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  1. Bug Repository
  2. BUG-475

Splitting joined tracks causes NPE

          Details

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

            Description

            join 2 graphs. the split. Get:
            Exception 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)

              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
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  rev 12053
                  cannot reproduce, please give exact steps

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - rev 12053 cannot reproduce, please give exact steps
                  Hide
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  can reproduce

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - can reproduce
                  Hide
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  can't reproduce, I think this was fixed
                  due to another change (by looking at
                  the stack trace)

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - can't reproduce, I think this was fixed due to another change (by looking at the stack trace)
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Windows v12138

                  Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: com/affymetrix/igb/viewmode/ComboGlyphFactory$ComboGlyph
                  at com.affymetrix.igb.trackOperations.SplitGraphsAction.actionPerformed(SplitGraphsAction.java:38)
                  at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
                  at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
                  at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
                  at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
                  at java.awt.Component.processMouseEvent(Unknown Source)
                  at javax.swing.JComponent.processMouseEvent(Unknown Source)
                  at java.awt.Component.processEvent(Unknown Source)
                  at java.awt.Container.processEvent(Unknown Source)
                  at java.awt.Component.dispatchEventImpl(Unknown Source)
                  at java.awt.Container.dispatchEventImpl(Unknown Source)
                  at java.awt.Component.dispatchEvent(Unknown Source)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
                  at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
                  at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
                  at java.awt.Container.dispatchEventImpl(Unknown Source)
                  at java.awt.Window.dispatchEventImpl(Unknown Source)
                  at java.awt.Component.dispatchEvent(Unknown Source)
                  at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
                  at java.awt.EventQueue.access$000(Unknown Source)
                  at java.awt.EventQueue$1.run(Unknown Source)
                  at java.awt.EventQueue$1.run(Unknown Source)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
                  at java.awt.EventQueue$2.run(Unknown Source)
                  at java.awt.EventQueue$2.run(Unknown Source)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
                  at java.awt.EventQueue.dispatchEvent(Unknown Source)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                  at java.awt.EventDispatchThread.run(Unknown Source)
                  Caused by: java.lang.ClassNotFoundException: com.affymetrix.igb.viewmode.ComboGlyphFactory$ComboGlyph not found by com.affymetrix.igb.TrackOperations [14]
                  at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1460)
                  at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:72)
                  at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1843)
                  at java.lang.ClassLoader.loadClass(Unknown Source)
                  ... 38 more

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Windows v12138 Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: com/affymetrix/igb/viewmode/ComboGlyphFactory$ComboGlyph at com.affymetrix.igb.trackOperations.SplitGraphsAction.actionPerformed(SplitGraphsAction.java:38) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.ClassNotFoundException: com.affymetrix.igb.viewmode.ComboGlyphFactory$ComboGlyph not found by com.affymetrix.igb.TrackOperations [14] at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1460) at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:72) at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1843) at java.lang.ClassLoader.loadClass(Unknown Source) ... 38 more
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  fixed
                  rev 12143

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - fixed rev 12143
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed Windows v12143

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v12143
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13674, Mac, Java 1.7.0_9

                  No Exceptions or Errors thrown when splitting graphs. Tested with 2 and 3 joined graphs without problems.

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13674, Mac, Java 1.7.0_9 No Exceptions or Errors thrown when splitting graphs. Tested with 2 and 3 joined graphs without problems.

                    People

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

                      • Created:
                        Updated:
                        Resolved: