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  1. Bug Repository
  2. BUG-359

Sliced View improvements; specifically for ORF view

          Details

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

            Description

            Sliced View can be improved in 2 ways.

            1. The background color for ORF view should be changeable. We can change stop and dynamic orf colors, but the background is always gray - we need access to colors (specifically white) so that it can be used for publication. The BG color box can easily be added to Preference > other > ORF analyzer.

            2. When 'Analyze ORFs' box is selected, it should AUTOMATICALLY change Slice buffer to '0' and become grayed out/unchangeable. This will make using the ORF analyzer much easier and much more obvious.

              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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                  imnick Nick Ren (Inactive) added a comment -

                  Fixed in truck version 10477.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Fixed in truck version 10477.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  LOVE it! The colors work fine. However, after you UNcheck the ORF box, you can NOT go back and change the slice buffer to any other number...

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - LOVE it! The colors work fine. However, after you UNcheck the ORF box, you can NOT go back and change the slice buffer to any other number...
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Also, UNchecking the ORF box generates this error:
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.shared.TierGlyph.pack(TierGlyph.java:214)
                  at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:186)
                  at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
                  at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:144)
                  at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
                  at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:302)
                  at com.affymetrix.genometryImpl.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:29)
                  at com.affymetrix.igb.view.OrfAnalyzer.adjustMap(OrfAnalyzer.java:293)
                  at com.affymetrix.igb.view.OrfAnalyzer.actionPerformed(OrfAnalyzer.java:121)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
                  at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
                  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)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Also, UNchecking the ORF box generates this error: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.shared.TierGlyph.pack(TierGlyph.java:214) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:186) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166) at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:144) at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159) at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:302) at com.affymetrix.genometryImpl.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:29) at com.affymetrix.igb.view.OrfAnalyzer.adjustMap(OrfAnalyzer.java:293) at com.affymetrix.igb.view.OrfAnalyzer.actionPerformed(OrfAnalyzer.java:121) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) 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)
                  Hide
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                  imnick Nick Ren (Inactive) added a comment -

                  Can't reproduce the bug.

                  Show
                  imnick Nick Ren (Inactive) added a comment - Can't reproduce the bug.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Lemme know when sliced view is functioning normally again

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Lemme know when sliced view is functioning normally again
                  Hide
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                  imnick Nick Ren (Inactive) added a comment -

                  I think this bug is related to the new feature you added recently.

                  Please take a look.

                  Show
                  imnick Nick Ren (Inactive) added a comment - I think this bug is related to the new feature you added recently. Please take a look.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  I can't get the sliced view to work properly at all:
                  Select gene, select sliced view. range box reports 'working...' but nothing ever shows up,
                  console says:

                  Exception in thread "pool-11-thread-1" java.lang.NullPointerException
                  at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1342)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:801)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:278)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:658)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:55)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:646)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:251)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:28)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:117)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
                  at java.lang.Thread.run(Thread.java:680)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - I can't get the sliced view to work properly at all: Select gene, select sliced view. range box reports 'working...' but nothing ever shows up, console says: Exception in thread "pool-11-thread-1" java.lang.NullPointerException at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1342) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:801) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:278) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:658) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:55) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:646) at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:251) at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:28) at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:117) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Made fix. Give it a try.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Made fix. Give it a try.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  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)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - 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)
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  However, every other aspect finally seems to be working GREAT!

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - However, every other aspect finally seems to be working GREAT!
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Currently in v. 11279, just trying to open sliced view at all throws:

                  Exception in thread "pool-13-thread-1" java.lang.NullPointerException
                  at com.affymetrix.genometryImpl.util.GeneralUtils.stripEndings(GeneralUtils.java:72)
                  at com.affymetrix.genometryImpl.parsers.FileTypeHolder.getFileTypeHandlerForURI(FileTypeHolder.java:442)
                  at com.affymetrix.igb.viewmode.MapViewModeHolder.getAutoloadFactory(MapViewModeHolder.java:118)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:831)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.getTrack(AltSpliceSeqMapView.java:73)
                  at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:230)
                  at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1121)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:894)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:727)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:287)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:56)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:639)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:255)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:29)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:121)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
                  at java.lang.Thread.run(Thread.java:680)

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                  alyssa Alyssa Gulledge (Inactive) added a comment - Currently in v. 11279, just trying to open sliced view at all throws: Exception in thread "pool-13-thread-1" java.lang.NullPointerException at com.affymetrix.genometryImpl.util.GeneralUtils.stripEndings(GeneralUtils.java:72) at com.affymetrix.genometryImpl.parsers.FileTypeHolder.getFileTypeHandlerForURI(FileTypeHolder.java:442) at com.affymetrix.igb.viewmode.MapViewModeHolder.getAutoloadFactory(MapViewModeHolder.java:118) at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:831) at com.affymetrix.igb.view.AltSpliceSeqMapView.getTrack(AltSpliceSeqMapView.java:73) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:230) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1121) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:894) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:727) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:287) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:56) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:639) at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:255) at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:29) at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:121) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed.
                  Hide
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Passed on 7.0.0 (11804) Mac.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11804) Mac.

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

                      • Created:
                        Updated:
                        Resolved: