org.biojava.bio.gui.sequence
Class AbiTraceRenderer

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

public class AbiTraceRenderer
extends AbstractChangeable
implements SequenceRenderer

Renders an ABI trace file as a chromatogram graph.

Author:
Matthew Pocock, Mark Schreiber

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.gui.sequence.SequenceRenderer
SequenceRenderer.RendererForwarder
 
Field Summary
static ChangeType DEPTH
           
static ChangeType TRACE
           
 
Constructor Summary
AbiTraceRenderer()
           
 
Method Summary
 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.
 ABITrace getTrace()
           
 void paint(java.awt.Graphics2D g, SequenceRenderContext ctxt)
          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 setDepth(double depth)
           
 void setTrace(ABITrace trace)
           
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

TRACE

public static final ChangeType TRACE

DEPTH

public static final ChangeType DEPTH
Constructor Detail

AbiTraceRenderer

public AbiTraceRenderer()
Method Detail

paint

public void paint(java.awt.Graphics2D g,
                  SequenceRenderContext ctxt)
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
ctxt - the SequenceRenderContext that encapsulates the information to render

setTrace

public void setTrace(ABITrace trace)
              throws ChangeVetoException
Throws:
ChangeVetoException

getTrace

public ABITrace getTrace()

setDepth

public void setDepth(double depth)
              throws ChangeVetoException
Throws:
ChangeVetoException

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

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