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  1. Jalview
  2. JAL-2697

Exceptions and problems working with wrapped alignments (in develop/2.10.3)

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Cannot Reproduce
    • Affects Version/s: None
    • Fix Version/s: 2.10.3
    • Component/s: gui
    • Labels:

      Description

      While testing JAL-2665 I picked up some exceptions while working with wrapped alignments. I was unable to reproduce any of these. Also see attached screenshot which occurred after printing (to pdf) the wrapped alignment - no exceptions were thrown and the alignment was printed correctly.

      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at jalview.renderer.AnnotationRenderer.drawComponent(AnnotationRenderer.java:655)
      at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:725)
      at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
      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.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:76)
      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:76)
      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)


      Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
      at java.util.Vector$Itr.checkForComodification(Vector.java:1184)
      at java.util.Vector$Itr.remove(Vector.java:1150)
      at sun.java2d.Spans.sortAndCollapse(Spans.java:186)
      at sun.java2d.Spans.add(Spans.java:77)
      at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1801)
      at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1777)
      at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1767)
      at sun.print.PeekGraphics.drawString(PeekGraphics.java:1470)
      at sun.print.PeekGraphics.drawString(PeekGraphics.java:861)
      at jalview.gui.SequenceRenderer.drawText(SequenceRenderer.java:423)
      at jalview.gui.SequenceRenderer.drawSequence(SequenceRenderer.java:186)
      at jalview.gui.SeqCanvas.draw(SeqCanvas.java:941)
      at jalview.gui.SeqCanvas.drawPanel(SeqCanvas.java:837)
      at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:715)
      at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
      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.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:76)
      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:76)
      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)

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            Assignee:
            jprocter Jim Procter
            Reporter:
            kmourao Kira Mourão
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              Dates

              Created:
              Updated:
              Resolved: