatureFilter.

recurse - a boolean.

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

getRenderer

public PairwiseSequenceRenderer getRenderer()

getRenderer return the current renderer.

Returns:

a PairwiseSequenceRenderer.

setRenderer

public void setRenderer(PairwiseSequenceRenderer renderer)
                 throws ChangeVetoException

setRenderer sets the renderer.

Parameters:

renderer - a PairwiseSequenceRenderer.

Throws:

ChangeVetoException - if the change is vetoed.

getFilter

public FeatureFilter getFilter()

getFilter returns the current filter.

Returns:

a FeatureFilter.

setFilter

public void setFilter(FeatureFilter filter)
               throws ChangeVetoException

setFilter sets the filter.

Parameters:

filter - a FeatureFilter.

Throws:

ChangeVetoException - if the change is vetoed.

getRecurse

public boolean getRecurse()

getRecurse returns the recursion flag of the filter.

Returns:

a boolean.

setRecurse

public void setRecurse(boolean recurse)
                throws ChangeVetoException

setRecurse sets the recursion flag on the filter.

Parameters:

recurse - a boolean.

Throws:

ChangeVetoException - if the change is vetoed.

paint

public void paint(Graphics2D g2,
                  PairwiseRenderContext context)

Description copied from interface: PairwiseSequenceRenderer

paints some or all of the information about the sequence pair.

Specified by:

paint in interface PairwiseSequenceRenderer

Parameters:

g2 - a Graphics2D.

context - a PairwiseRenderContext encapsulating the information to be displayed.

processMouseEvent

public SequenceViewerEvent processMouseEvent(PairwiseRenderContext context,
                                             MouseEvent me,
                                             List path)

Description copied from interface: PairwiseSequenceRenderer

processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.

Specified by:

processMouseEvent in interface PairwiseSequenceRenderer

Parameters:

context - a PairwiseRenderContext.

me - a MouseEvent that caused the request.

path - a List of PairwiseSequenceRenderer instances passed through so far.

Returns:

a SequenceViewerEvent encapsulating the mouse gesture.

getSubContext

protected PairwiseRenderContext getSubContext(PairwiseRenderContext context)

getSubContext creates a new context which has FeatureHolders filtered using the current filter.

Parameters:

context - a PairwiseRenderContext.

Returns:

a PairwiseRenderContext.