Details

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

      Description

      H sapiens
      refseq
      gsnap4
      cpg Islands (http://bioviz.org/filerepo/CpG%20Islands.bed.gz)

      java.lang.NullPointerException
      at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getStartEnd(Sym
      LoaderTabix.java:159)
      at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLo
      aderTabix.java:143)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(Q
      uickLoadSymLoader.java:257)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddS
      ymmetries(QuickLoadSymLoader.java:134)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetr
      iesThread(QuickLoadSymLoader.java:108)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeature
      s(QuickLoadSymLoader.java:94)
      at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(L
      ocalFilesServerType.java:99)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(Gene
      ralLoadUtils.java:816)
      at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
      nticZoomGlyph.getDetailGlyph(IndexedSemanticZoomGlyphFactory.java:102)
      at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
      nticZoomGlyph.getGlyph(IndexedSemanticZoomGlyphFactory.java:151)
      at com.affymetrix.igb.shared.SemanticZoomGlyphFactory$SemanticZoomGlyph.
      rangeChanged(SemanticZoomGlyphFactory.java:65)
      at com.affymetrix.igb.view.SeqMapView$2.rangeChanged(SeqMapView.java:288
      )
      at com.affymetrix.genoviz.widget.NeoMap.viewBoxChanged(NeoMap.java:1576)

      at com.affymetrix.genoviz.bioviews.View.draw(View.java:396)
      at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869)
      at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72
      )
      at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47
      )
      at javax.swing.JComponent.paint(Unknown Source)
      at javax.swing.JComponent.paintToOffscreen(Unknown Source)
      at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown S
      ource)
      at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
      at javax.swing.RepaintManager.paint(Unknown Source)
      at javax.swing.JComponent._paintImmediately(Unknown Source)
      at javax.swing.JComponent.paintImmediately(Unknown Source)
      at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
      at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
      at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
      at javax.swing.RepaintManager.access$700(Unknown Source)
      at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
      at java.awt.event.InvocationEvent.dispatch(Unknown Source)
      at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
      at java.awt.EventQueue.access$000(Unknown Source)
      at java.awt.EventQueue$3.run(Unknown Source)
      at java.awt.EventQueue$3.run(Unknown Source)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Sour
      ce)
      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)

        Attachments

          Issue Links

            Activity

            lfrohman Lance Frohman (Inactive) created issue -
            lfrohman Lance Frohman (Inactive) made changes -
            Field Original Value New Value
            Project IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
            Key IGBC-276 BUG-434
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Lance Frohman [ lfrohman ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Description H sapiens
            refseq
            gsnap4
            cpg Islands

            java.lang.NullPointerException
                    at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getStartEnd(Sym
            LoaderTabix.java:159)
                    at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLo
            aderTabix.java:143)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(Q
            uickLoadSymLoader.java:257)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddS
            ymmetries(QuickLoadSymLoader.java:134)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetr
            iesThread(QuickLoadSymLoader.java:108)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeature
            s(QuickLoadSymLoader.java:94)
                    at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(L
            ocalFilesServerType.java:99)
                    at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(Gene
            ralLoadUtils.java:816)
                    at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
            nticZoomGlyph.getDetailGlyph(IndexedSemanticZoomGlyphFactory.java:102)
                    at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
            nticZoomGlyph.getGlyph(IndexedSemanticZoomGlyphFactory.java:151)
                    at com.affymetrix.igb.shared.SemanticZoomGlyphFactory$SemanticZoomGlyph.
            rangeChanged(SemanticZoomGlyphFactory.java:65)
                    at com.affymetrix.igb.view.SeqMapView$2.rangeChanged(SeqMapView.java:288
            )
                    at com.affymetrix.genoviz.widget.NeoMap.viewBoxChanged(NeoMap.java:1576)

                    at com.affymetrix.genoviz.bioviews.View.draw(View.java:396)
                    at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869)
                    at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72
            )
                    at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47
            )
                    at javax.swing.JComponent.paint(Unknown Source)
                    at javax.swing.JComponent.paintToOffscreen(Unknown Source)
                    at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown S
            ource)
                    at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
                    at javax.swing.RepaintManager.paint(Unknown Source)
                    at javax.swing.JComponent._paintImmediately(Unknown Source)
                    at javax.swing.JComponent.paintImmediately(Unknown Source)
                    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.access$700(Unknown Source)
                    at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
                    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
                    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
                    at java.awt.EventQueue.access$000(Unknown Source)
                    at java.awt.EventQueue$3.run(Unknown Source)
                    at java.awt.EventQueue$3.run(Unknown Source)
                    at java.security.AccessController.doPrivileged(Native Method)
                    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Sour
            ce)
                    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)
            H sapiens
            refseq
            gsnap4
            cpg Islands (http://bioviz.org/filerepo/CpG%20Islands.bed.gz)

            java.lang.NullPointerException
                    at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getStartEnd(Sym
            LoaderTabix.java:159)
                    at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLo
            aderTabix.java:143)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(Q
            uickLoadSymLoader.java:257)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddS
            ymmetries(QuickLoadSymLoader.java:134)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetr
            iesThread(QuickLoadSymLoader.java:108)
                    at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeature
            s(QuickLoadSymLoader.java:94)
                    at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(L
            ocalFilesServerType.java:99)
                    at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(Gene
            ralLoadUtils.java:816)
                    at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
            nticZoomGlyph.getDetailGlyph(IndexedSemanticZoomGlyphFactory.java:102)
                    at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSema
            nticZoomGlyph.getGlyph(IndexedSemanticZoomGlyphFactory.java:151)
                    at com.affymetrix.igb.shared.SemanticZoomGlyphFactory$SemanticZoomGlyph.
            rangeChanged(SemanticZoomGlyphFactory.java:65)
                    at com.affymetrix.igb.view.SeqMapView$2.rangeChanged(SeqMapView.java:288
            )
                    at com.affymetrix.genoviz.widget.NeoMap.viewBoxChanged(NeoMap.java:1576)

                    at com.affymetrix.genoviz.bioviews.View.draw(View.java:396)
                    at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869)
                    at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72
            )
                    at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47
            )
                    at javax.swing.JComponent.paint(Unknown Source)
                    at javax.swing.JComponent.paintToOffscreen(Unknown Source)
                    at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown S
            ource)
                    at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
                    at javax.swing.RepaintManager.paint(Unknown Source)
                    at javax.swing.JComponent._paintImmediately(Unknown Source)
                    at javax.swing.JComponent.paintImmediately(Unknown Source)
                    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
                    at javax.swing.RepaintManager.access$700(Unknown Source)
                    at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
                    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
                    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
                    at java.awt.EventQueue.access$000(Unknown Source)
                    at java.awt.EventQueue$3.run(Unknown Source)
                    at java.awt.EventQueue$3.run(Unknown Source)
                    at java.security.AccessController.doPrivileged(Native Method)
                    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Sour
            ce)
                    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)
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Fixed in r12031.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Fixed in r12031.
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ]
            kkubiak Katharine Kubiak (Inactive) made changes -
            Status Open [ 1 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            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-622 [ BUG-622 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]

              People

              • Assignee:
                Unassigned
                Reporter:
                lfrohman Lance Frohman (Inactive)
              • Votes:
                0 Vote for this issue
                Watchers:
                0 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: