Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1982

jalviewLite fails on Jpred4 site with null pointer exception

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.9, 2.9.0b1, 2.9.0b2
    • Fix Version/s: 2.10.0
    • Component/s: jvlite
    • Labels:
    • Environment:
      Reproduced in IDE on OSX Java 1.9 & 1.8 with specific init parameters used by Jpred (alignment + concise file with no consensus, conservation or quality calc)

      Description

      JalviewLite shows a button but fails to start with the following exception:

      In 2.9.0b2:
      Exception in thread "Thread-15" java.lang.NullPointerException
      at jalview.appletgui.AlignFrame.setAnnotationsVisibility(AlignFrame.java:933)
      at jalview.appletgui.AlignFrame.<init>(AlignFrame.java:309)
      at jalview.appletgui.AlignFrame.<init>(AlignFrame.java:163)
      at jalview.bin.JalviewLite$LoadingThread.readAlignment(JalviewLite.java:1981)
      at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:1897)
      at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1883)

      When obfuscated:
      Dec 09, 2015 3:24:02 P.M. jalview.o.k <clinit>
      INFO: Getting messages for lang: en_US
      Exception in thread "Thread-30" java.lang.NullPointerException
      at jalview.appletgui.AlignFrame.d(Unknown Source)
      at jalview.appletgui.AlignFrame.<init>(Unknown Source)
      at jalview.appletgui.AlignFrame.<init>(Unknown Source)
      at jalview.bin.m.c(Unknown Source)
      at jalview.bin.m.run(Unknown Source)

      In IDE with debug enabled:

      Dec 09, 2015 3:22:01 PM jalview.util.MessageManager <clinit>
      INFO: Getting messages for lang: en_US
      Warning: No JalviewLite javascript callbacks available.
      Exception in thread "Thread-2" java.lang.NullPointerException
      at jalview.appletgui.AlignFrame.setAnnotationsVisibility(AlignFrame.java:934)
      at jalview.appletgui.AlignFrame.<init>(AlignFrame.java:309)
      at jalview.appletgui.AlignFrame.<init>(AlignFrame.java:163)
      at jalview.bin.JalviewLite$LoadingThread.readAlignment(JalviewLite.java:1981)
      at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:1897)
      at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1883)

        Attachments

          Issue Links

          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1983 annotation dependent dialogs should be inaccessible when no annotation available

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Open

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              drozdets Alexey Drozdetskiy
              Votes:
              0 Vote for this issue
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: