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  1. IGB
  2. IGBF-621

Deleting a track loaded into an "incorrect" genome generates an exception

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      Description

      Version found: 8.4.0 (on WIndows)

      While testing scripting issues I noticed that a null pointer exception was being generated when deleting tracks loaded from scripts.

      *Before reading further, please see comments listed below:

      To reproduce:

      1) Open IGB and drop the test.igb script (attached) onto the IGB window to run the script.

      2) Right-click on the track that the script opened and delete the track.

      *Observe: Upon confirming your deletion, a null pointer exception is generated in the console (see below for exception). After the exception is generated the user is not able to right-click on tracks to show the context menu.

      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at com.affymetrix.igb.tabs.annotation.AnnotationPanelImpl.labelFieldComboBoxReset(AnnotationPanelImpl.java:246)
      at com.affymetrix.igb.tabs.annotation.AnnotationPanel.resetAll(AnnotationPanel.java:483)
      at com.affymetrix.igb.tabs.annotation.AnnotationPanelImpl.selectionRefreshed(AnnotationPanelImpl.java:408)
      at com.affymetrix.igb.shared.Selections.notifyRefreshListener(Selections.java:346)
      at com.affymetrix.igb.shared.Selections.refreshSelection(Selections.java:150)
      at com.affymetrix.igb.shared.Selections.access$100(Selections.java:36)
      at com.affymetrix.igb.shared.Selections$Listeners.seqSelectionChanged(Selections.java:386)
      at com.affymetrix.genometry.GenometryModel.fireSeqSelectionEvent(GenometryModel.java:214)
      at com.affymetrix.genometry.GenometryModel.setSelectedSeq(GenometryModel.java:194)
      at com.affymetrix.genometry.GenometryModel.setSelectedSeq(GenometryModel.java:180)
      at com.affymetrix.igb.view.load.GeneralLoadView$5.finished(GeneralLoadView.java:634)
      at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:48)
      at javax.swing.SwingWorker$5.run(Unknown Source)
      at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
      at sun.swing.AccumulativeRunnable.run(Unknown Source)
      at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
      at javax.swing.Timer.fireActionPerformed(Unknown Source)
      at javax.swing.Timer$DoPostEvent.run(Unknown Source)
      at java.awt.event.InvocationEvent.dispatch(Unknown Source)
      at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
      at java.awt.EventQueue.access$500(Unknown Source)
      at java.awt.EventQueue$3.run(Unknown Source)
      at java.awt.EventQueue$3.run(Unknown Source)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
      at java.awt.EventQueue.dispatchEvent(Unknown Source)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
      at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
      at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
      at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
      at java.awt.EventDispatchThread.run(Unknown Source)

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            mason Mason Meyer (Inactive) added a comment -

            On further examination it seems that this exception is generated when deleting any files. This exception is even seen on the live version when attempting to delete 2-bit files.

            Show
            mason Mason Meyer (Inactive) added a comment - On further examination it seems that this exception is generated when deleting any files. This exception is even seen on the live version when attempting to delete 2-bit files.
            Hide
            mason Mason Meyer (Inactive) added a comment -

            It seems like this exception is NOT seen when deleting a file that was loaded into the "correct" genome (ask David for further clarification).

            When deleting a file loaded into a custom genome the exception seems to happen as well. Also, this exception only seems to happen when deleting from the track label context menu.

            Show
            mason Mason Meyer (Inactive) added a comment - It seems like this exception is NOT seen when deleting a file that was loaded into the "correct" genome (ask David for further clarification). When deleting a file loaded into a custom genome the exception seems to happen as well. Also, this exception only seems to happen when deleting from the track label context menu.
            Hide
            mason Mason Meyer (Inactive) added a comment -

            This particular issue has been resolved but I created a a new issue, IGBF-675, to track a slightly related issue that I noticed while testing this issue. Since testing verifies that this story is now resolved it will now be closed.

            Show
            mason Mason Meyer (Inactive) added a comment - This particular issue has been resolved but I created a a new issue, IGBF-675 , to track a slightly related issue that I noticed while testing this issue. Since testing verifies that this story is now resolved it will now be closed.

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              • Assignee:
                mason Mason Meyer (Inactive)
                Reporter:
                mason Mason Meyer (Inactive)
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                • Created:
                  Updated:
                  Resolved: