brkmyr / co-ode-owl-plugins Goto Github PK

We can filter by lang for untyped values.
It would be good if we could filter by type aswell.

Reported by Alan. Steps unknown.

java.lang.NullPointerException
at java.util.TreeMap.compare(TreeMap.java:1093)
at java.util.TreeMap.put(TreeMap.java:465)
at java.util.TreeSet.add(TreeSet.java:210)
at java.util.AbstractCollection.addAll(AbstractCollection.java:318)
at java.util.TreeSet.addAll(TreeSet.java:258)
at java.util.TreeSet.<init>(TreeSet.java:143)
at 
uk.ac.manchester.cs.owl.OWLNaryClassAxiomImpl.<init>(OWLNaryClassAxiomImpl.java:
49)
at 
uk.ac.manchester.cs.owl.OWLSubClassAxiomImpl.<init>(OWLSubClassAxiomImpl.java:46
)
at 
uk.ac.manchester.cs.owl.OWLDataFactoryImpl.getOWLSubClassAxiom(OWLDataFactoryImp
l.java:670)
at org.coode.matrix.model.helper.FillerHelper.setFillers(FillerHelper.java:132)
at 
org.coode.matrix.model.impl.RestrictionTreeMatrixModel.setMatrixValue(Restrictio
nTreeMatrixModel.java:90)
at 
org.coode.matrix.model.impl.RestrictionTreeMatrixModel.setMatrixValue(Restrictio
nTreeMatrixModel.java:45)
at 
org.coode.matrix.model.api.AbstractMatrixModel.setValueAt(AbstractMatrixModel.ja
va:131)
at 
org.coode.matrix.model.api.AbstractMatrixModel.setValueAt(AbstractMatrixModel.ja
va:48)
at 
uk.ac.manchester.cs.bhig.jtreetable.AbstractTreeTableModel.setValueAt(AbstractTr
eeTableModel.java:163)
at javax.swing.JTable.setValueAt(JTable.java:1926)
at javax.swing.JTable.editingStopped(JTable.java:3339)
at 
javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:124)
at javax.swing.AbstractCellEditor.stopCellEditing(AbstractCellEditor.java:67)
at 
org.coode.matrix.ui.editor.OWLObjectListEditor.stopCellEditing(OWLObjectListEdit
or.java:115)
at javax.swing.JTable.editCellAt(JTable.java:2667)
at 
javax.swing.plaf.basic.BasicTableUI$Handler.adjustFocusAndSelection(BasicTableUI
.java:952)
at 
javax.swing.plaf.basic.BasicTableUI$Handler.mousePressed(BasicTableUI.java:919)
at 
javax.swing.plaf.basic.BasicTableUI$MouseInputHandler.mousePressed(BasicTableUI.
java:749)
at apple.laf.CUIAquaTable$MouseInputHandler.mousePressed(CUIAquaTable.java:73)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:222)
...

The colon gets escaped as %3.

Links are correct but safari for example refuses to follow them.
Opening an html file directly from Finder with double click causes the URL
to contain %253 instead. Changing this to %3 fails.

This will make it easier to see why certain results have matched.
Hard to do with regexp.

Ctrl-Tab moves between fields, but tab does nothing (either it should enter
a tab character or it should switch focus).

Would be nice to have, in addition to text and and multiline, a choice that 
lets you select an entity 
as the target of the annotation

What steps will reproduce the problem?
  In Protege 4 (build 113) select Tools/Export OWLDoc

What is the expected output? What do you see instead?

  For Classes with more than 3 subclasses there is a "N more..." link at 
the end of the Asserted class hierarchy where N is the number of more 
subclasses. Nothing happens when clicking this link. JavaScript Debugger 
says:

> missing ) after argument list 
>   showSubs(''Behaviour Characteristic'');

Using the online version from http://code.google.com/p/ontology-browser/ 
the "N more..." links are working perfect...


What version of the product are you using? On what operating system?
  Protege 4, build 113
  OWLDoc plugin 1.0.9


Christian.

What steps will reproduce the problem?
1. Load bibo.owl
2. Run OWLDoc

What is the expected output? What do you see instead?

If you check the generated HTML, there will be missing annotations fo the
object property "dcterms:format". I am wondering if it is caused by the
skos:example Annotation Property?

What version of the product are you using? On what operating system?

1.0.6

Please provide any additional information below.

All information is above.

Allow the user to save and recover the layout (columns etc)

Needs to be able to handle data values/ranges

in annotations

What steps will reproduce the problem?
1. Start Protege 4.1 (Windows 64 bit) after installing the Annotation Template 
plugin and click on the Entities Tab
2. Create a new ontology and specify OWL/XML as the Ontology Format
3. Attempt to display the Annotation template using Window->Views-Misc 
Views->Annotation Template
4. Position the black circle to designate a location for the Annotation 
Template Window - in this case on the top of the right side
5. When the mouse is clicked to designate the location of the Annotation 
Template Window the red triangle appears to the right of the search window at 
the top of the Protege main window.  The stack trace shown below is displayed.

What is the expected output? What do you see instead?
I expect to see a window that allows me to edit and view annotations.  The 
stack trace displayed by the error dialog is shown here:

Error 1 Logged at Fri Jun 29 10:52:19 EDT 2012
NoClassDefFoundError: 
org/protege/editor/owl/ui/renderer/OWLAnnotationCellRenderer2
    org.coode.annotate.Template.<clinit>(Template.java:45)
    org.coode.annotate.AnnotationTemplateView.initialiseView(AnnotationTemplateView.java:60)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.initialiseOWLView(AbstractOWLSelectionViewComponent.java:118)
    org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:61)
    org.protege.editor.core.ui.view.View.createContent(View.java:439)
    org.protege.editor.core.ui.view.View.createUI(View.java:219)
    org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:149)
    java.awt.Component.processHierarchyEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.Component.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addImpl(Unknown Source)
    java.awt.Container.add(Unknown Source)
    org.coode.mdock.NodePanel.addNode(NodePanel.java:65)
    org.coode.mdock.NodePanel.addNode(NodePanel.java:71)
    org.coode.mdock.NodePanel.addNode(NodePanel.java:71)
    org.coode.mdock.NodePanel.rebuild(NodePanel.java:59)
    org.coode.mdock.DynamicConfigPanel$2.mouseClicked(DynamicConfigPanel.java:82)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue$2.run(Unknown Source)
    java.awt.EventQueue$2.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
--------------------------------------------------------------------------------
-------------------

What version of the product are you using? On what operating system?
Protege 4.1 hosted on windows 64-bit

Please provide any additional information below.
I am new to Protege and don't know what other information would be helpffull

See:

http://www.nabble.com/Matrix-not-showing-ans-and-Property-Matrix-exception-throw
n-td22291470.html

Implement Findable on tree

Annotations are rendered as OWL constants with "" etc
Entering anything without it being valid format will not parse and therefore 
the edit will have no 
effect - we should have a dropthrough parser that just inserts the value into 
an untyped literal with 
no language.
Further edits of an existing value also get ignored sometimes

Also, editing requires "" around the values which is a pain if there is a
single untyped literal value with no language.

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

Only updates when the selection is changed.

What steps will reproduce the problem?
1. Start protege
2. Error on load

What is the expected output? What do you see instead?
The plugin is not started.
I got the error in console
Problem starting plugin Annotation Template View
org.osgi.framework.BundleException: The bundle could not be resolved. Reason: Mi
ssing Constraint: Require-Bundle: org.protege.editor.core.application; bundle-ve
rsion="4.1.0"
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.getResolverEr
ror(AbstractBundle.java:1313)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.getResolution
FailureException(AbstractBundle.java:1297)
        at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(Bundl
eHost.java:309)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(Abstrac
tBundle.java:280)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(Abstrac
tBundle.java:272)
        at org.protege.editor.core.BundleManager.startPlugins(BundleManager.java
:144)
        at org.protege.editor.core.BundleManager.loadPlugins(BundleManager.java:
45)
        at org.protege.editor.core.ProtegeApplication.loadPlugins(ProtegeApplica
tion.java:263)
        at org.protege.editor.core.ProtegeApplication.initApplication(ProtegeApp
lication.java:158)
        at org.protege.editor.core.ProtegeApplication.start(ProtegeApplication.j
ava:105)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(Bund
leContextImpl.java:782)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActiv
ator(BundleContextImpl.java:773)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(Bund
leContextImpl.java:754)
        at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(Bundl
eHost.java:352)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.resume(Abstra
ctBundle.java:370)
        at org.eclipse.osgi.framework.internal.core.Framework.resumeBundle(Frame
work.java:1068)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.resumeBund
les(StartLevelManager.java:557)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.incFWSL(St
artLevelManager.java:464)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.doSetStart
Level(StartLevelManager.java:248)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.dispatchEv
ent(StartLevelManager.java:445)
        at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventM
anager.java:220)
        at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(Even
tManager.java:330)
Problem starting plugin Matrix Views
org.osgi.framework.BundleException: The bundle could not be resolved. Reason: Mi
ssing Constraint: Require-Bundle: org.protege.editor.core.application; bundle-ve
rsion="4.1.0"
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.getResolverEr
ror(AbstractBundle.java:1313)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.getResolution
FailureException(AbstractBundle.java:1297)
        at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(Bundl
eHost.java:309)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(Abstrac
tBundle.java:280)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(Abstrac
tBundle.java:272)
        at org.protege.editor.core.BundleManager.startPlugins(BundleManager.java
:144)
        at org.protege.editor.core.BundleManager.loadPlugins(BundleManager.java:
45)
        at org.protege.editor.core.ProtegeApplication.loadPlugins(ProtegeApplica
tion.java:263)
        at org.protege.editor.core.ProtegeApplication.initApplication(ProtegeApp
lication.java:158)
        at org.protege.editor.core.ProtegeApplication.start(ProtegeApplication.j
ava:105)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(Bund
leContextImpl.java:782)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActiv
ator(BundleContextImpl.java:773)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(Bund
leContextImpl.java:754)
        at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(Bundl
eHost.java:352)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.resume(Abstra
ctBundle.java:370)
        at org.eclipse.osgi.framework.internal.core.Framework.resumeBundle(Frame
work.java:1068)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.resumeBund
les(StartLevelManager.java:557)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.incFWSL(St
artLevelManager.java:464)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.doSetStart
Level(StartLevelManager.java:248)
        at org.eclipse.osgi.framework.internal.core.StartLevelManager.dispatchEv
ent(StartLevelManager.java:445)
        at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventM
anager.java:220)
        at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(Even
tManager.java:330)

What version of the product are you using? On what operating system?
Protege 4.0.2
I test the versions 1_1_0 and 1_1_1, I'm on Windows XP

The browser and OWLDoc cannot display non-ascii characters.
For example the chinese version of the amino acid ontology.

Current Protégé, i.e. 4.1 or 4.2, comes with an updated version of the OWL 
API, which does not contain an org.semanticweb.owl package any more:

java.lang.ClassNotFoundException: 
org.semanticweb.owl.inference.OWLReasonerException not found by org.coode.oae 
[16]

http://www.cs.man.ac.uk/~iannonel/owlcalculations/downloads.html says OWL API 
2.1.1 *or later*. However it seems that since rev. 1209 org.semanticweb.owl has 
been renamed to org.semanticweb.owlapi: 
http://owlapi.svn.sourceforge.net/viewvc/owlapi/v3/trunk/api/src/main/java/org/s
emanticweb/?pathrev=1209

What steps will reproduce the problem?
1. try to use "класс_1", "класс_2" as class names in Protege 4.
2. make them equ.
3. create OWLDoc pages.

What is the expected output? What do you see instead?
"класс_1", "класс_2". abrakadabra in IE8. link does not work in IE, 
Firefox and Chrom.

What version of the product are you using? On what operating system?

Protege 4.0 (Build 113)
Please provide any additional information below.

in file there are ontology and OWLDoc.

Not sure how this should work.
Either 
- a column only specifies a particular cardinality or
- some notation is used for each value (bracketed cardinality?) but this 
requires a new parser

What steps will reproduce the problem?
1. Open a new OWL file with default settings
2. Goto Classes tab
3. Set view to Annotation template
4. Create new class (sub class of Thing)
5. Enter text into a field on Annotation template (such as comment)

What is the expected output? What do you see instead?
Error triangle shown to the right of the search window
In command window the following text is shown in the attached file

What version of the product are you using? On what operating system?
Protege 4.2.0 (build 249)
Annotation Template 1.1.1
Windows 7 Ultimate x64

Please provide any additional information below.
Annotation fields with language attribute settings are what I am looking for if 
this bug can be resolved.

1 pound spaghetti
For Sauce: Heat oil in heavy large pot over medium-low heat. Add onion; saute 
until golden, about 10 minutes. Add garlic; stir 1 minute. Add sherry and stir 
30 seconds. Add tomatoes with juices, Romano cheese, and 2 tablespoons basil; 
bring to boil. Reduce heat; simmer until sauce thickens, breaking up tomatoes 
with fork, about 1 hour. Mix in 2 tablespoons basil. Season with salt and 
pepper. Set sauce aside.
For Meatballs: Preheat oven to 350F. Lightly oil baking sheet. Mix crumbs and 
milk in medium bowl; let stand 5 minutes. Mix in Parmesan, onion, basil, egg, 
garlic and pepper. Add sausage, ground beef, pine nuts and currants; blend 
well. Using wet hands, form mixture into 1 1/4-inch balls. Place on baking 
sheet. Bake until meatballs are light brown and cooked through, about 30 
minutes. Add to sauce.
Cook spaghetti in large pot of boiling salted water until just tender but still 
firm to bite. Drain. Mound in dish. Bring sauce and meatballs to simmer. Spoon 
over spaghetti.

Add an annotation column.

java.lang.NullPointerException
    at
org.coode.matrix.ui.view.AbstractTreeMatrixView$2.getTableCellRendererComponent(
AbstractTreeMatrixView.java:106)
    at javax.swing.JTable.prepareRenderer(JTable.java:3928)
    at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2072)
    at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:1974)
    at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1897)
    at javax.swing.plaf.ComponentUI.update(ComponentUI.java:154)
    at javax.swing.JComponent.paintComponent(JComponent.java:743)

What steps will reproduce the problem?
1. install termine plugin as from the instruction
2. open protege 4.0.2
3. launch Tools->Import from TerMine

What is the expected output? What do you see instead?

see nothing but the 
following exception:


Error 1 Logged at Tue Oct 05 14:25:05 CEST 2010
NullPointerException: null
    javax.swing.text.JTextComponent.setCaretPosition(Unknown Source)
    javax.swing.text.DefaultFormatter.positionCursorAtInitialLocation(Unknown Source)
    javax.swing.text.DefaultFormatter.install(Unknown Source)
    javax.swing.text.InternationalFormatter.install(Unknown Source)
    javax.swing.JFormattedTextField.setFormatter(Unknown Source)
    javax.swing.JFormattedTextField.setValue(Unknown Source)
    javax.swing.JFormattedTextField.setFormatterFactory(Unknown Source)
    javax.swing.JFormattedTextField.setValue(Unknown Source)
    javax.swing.JSpinner$DefaultEditor.<init>(Unknown Source)
    javax.swing.JSpinner$NumberEditor.<init>(Unknown Source)
    javax.swing.JSpinner$NumberEditor.<init>(Unknown Source)
    javax.swing.JSpinner$NumberEditor.<init>(Unknown Source)
    javax.swing.JSpinner.createEditor(Unknown Source)
    javax.swing.JSpinner.<init>(Unknown Source)
    uk.ac.nactem.owl.termine.TermineResultsPanel.buildPane(TermineResultsPanel.java:132)
    uk.ac.nactem.owl.termine.TermineResultsPanel.<init>(TermineResultsPanel.java:77)
    uk.ac.nactem.owl.termine.TermineWizardResultsPage.createUI(TermineWizardResultsPage.java:59)
    org.protege.editor.core.ui.wizard.AbstractWizardPanel.createUI(AbstractWizardPanel.java:132)
    org.protege.editor.core.ui.wizard.AbstractWizardPanel.<init>(AbstractWizardPanel.java:73)
    org.protege.editor.owl.ui.AbstractOWLWizardPanel.<init>(AbstractOWLWizardPanel.java:21)
    uk.ac.nactem.owl.termine.TermineWizardResultsPage.<init>(TermineWizardResultsPage.java:51)
    uk.ac.nactem.owl.termine.TermineWizard.<init>(TermineWizard.java:45)
    uk.ac.nactem.owl.termine.TermineMenuItem.actionPerformed(TermineMenuItem.java:42)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
--------------------------------------------------------------------------------
-------------------



What version of the product are you using? On what operating system?

Termine plugin 1.0
Protege 4.0.115
JVM 1.5.0_11_b03  (also tried with Java6)
Windows XP


Please provide any additional information below.

What steps will reproduce the problem?
1. Install the latest Bookmark View plugin (1.2.1) for Protege 4.1 (102) alpha
2. Close Protege (as per plugin instructions)
3. Open some ontology in Protege
4. Click on Bookmarks menu option

What is the expected output? What do you see instead?
The expected output is a Bookmarks window. I get some errors instead, with
no other visible outcome:

Error 1 Logged at Mon Mar 22 15:52:09 ADT 2010
NoSuchMethodError:
org.protege.editor.owl.model.OWLModelManager.getOWLOntologyManager()Lorg/semanti
cweb/owlapi/model/OWLOntologyManager;
    org.coode.bookmark.BookmarkModel.refill(BookmarkModel.java:157)
    org.coode.bookmark.BookmarkModel.<init>(BookmarkModel.java:84)
    org.coode.bookmark.BookmarkList.<init>(BookmarkList.java:63)
    org.coode.bookmark.BookmarkView.initialiseView(BookmarkView.java:86)

org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.initialiseOWLVi
ew(AbstractOWLSelectionViewComponent.java:110)

org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLVi
ewComponent.java:61)
    org.protege.editor.core.ui.view.View.createContent(View.java:416)
    org.protege.editor.core.ui.view.View.createUI(View.java:196)
    org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:126)
    java.awt.Component.processHierarchyEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.Component.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addNotify(Unknown Source)
    javax.swing.JComponent.addNotify(Unknown Source)
    java.awt.Container.addImpl(Unknown Source)
    javax.swing.JSplitPane.addImpl(Unknown Source)
    java.awt.Container.add(Unknown Source)

org.protege.editor.core.ui.view.ViewHolder$1.componentAdded(ViewHolder.java:50)
    java.awt.Container.processContainerEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.Container.addImpl(Unknown Source)
    java.awt.Container.add(Unknown Source)

org.protege.editor.core.ui.view.ViewHolder$2.componentAdded(ViewHolder.java:84)
    java.awt.AWTEventMulticaster.componentAdded(Unknown Source)
    java.awt.Container.processContainerEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.Container.addImpl(Unknown Source)
    javax.swing.JTabbedPane.insertTab(Unknown Source)
    javax.swing.JTabbedPane.addTab(Unknown Source)
    org.protege.editor.core.ui.view.ViewHolder.addView(ViewHolder.java:104)

org.protege.editor.core.ui.workspace.Workspace.showResultsView(Workspace.java:36
2)

org.protege.editor.core.ui.workspace.Workspace.showResultsView(Workspace.java:33
6)
    org.coode.bookmark.BookmarkAction.actionPerformed(BookmarkAction.java:43)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)

What version of the product are you using? On what operating system?
Bookmarks View 1.2.1. OS: Windows 7 x64

Please provide any additional information below.

Annotation Template View 2.0.0 is in the plugin registry of 
Protege 4.2 alpha (build 249)

But when you try to install it, you get this error:
java.io.FileNotFoundException: 
http://co-ode-owl-plugins.googlecode.com/files/org.coode.annotate_2_0_0.zip

It's not available for manual download at
http://code.google.com/p/co-ode-owl-plugins/downloads/list
either

Enable editing on the resulting rows.
So the author doesn't have to navigate to the entity and then use the 
annotation view

p 4.1 annotation properties tab. Add a URI view. Selecting different annotation 
properties doesn't 
change URI

What steps will reproduce the problem?
1. open Protege 4.3.0
2. Click on any matrix tab

What is the expected output? What do you see instead?
Expected output is the matrix screen would display normally.
Instead I see disjointed buttons/fields that only appear once I scroll over the 
screen. 

What version of the product are you using? On what operating system?
4.3.0 build 304

Please provide any additional information below.
If I open an existing OWL file, it will black the screen out and freeze the 
tool if I select a matrix tab. I then have to restart the tool.

For
- property chains
- equiv props
- superprops
- disjoint props

What steps will reproduce the problem?
1. simply place the BeanShell view onto the workspace

What is the expected output? What do you see instead?
a shell. Instead I see a red warning stating an NPE.

What version of the product are you using? On what operating system?
4.1 alpha (build 100) / openSUSE 11.2 x86_64

Please provide any additional information below.
...
Error logged
java.lang.NullPointerException
        at 
org.apache.felix.framework.FelixResolverState.getResolvedCandidates(FelixR
esolverState.java:649)
        at 
org.apache.felix.framework.Felix$FelixResolver.getResolvedCandidates(Felix
.java:3977)
        at 
org.apache.felix.framework.ModuleImpl.diagnoseClassLoadError(ModuleImpl.ja
va:2163)
        at 
org.apache.felix.framework.ModuleImpl.access$400(ModuleImpl.java:60)
        at 
org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleIm
pl.java:1663)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at bsh.classpath.ClassManagerImpl.classForName(Unknown Source)
        at bsh.NameSpace.classForName(Unknown Source)
        at bsh.NameSpace.getClassImpl(Unknown Source)
        at bsh.NameSpace.getClass(Unknown Source)
        at bsh.Name.consumeNextObjectField(Unknown Source)
        at bsh.Name.toObject(Unknown Source)
        at bsh.Name.toObject(Unknown Source)
        at bsh.NameSpace.get(Unknown Source)
        at bsh.Interpreter.get(Unknown Source)
        at bsh.Interpreter.getu(Unknown Source)
        at bsh.Interpreter.<init>(Unknown Source)
        at bsh.Interpreter.<init>(Unknown Source)
        at bsh.Interpreter.<init>(Unknown Source)
        at bsh.Interpreter.<init>(Unknown Source)
        at 
org.coode.shell.view.BeanShellView.initialiseOWLView(BeanShellView.java:11
3)
        at 
org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(Abstrac
tOWLViewComponent.java:61)
        at 
org.protege.editor.core.ui.view.View.createContent(View.java:416)
        at org.protege.editor.core.ui.view.View.createUI(View.java:196)
        at 
org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:126)
        at java.awt.Component.processHierarchyEvent(Component.java:6430)
        at java.awt.Component.processEvent(Component.java:6049)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4630)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4460)
        at java.awt.Component.createHierarchyEvents(Component.java:5280)
        at java.awt.Container.createHierarchyEvents(Container.java:1360)
        at java.awt.Component.show(Component.java:1531)
        at java.awt.Component.show(Component.java:1563)
        at java.awt.Component.setVisible(Component.java:1515)
        at javax.swing.JComponent.setVisible(JComponent.java:2612)
        at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:378)
        at 
javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:253)
        at 
javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSele
ctionModel.java:116)
        at 
javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSele
ctionModel.java:50)
        at 
javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:599)
        at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:574)
        at 
javax.swing.JTabbedPane.setSelectedComponent(JTabbedPane.java:657)
        at org.coode.mdock.Util.bringToFront(Util.java:123)
        at 
org.coode.mdock.DynamicConfigPanel$CentreAddMode.doAdd(DynamicConfigPanel.
java:344)
        at 
org.coode.mdock.DynamicConfigPanel$2.mouseClicked(DynamicConfigPanel.java:
80)
        at java.awt.Component.processMouseEvent(Component.java:6266)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6028)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4630)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4460)
        at 
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
        at 
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4247)
        at 
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4460)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
        at 
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.ja
va:269)
        at 
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:
184)
        at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.ja
va:174)
        at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
        at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Take this OWLDoc as an example: 

http://bibotools.googlecode.com/svn/bibo-ontology/trunk/doc/index.html

Check the list of "All Resources". Currently, some items appears to be
duplicated. I would suggest to change the color, or add small icons, to
distinguish what is what. For example, displaying an icon for the different
kind of resources that exists: classes, object/data properties,
individuals, etc.

[deleted issue]

What steps will reproduce the problem?
1. Open pizza.owl
2. click on owlviz tab
3. click on thing
then error occures then crashes

What is the expected output? What do you see instead?
I expected to see the links between entities.

What version of the product are you using? On what operating system?

Protege 4.0 beta

Please provide any additional information below.
the log is as following;

INFO  ... active ontology changed 
org.protege.editor.owl.model.OWLModelManagerImpl[AWT-EventQueue-0]
WARN  BAD LISTENER: ()  
org.protege.editor.owl.model.selection.OWLSelectionModelImpl[AWT-EventQueue-0]
WARN  Error logged  org.protege.editor.core.ui.error.ErrorLog[AWT-EventQueue-0]
java.lang.NumberFormatException: For input string: "190.57"
    at java.lang.NumberFormatException.forInputString(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParameterSetter.
parsePoint(DotParameterSetter.java:329)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParameterSetter.
setEdgePath(DotParameterSetter.java:230)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParameterSetter.
setEdgeAttribute(DotParameterSetter.java:176)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.setEdgeAt
tribute(DotParser.java:56)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.node_or_e
dge_stmt(DotParser.java:198)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.stmt(DotP
arser.java:127)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.graph(Dot
Parser.java:107)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.start(Dot
Parser.java:72)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParser.parse(Dot
Parser.java:25)
    at
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.DotGraphLayoutEngine.layoutGr
aph(DotGraphLayoutEngine.java:111)
    at
uk.ac.man.cs.mig.util.graph.ui.GraphView.revalidateGraph(GraphView.java:308)
    at uk.ac.man.cs.mig.util.graph.ui.GraphView$3.graphChanged(GraphView.java:141)
    at
uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator.fireGraphChang
edEvent(DefaultGraphGenerator.java:613)
    at
uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator$1.objectsAdded
(DefaultGraphGenerator.java:171)
    at
uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectManager.fireO
bjectAddedEvent(DefaultVisualisedObjectManager.java:731)
    at
uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectManager.showO
bject(DefaultVisualisedObjectManager.java:320)
    at
uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizGraphPanel$3.selectionChanged(OWLVizGraph
Panel.java:153)
    at
uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.fireSelectionChanged(OWLVi
zSelectionModel.java:69)
    at
uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.setSelectedClass(OWLVizSel
ectionModel.java:54)
    at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizView.updateView(OWLVizView.java:85)
    at
org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateView(Abstract
OWLClassViewComponent.java:29)
    at
org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateView(Abstract
OWLClassViewComponent.java:18)
    at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewConte
ntAndHeader(AbstractOWLSelectionViewComponent.java:189)
    at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChan
ged(AbstractOWLSelectionViewComponent.java:67)
    at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSelectionChange
d(OWLSelectionModelImpl.java:100)
    at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSelectedObjec
t(OWLSelectionModelImpl.java:88)
    at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedObject(O
WLSelectionModelImpl.java:76)
    at
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedEntity(O
WLSelectionModelImpl.java:111)
    at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setSelectedEnti
ty(AbstractOWLSelectionViewComponent.java:122)
    at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewComponent.tr
ansmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
    at
org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewComponent$6.
valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
    at javax.swing.JTree.fireValueChanged(Unknown Source)
    at javax.swing.JTree$TreeSelectionRedirector.valueChanged(Unknown Source)
    at javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(Unknown Source)
    at javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(Unknown Source)
    at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(Unknown
Source)
    at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(Unknown Source)
    at javax.swing.JTree.setSelectionPath(Unknown Source)
    at javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(Unknown Source)
    at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelectionImpl(Unknown
Source)
    at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(Unknown Source)
    at javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)