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 final 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 final ChangeType

RECURSE

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

static final 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 Details
- 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 Details
- 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 Details
- 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.

Class PairwiseFilteringRenderer

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Field Details

FILTER

RECURSE

RENDERER

filter

recurse

Constructor Details

PairwiseFilteringRenderer

PairwiseFilteringRenderer

Method Details

getChangeSupport

getRenderer

setRenderer

getFilter

setFilter

getRecurse

setRecurse

paint

processMouseEvent

getSubContext