Bug in P4

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Bug in P4

samsontu
It appears that the P4 release build 113 is not compatible with
Annotation Template view. Select a class triggers the following exception

BAD LISTENER: ()
Error logged
java.lang.NullPointerException
        at
uk.ac.manchester.cs.owl.OWLOntologyImpl.containsAxiom(OWLOntologyImpl
.java:422)
        at
org.coode.annotate.TemplateModel.getOntologiesContainingAnnotation(Te
mplateModel.java:103)
        at org.coode.annotate.Template.getToolTipText(Template.java:116)
        at org.coode.annotate.Template.rebuildUI(Template.java:94)
        at org.coode.annotate.Template.access$000(Template.java:43)
        at
org.coode.annotate.Template$1.modelStructureChanged(Template.java:53)

        at
org.coode.annotate.TemplateModel.notifyStructureChanged(TemplateModel
.java:178)
        at
org.coode.annotate.TemplateModel.setEntity(TemplateModel.java:157)
        at org.coode.annotate.Template.setEntity(Template.java:67)
        at
org.coode.annotate.AnnotationTemplateView.updateView(AnnotationTempla
teView.java:73)
        at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.upda
teViewContentAndHeader(AbstractOWLSelectionViewComponent.java:189)
        at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.se
lectionChanged(AbstractOWLSelectionViewComponent.java:67)
        at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSele
ctionChanged(OWLSelectionModelImpl.java:103)
        at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSe
lectedObject(OWLSelectionModelImpl.java:91)
        at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedObject(OWLSelectionModelImpl.java:82)
        at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedEntity(OWLSelectionModelImpl.java:114)
        at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setS
electedEntity(AbstractOWLSelectionViewComponent.java:122)
        at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent.transmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
        at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent$6.valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
        at javax.swing.JTree.fireValueChanged(JTree.java:2823)
        at
javax.swing.JTree$TreeSelectionRedirector.valueChanged(JTree.java:319
4)
        at
javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(DefaultTr
eeSelectionModel.java:629)
        at
javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(DefaultTr
eeSelectionModel.java:1078)
        at
javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(DefaultT
reeSelectionModel.java:287)
        at
javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(DefaultTr
eeSelectionModel.java:170)
        at javax.swing.JTree.setSelectionPath(JTree.java:1598)
        at
javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(BasicTreeUI.jav
a:2316)
        at
javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(BasicTreeU
I.java:3517)
        at
javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(BasicTreeUI.j
ava:3456)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
        at java.awt.Component.processMouseEvent(Component.java:6038)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
        at java.awt.Component.processEvent(Component.java:5806)
        at java.awt.Container.processEvent(Container.java:2058)
        at java.awt.Component.dispatchEventImpl(Component.java:4413)
        at java.awt.Container.dispatchEventImpl(Container.java:2116)
        at java.awt.Component.dispatchEvent(Component.java:4243)
        at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322
)
        at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3983)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
        at java.awt.Container.dispatchEventImpl(Container.java:2102)
        at java.awt.Window.dispatchEventImpl(Window.java:2440)
        at java.awt.Component.dispatchEvent(Component.java:4243)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
        at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:273)
        at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:183)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:173)
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)

        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)


--
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

_______________________________________________
p4-feedback mailing list
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Re: Bug in P4

Nick Drummond
Hi Samson,

What version of the plugin are you using? (See the About box)
Annotation template 1.0.7 appears to work for me.
Could you send me your ontology?

Nick


2009/6/18 Samson Tu <[hidden email]>
It appears that the P4 release build 113 is not compatible with
Annotation Template view. Select a class triggers the following exception

BAD LISTENER: ()
Error logged
java.lang.NullPointerException
       at
uk.ac.manchester.cs.owl.OWLOntologyImpl.containsAxiom(OWLOntologyImpl
.java:422)
       at
org.coode.annotate.TemplateModel.getOntologiesContainingAnnotation(Te
mplateModel.java:103)
       at org.coode.annotate.Template.getToolTipText(Template.java:116)
       at org.coode.annotate.Template.rebuildUI(Template.java:94)
       at org.coode.annotate.Template.access$000(Template.java:43)
       at
org.coode.annotate.Template$1.modelStructureChanged(Template.java:53)

       at
org.coode.annotate.TemplateModel.notifyStructureChanged(TemplateModel
.java:178)
       at
org.coode.annotate.TemplateModel.setEntity(TemplateModel.java:157)
       at org.coode.annotate.Template.setEntity(Template.java:67)
       at
org.coode.annotate.AnnotationTemplateView.updateView(AnnotationTempla
teView.java:73)
       at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.upda
teViewContentAndHeader(AbstractOWLSelectionViewComponent.java:189)
       at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.se
lectionChanged(AbstractOWLSelectionViewComponent.java:67)
       at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSele
ctionChanged(OWLSelectionModelImpl.java:103)
       at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSe
lectedObject(OWLSelectionModelImpl.java:91)
       at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedObject(OWLSelectionModelImpl.java:82)
       at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedEntity(OWLSelectionModelImpl.java:114)
       at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setS
electedEntity(AbstractOWLSelectionViewComponent.java:122)
       at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent.transmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
       at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent$6.valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
       at javax.swing.JTree.fireValueChanged(JTree.java:2823)
       at
javax.swing.JTree$TreeSelectionRedirector.valueChanged(JTree.java:319
4)
       at
javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(DefaultTr
eeSelectionModel.java:629)
       at
javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(DefaultTr
eeSelectionModel.java:1078)
       at
javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(DefaultT
reeSelectionModel.java:287)
       at
javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(DefaultTr
eeSelectionModel.java:170)
       at javax.swing.JTree.setSelectionPath(JTree.java:1598)
       at
javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(BasicTreeUI.jav
a:2316)
       at
javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(BasicTreeU
I.java:3517)
       at
javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(BasicTreeUI.j
ava:3456)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at
java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:26
2)
       at java.awt.Component.processMouseEvent(Component.java:6038)
       at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
       at java.awt.Component.processEvent(Component.java:5806)
       at java.awt.Container.processEvent(Container.java:2058)
       at java.awt.Component.dispatchEventImpl(Component.java:4413)
       at java.awt.Container.dispatchEventImpl(Container.java:2116)
       at java.awt.Component.dispatchEvent(Component.java:4243)
       at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322
)
       at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3983)

       at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
       at java.awt.Container.dispatchEventImpl(Container.java:2102)
       at java.awt.Window.dispatchEventImpl(Window.java:2440)
       at java.awt.Component.dispatchEvent(Component.java:4243)
       at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
       at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:273)
       at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:183)
       at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:173)
       at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)

       at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)

       at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)


--
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback
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Re: Bug in P4

samsontu

Checked and found the Annotation Template version was 1.0. Version 1.0.7
works for me.

Earlier, when I checked File/Preference/Plugins Autot update, it  said
no update.

Thanks.

Samson

Nick Drummond wrote:
> Hi Samson,
>
> What version of the plugin are you using? (See the About box)
> Annotation template 1.0.7 appears to work for me.
> Could you send me your ontology?
>

--
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback
Reply | Threaded
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Re: Bug in P4

Nick Drummond
Hi Samson,

Yes, this version was before auto-update was written.

Nick


2009/6/18 Samson Tu <[hidden email]>

Checked and found the Annotation Template version was 1.0. Version 1.0.7
works for me.

Earlier, when I checked File/Preference/Plugins Autot update, it  said
no update.

Thanks.

Samson

Nick Drummond wrote:
> Hi Samson,
>
> What version of the plugin are you using? (See the About box)
> Annotation template 1.0.7 appears to work for me.
> Could you send me your ontology?
>

--
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback