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  1. Bug Repository
  2. BUG-201

Autoload is not consistantly reloading data after 'clear data from tracks' is used

          Details

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

            Description

            Set to autoload, allow data to load. Zoom out to larger than the autoload threshold. Clear data from track. Zoom in again. Sometimes the data reloads, sometime it doesn't reload anything, sometime it reloads pieces. Also do this under the threshold. Again, what it load, if it loads, seems random.

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                relates to

                Task - A task that needs to be done. BUG-663 Load Modes

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  hiralv Hiral Vora (Inactive) added a comment -

                  It's not throwing exception.
                  And it seems to be loading data fine.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - It's not throwing exception. And it seems to be loading data fine.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Broken again... make sure the bam track is set to 'view mode > annotations', repeat described actions, and it fails to load data. Instead, this error:

                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at java.util.concurrent.CopyOnWriteArrayList.<init>(CopyOnWriteArrayList.java:91)
                  at com.affymetrix.genometryImpl.symmetry.SimpleSeqSymmetry.equals(SimpleSeqSymmetry.java:118)
                  at com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.equals(SimpleSymWithProps.java:122)
                  at java.util.ArrayList.indexOf(ArrayList.java:216)
                  at java.util.ArrayList.contains(ArrayList.java:199)
                  at com.affymetrix.igb.trackOperations.TrackOperationsTab.collectGraphsAndGlyphs(TrackOperationsTab.java:171)
                  at com.affymetrix.igb.trackOperations.TrackOperationsTab.resetSelectedGlyphs(TrackOperationsTab.java:138)
                  at com.affymetrix.igb.trackOperations.TrackOperationsTab.symSelectionChanged(TrackOperationsTab.java:132)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241)
                  at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1460)
                  at com.affymetrix.igb.view.SeqMapView.select(SeqMapView.java:1441)
                  at com.affymetrix.igb.view.SeqMapView.symSelectionChanged(SeqMapView.java:1831)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241)
                  at com.affymetrix.igb.tiers.TierLabelManager.doGraphSelections(TierLabelManager.java:404)
                  at com.affymetrix.igb.tiers.TierLabelManager.access$300(TierLabelManager.java:37)
                  at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:129)
                  at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1277)
                  at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540)
                  at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814)
                  at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:921)
                  at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:837)
                  at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:262)
                  at java.awt.Component.processMouseEvent(Component.java:6372)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6140)
                  at java.awt.Container.processEvent(Container.java:2083)
                  at java.awt.Component.dispatchEventImpl(Component.java:4737)
                  at java.awt.Container.dispatchEventImpl(Container.java:2141)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
                  at java.awt.Container.dispatchEventImpl(Container.java:2127)
                  at java.awt.Window.dispatchEventImpl(Window.java:2482)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:643)
                  at java.awt.EventQueue$1.run(EventQueue.java:641)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
                  at java.awt.EventQueue$2.run(EventQueue.java:657)
                  at java.awt.EventQueue$2.run(EventQueue.java:655)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Broken again... make sure the bam track is set to 'view mode > annotations', repeat described actions, and it fails to load data. Instead, this error: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at java.util.concurrent.CopyOnWriteArrayList.<init>(CopyOnWriteArrayList.java:91) at com.affymetrix.genometryImpl.symmetry.SimpleSeqSymmetry.equals(SimpleSeqSymmetry.java:118) at com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.equals(SimpleSymWithProps.java:122) at java.util.ArrayList.indexOf(ArrayList.java:216) at java.util.ArrayList.contains(ArrayList.java:199) at com.affymetrix.igb.trackOperations.TrackOperationsTab.collectGraphsAndGlyphs(TrackOperationsTab.java:171) at com.affymetrix.igb.trackOperations.TrackOperationsTab.resetSelectedGlyphs(TrackOperationsTab.java:138) at com.affymetrix.igb.trackOperations.TrackOperationsTab.symSelectionChanged(TrackOperationsTab.java:132) at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226) at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241) at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1460) at com.affymetrix.igb.view.SeqMapView.select(SeqMapView.java:1441) at com.affymetrix.igb.view.SeqMapView.symSelectionChanged(SeqMapView.java:1831) at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226) at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241) at com.affymetrix.igb.tiers.TierLabelManager.doGraphSelections(TierLabelManager.java:404) at com.affymetrix.igb.tiers.TierLabelManager.access$300(TierLabelManager.java:37) at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:129) at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1277) at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540) at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814) at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:921) at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:837) at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:262) at java.awt.Component.processMouseEvent(Component.java:6372) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6140) at java.awt.Container.processEvent(Container.java:2083) at java.awt.Component.dispatchEventImpl(Component.java:4737) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210) at java.awt.Container.dispatchEventImpl(Container.java:2127) at java.awt.Window.dispatchEventImpl(Window.java:2482) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:643) at java.awt.EventQueue$1.run(EventQueue.java:641) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:657) at java.awt.EventQueue$2.run(EventQueue.java:655) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:654) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r9638.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r9638.

                    People

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

                      • Created:
                        Updated:
                        Resolved: