Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
When adding to the toolbar from Preferences > Shortcuts
1) 'View Genomic Sequence in Sequence Viewer...' and 'View Read Sequence in Sequence Viewer...' are NOT added to toolbar when check box is selected
2) Appears that there are a set limit of spaces for main toolbar, when tools already in the bar are de-selected, the newly requested tools appear. However, it throws NegativeArraySizeException:
Exception in thread "AWT-EventQueue-0" java.lang.NegativeArraySizeException
at com.affymetrix.genoviz.datamodel.Sequence.getResidues(Sequence.java:237)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:232)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:110)
at com.affymetrix.genoviz.widget.neoseq.WrapFontColors.draw(WrapFontColors.java:51)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:128)
at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawTraversal(WrapSequence.java:450)
at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129)
at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74)
at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:450)
at com.affymetrix.genoviz.bioviews.View.draw(View.java:359)
at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869)
at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72)
at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47)
at javax.swing.JComponent.paint(Unknown Source)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1235)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JLayeredPane.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paintToOffscreen(Unknown Source)
at javax.swing.BufferStrategyPaintManager.paint(Unknown Source)
at javax.swing.RepaintManager.paint(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at java.awt.Window.paint(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.access$700(Unknown Source)
at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Attachments
Issue Links
- relates to
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BUG-651 Windows specific bugs
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- Closed
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Activity
Definitely a button number limit - you cannot make more than 9 buttons appear. If you check on a 10th, you must check off a preset to get it to appear. Also, if you check off all but 3 buttons, then start adding 6 back in, they add in weirdly - ie, first three fill in the first 3 spots, then a previously checked then a new, then a previous then a new, then a previous then a new.... very odd.
AHA! This is a problem BEFORE loading a species/genome. After choosing A. thal from home screen, I could add more buttons! No, that's not right either - it looks like you can add buttons while it is loading data, but NOT while the main scree is static... VERY weird... Once loaded, I cannot add new numbers of buttons - it did increase the set number though...
I never got it to throw the exception.
Fixed the odd behavior in r13659.
But I don't see any button limits except when it reaches to right where selection info is. And even then you can continue to add but it would start covering selection info.
Start IGB from a clean build on a windows computer. WithOUT selecting a species, open preferences and start checking on ~5 buttons. No buttons are added. NOW select a species from the clickable pictures of the start page. Notice how now the 5 selected buttons appear. After all tracks are fully loaded and IGB is no longer trying to load anything select 5 more. They do not appear. Add a new track to the DMT using the available data panel. As soon as a track is selected, all selected buttons appear. This happens consistently on my Windows 7 machine.
Fixed in r13694.
Cannot reproduce. Can you?