Details
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Type: Bug
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Status: Closed
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Priority: Minor
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Resolution: Fixed
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Affects Version/s: 2.10.2b1
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Component/s: None
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Labels:
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Environment:Jalview Version: 2.10.2b1 Next-Release Branch Build
Jalview Installation: webstart git-commit:f057bbd [releases/Release_2_10_2b1_Branch]
Build Date: 04 September 2017
Java version: 1.8.0_144
x86_64 Mac OS X 10.10.5
Description
Doing the following on 2.10.2b1 rc build :
1. import example uniref50 - alignment window should be default size (ie just a bit bigger than the alignment)
2. Set fontsize to something very large (e.g. 45 points)
The sequence and annotation labels are now offset relative to the sequence and annotation rows.
3. Change fontsize again - to something small (e.g. 5)
I noticed an exception in fastpaint:
File format identified as Fasta
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
at jalview.gui.SeqCanvas.fastPaint(SeqCanvas.java:300)
at jalview.gui.SeqCanvas.propertyChange(SeqCanvas.java:1356)
at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:283)
at jalview.viewmodel.ViewportRanges.setStartEndRes(ViewportRanges.java:166)
at jalview.viewmodel.ViewportRanges.setViewportStartAndWidth(ViewportRanges.java:345)
at jalview.gui.AlignmentPanel.adjustmentValueChanged(AlignmentPanel.java:760)
at javax.swing.JScrollBar.fireAdjustmentValueChanged(JScrollBar.java:705)
at javax.swing.JScrollBar.access$100(JScrollBar.java:81)
at javax.swing.JScrollBar$ModelListener.stateChanged(JScrollBar.java:727)
at javax.swing.DefaultBoundedRangeModel.fireStateChanged(DefaultBoundedRangeModel.java:364)
at javax.swing.DefaultBoundedRangeModel.setRangeProperties(DefaultBoundedRangeModel.java:302)
at javax.swing.JScrollBar.setValues(JScrollBar.java:623)
at jalview.gui.AlignmentPanel.setScrollValues(AlignmentPanel.java:725)
at jalview.gui.AlignmentPanel.paintComponent(AlignmentPanel.java:891)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
1. import example uniref50 - alignment window should be default size (ie just a bit bigger than the alignment)
2. Set fontsize to something very large (e.g. 45 points)
The sequence and annotation labels are now offset relative to the sequence and annotation rows.
3. Change fontsize again - to something small (e.g. 5)
I noticed an exception in fastpaint:
File format identified as Fasta
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
at jalview.gui.SeqCanvas.fastPaint(SeqCanvas.java:300)
at jalview.gui.SeqCanvas.propertyChange(SeqCanvas.java:1356)
at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:283)
at jalview.viewmodel.ViewportRanges.setStartEndRes(ViewportRanges.java:166)
at jalview.viewmodel.ViewportRanges.setViewportStartAndWidth(ViewportRanges.java:345)
at jalview.gui.AlignmentPanel.adjustmentValueChanged(AlignmentPanel.java:760)
at javax.swing.JScrollBar.fireAdjustmentValueChanged(JScrollBar.java:705)
at javax.swing.JScrollBar.access$100(JScrollBar.java:81)
at javax.swing.JScrollBar$ModelListener.stateChanged(JScrollBar.java:727)
at javax.swing.DefaultBoundedRangeModel.fireStateChanged(DefaultBoundedRangeModel.java:364)
at javax.swing.DefaultBoundedRangeModel.setRangeProperties(DefaultBoundedRangeModel.java:302)
at javax.swing.JScrollBar.setValues(JScrollBar.java:623)
at jalview.gui.AlignmentPanel.setScrollValues(AlignmentPanel.java:725)
at jalview.gui.AlignmentPanel.paintComponent(AlignmentPanel.java:891)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Attachments
Issue Links
- related with
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JAL-2511 Sequence ids lose vertical position during middle mouse vertical drag
- Closed