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  1. Bug Repository
  2. BUG-361

Sliced View: unchecking the Analyze ORF box throws and error.

          Details

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

            Description

            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)

              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
                  hiralv Hiral Vora (Inactive) created issue -
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                  hiralv Hiral Vora (Inactive) added a comment -

                  I think the bug is fixed. Please go ahead and test it.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - I think the bug is fixed. Please go ahead and test it.
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Can't test this bug until the main bug is fixed - see the comment added to the bottom of the main issue.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Can't test this bug until the main bug is fixed - see the comment added to the bottom of the main issue.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Made a fix. Test it out.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Made a fix. Test it out.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Ummm - now I can not click the box ON... can't get it to activate Analyze ORFs

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Ummm - now I can not click the box ON... can't get it to activate Analyze ORFs
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Nick Ren [ imnick ]
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                  imnick Nick Ren (Inactive) added a comment -

                  UNchecking the ORF box generates this error:
                  Exception in thread "pool-11-thread-1" java.lang.NullPointerException
                  at java.util.ArrayList.addAll(ArrayList.java:472)
                  at com.affymetrix.igb.shared.AbstractViewModeGlyph.copyChildren(AbstractViewModeGlyph.java:177)
                  at com.affymetrix.igb.shared.SemanticZoomGlyphFactory$SemanticZoomGlyph.copyChildren(SemanticZoomGlyphFactory.java:464)
                  at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:72)
                  at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:102)
                  at com.affymetrix.igb.shared.TierGlyph.setInfo(TierGlyph.java:459)
                  at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:240)
                  at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1072)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:845)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:678)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:283)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:604)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:57)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:592)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:256)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:30)
                  at com.affymetrix.igb.view.AltSpliceSeqMapView$2.run(AltSpliceSeqMapView.java:97)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
                  at java.lang.Thread.run(Thread.java:680)

                  Show
                  imnick Nick Ren (Inactive) added a comment - UNchecking the ORF box generates this error: Exception in thread "pool-11-thread-1" java.lang.NullPointerException at java.util.ArrayList.addAll(ArrayList.java:472) at com.affymetrix.igb.shared.AbstractViewModeGlyph.copyChildren(AbstractViewModeGlyph.java:177) at com.affymetrix.igb.shared.SemanticZoomGlyphFactory$SemanticZoomGlyph.copyChildren(SemanticZoomGlyphFactory.java:464) at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:72) at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:102) at com.affymetrix.igb.shared.TierGlyph.setInfo(TierGlyph.java:459) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:240) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1072) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:845) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:678) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:283) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:604) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:57) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:592) at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:256) at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:30) at com.affymetrix.igb.view.AltSpliceSeqMapView$2.run(AltSpliceSeqMapView.java:97) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)
                  imnick Nick Ren (Inactive) made changes -
                  Assignee Nick Ren [ imnick ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  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 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
                  Key IGBC-140 BUG-361
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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited

                  Pass on 7.0.0 (11804) Mac.

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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited Pass on 7.0.0 (11804) Mac.
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Fuquan Wang [ fwang4 ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Summary Test the bug Sliced View: unchecking the Analyze ORF box throws and error.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Parent BUG-359 [ 11282 ]
                  Issue Type Sub-task [ 5 ] Bug [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-661 [ BUG-661 ]
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13772, Mac, Java 1.7.0_09

                  No errors are thrown in the Java console when checking or unchecking the 'Analyze ORFs' option in 'Sliced View' Tab.

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13772, Mac, Java 1.7.0_09 No errors are thrown in the Java console when checking or unchecking the 'Analyze ORFs' option in 'Sliced View' Tab.
                  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:
                      hiralv Hiral Vora (Inactive)
                    • Votes:
                      0 Vote for this issue
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                      Dates

                      • Created:
                        Updated:
                        Resolved: