[BUG-146] Exception when trying to change load mode of 'no data loaded' files IF they are set to whole genome - JIRA UNCC

Details

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

Description

To generate this exception, load the test gff into igb (from desktop), notice chr22 in current sequences. Load the test wig file (again from desktop). Set the wig to 'whole chromosome'. Wait for igb to respod and 'gray out' the load data buttons. Notice that there is now a chrblah in current sequences. Now, click on the 'load mode' for the wig file in the load mode table. It will throw an exception (see below). Also, the track does NOT show the 'warning' symbol, although the track name says data not loaded. Select the chrblah in current seq, data appears, but a similar thing happens to the gff file - it says data not loaded, with no symbol, and if you try to click on load mode, you get the exception.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.LoadModeTable$ColumnRenderer.getTableCellRendererComponent(LoadModeTable.java:167)
at javax.swing.JTable$AccessibleJTable.getAccessibleChild(JTable.java:7023)
at javax.swing.JTable$AccessibleJTable.getAccessibleAt(JTable.java:7410)
at javax.swing.JTable$AccessibleJTable.valueChanged(JTable.java:6925)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:167)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:147)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:194)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:388)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:398)
at javax.swing.DefaultListSelectionModel.setSelectionInterval(DefaultListSelectionModel.java:442)
at javax.swing.JTable.changeSelectionModel(JTable.java:2352)
at javax.swing.JTable.changeSelection(JTable.java:2421)
at javax.swing.plaf.basic.BasicTableUI$Handler.adjustSelection(BasicTableUI.java:1085)
at javax.swing.plaf.basic.BasicTableUI$Handler.mousePressed(BasicTableUI.java:1008)
at javax.swing.plaf.basic.BasicTableUI$MouseInputHandler.mousePressed(BasicTableUI.java:768)
at com.apple.laf.AquaTableUI$MouseInputHandler.mousePressed(AquaTableUI.java:82)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:263)
at java.awt.Component.processMouseEvent(Component.java:6349)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6117)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4714)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
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)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.LoadModeTable$ColumnRenderer.getTableCellRendererComponent(LoadModeTable.java:167)
at javax.swing.JTable$AccessibleJTable.getAccessibleChild(JTable.java:7023)
at javax.swing.JTable$AccessibleJTable.getAccessibleAt(JTable.java:7410)
at javax.swing.JTable$AccessibleJTable.valueChanged(JTable.java:6925)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:167)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:137)
at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:668)
at javax.swing.plaf.basic.BasicTableUI$Handler.setValueIsAdjusting(BasicTableUI.java:923)
at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1136)
at javax.swing.plaf.basic.BasicTableUI$MouseInputHandler.mouseReleased(BasicTableUI.java:772)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273)
at java.awt.Component.processMouseEvent(Component.java:6352)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6117)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4714)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
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)

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Attachments

GSM535746_3T3L1t1.H3K36me3.density.wig.zip
2.77 MB
05/Dec/12 4:38 AM
tester with sequence in it.gff3
0.3 kB
05/Dec/12 4:38 AM

Issue Links

relates to

BUG-663 Load Modes

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Alyssa Gulledge (Inactive) added a comment - 19/Aug/11 6:24 AM

IF data is successfully loaded, and set to whole genome, you get the following error when clicking on 'chose load mode'

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Alyssa Gulledge (Inactive) added a comment - 19/Aug/11 6:24 AM IF data is successfully loaded, and set to whole genome, you get the following error when clicking on 'chose load mode' Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.LoadModeTable$ColumnRenderer.getTableCellRendererComponent(LoadModeTable.java:167) at javax.swing.JTable$AccessibleJTable.getAccessibleChild(JTable.java:7023) at javax.swing.JTable$AccessibleJTable.getAccessibleAt(JTable.java:7410) at javax.swing.JTable$AccessibleJTable.valueChanged(JTable.java:6925) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:167) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:137) at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:668) at javax.swing.plaf.basic.BasicTableUI$Handler.setValueIsAdjusting(BasicTableUI.java:924) at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1136) at javax.swing.plaf.basic.BasicTableUI$MouseInputHandler.mouseReleased(BasicTableUI.java:772) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273) at java.awt.Component.processMouseEvent(Component.java:6352) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6117) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4714) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4544) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212) at java.awt.Container.dispatchEventImpl(Container.java:2129) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4544) at java.awt.EventQueue.dispatchEvent(EventQueue.java:635) 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)

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Hiral Vora (Inactive) added a comment - 19/Aug/11 11:07 AM

It doesn't seem to be consistent. I was not able to reproduce it. Can you try it out once more?

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Hiral Vora (Inactive) added a comment - 19/Aug/11 11:07 AM It doesn't seem to be consistent. I was not able to reproduce it. Can you try it out once more?

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Alyssa Gulledge (Inactive) added a comment - 22/Aug/11 8:12 AM

The actual bug seems to be clicking on "whole genome" throws the exception, no matter where the file is from, and no matter what file type.

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Alyssa Gulledge (Inactive) added a comment - 22/Aug/11 8:12 AM The actual bug seems to be clicking on "whole genome" throws the exception, no matter where the file is from, and no matter what file type.

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David Norris (Inactive) added a comment - 23/Aug/11 11:09 AM

I confirmed this bug. Its apparently an old bug which has gone unnoticed since I also found the bug in IGB 6.5.3.

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David Norris (Inactive) added a comment - 23/Aug/11 11:09 AM I confirmed this bug. Its apparently an old bug which has gone unnoticed since I also found the bug in IGB 6.5.3.

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David Norris (Inactive) added a comment - 23/Aug/11 11:31 AM

fixed in revision 8737

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David Norris (Inactive) added a comment - 23/Aug/11 11:31 AM fixed in revision 8737

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 7:33 AM

Passed v9845 Windows

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 7:33 AM Passed v9845 Windows

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Anuj Puram (Inactive) added a comment - 20/Jan/12 7:02 AM

Passed 6.7.0 (9891) on Mac

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Anuj Puram (Inactive) added a comment - 20/Jan/12 7:02 AM Passed 6.7.0 (9891) on Mac

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Vineeth Mylapur (Inactive) added a comment - 12/Jun/12 4:48 AM

Passed 7.0 (11934) on windows.

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Vineeth Mylapur (Inactive) added a comment - 12/Jun/12 4:48 AM Passed 7.0 (11934) on windows.

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Richard Linchangco (Inactive) added a comment - 29/Nov/12 10:07 AM

Please attach test files (gff and wig).

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Richard Linchangco (Inactive) added a comment - 29/Nov/12 10:07 AM Please attach test files (gff and wig).

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Richard Linchangco (Inactive) added a comment - 05/Dec/12 12:13 PM

Passed V.13674, Mac, Java 1.7.0_09

No exceptions when clicking on 'Load Mode' > 'Genome'

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Richard Linchangco (Inactive) added a comment - 05/Dec/12 12:13 PM Passed V.13674, Mac, Java 1.7.0_09 No exceptions when clicking on 'Load Mode' > 'Genome'

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

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Dates

Created:

19/Aug/11 6:22 AM

Updated:

10/Dec/12 8:05 AM

Resolved:

06/Dec/12 7:48 AM