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  1. Bug Repository
  2. BUG-347

Creating a second depth graph causes some odd behavior

    Details

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

      Description

      Create a depth graph. Create a second one. A seoncd one appears in the Data management track list, but does not appear in the window. If you delete the second track (no data) from the table, the data disappears from the one that is shown. refresh (but don't MOVE the zoom, still shows nothing. Now zoom out to new data and refresh, everything reappears.

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            alyssa Alyssa Gulledge (Inactive) added a comment -

            Somewhere in this process, IGB threw:

            Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
            at java.util.Arrays.binarySearch(Arrays.java:1417)
            at com.affymetrix.genometryImpl.symmetry.GraphSym.determineBegIndex(GraphSym.java:338)
            at com.affymetrix.igb.shared.AbstractGraphGlyph.DrawTheGraph(AbstractGraphGlyph.java:332)
            at com.affymetrix.igb.shared.AbstractGraphGlyph.oldDraw(AbstractGraphGlyph.java:280)
            at com.affymetrix.igb.shared.AbstractGraphGlyph.doDraw(AbstractGraphGlyph.java:1259)
            at com.affymetrix.igb.shared.AbstractGraphGlyph.draw(AbstractGraphGlyph.java:1275)
            at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:127)
            at com.affymetrix.igb.shared.TierGlyph.drawTraversal(TierGlyph.java:388)
            at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:168)
            at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:128)
            at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74)
            at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:446)
            at com.affymetrix.genoviz.bioviews.View.draw(View.java:357)
            at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:865)
            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(JComponent.java:1029)
            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.JSplitPane.paintChildren(JSplitPane.java:1030)
            at javax.swing.JComponent.paint(JComponent.java:1038)
            at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:34)
            at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60)
            at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97)
            at java.awt.Container.paint(Container.java:1793)
            at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1234)
            at javax.swing.JComponent.paintChildren(JComponent.java:876)
            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: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)

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - Somewhere in this process, IGB threw: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at java.util.Arrays.binarySearch(Arrays.java:1417) at com.affymetrix.genometryImpl.symmetry.GraphSym.determineBegIndex(GraphSym.java:338) at com.affymetrix.igb.shared.AbstractGraphGlyph.DrawTheGraph(AbstractGraphGlyph.java:332) at com.affymetrix.igb.shared.AbstractGraphGlyph.oldDraw(AbstractGraphGlyph.java:280) at com.affymetrix.igb.shared.AbstractGraphGlyph.doDraw(AbstractGraphGlyph.java:1259) at com.affymetrix.igb.shared.AbstractGraphGlyph.draw(AbstractGraphGlyph.java:1275) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:127) at com.affymetrix.igb.shared.TierGlyph.drawTraversal(TierGlyph.java:388) at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:168) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:128) at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74) at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:446) at com.affymetrix.genoviz.bioviews.View.draw(View.java:357) at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:865) 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(JComponent.java:1029) 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.JSplitPane.paintChildren(JSplitPane.java:1030) at javax.swing.JComponent.paint(JComponent.java:1038) at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:34) at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60) at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97) at java.awt.Container.paint(Container.java:1793) at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1234) at javax.swing.JComponent.paintChildren(JComponent.java:876) 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: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)
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Fixed in r11025.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Fixed in r11025.
            Hide
            fwang4 Fuquan Wang (Inactive) added a comment -

            For 7.0.0 (11804) Mac:

            Sometimes the titles of the 2 depth graphs do not show in consistent alignment, in this case if you remove them - 2 depth graphs in data management table there will be an empty track remained in track list. At the same time, status bar is always showing 'Removing feature Depth: ...'.

            Show
            fwang4 Fuquan Wang (Inactive) added a comment - For 7.0.0 (11804) Mac: Sometimes the titles of the 2 depth graphs do not show in consistent alignment, in this case if you remove them - 2 depth graphs in data management table there will be an empty track remained in track list. At the same time, status bar is always showing 'Removing feature Depth: ...'.
            Hide
            fwang4 Fuquan Wang (Inactive) added a comment -

            Passed on 7.0.0 (11920) Mac.

            Show
            fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11920) Mac.

              People

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

                • Created:
                  Updated:
                  Resolved: