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  1. Bug Repository
  2. BUG-363

Concurrent modification error on Sliced View

          Details

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

            Description

            Currently, if I try to change the color of any of the elements (BG, stop, orf) they throw:

            Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
            at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
            at java.util.AbstractList$Itr.next(AbstractList.java:343)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:185)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
            at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
            at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
            at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
            at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
            at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
            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$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
            at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
            Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
            at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
            at java.util.AbstractList$Itr.next(AbstractList.java:343)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
            at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
            at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
            at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
            at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
            at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
            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$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
            at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
            Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
            at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
            at java.util.AbstractList$Itr.next(AbstractList.java:343)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211)
            at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
            at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
            at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
            at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
            at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
            at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
            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.awt.EventQueue.dispatchEvent(EventQueue.java:647)
            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)

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-661 Sliced View

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

                  Activity

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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13782, Mac ,Java 1.7.0_10

                  No errors occurred when changing 'ORF Analyzer (Sliced View tab)' colors under 'Other Options' in 'Preferences'.

                  'Sliced View' viewer was open throughout the modification process with an entire read or entire gene model selected.

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13782, Mac ,Java 1.7.0_10 No errors occurred when changing 'ORF Analyzer (Sliced View tab)' colors under 'Other Options' in 'Preferences'. 'Sliced View' viewer was open throughout the modification process with an entire read or entire gene model selected.
                  Hide
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                  darius darius added a comment -

                  passed 7.0.0 (11798)

                  Show
                  darius darius added a comment - passed 7.0.0 (11798)
                  Hide
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                  imnick Nick Ren (Inactive) added a comment -

                  Fixed in version 11053.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Fixed in version 11053.
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  make sure to select the WHOLE gene to view in Sliced View prior to testing this out.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - make sure to select the WHOLE gene to view in Sliced View prior to testing this out.
                  Hide
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                  imnick Nick Ren (Inactive) added a comment -

                  Fixed in version 11018.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Fixed in version 11018.

                    People

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

                      • Created:
                        Updated:
                        Resolved: