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  1. Bug Repository
  2. BUG-385

Intermittant bug: close IGB due to a bug (in the console) open withOUT clearing, and IGB opens with this bug

          Details

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

            Description

            While working in IGB, if an error gets thrown to the console, you typically close IGB and then restart. If you restart and do NOT clear the preferences/start from scratch, this error gets thrown.

            SEVERE: null
            java.lang.NullPointerException
            at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
            at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
            at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
            at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
            at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
            at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
            at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
            at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:686)
            at com.affymetrix.igb.view.SeqMapView.seqSelectionChanged(SeqMapView.java:2224)
            at com.affymetrix.genometryImpl.GenometryModel.fireSeqSelectionEvent(GenometryModel.java:208)
            at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:188)
            at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:171)
            at com.affymetrix.igb.view.SeqGroupView$9.finished(SeqGroupView.java:874)
            at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
            at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
            at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
            at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
            at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
            at javax.swing.Timer.fireActionPerformed(Timer.java:291)
            at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
            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)
            com.affymetrix.igb.trackAdjuster.Activator - Exception in Activator.createPage() -> null
            java.lang.NullPointerException
            at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
            at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
            at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
            at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
            at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
            at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
            at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
            at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
            at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2575)
            at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2583)
            at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab$2.actionPerformed(TrackAdjusterTab.java:202)
            at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
            at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
            at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
            at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
            at com.jidesoft.combobox.ColorComboBox.setSelectedColor(Unknown Source)
            at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetStylePanel(TrackAdjusterTab.java:483)
            at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:426)
            at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.<init>(TrackAdjusterTab.java:140)
            at com.affymetrix.igb.trackAdjuster.Activator.getPage(Activator.java:12)
            at com.affymetrix.igb.window.service.WindowActivator.createPage(WindowActivator.java:47)
            at com.affymetrix.igb.window.service.WindowActivator.access$000(WindowActivator.java:18)
            at com.affymetrix.igb.window.service.WindowActivator$1.addingService(WindowActivator.java:71)
            at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
            at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
            at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
            at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
            at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
            at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
            at java.security.AccessController.doPrivileged(Native Method)
            at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
            at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
            at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
            at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
            at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
            at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
            at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:352)
            at com.affymetrix.igb.Activator.run(Activator.java:221)
            at com.affymetrix.igb.Activator.access$000(Activator.java:63)
            at com.affymetrix.igb.Activator$1.addingService(Activator.java:141)
            at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
            at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
            at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
            at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
            at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
            at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
            at java.security.AccessController.doPrivileged(Native Method)
            at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
            at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
            at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
            at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
            at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
            at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
            at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:320)
            at com.affymetrix.igb.window.service.def.Activator.start(Activator.java:57)
            at org.apache.felix.framework.util.SecureAction$Actions.run(SecureAction.java:1600)
            at java.security.AccessController.doPrivileged(Native Method)
            at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:632)
            at org.apache.felix.framework.Felix.activateBundle(Felix.java:1977)
            at org.apache.felix.framework.Felix.startBundle(Felix.java:1895)
            at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
            at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
            at java.lang.Thread.run(Thread.java:680)
            Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.SimpleBookmarkServer findAvailablePort
            INFO: Found available port for bookmark server: 7085
            Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.action.BookmarkActionManager addDefaultBookmarks
            INFO: Loading bookmarks from file /Users/auser/.igb/bookmarks.html
            Jun 6, 2012 11:21:51 AM com.affymetrix.main.OSGiHandler startOSGi
            INFO: OSGi is started with org.apache.felix.framework version 4.0.1

                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****
                          • WARNING: Coordbox height is not a number! How did this happen? *****

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-689 IGB start up and Help menu issues

                • 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 -
                  Hide
                  Permalink
                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r11849.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r11849.
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Summary Intermittant bug: close IGB while viewing h. sapiens. Open IGB (no clear) and this bug happens Intermittant bug: close IGB due to a bug (in the console) open withOUT clearing, and IGB opens with this bug
                  Description Nothing loads! Usually, while viewing homo sapiens, IGB does something 'wrong' (fails to load sequence when I click it, or I switched genome versions too quickly and it failed to load) and I close IGB entirely. When I reopen (no clearing!) it opens but no models appear, and cole throws the same bug (I think)

                  SEVERE: null
                  java.lang.NullPointerException
                  at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
                  at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
                  at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
                  at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
                  at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
                  at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:686)
                  at com.affymetrix.igb.view.SeqMapView.seqSelectionChanged(SeqMapView.java:2224)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSeqSelectionEvent(GenometryModel.java:208)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:188)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:171)
                  at com.affymetrix.igb.view.SeqGroupView$9.finished(SeqGroupView.java:874)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
                  at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
                  at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
                  at javax.swing.Timer.fireActionPerformed(Timer.java:291)
                  at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
                  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)
                  com.affymetrix.igb.trackAdjuster.Activator - Exception in Activator.createPage() -> null
                  java.lang.NullPointerException
                  at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
                  at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
                  at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
                  at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
                  at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
                  at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
                  at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2575)
                  at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2583)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab$2.actionPerformed(TrackAdjusterTab.java:202)
                  at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
                  at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.ColorComboBox.setSelectedColor(Unknown Source)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetStylePanel(TrackAdjusterTab.java:483)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:426)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.<init>(TrackAdjusterTab.java:140)
                  at com.affymetrix.igb.trackAdjuster.Activator.getPage(Activator.java:12)
                  at com.affymetrix.igb.window.service.WindowActivator.createPage(WindowActivator.java:47)
                  at com.affymetrix.igb.window.service.WindowActivator.access$000(WindowActivator.java:18)
                  at com.affymetrix.igb.window.service.WindowActivator$1.addingService(WindowActivator.java:71)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
                  at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
                  at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
                  at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
                  at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
                  at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
                  at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
                  at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:352)
                  at com.affymetrix.igb.Activator.run(Activator.java:221)
                  at com.affymetrix.igb.Activator.access$000(Activator.java:63)
                  at com.affymetrix.igb.Activator$1.addingService(Activator.java:141)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
                  at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
                  at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
                  at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
                  at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
                  at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
                  at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
                  at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:320)
                  at com.affymetrix.igb.window.service.def.Activator.start(Activator.java:57)
                  at org.apache.felix.framework.util.SecureAction$Actions.run(SecureAction.java:1600)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:632)
                  at org.apache.felix.framework.Felix.activateBundle(Felix.java:1977)
                  at org.apache.felix.framework.Felix.startBundle(Felix.java:1895)
                  at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
                  at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
                  at java.lang.Thread.run(Thread.java:680)
                  Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.SimpleBookmarkServer findAvailablePort
                  INFO: Found available port for bookmark server: 7085
                  Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.action.BookmarkActionManager addDefaultBookmarks
                  INFO: Loading bookmarks from file /Users/auser/.igb/bookmarks.html
                  Jun 6, 2012 11:21:51 AM com.affymetrix.main.OSGiHandler startOSGi
                  INFO: OSGi is started with org.apache.felix.framework version 4.0.1
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****                   		While working in IGB, if an error gets thrown to the console, you typically close IGB and then restart. If you restart and do NOT clear the preferences/start from scratch, this error gets thrown.

                  SEVERE: null
                  java.lang.NullPointerException
                  at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
                  at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
                  at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
                  at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
                  at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
                  at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:686)
                  at com.affymetrix.igb.view.SeqMapView.seqSelectionChanged(SeqMapView.java:2224)
                  at com.affymetrix.genometryImpl.GenometryModel.fireSeqSelectionEvent(GenometryModel.java:208)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:188)
                  at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:171)
                  at com.affymetrix.igb.view.SeqGroupView$9.finished(SeqGroupView.java:874)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
                  at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
                  at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
                  at javax.swing.Timer.fireActionPerformed(Timer.java:291)
                  at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
                  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)
                  com.affymetrix.igb.trackAdjuster.Activator - Exception in Activator.createPage() -> null
                  java.lang.NullPointerException
                  at com.affymetrix.igb.shared.ViewModeGlyph.setMinimumPixelBounds(ViewModeGlyph.java:72)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.createViewModeGlyph(AnnotationGlyphFactory.java:551)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:559)
                  at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:902)
                  at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:898)
                  at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
                  at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
                  at com.affymetrix.igb.view.TrackView.addDependentAndEmptyTrack(TrackView.java:163)
                  at com.affymetrix.igb.view.SeqMapView.addDependentAndEmptyTrack(SeqMapView.java:1267)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1198)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
                  at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2575)
                  at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2583)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab$2.actionPerformed(TrackAdjusterTab.java:202)
                  at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
                  at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
                  at com.jidesoft.combobox.ColorComboBox.setSelectedColor(Unknown Source)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetStylePanel(TrackAdjusterTab.java:483)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:426)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.<init>(TrackAdjusterTab.java:140)
                  at com.affymetrix.igb.trackAdjuster.Activator.getPage(Activator.java:12)
                  at com.affymetrix.igb.window.service.WindowActivator.createPage(WindowActivator.java:47)
                  at com.affymetrix.igb.window.service.WindowActivator.access$000(WindowActivator.java:18)
                  at com.affymetrix.igb.window.service.WindowActivator$1.addingService(WindowActivator.java:71)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
                  at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
                  at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
                  at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
                  at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
                  at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
                  at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
                  at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:352)
                  at com.affymetrix.igb.Activator.run(Activator.java:221)
                  at com.affymetrix.igb.Activator.access$000(Activator.java:63)
                  at com.affymetrix.igb.Activator$1.addingService(Activator.java:141)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:980)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:906)
                  at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:262)
                  at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:234)
                  at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:941)
                  at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
                  at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
                  at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
                  at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4252)
                  at org.apache.felix.framework.Felix.registerService(Felix.java:3275)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
                  at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:320)
                  at com.affymetrix.igb.window.service.def.Activator.start(Activator.java:57)
                  at org.apache.felix.framework.util.SecureAction$Actions.run(SecureAction.java:1600)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:632)
                  at org.apache.felix.framework.Felix.activateBundle(Felix.java:1977)
                  at org.apache.felix.framework.Felix.startBundle(Felix.java:1895)
                  at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
                  at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
                  at java.lang.Thread.run(Thread.java:680)
                  Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.SimpleBookmarkServer findAvailablePort
                  INFO: Found available port for bookmark server: 7085
                  Jun 6, 2012 11:21:50 AM com.affymetrix.igb.bookmarks.action.BookmarkActionManager addDefaultBookmarks
                  INFO: Loading bookmarks from file /Users/auser/.igb/bookmarks.html
                  Jun 6, 2012 11:21:51 AM com.affymetrix.main.OSGiHandler startOSGi
                  INFO: OSGi is started with org.apache.felix.framework version 4.0.1
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  ******** WARNING: Coordbox height is not a number! How did this happen? *****
                  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-252 BUG-385
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-689 [ BUG-689 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Resolution Fixed [ 1 ]

                    People

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

                      • Created:
                        Updated:
                        Resolved: