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  1. Bug Repository
  2. BUG-455

Join two graphs throwing exception

          Details

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

            Description

            After joining two graphs, there is immediately the following errors. The reoccur every time you click the joined track label

            Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException: Not supported yet.
            at com.affymetrix.genometryImpl.style.SimpleTrackStyle.getSummaryThreshold(SimpleTrackStyle.java:233)
            at com.affymetrix.igb.view.SeqMapView$ThresholdXZoomer.drawTrackThresholdPoint(SeqMapView.java:511)
            at com.affymetrix.igb.view.SeqMapView$ThresholdXZoomer.paint(SeqMapView.java:501)
            at javax.swing.JComponent.paintChildren(JComponent.java:862)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at javax.swing.JComponent.paintChildren(JComponent.java:862)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at javax.swing.JComponent.paintChildren(JComponent.java:862)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at javax.swing.JComponent._paintImmediately(JComponent.java:5098)
            at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
            at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:812)
            at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)
            at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:694)
            at javax.swing.RepaintManager.access$700(RepaintManager.java:41)
            at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1672)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
            at java.awt.EventQueue.access$000(EventQueue.java:85)
            at java.awt.EventQueue$1.run(EventQueue.java:643)
            at java.awt.EventQueue$1.run(EventQueue.java:641)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
            at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
            Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException: Not supported yet.
            at com.affymetrix.genometryImpl.style.SimpleTrackStyle.getSummaryThreshold(SimpleTrackStyle.java:233)
            at com.affymetrix.igb.view.SeqMapView$ThresholdXZoomer.drawTrackThresholdPoint(SeqMapView.java:511)
            at com.affymetrix.igb.view.SeqMapView$ThresholdXZoomer.paint(SeqMapView.java:501)
            at javax.swing.JComponent.paintChildren(JComponent.java:862)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at javax.swing.JComponent.paintChildren(JComponent.java:862)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at javax.swing.JComponent._paintImmediately(JComponent.java:5098)
            at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
            at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:812)
            at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)
            at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:694)
            at javax.swing.RepaintManager.access$700(RepaintManager.java:41)
            at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1672)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
            at java.awt.EventQueue.access$000(EventQueue.java:85)
            at java.awt.EventQueue$1.run(EventQueue.java:643)
            at java.awt.EventQueue$1.run(EventQueue.java:641)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
            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-637 Graph >Join/Split bugs

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

                  Activity

                  Ascending order - Click to sort in descending order
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r11962.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r11962.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  v.11986 seeing a new error:

                  Graph has no info! com.affymetrix.igb.viewmode.ComboGlyphFactory$ComboGlyph@60db68c6
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.shared.AbstractGraphGlyph.copyYCoords(AbstractGraphGlyph.java:143)
                  at com.affymetrix.igb.shared.GraphGlyphUtils.getPercents2Scores(GraphGlyphUtils.java:139)
                  at com.affymetrix.igb.shared.GraphGlyphUtils.getPercentForValue(GraphGlyphUtils.java:166)
                  at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.initPercents(GraphVisibleBoundsSetter.java:309)
                  at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.setGraphs(GraphVisibleBoundsSetter.java:189)
                  at com.affymetrix.igb.trackAdjuster.YScaleAxisGUI.resetAll(YScaleAxisGUI.java:327)
                  at com.affymetrix.igb.trackAdjuster.YScaleAxisGUI.symSelectionChanged(YScaleAxisGUI.java:310)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241)
                  at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1455)
                  at com.affymetrix.igb.view.SeqMapView.select(SeqMapView.java:1436)
                  at com.affymetrix.igb.view.SeqMapView.symSelectionChanged(SeqMapView.java:1822)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241)
                  at com.affymetrix.igb.tiers.TierLabelManager.doGraphSelections(TierLabelManager.java:404)
                  at com.affymetrix.igb.tiers.TierLabelManager.access$300(TierLabelManager.java:37)
                  at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:129)
                  at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1277)
                  at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540)
                  at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814)
                  at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:921)
                  at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:837)
                  at java.awt.Component.processMouseEvent(Component.java:6372)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6140)
                  at java.awt.Container.processEvent(Container.java:2083)
                  at java.awt.Component.dispatchEventImpl(Component.java:4737)
                  at java.awt.Container.dispatchEventImpl(Container.java:2141)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
                  at java.awt.Container.dispatchEventImpl(Container.java:2127)
                  at java.awt.Window.dispatchEventImpl(Window.java:2482)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:643)
                  at java.awt.EventQueue$1.run(EventQueue.java:641)
                  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:657)
                  at java.awt.EventQueue$2.run(EventQueue.java:655)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
                  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 - v.11986 seeing a new error: Graph has no info! com.affymetrix.igb.viewmode.ComboGlyphFactory$ComboGlyph@60db68c6 Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.shared.AbstractGraphGlyph.copyYCoords(AbstractGraphGlyph.java:143) at com.affymetrix.igb.shared.GraphGlyphUtils.getPercents2Scores(GraphGlyphUtils.java:139) at com.affymetrix.igb.shared.GraphGlyphUtils.getPercentForValue(GraphGlyphUtils.java:166) at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.initPercents(GraphVisibleBoundsSetter.java:309) at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.setGraphs(GraphVisibleBoundsSetter.java:189) at com.affymetrix.igb.trackAdjuster.YScaleAxisGUI.resetAll(YScaleAxisGUI.java:327) at com.affymetrix.igb.trackAdjuster.YScaleAxisGUI.symSelectionChanged(YScaleAxisGUI.java:310) at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226) at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241) at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1455) at com.affymetrix.igb.view.SeqMapView.select(SeqMapView.java:1436) at com.affymetrix.igb.view.SeqMapView.symSelectionChanged(SeqMapView.java:1822) at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226) at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241) at com.affymetrix.igb.tiers.TierLabelManager.doGraphSelections(TierLabelManager.java:404) at com.affymetrix.igb.tiers.TierLabelManager.access$300(TierLabelManager.java:37) at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:129) at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1277) at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540) at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814) at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:921) at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:837) at java.awt.Component.processMouseEvent(Component.java:6372) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6140) at java.awt.Container.processEvent(Container.java:2083) at java.awt.Component.dispatchEventImpl(Component.java:4737) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210) at java.awt.Container.dispatchEventImpl(Container.java:2127) at java.awt.Window.dispatchEventImpl(Window.java:2482) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:643) at java.awt.EventQueue$1.run(EventQueue.java:641) 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:657) at java.awt.EventQueue$2.run(EventQueue.java:655) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:654) 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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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r11990.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r11990.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  And now... bug #3... join 2 graphs, split, get this NPEException in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.collectSymsAndGlyphs(TrackPreferencesSeqMapViewPanel.java:55)
                  at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.refreshSelection(TrackPreferencesSeqMapViewPanel.java:118)
                  at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.trackstylePropertyChanged(TrackPreferencesSeqMapViewPanel.java:170)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:47)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:29)
                  at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
                  at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
                  at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:237)
                  at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:893)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:724)
                  at com.affymetrix.igb.trackOperations.TrackOperationsTab$5.run(TrackOperationsTab.java:204)
                  at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:643)
                  at java.awt.EventQueue$1.run(EventQueue.java:641)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
                  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 - And now... bug #3... join 2 graphs, split, get this NPEException in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.collectSymsAndGlyphs(TrackPreferencesSeqMapViewPanel.java:55) at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.refreshSelection(TrackPreferencesSeqMapViewPanel.java:118) at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.trackstylePropertyChanged(TrackPreferencesSeqMapViewPanel.java:170) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:47) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:29) at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280) at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182) at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:237) at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:893) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:724) at com.affymetrix.igb.trackOperations.TrackOperationsTab$5.run(TrackOperationsTab.java:204) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:643) at java.awt.EventQueue$1.run(EventQueue.java:641) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:652) 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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                  hiralv Hiral Vora (Inactive) added a comment -

                  I have fixed it. Test it now.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - I have fixed it. Test it now.
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed Windows v12145

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v12145
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13674, Mac, Java 1.7.0_9

                  'Join' Option

                  • No exceptions

                  'Split' Option

                  • No exceptions
                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13674, Mac, Java 1.7.0_9 'Join' Option No exceptions 'Split' Option No exceptions

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      0 Vote for this issue
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                      Dates

                      • Created:
                        Updated:
                        Resolved: