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  1. Jalview
  2. JAL-2065

Catastrophic NPE during redraw with show non-conserved and group-based consensus

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.9, 2.9.0b1, 2.9.0b2
    • Fix Version/s: 2.10.0
    • Component/s: renderer
    • Labels:
      None
    • Environment:
      Java version: 1.8.0_77
      x86_64 Mac OS X 10.10.5
      Jalview Version: 2.9.0b2 (webstart git-commit:f92b601 [Release_2_9_0b1_Branch])

      Description

      Problem due to group consensus lines not extending the full width of the alignment.

      To reproduce:
      1. import feredoxin alignment.
      2. create a group that does not cover the full extent of the alignment (say columns 2-45)
      3. Select Annotations->Autocalculated->Group Consensus'
      4. Select Format->Show nonconserved

      NPE like appear on each redraw:
      Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
      at jalview.gui.SequenceRenderer.getDisplayChar(SequenceRenderer.java:450)
      at jalview.gui.SequenceRenderer.drawText(SequenceRenderer.java:420)
      at jalview.gui.SequenceRenderer.drawSequence(SequenceRenderer.java:194)
      at jalview.gui.SeqCanvas.draw(SeqCanvas.java:720)
      at jalview.gui.SeqCanvas.drawPanel(SeqCanvas.java:646)
      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.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)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated:
              Resolved: