Class SixFrameRenderer
- All Implemented Interfaces:
SequenceRenderer
,Changeable
Partly based on Matthew Pocock's ZiggyFeatureRenderer.
- Author:
- David Huen
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer
SequenceRenderer.RendererForwarder
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
drawLine
(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) draws required bar in correct translation frame.double
double
Retrieve the depth of this renderer when rendering src.getFill()
double
Retrieve the minimum leading distance for this renderer when rendering src.double
Retrieve the minimum trailing distance for this renderer when rendering src.void
paint
(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.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) Produce a SequenceViewerEvent in response to a mouse gesture.void
renderLocation
(Graphics2D g, SequenceRenderContext src, Location loc) Render another "exon" in the correct translation frame.void
setBlockWidth
(double width) void
void
setOutline
(Paint p) void
startZiggy
(StrandedFeature.Strand strand) Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.void
startZiggy
(StrandedFeature.Strand strand, int phase) This method is called to initialise the renderer for a spliced transcript.Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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SixFrameRenderer
public SixFrameRenderer()
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Method Details
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getDepth
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 interfaceSequenceRenderer
- Parameters:
src
- the SequenceRenderContext to return info for- Returns:
- the depth of the renderer for that sequence panel
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getMinimumLeader
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 interfaceSequenceRenderer
- Parameters:
src
- the SequenceRenderContext to return info for- Returns:
- the leading distance of the renderer for that sequence panel
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getMinimumTrailer
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 interfaceSequenceRenderer
- Parameters:
src
- the SequenceRenderContext to return info for- Returns:
- the trailing distance of the renderer for that sequence panel
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setFill
- Throws:
ChangeVetoException
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getFill
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setOutline
- Throws:
ChangeVetoException
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getOutline
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setBlockWidth
- Throws:
ChangeVetoException
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getBlockWidth
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startZiggy
Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature. -
startZiggy
This method is called to initialise the renderer for a spliced transcript.- Parameters:
strand
- the strand that the transcipt is on.phase
- the initial translation phase of transcript coding region.
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renderLocation
Render another "exon" in the correct translation frame. -
sequenceExtentOfPixels
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drawLine
public void drawLine(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) draws required bar in correct translation frame.- Parameters:
base
- the sequence coordinate of the bar.strand
- strand that the bar annotates.
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paint
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 interfaceSequenceRenderer
- Parameters:
g
- the Graphics2D to render tosrc
- the SequenceRenderContext that encapsulates the information to render
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processMouseEvent
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 interfaceSequenceRenderer
- Parameters:
src
- the SequenceRenderContext currently in scopeme
- a MouseEvent that caused this requestpath
- the List of SequenceRenderer instances passed through so far- Returns:
- a SequenceViewerEvent encapsulating the mouse gesture
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