Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2238

Cannot create groups from a tree on alignment with t-coffee scores

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.9.0b2
    • Fix Version/s: 2.10.0
    • Component/s: None
    • Labels:
      None

      Description

      An exception is raised and rendering of the alignment window breaks when trying to define subgroups on an alignment when t-coffee shading is enabled.

      To reproduce:
      1. import examples/uniref50.fa
      2. Add examples/uniref50.score_ascii (drag and drop or load annotations)
      3. Calculate a tree
      4. click on the tree to create subgroups.

      Exception is:

      Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
      at jalview.schemes.TCoffeeColourScheme.alignmentChanged(TCoffeeColourScheme.java:90)
      at jalview.schemes.TCoffeeColourScheme.<init>(TCoffeeColourScheme.java:71)
      at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:514)
      at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:428)
      at jalview.gui.TreeCanvas.colourGroups(TreeCanvas.java:962)
      at jalview.gui.TreeCanvas.mousePressed(TreeCanvas.java:913)
      at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
      at java.awt.Component.processMouseEvent(Component.java:6530)

        Attachments

          Activity

            People

            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
            Votes:
            0 Vote for this issue
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: