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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.gui.sequence.AbiTraceRenderer
public class AbiTraceRenderer
Renders an ABI trace file as a chromatogram graph.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer |
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SequenceRenderer.RendererForwarder |
Field Summary | |
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static ChangeType |
DEPTH
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static ChangeType |
TRACE
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Constructor Summary | |
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AbiTraceRenderer()
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Method Summary | |
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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)
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void |
setTrace(ABITrace trace)
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Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final ChangeType TRACE
public static final ChangeType DEPTH
Constructor Detail |
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public AbiTraceRenderer()
Method Detail |
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public void paint(Graphics2D g, SequenceRenderContext ctxt)
SequenceRenderer
paint
in interface SequenceRenderer
g
- the Graphics2D to render toctxt
- the SequenceRenderContext that encapsulates the information to renderpublic void setTrace(ABITrace trace) throws ChangeVetoException
ChangeVetoException
public ABITrace getTrace()
public void setDepth(double depth) throws ChangeVetoException
ChangeVetoException
public double getDepth(SequenceRenderContext src)
SequenceRenderer
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.
getDepth
in interface SequenceRenderer
src
- the SequenceRenderContext to return info for
public double getMinimumLeader(SequenceRenderContext src)
SequenceRenderer
The leading distance may vary between sequence panels - for example based upon sequence length.
getMinimumLeader
in interface SequenceRenderer
src
- the SequenceRenderContext to return info for
public double getMinimumTrailer(SequenceRenderContext src)
SequenceRenderer
The trailing distance may vary between sequence panels - for example based upon sequence length.
getMinimumTrailer
in interface SequenceRenderer
src
- the SequenceRenderContext to return info for
public SequenceViewerEvent processMouseEvent(SequenceRenderContext src, MouseEvent me, List path)
SequenceRenderer
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.
processMouseEvent
in interface SequenceRenderer
src
- the SequenceRenderContext currently in scopeme
- a MouseEvent that caused this requestpath
- the List of SequenceRenderer instances passed through so far
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