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  1. Bug Repository
  2. BUG-468

Sliced View has some significant issues with showing bam files

    Details

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

      Description

      Usually I just get 3 pages of 'stack overflow errors.

      This time, I loaded a bam track, picked a gene with a low number of reads and then went to sliced view, got this error:

      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at com.affymetrix.genoviz.bioviews.Scene.removeGlyph(Scene.java:391)
      at com.affymetrix.genoviz.widget.NeoMap.removeItem(NeoMap.java:1021)
      at com.affymetrix.igb.tiers.AffyTieredMap.removeItem(AffyTieredMap.java:277)
      at com.affymetrix.igb.tiers.AffyTieredMap.removeTier(AffyTieredMap.java:296)
      at com.affymetrix.igb.tiers.AffyLabelledTierMap.removeTier(AffyLabelledTierMap.java:251)
      at com.affymetrix.igb.view.SeqMapView.copyMapTierGlyphs(SeqMapView.java:946)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:752)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:327)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:62)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:686)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:295)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.mapRefresh(AltSpliceSeqMapView.java:215)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:869)
      at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2575)
      at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2583)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab$2.actionPerformed(TrackAdjusterTab.java:213)
      at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
      at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.ColorComboBox.setSelectedColor(Unknown Source)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetStylePanel(TrackAdjusterTab.java:537)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:480)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.symSelectionChanged(TrackAdjusterTab.java:462)
      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:1436)
      at com.affymetrix.igb.view.SeqMapViewMouseListener.processSelections(SeqMapViewMouseListener.java:335)
      at com.affymetrix.igb.view.SeqMapViewMouseListener.mouseReleased(SeqMapViewMouseListener.java:131)
      at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1279)
      at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540)
      at com.affymetrix.genoviz.widget.NeoAbstractWidget.mouseReleased(NeoAbstractWidget.java:815)
      at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:923)
      at com.affymetrix.genoviz.bioviews.View.mouseReleased(View.java:841)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.Component.processMouseEvent(Component.java:6373)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      at java.awt.EventQueue.access$000(EventQueue.java:85)
      at java.awt.EventQueue$1.run(EventQueue.java:638)
      at java.awt.EventQueue$1.run(EventQueue.java:636)
      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:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      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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              • Assignee:
                Unassigned
                Reporter:
                alyssa Alyssa Gulledge (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: