org.biojava.bio.gui.sequence
Class FeatureBlockSequenceRenderer

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
All Implemented Interfaces:
Changeable, SequenceRenderer

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 inherited from class org.biojava.bio.gui.sequence.SequenceRenderer
SequenceRenderer.RendererForwarder
 
Field Summary
static ChangeType FEATURE_COLLAPSING
           
static ChangeType FEATURE_RENDERER
           
 
Constructor Summary
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
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(java.awt.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, java.awt.event.MouseEvent me, java.util.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, 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

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(java.awt.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,
                                             java.awt.event.MouseEvent me,
                                             java.util.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