[BUG-839] implement Cufflinks GTF parser for IGB 7.0 (as plugin?) - JIRA UNCC

Details

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

Description

Please support CuffLinks GTF - this is a pretty important format and would help us get more users if we support it.
I attach an example.
Note that some "extra feature" fields are quantitative. It would be good to ensure that these are read in as floats not character strings and that they be available for the "color by score" feature. Note also that individual exons have scores and that the transcript as a whole has a score.
The attached file (Cufflinks_6K.gtf.gz) and its tabix index is from blueberry genome:
Vaccinium corymbosum genome versions V_corymbosum_scaffold_May_2013
Access it via private Loraine Lab RNASeq QL server http://transvar.org/illumina/ using your transvar user name and password.
I also attach an image showing how the file looks when parsed into IGB.
Note that CuffLinks probably has a non-standard implementation of GTF. However, the CuffLinks software is very, very widely used and even if the format is non-standard, IGB needs to support it.
Note that the second field is "Cufflinks" which is one way IGB can tell that the file is Cufflinks GTF.
Another option would be for the parser to detect that there are "exon" features that are not part of any parent "sim"
When that happens, IGB could open a window that asks the user about the format what the grouping feature can be.

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Cufflinks_6K.gtf.gz
4.80 MB
13/Jun/13 6:47 AM
Cufflinks_6K.gtf.gz.tbi
239 kB
13/Jun/13 6:47 AM
GTFinIGB.png
180 kB
13/Jun/13 6:47 AM

Issue Links

relates to

BUG-622 File format issues

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Ann Loraine created issue - 13/Jun/13 6:47 AM

Hiral Vora (Inactive) made changes - 24/Jun/13 6:53 AM

Field	Original Value	New Value
Project	IGB 7.0 [ 10140 ]	IGB 7.1 [ 10240 ]
Key	~~IGBC-1020~~	~~IGBD-252~~

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Hiral Vora (Inactive) added a comment - 24/Jun/13 6:53 AM

Fixed in r14748.

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Hiral Vora (Inactive) added a comment - 24/Jun/13 6:53 AM Fixed in r14748.

Hiral Vora (Inactive) made changes - 24/Jun/13 6:53 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 02/Jul/13 6:06 AM - edited

I do not have the bluebaerry set up as a genome, and I do not have the ref seq. When I drag it in as a custom genome:

every scaffold reports as 1000000000

If I drag it in the first time, it will load. If I drag it in from scratch the second time (ie make a second custom genome), it will NOT load.

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Alyssa Gulledge (Inactive) added a comment - 02/Jul/13 6:06 AM - edited I do not have the bluebaerry set up as a genome, and I do not have the ref seq. When I drag it in as a custom genome: every scaffold reports as 1000000000 If I drag it in the first time, it will load. If I drag it in from scratch the second time (ie make a second custom genome), it will NOT load.

Alyssa Gulledge (Inactive) made changes - 02/Jul/13 6:06 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 03/Jul/13 10:38 AM

Could not reproduce.

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Hiral Vora (Inactive) added a comment - 03/Jul/13 10:38 AM Could not reproduce.

Hiral Vora (Inactive) made changes - 03/Jul/13 10:38 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 22/Jul/13 10:25 AM

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

Alyssa Gulledge (Inactive) made changes - 22/Jul/13 10:25 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 01/Oct/13 7:06 AM

Issue Type

Improvement [ 4 ]

Bug [ 1 ]

Alyssa Gulledge (Inactive) made changes - 01/Oct/13 7:19 AM

Project	IGB 7.1 [ 10240 ]	Bug Repository [ 10030 ]
Key	~~IGBD-252~~	~~BUG-839~~

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:58 AM

Link

This issue relates to ~~BUG-622~~ [ ~~BUG-622~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 10:23 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Tarun Santosh [ tkanapar ]

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Tarun Santosh (Inactive) added a comment - 04/Oct/13 11:46 AM - edited

I was unable to load the files that are attached .Please look into this
It displays the following information
"Unable to load data set from the file "

The following error was displayed in the console

Exception in thread "AWT-EventQueue-3" java.lang.NullPointerException
at com.affymetrix.igb.view.load.JTableX.getCellRenderer(DataManagementTable.java:223)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(ComponentUI.java:153)
at javax.swing.JComponent.paintComponent(JComponent.java:760)
at javax.swing.JComponent.paint(JComponent.java:1037)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JViewport.paint(JViewport.java:795)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent._paintImmediately(JComponent.java:5106)
at javax.swing.JComponent.paintImmediately(JComponent.java:4890)
at javax.swing.RepaintManager$3.run(RepaintManager.java:814)
at javax.swing.RepaintManager$3.run(RepaintManager.java:802)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725)
at javax.swing.RepaintManager.access$1000(RepaintManager.java:46)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
at java.awt.Dialog$1.run(Dialog.java:1049)
at java.awt.Dialog$3.run(Dialog.java:1101)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1099)
at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:853)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621)
at com.affymetrix.igb.Application.infoPanel(Application.java:234)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.finished(GeneralLoadUtils.java:1323)
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:715)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
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-3" java.lang.NullPointerException
at com.affymetrix.igb.view.load.JTableX.getCellRenderer(DataManagementTable.java:223)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(ComponentUI.java:153)
at javax.swing.JComponent.paintComponent(JComponent.java:760)
at javax.swing.JComponent.paint(JComponent.java:1037)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JViewport.paint(JViewport.java:795)
at javax.swing.JComponent.paintChildren(JComponent.java:870)
at javax.swing.JComponent.paint(JComponent.java:1046)
at javax.swing.JComponent._paintImmediately(JComponent.java:5106)
at javax.swing.JComponent.paintImmediately(JComponent.java:4890)
at javax.swing.RepaintManager$3.run(RepaintManager.java:814)
at javax.swing.RepaintManager$3.run(RepaintManager.java:802)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725)
at javax.swing.RepaintManager.access$1000(RepaintManager.java:46)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
at java.awt.Dialog$1.run(Dialog.java:1049)
at java.awt.Dialog$3.run(Dialog.java:1101)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1099)
at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:853)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621)
at com.affymetrix.igb.Application.infoPanel(Application.java:234)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.finished(GeneralLoadUtils.java:1323)
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:715)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
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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Tarun Santosh (Inactive) added a comment - 04/Oct/13 11:46 AM - edited I was unable to load the files that are attached .Please look into this It displays the following information "Unable to load data set from the file " The following error was displayed in the console Exception in thread "AWT-EventQueue-3" java.lang.NullPointerException at com.affymetrix.igb.view.load.JTableX.getCellRenderer(DataManagementTable.java:223) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUI.paint(Unknown Source) at javax.swing.plaf.ComponentUI.update(ComponentUI.java:153) at javax.swing.JComponent.paintComponent(JComponent.java:760) at javax.swing.JComponent.paint(JComponent.java:1037) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205) at java.awt.Dialog$1.run(Dialog.java:1049) at java.awt.Dialog$3.run(Dialog.java:1101) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Dialog.show(Dialog.java:1099) at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:853) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621) at com.affymetrix.igb.Application.infoPanel(Application.java:234) at com.affymetrix.igb.view.load.GeneralLoadUtils$5.finished(GeneralLoadUtils.java:1323) 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:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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-3" java.lang.NullPointerException at com.affymetrix.igb.view.load.JTableX.getCellRenderer(DataManagementTable.java:223) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUI.paint(Unknown Source) at javax.swing.plaf.ComponentUI.update(ComponentUI.java:153) at javax.swing.JComponent.paintComponent(JComponent.java:760) at javax.swing.JComponent.paint(JComponent.java:1037) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205) at java.awt.Dialog$1.run(Dialog.java:1049) at java.awt.Dialog$3.run(Dialog.java:1101) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Dialog.show(Dialog.java:1099) at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:853) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621) at com.affymetrix.igb.Application.infoPanel(Application.java:234) at com.affymetrix.igb.view.load.GeneralLoadUtils$5.finished(GeneralLoadUtils.java:1323) 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:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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)

Tarun Santosh (Inactive) made changes - 04/Oct/13 11:47 AM

Assignee

Tarun Santosh [ tkanapar ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 08/Oct/13 5:16 AM

I had no problems - none of the reported problems appeared v. 15424, so closing this issue.

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Alyssa Gulledge (Inactive) added a comment - 08/Oct/13 5:16 AM I had no problems - none of the reported problems appeared v. 15424, so closing this issue.

Alyssa Gulledge (Inactive) made changes - 08/Oct/13 5:16 AM

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

Alyssa Gulledge (Inactive) made changes - 08/Oct/13 5:16 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

Assignee:

Unassigned

Reporter:

Ann Loraine

Votes:

0 Vote for this issue

Watchers:

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Dates

Created:

13/Jun/13 6:47 AM

Updated:

08/Oct/13 5:16 AM

Resolved:

08/Oct/13 5:16 AM