[Biojava-l] How to Use SixFrameRenderer and related classes? (fwd)

[hywang]

Hi, 

Ok. 

I had just test the codes again and found that among the code to set 
sixframe renderer below: 

   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
0, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
1, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
2, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
0, StrandedFeature.NEGATIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
1, StrandedFeature.NEGATIVE)));
   //********erro seems exist the line below*****
   zml.addRenderer(new StopRenderer(sixFramePane, 2, 
StrandedFeature.NEGATIVE)); 

The bug seems lies in the line:
   zml.addRenderer(new StopRenderer(sixFramePane, 2, 
StrandedFeature.NEGATIVE)); 

I have committed the lines of code one by one ,and the error info 

won't disappear until I commented the that line codes. I wonder if 

it is beacause it's difference with others, so then I change it into: 

zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 

2, StrandedFeature.NEGATIVE))); 

But the same error info still came out, I have read the code of 

sixframerenderer.java , but still no idea to me.;-( 

Thanks a lot, and waiting for your help ;-). 

Haiyan Wang, 

The whole error info is : 

java.lang.IndexOutOfBoundsException: Index out of range: 0
	at 
org.biojava.bio.seq.io.SubArraySymbolList.symbolAt(SubArraySymbolList.java:7 
7)
	at 
org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:101)
	at org.biojava.bio.gui.sequence.StopRenderer.isStop(StopRenderer.java:123)
	at 
org.biojava.bio.gui.sequence.StopRenderer.renderOneFrame(StopRenderer.java:1 
61)
	at org.biojava.bio.gui.sequence.StopRenderer.paint(StopRenderer.java:197)
	at 
org.biojava.bio.gui.sequence.OverlayRendererWrapper.paint(OverlayRendererWra 
pper.java:145)
	at 
org.biojava.bio.gui.sequence.LayeredRenderer.paint(LayeredRenderer.java:186)
	at 
org.biojava.bio.gui.sequence.MultiLineRenderer.paint(MultiLineRenderer.java: 
186)
	at 
org.biojava.bio.gui.sequence.SequencePanel.paintComponent(SequencePanel.java 
:471)
	at javax.swing.JComponent.paint(JComponent.java:808)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JViewport.paint(JViewport.java:707)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4771)
	at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4724)
	at javax.swing.JComponent._paintImmediately(JComponent.java:4668)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4477)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:410)
	at 
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQu 
eueUtilities.java:117)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:178)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:448)
	at 
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja 
va:197)
	at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java 
:150)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:144)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:136)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:99)
java.lang.IndexOutOfBoundsException: Index out of range: 0
	at 
org.biojava.bio.seq.io.SubArraySymbolList.symbolAt(SubArraySymbolList.java:7 
7)
	at 
org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:101)
	at org.biojava.bio.gui.sequence.StopRenderer.isStop(StopRenderer.java:123)
	at 
org.biojava.bio.gui.sequence.StopRenderer.renderOneFrame(StopRenderer.java:1 
61)
	at org.biojava.bio.gui.sequence.StopRenderer.paint(StopRenderer.java:197)
	at 
org.biojava.bio.gui.sequence.OverlayRendererWrapper.paint(OverlayRendererWra 
pper.java:145)
	at 
org.biojava.bio.gui.sequence.LayeredRenderer.paint(LayeredRenderer.java:186)
	at 
org.biojava.bio.gui.sequence.MultiLineRenderer.paint(MultiLineRenderer.java: 
186)
	at 
org.biojava.bio.gui.sequence.SequencePanel.paintComponent(SequencePanel.java 
:471)
	at javax.swing.JComponent.paint(JComponent.java:808)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JViewport.paint(JViewport.java:707)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1021)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1021)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1021)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1021)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paint(JComponent.java:817)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:552)
	at javax.swing.JComponent.paintChildren(JComponent.java:647)
	at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4778)
	at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4724)
	at javax.swing.JComponent.paint(JComponent.java:798)
	at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:21)
	at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60)
	at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97)
	at java.awt.Container.paint(Container.java:1309)
	at sun.awt.RepaintArea.paint(RepaintArea.java:177)
	at sun.awt.windows.WComponentPeer.handleEvent(WComponentPeer.java:260)
	at java.awt.Component.dispatchEventImpl(Component.java:3699)
	at java.awt.Container.dispatchEventImpl(Container.java:1623)
	at java.awt.Window.dispatchEventImpl(Window.java:1590)
	at java.awt.Component.dispatchEvent(Component.java:3480)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:450)
	at 
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja 
va:197)
	at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java 
:150)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:144)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:136)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:99) 

 

 

 

 

 

 

 

 

 

David Huen wrote: 

> On Sat, 2 Aug 2003, hywang wrote:  
> 
> Could we have the whole stack trace please?  The top end seems missing so
> I don't even know the Exception thrown.  
>