[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)

Attachments

Options
- Sort By Name
- Sort By Date
- Ascending
- Descending
- Thumbnails
- List
- Download All

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

Closed

Activity

Ascending order - Click to sort in descending order

Alyssa Gulledge (Inactive) created issue - 19/Aug/11 6:22 AM

Hide

Permalink

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'

Show

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)

Hide

Permalink

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?

Show

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?

Hiral Vora (Inactive) made changes - 19/Aug/11 11:07 AM

Field	Original Value	New Value
Assignee	Hiral Vora [ hiralv ]	Alyssa Gulledge [ alyssa ]

Hide

Permalink

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.

Show

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.

Alyssa Gulledge (Inactive) made changes - 22/Aug/11 8:12 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hiral Vora [ hiralv ]

Hiral Vora (Inactive) made changes - 22/Aug/11 11:18 AM

Assignee

Hiral Vora [ hiralv ]

David Norris [ david ]

Hide

Permalink

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.

Show

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.

Hide

Permalink

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

fixed in revision 8737

Show

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

David Norris (Inactive) made changes - 23/Aug/11 11:31 AM

Assignee

David Norris [ david ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 24/Aug/11 12:28 PM

Status	Open [ 1 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 24/Aug/11 12:28 PM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 24/Aug/11 12:28 PM

Project	IGB6.6 [ 10021 ]	Bug Repository [ 10030 ]
Key	~~IGBA-171~~	~~BUG-146~~

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 6:57 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee	Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 6:57 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 10/Jan/12 9:46 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Katharine Kubiak [ kkubiak ]

Hide

Permalink

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

Passed v9845 Windows

Show

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

Katharine Kubiak (Inactive) made changes - 18/Jan/12 7:33 AM

Assignee

Katharine Kubiak [ kkubiak ]

Anuj Puram [ anuj ]

Hide

Permalink

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

Passed 6.7.0 (9891) on Mac

Show

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

Anuj Puram (Inactive) made changes - 20/Jan/12 7:02 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:19 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:19 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Vineeth Mylapur (Inactive) made changes - 12/Jun/12 4:44 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Vineeth Mylapur [ smylapur ]

Hide

Permalink

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

Passed 7.0 (11934) on windows.

Show

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

Vineeth Mylapur (Inactive) made changes - 12/Jun/12 4:49 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Vineeth Mylapur [ smylapur ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 10:14 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:00 AM

Link

This issue relates to ~~BUG-623~~ [ ~~BUG-623~~ ]

Hide

Permalink

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

Please attach test files (gff and wig).

Show

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

Richard Linchangco (Inactive) made changes - 29/Nov/12 10:07 AM

Assignee

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 05/Dec/12 4:38 AM

Attachment		tester with sequence in it.gff3 [ 11768 ]
Attachment		GSM535746_3T3L1t1.H3K36me3.density.wig.zip [ 11769 ]

Alyssa Gulledge (Inactive) made changes - 05/Dec/12 4:38 AM

Assignee

Alyssa Gulledge [ alyssa ]

Richard Linchangco [ richard ]

Hide

Permalink

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'

Show

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'

Richard Linchangco (Inactive) made changes - 05/Dec/12 12:13 PM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 05/Dec/12 12:13 PM

Status	Resolved [ 5 ]	Closed [ 6 ]
Assignee	Richard Linchangco [ richard ]	Alyssa Gulledge [ alyssa ]

Richard Linchangco (Inactive) made changes - 05/Dec/12 12:14 PM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee	Alyssa Gulledge [ alyssa ]

Richard Linchangco (Inactive) made changes - 05/Dec/12 12:14 PM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee		Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:44 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:46 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:48 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 7:51 AM

Link

This issue relates to ~~BUG-663~~ [ ~~BUG-663~~ ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:01 AM

Link

This issue relates to BUG-664 [ BUG-664 ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:03 AM

Link

This issue relates to BUG-664 [ BUG-664 ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:05 AM

Link

This issue relates to ~~BUG-623~~ [ ~~BUG-623~~ ]

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

Votes:

0 Vote for this issue

Watchers:

0 Start watching this issue

Dates

Created:

19/Aug/11 6:22 AM

Updated:

10/Dec/12 8:05 AM

Resolved:

06/Dec/12 7:48 AM