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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.gui.sequence.SequenceRendererWrapper
org.biojava.bio.gui.sequence.GappedRenderer
public class GappedRenderer
A renderer that will display a gapped sequence as a discontinuous series of regions.
Each ungapped block in the gapped symbol list will be displayed as a contiguous region by this renderer. Where there are gaps, this renderer will display nothing. Then, when the gaps are over, it will continue to render the ungapped sequence. This has the effect of snapping the image of the ungapped sequence where there are gaps, so as to allow it to be viewed in the gapped co-ordinate system.
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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Fields inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper |
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RENDERER |
Constructor Summary | |
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GappedRenderer()
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GappedRenderer(SequenceRenderer renderer)
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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. |
protected SequenceRenderContext |
makeContext(SequenceRenderContext src,
RangeLocation loc)
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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. |
Methods inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper |
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getChangeSupport, getRenderer, processMouseEvent, setRenderer |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, 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 |
Constructor Detail |
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public GappedRenderer()
public GappedRenderer(SequenceRenderer renderer)
Method Detail |
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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
getDepth
in class SequenceRendererWrapper
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
getMinimumLeader
in class SequenceRendererWrapper
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
getMinimumTrailer
in class SequenceRendererWrapper
src
- the SequenceRenderContext to return info for
public void paint(Graphics2D g, SequenceRenderContext src)
SequenceRenderer
paint
in interface SequenceRenderer
paint
in class SequenceRendererWrapper
g
- the Graphics2D to render tosrc
- the SequenceRenderContext that encapsulates the information to renderprotected SequenceRenderContext makeContext(SequenceRenderContext src, RangeLocation loc)
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