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  1. Bug Repository
  2. BUG-25

Make mismatch graph can be run without BAM file loaded.

          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

                Task - A task that needs to be done. BUG-639 IGB generated graphs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  adam Adam Baxter (Inactive) added a comment -

                  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 Adam Baxter (Inactive) added a comment - 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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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9854 Windows

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                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9854 Windows
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed (v9906) on Mac

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                  anuj Anuj Puram (Inactive) added a comment - Passed (v9906) on Mac
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  originally reported by Adam Baxter

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                  alyssa Alyssa Gulledge (Inactive) added a comment - originally reported by Adam Baxter
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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited

                  Passed on 7.0.0 (11982) Mac.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - - edited Passed on 7.0.0 (11982) Mac.

                    People

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

                      • Created:
                        Updated:
                        Resolved: