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? *****