[BUG-25] Make mismatch graph can be run without BAM file loaded. - JIRA UNCC

Details

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

OS X: 10.6
Java: "1.6.0_24"
IGB: 7791

Description

Steps to reproduce:
Load Arabidopsis thaliana version 'A_thaliana_Jun_2009'.
Right click on a track (+ or -) and choose "Make Mismatch Graph"

UI becomes unresponsive. IGB generates an exception, added in comments.
UI eventually becomes responsive even though the loading bar is still animating.

Attachments

Issue Links

is blocked by

BUG-639 IGB generated graphs

Closed

Activity

Ascending order - Click to sort in descending order

Adam Baxter (Inactive) created issue - 21/Mar/11 9:48 AM

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Adam Baxter (Inactive) added a comment - 21/Mar/11 9:48 AM

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 0
at com.affymetrix.genometryImpl.GraphSym.<init>(GraphSym.java:69)
at com.affymetrix.genometryImpl.MisMatchGraphSym.<init>(MisMatchGraphSym.java:33)
at com.affymetrix.genometryImpl.SeqSymSummarizer.createMisMatchGraph(SeqSymSummarizer.java:115)
at com.affymetrix.genometryImpl.SeqSymSummarizer.getMismatchGraph(SeqSymSummarizer.java:100)
at com.affymetrix.igb.view.DependentData.createMisMatchGraph(DependentData.java:85)
at com.affymetrix.igb.view.DependentData.createTier(DependentData.java:54)
at com.affymetrix.igb.view.TrackView.addToDependentList(TrackView.java:260)
at com.affymetrix.igb.tiers.SeqMapViewPopup.addMisMatchTier(SeqMapViewPopup.java:553)
at com.affymetrix.igb.tiers.SeqMapViewPopup.access$800(SeqMapViewPopup.java:48)
at com.affymetrix.igb.tiers.SeqMapViewPopup$19.actionPerformed(SeqMapViewPopup.java:219)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
at java.awt.Component.processMouseEvent(Component.java:6374)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6139)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4736)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4566)
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:4566)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
at java.awt.EventQueue.access$000(EventQueue.java:86)
at java.awt.EventQueue$1.run(EventQueue.java:639)
at java.awt.EventQueue$1.run(EventQueue.java:637)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:653)
at java.awt.EventQueue$2.run(EventQueue.java:651)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
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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Adam Baxter (Inactive) added a comment - 21/Mar/11 9:48 AM Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 0 at com.affymetrix.genometryImpl.GraphSym.<init>(GraphSym.java:69) at com.affymetrix.genometryImpl.MisMatchGraphSym.<init>(MisMatchGraphSym.java:33) at com.affymetrix.genometryImpl.SeqSymSummarizer.createMisMatchGraph(SeqSymSummarizer.java:115) at com.affymetrix.genometryImpl.SeqSymSummarizer.getMismatchGraph(SeqSymSummarizer.java:100) at com.affymetrix.igb.view.DependentData.createMisMatchGraph(DependentData.java:85) at com.affymetrix.igb.view.DependentData.createTier(DependentData.java:54) at com.affymetrix.igb.view.TrackView.addToDependentList(TrackView.java:260) at com.affymetrix.igb.tiers.SeqMapViewPopup.addMisMatchTier(SeqMapViewPopup.java:553) at com.affymetrix.igb.tiers.SeqMapViewPopup.access$800(SeqMapViewPopup.java:48) at com.affymetrix.igb.tiers.SeqMapViewPopup$19.actionPerformed(SeqMapViewPopup.java:219) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.AbstractButton.doClick(AbstractButton.java:389) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850) at java.awt.Component.processMouseEvent(Component.java:6374) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6139) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4736) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4566) 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:4566) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680) at java.awt.EventQueue.access$000(EventQueue.java:86) at java.awt.EventQueue$1.run(EventQueue.java:639) at java.awt.EventQueue$1.run(EventQueue.java:637) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:653) at java.awt.EventQueue$2.run(EventQueue.java:651) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:650) 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)

Hiral Vora (Inactive) made changes - 21/Mar/11 10:43 AM

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

Alyssa Gulledge (Inactive) made changes - 22/Mar/11 6:18 AM

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

Alyssa Gulledge (Inactive) made changes - 22/Mar/11 6:18 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 08/Apr/11 10:45 AM

Project	IGB6.5 [ 10010 ]	Bug Repository [ 10030 ]
Key	~~IGB-109~~	~~BUG-25~~

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 5:25 AM

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

David Norris (Inactive) made changes - 01/Sep/11 5:52 AM

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

David Norris (Inactive) made changes - 01/Sep/11 5:52 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 10/Jan/12 8:42 AM

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

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 12:00 PM

Passed v9854 Windows

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 12:00 PM Passed v9854 Windows

Katharine Kubiak (Inactive) made changes - 18/Jan/12 12:00 PM

Assignee

Katharine Kubiak [ kkubiak ]

Anuj Puram [ anuj ]

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Anuj Puram (Inactive) added a comment - 23/Jan/12 4:43 AM

Passed (v9906) on Mac

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Anuj Puram (Inactive) added a comment - 23/Jan/12 4:43 AM Passed (v9906) on Mac

Anuj Puram (Inactive) made changes - 23/Jan/12 4:43 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:57 AM

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

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:57 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 30/Apr/12 8:25 AM

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

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Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 8:25 AM

originally reported by Adam Baxter

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Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 8:25 AM originally reported by Adam Baxter

Alyssa Gulledge (Inactive) made changes - 30/Apr/12 8:25 AM

Reporter

Adam Baxter [ adam ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 30/Apr/12 8:25 AM

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

Fuquan Wang (Inactive) made changes - 12/Jun/12 11:12 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Fuquan Wang [ fwang4 ]

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 11:13 AM - edited

Passed on 7.0.0 (11982) Mac.

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 11:13 AM - edited Passed on 7.0.0 (11982) Mac.

Fuquan Wang (Inactive) made changes - 14/Jun/12 8:51 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Fuquan Wang [ fwang4 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 10:25 AM

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

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 8:48 AM

Link

This issue is blocked by ~~BUG-639~~ [ ~~BUG-639~~ ]

Alyssa Gulledge (Inactive) made changes - 13/Dec/12 10:58 AM

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

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

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Dates

Created:

21/Mar/11 9:48 AM

Updated:

13/Dec/12 10:58 AM

Resolved:

13/Dec/12 10:58 AM