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  1. Bug Repository
  2. BUG-443

Search Tab: When searching for residues an exception is thrown and main view changes

          Details

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

            Description

            Windows v11949

            Exception thrown and half of the main view is blacked out and labels disappear.

            To reproduce:
            A_thal_2009
            Search tab > Residues > in any Chr > for any residue

            Exception:
            Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
            at java.util.AbstractList$Itr.checkForComodification(Unknown Source)
            at java.util.AbstractList$Itr.next(Unknown Source)
            at com.affymetrix.igb.shared.FasterExpandPacker.pack(FasterExpandPacker.java:224)
            at com.affymetrix.genoviz.bioviews.Glyph.pack(Glyph.java:628)
            at com.affymetrix.igb.shared.TierGlyph.pack(TierGlyph.java:420)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:187)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:178)
            at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:167)
            at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:162)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:806)
            at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:88)
            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)

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                Issue Links

                is blocked by

                Task - A task that needs to be done. BUG-648 Search bugs

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

                  Activity

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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Windows v11959
                  I am now getting this exception:

                  Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
                  at java.util.AbstractList$Itr.checkForComodification(Unknown Source)
                  at java.util.AbstractList$Itr.next(Unknown Source)
                  at com.affymetrix.igb.IGBServiceImpl.mapRefresh(IGBServiceImpl.java:217)
                  at com.affymetrix.igb.search.SearchModeResidue.mapRefresh(SearchModeResidue.java:106)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:894)
                  at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:88)
                  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 v11959 I am now getting this exception: Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException at java.util.AbstractList$Itr.checkForComodification(Unknown Source) at java.util.AbstractList$Itr.next(Unknown Source) at com.affymetrix.igb.IGBServiceImpl.mapRefresh(IGBServiceImpl.java:217) at com.affymetrix.igb.search.SearchModeResidue.mapRefresh(SearchModeResidue.java:106) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:894) at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:88) 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)
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  fixed
                  I could not reproduce, but I could fix
                  the problem from the stack trace.

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - fixed I could not reproduce, but I could fix the problem from the stack trace.
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Windows v11961

                  There are no longer any issues to the main view or to the labels. Everything looks good, but I am getting this exception.

                  Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
                  at java.util.AbstractList$Itr.checkForComodification(Unknown Source)
                  at java.util.AbstractList$Itr.next(Unknown Source)
                  at com.affymetrix.igb.IGBServiceImpl.mapRefresh(IGBServiceImpl.java:217)
                  at com.affymetrix.igb.search.SearchModeResidue.mapRefresh(SearchModeResidue.java:106)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:894)
                  at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:88)
                  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 v11961 There are no longer any issues to the main view or to the labels. Everything looks good, but I am getting this exception. Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException at java.util.AbstractList$Itr.checkForComodification(Unknown Source) at java.util.AbstractList$Itr.next(Unknown Source) at com.affymetrix.igb.IGBServiceImpl.mapRefresh(IGBServiceImpl.java:217) at com.affymetrix.igb.search.SearchModeResidue.mapRefresh(SearchModeResidue.java:106) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:894) at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:88) 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)
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  fixed

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - fixed
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed Windows v11986

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v11986
                  Hide
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                  tkanapar Tarun Santosh (Inactive) added a comment - - edited

                  In(7.0.4) 15389(Mac)
                  A_Thal_2009 -> Search Tab -> Residue -> CCCA

                  Exception in thread "AWT-EventQueue-3" java.lang.NullPointerException
                  at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:171)
                  at com.affymetrix.igb.view.factories.AbstractTransformTierGlyph.superDrawChildren(AbstractTransformTierGlyph.java:33)
                  at com.affymetrix.igb.view.factories.AbstractTransformTierGlyph.drawChildren(AbstractTransformTierGlyph.java:74)
                  at com.affymetrix.igb.view.factories.AbstractTierGlyph.drawTraversal(AbstractTierGlyph.java:291)
                  at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:171)
                  at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:131)
                  at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74)
                  at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:453)
                  at com.affymetrix.genoviz.bioviews.View.draw(View.java:362)
                  at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:882)
                  at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72)
                  at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47)
                  at javax.swing.JComponent.paint(JComponent.java:1037)
                  at javax.swing.JComponent.paintChildren(JComponent.java:870)
                  at javax.swing.JComponent.paint(JComponent.java:1046)
                  at javax.swing.JComponent.paintChildren(JComponent.java:870)
                  at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030)
                  at javax.swing.JComponent.paint(JComponent.java:1046)
                  at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:34)
                  at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60)
                  at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97)
                  at java.awt.Container.paint(Container.java:1791)
                  at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1235)
                  at javax.swing.JComponent.paintChildren(JComponent.java:884)
                  at javax.swing.JComponent.paint(JComponent.java:1046)
                  at javax.swing.JComponent._paintImmediately(JComponent.java:5106)
                  at javax.swing.JComponent.paintImmediately(JComponent.java:4890)
                  at javax.swing.RepaintManager$3.run(RepaintManager.java:814)
                  at javax.swing.RepaintManager$3.run(RepaintManager.java:802)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
                  at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802)
                  at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745)
                  at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725)
                  at javax.swing.RepaintManager.access$1000(RepaintManager.java:46)
                  at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680)
                  at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
                  at java.awt.EventQueue.access$400(EventQueue.java:82)
                  at java.awt.EventQueue$2.run(EventQueue.java:676)
                  at java.awt.EventQueue$2.run(EventQueue.java:674)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
                  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
                  tkanapar Tarun Santosh (Inactive) added a comment - - edited In(7.0.4) 15389(Mac) A_Thal_2009 -> Search Tab -> Residue -> CCCA Exception in thread "AWT-EventQueue-3" java.lang.NullPointerException at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:171) at com.affymetrix.igb.view.factories.AbstractTransformTierGlyph.superDrawChildren(AbstractTransformTierGlyph.java:33) at com.affymetrix.igb.view.factories.AbstractTransformTierGlyph.drawChildren(AbstractTransformTierGlyph.java:74) at com.affymetrix.igb.view.factories.AbstractTierGlyph.drawTraversal(AbstractTierGlyph.java:291) at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:171) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:131) at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74) at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:453) at com.affymetrix.genoviz.bioviews.View.draw(View.java:362) at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:882) at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72) at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47) at javax.swing.JComponent.paint(JComponent.java:1037) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030) at javax.swing.JComponent.paint(JComponent.java:1046) at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:34) at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60) at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97) at java.awt.Container.paint(Container.java:1791) at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1235) at javax.swing.JComponent.paintChildren(JComponent.java:884) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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 -

                  Cannot reproduce on r15390.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Cannot reproduce on r15390.
                  Hide
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                  tkanapar Tarun Santosh (Inactive) added a comment -

                  Passed (7.0.4) 15393(Mac)

                  Show
                  tkanapar Tarun Santosh (Inactive) added a comment - Passed (7.0.4) 15393(Mac)

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      kkubiak Katharine Kubiak (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: