org.biojava.bio.gui.sequence

Class AbiTraceRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.AbiTraceRenderer

All Implemented Interfaces:

SequenceRenderer, Changeable

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/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer

SequenceRenderer.RendererForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	DEPTH
static ChangeType	TRACE

Constructor Summary

Constructors

Constructor and Description
AbiTraceRenderer()

Method Summary

Methods

Modifier and Type	Method and Description
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(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, MouseEvent me, 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, 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(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,
                                    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