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  1. Bugs That Are No Longer Relevant
  2. OLD-60

Activating Single-Track Operation on depth track throws exception

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None

            Description

            Windows v12291

            A_thal
            Rt click > Transform < Depth
            Click on track label
            Track Operations > Single-Track Operations > Any option > Go

            Exception thrown:

            Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
            at com.affymetrix.igb.view.TrackView.getTier(TrackView.java:84)
            at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:97)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:942)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:938)
            at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:244)
            at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:154)
            at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1255)
            at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:1001)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:815)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:737)
            at com.affymetrix.igb.shared.TrackUtils.addTrack(TrackUtils.java:39)
            at com.affymetrix.igb.shared.TrackFunctionOperationA.addNonUpdateableTier(TrackFunctionOperationA.java:109)
            at com.affymetrix.igb.shared.TrackFunctionOperationA.addTier(TrackFunctionOperationA.java:48)
            at com.affymetrix.igb.shared.TrackTransformAction.actionPerformed(TrackTransformAction.java:24)
            at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
            at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
            at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
            at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
            at java.awt.Component.processMouseEvent(Unknown Source)
            at javax.swing.JComponent.processMouseEvent(Unknown Source)
            at java.awt.Component.processEvent(Unknown Source)
            at java.awt.Container.processEvent(Unknown Source)
            at java.awt.Component.dispatchEventImpl(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Window.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
            at java.awt.EventQueue.access$000(Unknown Source)
            at java.awt.EventQueue$1.run(Unknown Source)
            at java.awt.EventQueue$1.run(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
            at java.awt.EventQueue$2.run(Unknown Source)
            at java.awt.EventQueue$2.run(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$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)

              Attachments

                Activity

                Ascending order - Click to sort in descending order
                Hide
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                hiralv Hiral Vora (Inactive) added a comment -

                Fixed in r12302.

                Show
                hiralv Hiral Vora (Inactive) added a comment - Fixed in r12302.
                Hide
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                lfrohman Lance Frohman (Inactive) added a comment -

                I still get a NPE

                • pristine IGB
                • H sapiens
                • show 1 track
                • view mode semantic zoom
                • select track
                • open Track Operations
                • Single Track Operations = Depth
                • Go button
                Show
                lfrohman Lance Frohman (Inactive) added a comment - I still get a NPE pristine IGB H sapiens show 1 track view mode semantic zoom select track open Track Operations Single Track Operations = Depth Go button
                Hide
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                kkubiak Katharine Kubiak (Inactive) added a comment -

                Windows v12305

                My original instructions cause no error, but when I follow Lance's instructions to reproduce majority of the IGB window turns black (attached blank.png) and I get this NPE:

                Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                at com.affymetrix.igb.view.TrackView.getTier(TrackView.java:79)
                at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:92)
                at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:942)
                at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:938)
                at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:239)
                at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:149)
                at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1255)
                at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:1001)
                at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:815)
                at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:737)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:785)
                at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:54)
                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$000(Unknown Source)
                at java.awt.EventQueue$1.run(Unknown Source)
                at java.awt.EventQueue$1.run(Unknown Source)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.security.AccessControlContext$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)

                Show
                kkubiak Katharine Kubiak (Inactive) added a comment - Windows v12305 My original instructions cause no error, but when I follow Lance's instructions to reproduce majority of the IGB window turns black (attached blank.png) and I get this NPE: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.TrackView.getTier(TrackView.java:79) at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:92) at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:942) at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:938) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:239) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:149) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1255) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:1001) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:815) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:737) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:785) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:54) 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$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$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)
                Hide
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                hiralv Hiral Vora (Inactive) added a comment -

                Test r12307.

                Show
                hiralv Hiral Vora (Inactive) added a comment - Test r12307.
                Hide
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                kkubiak Katharine Kubiak (Inactive) added a comment -

                Passed Windows v12307

                It was extremely fast too.

                Show
                kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v12307 It was extremely fast too.

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    alyssa Alyssa Gulledge (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: