Uploaded image for project: 'Bug Repository'
  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

                  Ascending order - Click to sort in descending order
                  alyssa Alyssa Gulledge (Inactive) created issue -
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Nick Ren [ imnick ]
                  Hide
                  Permalink
                  imnick Nick Ren (Inactive) added a comment -

                  Fixed in version 11018.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Fixed in version 11018.
                  imnick Nick Ren (Inactive) made changes -
                  Assignee Nick Ren [ imnick ] Alyssa Gulledge [ alyssa ]
                  Hide
                  Permalink
                  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.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Nick Ren [ imnick ]
                  Hide
                  Permalink
                  imnick Nick Ren (Inactive) added a comment -

                  Fixed in version 11053.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Fixed in version 11053.
                  imnick Nick Ren (Inactive) made changes -
                  Assignee Nick Ren [ imnick ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
                  Key IGBC-154 BUG-363
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  darius darius made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Darius Bost [ darius ]
                  Hide
                  Permalink
                  darius darius added a comment -

                  passed 7.0.0 (11798)

                  Show
                  darius darius added a comment - passed 7.0.0 (11798)
                  darius darius made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Darius Bost [ darius ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-661 [ BUG-661 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Parent BUG-359 [ 11282 ]
                  Issue Type Sub-task [ 5 ] Bug [ 1 ]
                  Hide
                  Permalink
                  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.
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
                    • Votes:
                      0 Vote for this issue
                      Watchers:
                      0 Start watching this issue

                      Dates

                      • Created:
                        Updated:
                        Resolved: