├── protege-desktop └── src │ └── main │ ├── env │ ├── win │ │ ├── Protege.l4j.ini │ │ └── run.bat │ ├── os-x │ │ └── bundle-resources │ │ │ ├── MacOS │ │ │ └── JavaAppLauncher │ │ │ └── Resources │ │ │ └── Protege.icns │ └── platform-independent │ │ ├── run.command │ │ └── run.bat │ └── resources │ └── app │ ├── Protege.icns │ └── Protege.ico ├── protege-editor-owl ├── src │ ├── main │ │ ├── resources │ │ │ ├── A.png │ │ │ ├── AL.png │ │ │ ├── C.png │ │ │ ├── E.png │ │ │ ├── F.png │ │ │ ├── H.png │ │ │ ├── I.png │ │ │ ├── L.png │ │ │ ├── N.png │ │ │ ├── O.png │ │ │ ├── Q.png │ │ │ ├── S.png │ │ │ ├── U.png │ │ │ ├── FLM.png │ │ │ ├── FLO.png │ │ │ ├── False.gif │ │ │ ├── Help.gif │ │ │ ├── Top.gif │ │ │ ├── True.gif │ │ │ ├── Bottom.gif │ │ │ ├── Classes.gif │ │ │ ├── nav.fwd.png │ │ │ ├── Annotation.gif │ │ │ ├── Backspace.gif │ │ │ ├── Datatype.png │ │ │ ├── Deprecated.gif │ │ │ ├── Metadata.gif │ │ │ ├── class.add.png │ │ │ ├── datarange.png │ │ │ ├── individual.png │ │ │ ├── nav.back.png │ │ │ ├── ontology.png │ │ │ ├── prefix.add.png │ │ │ ├── OWLHasValue.gif │ │ │ ├── class.delete.png │ │ │ ├── class.usage.png │ │ │ ├── ontology.add.png │ │ │ ├── DefinedOWLClass.gif │ │ │ ├── OWLCardinality.gif │ │ │ ├── OWLIndividual.gif │ │ │ ├── OWLRestriction.gif │ │ │ ├── OWLUnionClass.gif │ │ │ ├── PrimitiveClass.gif │ │ │ ├── class.add.sib.png │ │ │ ├── class.add.sub.png │ │ │ ├── class.defined.png │ │ │ ├── class.expr.edit.png │ │ │ ├── class.primitive.png │ │ │ ├── datarange.add.png │ │ │ ├── individual.add.png │ │ │ ├── ontology.remove.png │ │ │ ├── prefix.generate.png │ │ │ ├── prefix.remove.png │ │ │ ├── property.data.png │ │ │ ├── property.object.png │ │ │ ├── property.usage.png │ │ │ ├── AddFromOntPolicy.gif │ │ │ ├── OWLAllValuesFrom.gif │ │ │ ├── OWLAnonymousClass.gif │ │ │ ├── OWLMaxCardinality.gif │ │ │ ├── OWLMinCardinality.gif │ │ │ ├── OWLObjectProperty.gif │ │ │ ├── OWLSomeValuesFrom.gif │ │ │ ├── class.defined.add.png │ │ │ ├── datarange.remove.png │ │ │ ├── individual.delete.png │ │ │ ├── individual.remove.png │ │ │ ├── individual.usage.png │ │ │ ├── ontology.library.png │ │ │ ├── property.data.add.png │ │ │ ├── repository.moveup.png │ │ │ ├── DatatypeSubProperty.gif │ │ │ ├── OWLComplementClass.gif │ │ │ ├── OWLDatatypeProperty.gif │ │ │ ├── OWLDisjointClasses.gif │ │ │ ├── OWLEnumeratedClass.gif │ │ │ ├── OWLIntersectionClass.gif │ │ │ ├── class.axiom.disjoint.png │ │ │ ├── class.axiom.subclass.png │ │ │ ├── hierarchy.collapsed.gif │ │ │ ├── hierarchy.expanded.gif │ │ │ ├── ontology.library.add.png │ │ │ ├── property.annotation.png │ │ │ ├── property.data.addsib.png │ │ │ ├── property.data.addsub.png │ │ │ ├── property.data.delete.png │ │ │ ├── property.data.remove.png │ │ │ ├── property.data.usage.png │ │ │ ├── property.object.add.png │ │ │ ├── repository.movedown.png │ │ │ ├── class.axiom.equivalent.png │ │ │ ├── class.defined.convert.png │ │ │ ├── class.disjointsib.add.png │ │ │ ├── property.object.addsib.png │ │ │ ├── property.object.addsub.png │ │ │ ├── property.object.delete.png │ │ │ ├── property.object.remove.png │ │ │ ├── class.disjointsib.remove.png │ │ │ ├── class.primitive.convert.png │ │ │ ├── class.sibs.disjoint.add.png │ │ │ ├── ontology.library.remove.png │ │ │ ├── property.annotation.add.png │ │ │ ├── property.annotation.usage.png │ │ │ ├── OWLAnnotationPropertyFrame.gif │ │ │ ├── OWLObjectPropertyInherited.gif │ │ │ ├── class.restriction.covering.png │ │ │ ├── property.annotation.addsib.png │ │ │ ├── property.annotation.addsub.png │ │ │ ├── property.annotation.delete.png │ │ │ ├── property.annotation.remove.png │ │ │ ├── OWLDatatypePropertyInherited.gif │ │ │ ├── DisplayedInferencesHelp.txt │ │ │ ├── viewconfig-sparqltab.xml │ │ │ ├── viewconfig-explanationtab.xml │ │ │ ├── InconsistentOntologyHelp.html │ │ │ └── PrecomputePreferencesHelp.txt │ │ └── java │ │ │ └── org │ │ │ └── protege │ │ │ ├── editor │ │ │ └── owl │ │ │ │ ├── ui │ │ │ │ ├── renderer │ │ │ │ │ ├── prefix │ │ │ │ │ │ └── PrefixBasedRenderer.java │ │ │ │ │ ├── AnnotationRenderingStyle.java │ │ │ │ │ ├── styledstring │ │ │ │ │ │ ├── FontWeight.java │ │ │ │ │ │ ├── StrikeThrough.java │ │ │ │ │ │ ├── Underline.java │ │ │ │ │ │ ├── LineIntroduction.java │ │ │ │ │ │ ├── BracketingStrategy.java │ │ │ │ │ │ └── PrettyPrintStrategy.java │ │ │ │ │ ├── InlineThumbnailRendering.java │ │ │ │ │ ├── InlineDatatypeRendering.java │ │ │ │ │ ├── InlineAnnotationRendering.java │ │ │ │ │ ├── LinkExtractor.java │ │ │ │ │ ├── OWLObjectRenderer.java │ │ │ │ │ ├── layout │ │ │ │ │ │ ├── Alignment.java │ │ │ │ │ │ └── PageLayoutState.java │ │ │ │ │ ├── context │ │ │ │ │ │ ├── LinkFactory.java │ │ │ │ │ │ ├── NullDeprecatedObjectChecker.java │ │ │ │ │ │ ├── NullLinkFactory.java │ │ │ │ │ │ ├── DefinedClassChecker.java │ │ │ │ │ │ ├── NullDataPropertySatisfiabilityChecker.java │ │ │ │ │ │ ├── DeprecatedObjectChecker.java │ │ │ │ │ │ └── NullObjectPropertySatisfiabilityChecker.java │ │ │ │ │ ├── OWLIconProvider.java │ │ │ │ │ ├── OWLEntityRendererListener.java │ │ │ │ │ ├── EntityActionIcon.java │ │ │ │ │ ├── OWLEntityColorProviderPlugin.java │ │ │ │ │ ├── plugin │ │ │ │ │ │ └── RendererPluginLoader.java │ │ │ │ │ └── menu │ │ │ │ │ │ └── ConfigureRenderer.java │ │ │ │ ├── action │ │ │ │ │ ├── export │ │ │ │ │ │ └── inferred │ │ │ │ │ │ │ └── ExportCancelledException.java │ │ │ │ │ ├── ActionTarget.java │ │ │ │ │ ├── OWLUIActionStrategy.java │ │ │ │ │ └── FindAction.java │ │ │ │ ├── explanation │ │ │ │ │ ├── ExplanationResult.java │ │ │ │ │ └── io │ │ │ │ │ │ └── InconsistentOntologyPluginInstance.java │ │ │ │ ├── tree │ │ │ │ │ └── TreeDragAndDropHandler.java │ │ │ │ ├── view │ │ │ │ │ ├── HasExpandAll.java │ │ │ │ │ ├── HasDisplayDeprecatedEntities.java │ │ │ │ │ ├── Deleteable.java │ │ │ │ │ ├── CreateNewTarget.java │ │ │ │ │ ├── HasCopySubHierarchyToClipboard.java │ │ │ │ │ ├── CreateNewChildTarget.java │ │ │ │ │ ├── CreateNewSiblingTarget.java │ │ │ │ │ ├── Findable.java │ │ │ │ │ ├── rdf │ │ │ │ │ │ └── RootTriple.java │ │ │ │ │ └── AbstractHierarchyViewComponent.java │ │ │ │ ├── editor │ │ │ │ │ └── OWLObjectEditorHandler.java │ │ │ │ ├── framelist │ │ │ │ │ └── ObjectEditorHandler.java │ │ │ │ ├── search │ │ │ │ │ ├── SearchOptionsChangedListener.java │ │ │ │ │ ├── SearchResultClickedListener.java │ │ │ │ │ └── SearchOptionsEditor.java │ │ │ │ ├── ontology │ │ │ │ │ ├── DefaultOntologyURIPanel.java │ │ │ │ │ └── wizard │ │ │ │ │ │ └── move │ │ │ │ │ │ ├── MoveAxiomsKitPlugin.java │ │ │ │ │ │ └── MoveType.java │ │ │ │ ├── metrics │ │ │ │ │ ├── MetricsTreeNode.java │ │ │ │ │ ├── ClassCountMetric.java │ │ │ │ │ ├── IndividualCountMetric.java │ │ │ │ │ └── ObjectPropertyCount.java │ │ │ │ ├── selector │ │ │ │ │ └── OWLObjectSelector.java │ │ │ │ ├── transfer │ │ │ │ │ ├── ObjectDropTarget.java │ │ │ │ │ └── OWLObjectDragSource.java │ │ │ │ ├── util │ │ │ │ │ └── ProgressView.java │ │ │ │ ├── find │ │ │ │ │ └── AbstractSearchResultsRow.java │ │ │ │ ├── table │ │ │ │ │ └── ProgrammaticEditEvent.java │ │ │ │ ├── frame │ │ │ │ │ ├── SWRLRulesFrame.java │ │ │ │ │ ├── InferredAxiomsFrame.java │ │ │ │ │ ├── OWLAnnotationsFrame.java │ │ │ │ │ ├── AxiomListFrame.java │ │ │ │ │ ├── OWLFrameListener.java │ │ │ │ │ └── OWLFrameObject.java │ │ │ │ ├── hierarchy │ │ │ │ │ └── creation │ │ │ │ │ │ └── TabIndentedHierachyTextPane.java │ │ │ │ ├── clsdescriptioneditor │ │ │ │ │ └── OWLClassAxiomEditor.java │ │ │ │ └── inference │ │ │ │ │ └── ExplainInconsistentOntologyAction.java │ │ │ │ └── model │ │ │ │ ├── inference │ │ │ │ ├── ReasonerPreferencesListener.java │ │ │ │ ├── ReasonerFilter.java │ │ │ │ ├── ReasonerDiedException.java │ │ │ │ ├── OWLReasonerExceptionHandler.java │ │ │ │ ├── ProtegeOWLReasonerFactoryAdapter.java │ │ │ │ └── DefaultOWLReasonerExceptionHandler.java │ │ │ │ ├── library │ │ │ │ ├── folder │ │ │ │ │ ├── Algorithm.java │ │ │ │ │ └── SAXParseCompletedException.java │ │ │ │ └── CatalogEntryManagerLoader.java │ │ │ │ ├── search │ │ │ │ ├── SearchMDImporter.java │ │ │ │ ├── SearchCategory.java │ │ │ │ ├── SearchResultHandler.java │ │ │ │ ├── SearchMetadataImporter.java │ │ │ │ ├── SearchMetadataImportManager.java │ │ │ │ ├── EntityBasedSearchMDImporter.java │ │ │ │ ├── OntologyBasedSearchMDImporter.java │ │ │ │ └── SearchMetadataDB.java │ │ │ │ ├── user │ │ │ │ ├── UserNameProvider.java │ │ │ │ ├── OrcidProvider.java │ │ │ │ └── UserPreferences.java │ │ │ │ ├── selection │ │ │ │ ├── SelectionModel.java │ │ │ │ ├── SelectionDriver.java │ │ │ │ ├── OWLSelectionModelListener.java │ │ │ │ └── OWLSelectionModelAdapter.java │ │ │ │ ├── HasActiveOntology.java │ │ │ │ ├── repository │ │ │ │ ├── extractors │ │ │ │ │ └── OntologyIdExtractor.java │ │ │ │ └── TONESRepository.java │ │ │ │ ├── axiom │ │ │ │ ├── FreshAxiomLocationStrategyFactory.java │ │ │ │ ├── AxiomSubjectProvider.java │ │ │ │ ├── TopologicallySortedImportsClosureProvider.java │ │ │ │ ├── FreshAxiomLocationStrategy.java │ │ │ │ ├── DefaultTopologicallySortedImportsClosureProvider.java │ │ │ │ └── ActiveOntologyLocationStrategy.java │ │ │ │ ├── io │ │ │ │ ├── IOListenerPlugin.java │ │ │ │ └── IOListener.java │ │ │ │ ├── util │ │ │ │ ├── DateFormatter.java │ │ │ │ └── TimestampFormatter.java │ │ │ │ ├── entity │ │ │ │ ├── Revertable.java │ │ │ │ ├── AutoIDGenerator.java │ │ │ │ ├── LabelDescriptor.java │ │ │ │ └── AutoIDException.java │ │ │ │ ├── hierarchy │ │ │ │ └── HasFilter.java │ │ │ │ ├── annotation │ │ │ │ ├── AnnotationValueProvider.java │ │ │ │ ├── EntityCreationMetadataPreferences.java │ │ │ │ └── EntityCreationMetadataProvider.java │ │ │ │ ├── event │ │ │ │ └── OWLModelManagerListener.java │ │ │ │ ├── OWLEntityDisplayProvider.java │ │ │ │ ├── OntologyVisibilityManagerListener.java │ │ │ │ ├── AnnotationContainer.java │ │ │ │ ├── namespace │ │ │ │ └── NamespaceManagerListener.java │ │ │ │ ├── IOListenerManager.java │ │ │ │ ├── OWLEditorKitOntologyShortFormProvider.java │ │ │ │ ├── MissingImportHandler.java │ │ │ │ ├── OWLEditorKitHook.java │ │ │ │ ├── history │ │ │ │ └── UndoManagerListener.java │ │ │ │ ├── refactor │ │ │ │ ├── ontology │ │ │ │ │ └── OntologyTargetResolver.java │ │ │ │ └── AnnotationDeleter.java │ │ │ │ └── OntologyFileFilter.java │ │ │ └── owlapi │ │ │ └── inference │ │ │ └── orphan │ │ │ ├── NamedClassExtractor.java │ │ │ └── Relation.java │ └── test │ │ └── resources │ │ ├── ontologies │ │ ├── catalog-existing-with-no-groups.xml │ │ └── VersionedOntology-functional.owl │ │ └── logback-test.xml └── etc │ ├── update.properties │ └── owleditor-readme.html ├── protege-editor-core └── src │ └── main │ ├── resources │ ├── back.gif │ ├── busy.gif │ ├── copy.gif │ ├── cut.gif │ ├── form.gif │ ├── home.gif │ ├── no.gif │ ├── ok.gif │ ├── redo.gif │ ├── slot.gif │ ├── undo.gif │ ├── yes.gif │ ├── blank.gif │ ├── class.gif │ ├── clear.gif │ ├── cut.24.gif │ ├── delete.gif │ ├── error.png │ ├── export.gif │ ├── facet.gif │ ├── logo16.gif │ ├── logo32.gif │ ├── paste.gif │ ├── query.gif │ ├── class.add.gif │ ├── clear.24.gif │ ├── copy.24.gif │ ├── copy.gray.gif │ ├── cut.gray.gif │ ├── facet.add.gif │ ├── form.add.gif │ ├── form.copy.gif │ ├── forward.gif │ ├── instance.gif │ ├── paste.24.gif │ ├── project.gif │ ├── redo.24.gif │ ├── redo.gray.gif │ ├── slot.add.gif │ ├── slot.copy.gif │ ├── slot.view.gif │ ├── slot_note.gif │ ├── undo.24.gif │ ├── undo.gray.gif │ ├── warning.png │ ├── zoom.in.png │ ├── zoom.out.png │ ├── class.copy.gif │ ├── class.view.gif │ ├── class_note.gif │ ├── clear.gray.gif │ ├── cut.gray.24.gif │ ├── facet.copy.gif │ ├── facet.view.gif │ ├── filter.add.png │ ├── form.create.gif │ ├── form.delete.gif │ ├── form.remove.gif │ ├── form.search.gif │ ├── logo.48x48.png │ ├── logo.banner.gif │ ├── logo.splash.gif │ ├── logo.wizard.png │ ├── object.add.gif │ ├── object.copy.gif │ ├── object.view.gif │ ├── paste.gray.gif │ ├── project.add.gif │ ├── project.new.gif │ ├── query.copy.gif │ ├── query.view.gif │ ├── slot.create.gif │ ├── slot.delete.gif │ ├── slot.remove.gif │ ├── slot.search.gif │ ├── view.close.gif │ ├── view.float.gif │ ├── class.abstract.gif │ ├── class.create.gif │ ├── class.delete.gif │ ├── class.instance.gif │ ├── class.move_up.gif │ ├── class.remove.gif │ ├── class.search.gif │ ├── clear.gray.24.gif │ ├── copy.gray.24.gif │ ├── facet.create.gif │ ├── facet.delete.gif │ ├── facet.move_up.gif │ ├── facet.remove.gif │ ├── filter.remove.png │ ├── form.move_down.gif │ ├── form.move_up.gif │ ├── form.relayout.gif │ ├── instance.add.gif │ ├── instance.copy.gif │ ├── instance.view.gif │ ├── instance_note.gif │ ├── logo.billboard.gif │ ├── logo.billboard.png │ ├── object.create.gif │ ├── object.delete.gif │ ├── object.move_up.gif │ ├── object.remove.gif │ ├── object.search.gif │ ├── paste.gray.24.gif │ ├── project.new.24.gif │ ├── project.open.gif │ ├── project.remove.gif │ ├── project.revert.gif │ ├── project.save.gif │ ├── project_select.gif │ ├── query.delete.gif │ ├── redo.gray.24.gif │ ├── slot.inherited.gif │ ├── slot.inverse.gif │ ├── slot.move_down.gif │ ├── slot.move_up.gif │ ├── slot_note.hide.gif │ ├── sort.ascending.png │ ├── undo.gray.24.gif │ ├── class.metaclass.gif │ ├── class.move_down.gif │ ├── class_note.hide.gif │ ├── facet.move_down.gif │ ├── form.customized.gif │ ├── form.layout_like.gif │ ├── instance.create.gif │ ├── instance.delete.gif │ ├── instance.move_up.gif │ ├── instance.remove.gif │ ├── instance.search.gif │ ├── object.move_down.gif │ ├── project.archive.gif │ ├── project.new.gray.gif │ ├── project.open.24.gif │ ├── project.save.24.gif │ ├── slot.overridden.gif │ ├── slot_note.create.gif │ ├── slot_note.delete.gif │ ├── view.close copy.gif │ ├── class.multiparents.gif │ ├── class_note.create.gif │ ├── class_note.delete.gif │ ├── close_all_windows.gif │ ├── form.multiparents.gif │ ├── hierarchy.collapsed.gif │ ├── hierarchy.expanded.gif │ ├── instance.move_down.gif │ ├── instance_note.hide.gif │ ├── project.archive.24.gif │ ├── project.new.gray.24.gif │ ├── project.open.gray.gif │ ├── project.revert.24.gif │ ├── project.revert.gray.gif │ ├── project.save.gray.gif │ ├── query.library.add.gif │ ├── slot.multiparents.gif │ ├── slot.view_overrides.gif │ ├── slot.view_top_level.gif │ ├── class.view_references.gif │ ├── close_all_window.gray.gif │ ├── close_all_windows.24.gif │ ├── instance_note.create.gif │ ├── instance_note.delete.gif │ ├── project.archive.gray.gif │ ├── project.open.gray.24.gif │ ├── project.save.gray.24.gif │ ├── slot.remove_overrides.gif │ ├── slot.view_references.gif │ ├── view.horizontalsplit.gif │ ├── view.splitvertically.gif │ ├── class.metaclass.abstract.gif │ ├── class.metaclass.default.gif │ ├── form.view_customizations.gif │ ├── instance.view_references.gif │ ├── object.view_in_browser.gif │ ├── object.view_references.gif │ ├── project.archive.gray.24.gif │ ├── project.revert.gray.24.gif │ ├── query.library.retrieve.gif │ ├── close_all_windows.gray.24.gif │ ├── form.remove_customizations.gif │ ├── slot.inherited.overridden.gif │ └── form.multiparents.customized.gif │ └── java │ └── org │ └── protege │ └── editor │ └── core │ ├── ui │ ├── list │ │ ├── RendererWithInsets.java │ │ ├── MListSectionHeader.java │ │ └── MListItem.java │ ├── view │ │ ├── ViewModeChangedHandler.java │ │ ├── ViewBarIcon.java │ │ ├── ViewActionPlugin.java │ │ ├── ViewAction.java │ │ └── DisposableAction.java │ ├── util │ │ ├── Resettable.java │ │ ├── UIConstants.java │ │ ├── InputVerificationStatusChangedListener.java │ │ ├── SelectionProviderListener.java │ │ ├── VerifiedInputEditor.java │ │ ├── TextFieldSearchHandler.java │ │ ├── OpenRequestHandler.java │ │ └── SelectionProvider.java │ ├── tabbedpane │ │ ├── TabCloseHandler.java │ │ └── NullTabCloseHandler.java │ ├── progress │ │ ├── BackgroundTask.java │ │ └── BackgroundTaskListener.java │ ├── error │ │ ├── SendErrorReportHandler.java │ │ └── ErrorLogListener.java │ ├── ProtegeWelcomePanel.java │ ├── action │ │ ├── start │ │ │ └── AltStartupAction.java │ │ └── ProtegeDynamicAction.java │ ├── workspace │ │ └── views │ │ │ └── ViewNodePanel.java │ ├── wizard │ │ └── WizardPanelNotFoundException.java │ ├── RefreshableComponent.java │ └── preferences │ │ ├── node │ │ └── PreferenceNode.java │ │ └── PreferencesPanelPlugin.java │ ├── plugin │ ├── BundleExceptionParser.java │ ├── BundleExceptionHandler.java │ └── DefaultPluginActivator.java │ ├── log │ ├── LogLevel.java │ └── LogView.java │ ├── HasUpdateState.java │ ├── util │ ├── HandlerRegistration.java │ └── Recommendation.java │ ├── Disposable.java │ ├── update │ ├── PluginDocumentParseException.java │ └── PluginRegistry.java │ ├── OntologyRepositoryFactoryPlugin.java │ ├── editorkit │ └── plugin │ │ └── EditorKitHookPlugin.java │ ├── OntologyRepositoryFactory.java │ └── ModelManager.java ├── .gitignore ├── .travis.yml └── protege-launcher └── src └── main └── java └── org └── protege └── osgi └── framework ├── service └── LaunchInfoService.java └── 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/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/prefix/PrefixBasedRenderer.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.prefix; 2 | 3 | public interface PrefixBasedRenderer { 4 | 5 | } 6 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/resources/DisplayedInferencesHelp.txt: -------------------------------------------------------------------------------- 1 | Use the checkboxes below to control which inferences are displayed in Protege. 2 | Selectively disabling automatic inferences may improve performance. -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/ReasonerPreferencesListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | public interface ReasonerPreferencesListener { 4 | 5 | void preferencesChanged(); 6 | } 7 | -------------------------------------------------------------------------------- /protege-desktop/src/main/env/platform-independent/run.command: -------------------------------------------------------------------------------- 1 | cd "$(dirname "$0")" 2 | 3 | CMD_OPTIONS="-Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Protege -Xdock:name=Protege -Xdock:icon=app/Protege.icns" sh run.sh $1 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/list/RendererWithInsets.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.list; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 05/03/15 7 | */ 8 | public interface RendererWithInsets { 9 | } 10 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/plugin/BundleExceptionParser.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.plugin; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 19/11/15 7 | */ 8 | public class BundleExceptionParser { 9 | 10 | } 11 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/ReasonerFilter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | public interface ReasonerFilter { 6 | 7 | OWLOntology getFilteredOntology(OWLOntology ontology); 8 | } 9 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Maven 2 | target/ 3 | 4 | # Eclipse 5 | .classpath 6 | .project 7 | .settings/ 8 | META-INF/ 9 | build.properties 10 | plugin.xml 11 | 12 | #intelliJ 13 | *.iws 14 | *.ipr 15 | .idea 16 | *.iml 17 | build/ 18 | 19 | _site 20 | _views 21 | _posts 22 | _menus 23 | assets 24 | installation 25 | 26 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: java 2 | 3 | jdk: 4 | - oraclejdk8 5 | 6 | notifications: 7 | email: 8 | recipients: 9 | - horridge@stanford.edu 10 | on_success: never 11 | on_failure: always 12 | 13 | before_install: 14 | - "export DISPLAY=:99.0" 15 | - "sh -e /etc/init.d/xvfb start" 16 | 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/library/folder/Algorithm.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.library.folder; 2 | 3 | import java.io.File; 4 | import java.net.URI; 5 | import java.util.Set; 6 | 7 | public interface Algorithm { 8 | Set getSuggestions(File f); 9 | } 10 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/export/inferred/ExportCancelledException.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.action.export.inferred; 2 | 3 | public class ExportCancelledException extends RuntimeException { 4 | private static final long serialVersionUID = -5179167522827367619L; 5 | 6 | } 7 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/owlapi/inference/orphan/NamedClassExtractor.java: -------------------------------------------------------------------------------- 1 | 2 | package org.protege.owlapi.inference.orphan; 3 | 4 | @Deprecated // todo: unused -> delete (used only inside ProtegeOrphanFinder - which is unused itself) 5 | public class NamedClassExtractor extends org.protege.owlapi.inference.cls.NamedClassExtractor { 6 | } -------------------------------------------------------------------------------- /protege-editor-owl/src/test/resources/ontologies/catalog-existing-with-no-groups.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/ReasonerDiedException.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | public class ReasonerDiedException extends RuntimeException { 4 | private static final long serialVersionUID = 1L; 5 | 6 | public ReasonerDiedException(Throwable t) { 7 | super(t); 8 | } 9 | } 10 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchMDImporter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | 4 | /** 5 | * Author: Matthew Horridge
6 | * Stanford University
7 | * Bio-Medical Informatics Research Group
8 | * Date: 03/10/2012 9 | */ 10 | public abstract class SearchMDImporter { 11 | 12 | } 13 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/explanation/ExplanationResult.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.explanation; 2 | 3 | import javax.swing.*; 4 | 5 | public abstract class ExplanationResult extends JPanel { 6 | private static final long serialVersionUID = -3168518791862105068L; 7 | 8 | public abstract void dispose(); 9 | 10 | } 11 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/log/LogLevel.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.log; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 04/11/15 7 | */ 8 | public enum LogLevel { 9 | 10 | TRACE, 11 | 12 | DEBUG, 13 | 14 | INFO, 15 | 16 | WARN, 17 | 18 | ERROR 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/resources/viewconfig-sparqltab.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /protege-launcher/src/main/java/org/protege/osgi/framework/service/LaunchInfoService.java: -------------------------------------------------------------------------------- 1 | package org.protege.osgi.framework.service; 2 | 3 | import org.protege.osgi.framework.BundleSearchPath; 4 | 5 | import java.util.List; 6 | 7 | public interface LaunchInfoService { 8 | 9 | String[] getCommandLineArguments(); 10 | List getSearchPath(); 11 | } 12 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/HasUpdateState.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 7 Nov 2016 7 | */ 8 | public interface HasUpdateState { 9 | 10 | /** 11 | * Update the state of this object 12 | */ 13 | void updateState(); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/user/UserNameProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.user; 2 | 3 | import java.util.Optional; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 20/11/15 9 | */ 10 | public interface UserNameProvider { 11 | 12 | Optional getUserName(); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/library/folder/SAXParseCompletedException.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.protege.editor.owl.model.library.folder; 5 | 6 | import org.xml.sax.SAXException; 7 | 8 | public class SAXParseCompletedException extends SAXException { 9 | private static final long serialVersionUID = -3132857052804332468L; 10 | 11 | } -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/selection/SelectionModel.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.selection; 2 | 3 | import javax.annotation.Nullable; 4 | 5 | /** 6 | * Created by @ssz on 07.01.2021. 7 | */ 8 | public interface SelectionModel { 9 | void setSelectedObject(@Nullable Object object); 10 | 11 | Object getSelectedObject(); 12 | } 13 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/AnnotationRenderingStyle.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | /** 4 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 28/05/2014 5 | */ 6 | public enum AnnotationRenderingStyle { 7 | 8 | COMFORTABLE, 9 | 10 | COSY, 11 | 12 | COMPACT 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/resources/viewconfig-explanationtab.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/FontWeight.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 20/09/2012 8 | */ 9 | public enum FontWeight { 10 | 11 | REGULAR, 12 | 13 | BOLD 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/owlapi/inference/orphan/Relation.java: -------------------------------------------------------------------------------- 1 | package org.protege.owlapi.inference.orphan; 2 | 3 | import java.util.Collection; 4 | 5 | /** 6 | * This interface simply represents a relation 7 | * R: X -> X. 8 | * 9 | * @author tredmond 10 | * 11 | */ 12 | 13 | public interface Relation { 14 | 15 | Collection getR(X x); 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/InlineThumbnailRendering.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 04/02/16 7 | */ 8 | public enum InlineThumbnailRendering { 9 | 10 | DO_NOT_DISPLAY_THUMBNAILS_INLINE, 11 | 12 | DISPLAY_THUMBNAILS_INLINE, 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/StrikeThrough.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 20/09/2012 8 | */ 9 | public enum StrikeThrough { 10 | 11 | NORMAL, 12 | 13 | SINGLE 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/Underline.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 24/09/2012 8 | */ 9 | public enum Underline { 10 | 11 | NONE, 12 | 13 | SINGLE 14 | 15 | } 16 | 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/tree/TreeDragAndDropHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.tree; 2 | 3 | /** 4 | * @param - anything 5 | */ 6 | public interface TreeDragAndDropHandler { 7 | 8 | boolean canDrop(Object child, Object parent); 9 | 10 | void move(N child, N fromParent, N toParent); 11 | 12 | void add(N child, N parent); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/HasExpandAll.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 31/08/15 9 | */ 10 | public interface HasExpandAll extends ActionTarget { 11 | 12 | void expandAll(); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/HasActiveOntology.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | /** 6 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 7 | */ 8 | public interface HasActiveOntology { 9 | 10 | OWLOntology getActiveOntology(); 11 | } 12 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/InlineDatatypeRendering.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | /** 4 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 28/05/2014 5 | */ 6 | public enum InlineDatatypeRendering { 7 | 8 | RENDER_DATATYPE_INLINE, 9 | 10 | DO_NOT_RENDER_DATATYPE_INLINE 11 | 12 | } 13 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/LineIntroduction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 01/10/2012 8 | */ 9 | public enum LineIntroduction { 10 | 11 | SAME_LINE, 12 | 13 | NEW_LINE 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewModeChangedHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.view; 2 | 3 | import java.util.Optional; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 26/01/16 9 | */ 10 | public interface ViewModeChangedHandler { 11 | 12 | void handleViewModeChanged(Optional viewMode); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/repository/extractors/OntologyIdExtractor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.repository.extractors; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntologyID; 4 | 5 | import java.net.URI; 6 | import java.util.Optional; 7 | 8 | public interface OntologyIdExtractor { 9 | 10 | Optional getOntologyId(URI location); 11 | 12 | } 13 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/log/LogView.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.log; 2 | 3 | import javax.swing.*; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 04/11/15 9 | */ 10 | public interface LogView { 11 | 12 | void clearView(); 13 | 14 | JComponent asJComponent(); 15 | 16 | void append(LogRecord logRecord); 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/util/HandlerRegistration.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.util; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 8 Aug 16 7 | */ 8 | public interface HandlerRegistration { 9 | 10 | /** 11 | * Removes the registered handler that this registration pertains to. 12 | */ 13 | void removeHandler(); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/InlineAnnotationRendering.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | /** 4 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 28/05/2014 5 | */ 6 | public enum InlineAnnotationRendering { 7 | 8 | DO_NOT_RENDER_COMPOUND_ANNOTATIONS_INLINE, 9 | 10 | RENDER_COMPOUND_ANNOTATIONS_INLINE 11 | 12 | 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/plugin/BundleExceptionHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.plugin; 2 | 3 | import org.osgi.framework.BundleException; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 19/11/15 9 | */ 10 | public class BundleExceptionHandler { 11 | 12 | public void handleBundleException(BundleException e) { 13 | 14 | } 15 | 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/Resettable.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 13-Aug-2007

14 | */ 15 | public interface Resettable { 16 | 17 | void reset(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchCategory.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 26/09/2012 8 | */ 9 | public enum SearchCategory { 10 | 11 | DISPLAY_NAME, 12 | 13 | IRI, 14 | 15 | ANNOTATION_VALUE, 16 | 17 | LOGICAL_AXIOM 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchResultHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import java.util.List; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 19/09/2012 10 | */ 11 | public interface SearchResultHandler { 12 | 13 | void searchFinished(List searchResults); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/LinkExtractor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | import org.protege.editor.owl.ui.renderer.layout.Link; 4 | 5 | import java.util.Optional; 6 | 7 | /** 8 | * Matthew Horridge 9 | * Stanford Center for Biomedical Informatics Research 10 | * 18 Aug 16 11 | */ 12 | public interface LinkExtractor { 13 | 14 | Optional extractLink(String s); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/editor/OWLObjectEditorHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.editor; 2 | 3 | import java.util.Set; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 15-Feb-2007

11 | */ 12 | public interface OWLObjectEditorHandler { 13 | 14 | void handleEditingFinished(Set editedObjects); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/framelist/ObjectEditorHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.framelist; 2 | 3 | import javax.swing.*; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 09-Feb-2007

11 | */ 12 | public interface ObjectEditorHandler { 13 | 14 | JComponent getEditingComponent(Object object); 15 | 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/HasDisplayDeprecatedEntities.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 16/11/15 9 | */ 10 | public interface HasDisplayDeprecatedEntities extends ActionTarget { 11 | 12 | void setShowDeprecatedEntities(boolean b); 13 | 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/search/SearchOptionsChangedListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.search; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 20/09/2012 8 | */ 9 | public interface SearchOptionsChangedListener { 10 | 11 | void searchRequestOptionChanged(); 12 | 13 | void searchResultsPresentationOptionChanged(); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/FreshAxiomLocationStrategyFactory.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | 5 | /** 6 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 7 | */ 8 | public interface FreshAxiomLocationStrategyFactory { 9 | 10 | FreshAxiomLocationStrategy getStrategy(OWLEditorKit editorKit); 11 | } 12 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/user/OrcidProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.user; 2 | 3 | import java.util.Optional; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 23/11/15 9 | */ 10 | public interface OrcidProvider { 11 | 12 | /** 13 | * Get the ORCID for the user. 14 | * @return The orcid. Not null. 15 | */ 16 | Optional getOrcid(); 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/OWLObjectRenderer.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * The University Of Manchester
6 | * Medical Informatics Group
7 | * Date: Apr 2, 2006

8 | 9 | * matthew.horridge@cs.man.ac.uk
10 | * www.cs.man.ac.uk/~horridgm

11 | */ 12 | public interface OWLObjectRenderer { 13 | 14 | String render(X object); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/tabbedpane/TabCloseHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.tabbedpane; 2 | 3 | import javax.swing.*; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 08/03/15 9 | */ 10 | public interface TabCloseHandler { 11 | 12 | boolean shouldCloseTab(int tabIndex, JTabbedPane tabbedPane); 13 | 14 | void handleCloseTab(int tabIndex, JTabbedPane tabbedPane); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/etc/update.properties: -------------------------------------------------------------------------------- 1 | 2 | id=org.protege.editor.owl 3 | version=4.2.0.b276_2012_06_08_1126 4 | download=https://protege.googlecode.com/files/org.protege.editor.owl-4.2.0.b276_2012_06_08_1126.jar 5 | name=OWL Editor 6 | readme=http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.editor.owl/trunk/etc/owleditor-readme.html 7 | license=http://opensource.org/licenses/BSD-2-Clause 8 | author=Protege Development Team (First working version by Matthew Horridge) 9 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/progress/BackgroundTask.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.progress; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: May 8, 2009

15 | */ 16 | public interface BackgroundTask { 17 | 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/Disposable.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: Sep 15, 2008

15 | */ 16 | public interface Disposable { 17 | 18 | public void dispose() throws Exception; 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/Deleteable.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 02-May-2007

11 | */ 12 | public interface Deleteable extends ActionTarget { 13 | 14 | boolean canDelete(); 15 | 16 | 17 | void handleDelete(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/list/MListSectionHeader.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.list; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 24-Feb-2007

14 | */ 15 | public interface MListSectionHeader { 16 | 17 | String getName(); 18 | 19 | boolean canAdd(); 20 | } 21 | -------------------------------------------------------------------------------- /protege-desktop/src/main/env/win/run.bat: -------------------------------------------------------------------------------- 1 | setlocal 2 | cd /d %~dp0 3 | jre\bin\java -Xmx${conf.mem.xmx}M -Xms${conf.mem.xms}M -Xss${conf.mem.xss}M ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1 4 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/error/SendErrorReportHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.error; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 28-Feb-2007

14 | */ 15 | public interface SendErrorReportHandler { 16 | 17 | boolean sendErrorReport(ErrorLog errorLog); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/io/IOListenerPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.io; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 8 | * 16-Sep-2008

9 | */ 10 | public interface IOListenerPlugin extends ProtegePlugin { 11 | 12 | public static final String ID = "io_listener"; 13 | 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/ontology/DefaultOntologyURIPanel.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.ontology; 2 | 3 | import javax.swing.*; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 28-Jun-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public class DefaultOntologyURIPanel extends JPanel { 16 | 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/error/ErrorLogListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.error; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 28-Feb-2007

14 | */ 15 | public interface ErrorLogListener { 16 | 17 | void errorLogged(); 18 | 19 | 20 | void errorLogCleared(); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/OWLReasonerExceptionHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | /* 4 | * Copyright (C) 2007, University of Manchester 5 | * 6 | * 7 | */ 8 | 9 | 10 | /** 11 | * Author: Matthew Horridge
12 | * The University Of Manchester
13 | * Bio-Health Informatics Group
14 | * Date: 26-Nov-2007

15 | */ 16 | public interface OWLReasonerExceptionHandler { 17 | 18 | void handle(Throwable t); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/selection/SelectionDriver.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.selection; 2 | 3 | import org.semanticweb.owlapi.model.OWLObject; 4 | 5 | import java.awt.*; 6 | import java.util.Optional; 7 | 8 | /** 9 | * Matthew Horridge 10 | * Stanford Center for Biomedical Informatics Research 11 | * 8 Aug 16 12 | */ 13 | public interface SelectionDriver { 14 | 15 | Component asComponent(); 16 | 17 | Optional getSelection(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/util/DateFormatter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.util; 2 | 3 | import org.semanticweb.owlapi.model.OWLDataFactory; 4 | import org.semanticweb.owlapi.model.OWLLiteral; 5 | 6 | import java.util.Date; 7 | 8 | /** 9 | * Matthew Horridge 10 | * Stanford Center for Biomedical Informatics Research 11 | * 20/11/15 12 | */ 13 | public interface DateFormatter { 14 | 15 | OWLLiteral formatDate(Date date, OWLDataFactory dataFactory); 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/BracketingStrategy.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | import org.semanticweb.owlapi.model.OWLObject; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public interface BracketingStrategy { 12 | 13 | boolean shouldBracket(OWLObject parentObject, OWLObject childObject); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/styledstring/PrettyPrintStrategy.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.styledstring; 2 | 3 | import org.semanticweb.owlapi.model.OWLObject; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public interface PrettyPrintStrategy { 12 | 13 | boolean shouldStartNewLine(OWLObject parentObject, OWLObject object); 14 | } 15 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/search/SearchResultClickedListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.search; 2 | 3 | import org.protege.editor.owl.model.search.SearchResult; 4 | 5 | import java.awt.event.MouseEvent; 6 | 7 | /** 8 | * Matthew Horridge 9 | * Stanford Center for Biomedical Informatics Research 10 | * 31/03/15 11 | */ 12 | public interface SearchResultClickedListener { 13 | 14 | void handleSearchResultClicked(SearchResult searchResult, MouseEvent e); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/CreateNewTarget.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 09-May-2007

11 | */ 12 | public interface CreateNewTarget extends ActionTarget { 13 | 14 | boolean canCreateNew(); 15 | 16 | 17 | void createNewObject(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-desktop/src/main/env/platform-independent/run.bat: -------------------------------------------------------------------------------- 1 | setlocal 2 | cd /d %~dp0 3 | java -Xmx${conf.mem.xmx}M -Xms${conf.mem.xms}M -Xss${conf.mem.xss}M ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1 4 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/ProtegeWelcomePanel.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Apr 27, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public class ProtegeWelcomePanel { 19 | 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/HasCopySubHierarchyToClipboard.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 31/08/15 9 | */ 10 | public interface HasCopySubHierarchyToClipboard extends ActionTarget { 11 | 12 | void copySubHierarchyToClipboard(); 13 | 14 | boolean canPerformCopySubHierarchyToClipboard(); 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/explanation/io/InconsistentOntologyPluginInstance.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.explanation.io; 2 | 3 | import org.protege.editor.core.plugin.ProtegePluginInstance; 4 | import org.protege.editor.owl.OWLEditorKit; 5 | import org.semanticweb.owlapi.model.OWLOntology; 6 | 7 | public interface InconsistentOntologyPluginInstance extends ProtegePluginInstance { 8 | 9 | void setup(OWLEditorKit editorKit); 10 | 11 | void explain(OWLOntology ontology); 12 | } 13 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/layout/Alignment.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.layout; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 03/11/2011 8 | *

9 | * This class is subject to change and it is therefore not recommended for public use. 10 | *

11 | */ 12 | public enum Alignment { 13 | 14 | LEFT, 15 | 16 | RIGHT, 17 | 18 | CENTRE 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/CreateNewChildTarget.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 09-May-2007

11 | */ 12 | public interface CreateNewChildTarget extends ActionTarget { 13 | 14 | boolean canCreateNewChild(); 15 | 16 | 17 | void createNewChild(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/AxiomSubjectProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import com.google.common.base.Optional; 4 | import org.semanticweb.owlapi.model.OWLAxiom; 5 | import org.semanticweb.owlapi.model.OWLObject; 6 | 7 | /** 8 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 9 | */ 10 | public interface AxiomSubjectProvider { 11 | 12 | Optional getAxiomSubject(OWLAxiom axiom); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/entity/Revertable.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.entity; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: Sep 18, 2008

15 | */ 16 | public interface Revertable { 17 | 18 | void checkpoint(); 19 | 20 | void revert(); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/metrics/MetricsTreeNode.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.metrics; 2 | 3 | import javax.swing.tree.DefaultMutableTreeNode; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 20-Feb-2007

11 | */ 12 | public class MetricsTreeNode extends DefaultMutableTreeNode { 13 | 14 | protected MetricsTreeNode(Metric metric) { 15 | super(metric); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/CreateNewSiblingTarget.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.ui.action.ActionTarget; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 09-May-2007

11 | */ 12 | public interface CreateNewSiblingTarget extends ActionTarget { 13 | 14 | boolean canCreateNewSibling(); 15 | 16 | 17 | void createNewSibling(); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/TopologicallySortedImportsClosureProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | import java.util.List; 6 | 7 | /** 8 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 9 | */ 10 | public interface TopologicallySortedImportsClosureProvider { 11 | 12 | List getTopologicallySortedImportsClosure(OWLOntology ontology); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/ActionTarget.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.action; 2 | 3 | import javax.swing.event.ChangeListener; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 02-May-2007

11 | */ 12 | public interface ActionTarget { 13 | 14 | public void addChangeListener(ChangeListener listener); 15 | 16 | 17 | public void removeChangeListener(ChangeListener listener); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/selector/OWLObjectSelector.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.selector; 2 | 3 | import java.util.Set; 4 | /* 5 | * Copyright (C) 2008, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 13 | * 21-Sep-2008

14 | */ 15 | public interface OWLObjectSelector { 16 | 17 | O getSelectedObject(); 18 | 19 | Set getSelectedObjects(); 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/Findable.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import java.util.List; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 11-Sep-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface Findable { 16 | 17 | List find(String match); 18 | 19 | 20 | void show(E owlEntity); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchMetadataImporter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | 5 | import java.util.Set; 6 | 7 | /** 8 | * Author: Matthew Horridge
9 | * Stanford University
10 | * Bio-Medical Informatics Research Group
11 | * Date: 18/09/2012 12 | */ 13 | public interface SearchMetadataImporter { 14 | 15 | SearchMetadataDB getSearchMetadata(OWLEditorKit editorKit, Set categories); 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/LinkFactory.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.protege.editor.owl.ui.renderer.layout.Link; 4 | import org.semanticweb.owlapi.model.OWLObject; 5 | 6 | import java.util.List; 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * Stanford University
11 | * Bio-Medical Informatics Research Group
12 | * Date: 01/10/2012 13 | */ 14 | public interface LinkFactory { 15 | 16 | List getLinks(OWLObject object); 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/search/SearchOptionsEditor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.search; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 29/10/2012 8 | */ 9 | public interface SearchOptionsEditor { 10 | 11 | void setSearchOptions(SearchOptions searchOptions); 12 | 13 | SearchOptions getSearchOptions(); 14 | 15 | void setSearchOptionsChangedListener(SearchOptionsChangedListener listener); 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/rdf/RootTriple.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view.rdf; 2 | 3 | import org.apache.jena.graph.Node; 4 | import org.apache.jena.graph.Triple; 5 | 6 | /** 7 | * A special triple to describe UI roots. 8 | */ 9 | public class RootTriple extends Triple { 10 | protected RootTriple(Triple t) { 11 | this(t.getSubject(), t.getPredicate(), t.getObject()); 12 | } 13 | 14 | protected RootTriple(Node s, Node p, Node o) { 15 | super(s, p, o); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/transfer/ObjectDropTarget.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.transfer; 2 | 3 | import org.protege.editor.owl.model.OWLModelManager; 4 | 5 | import javax.swing.*; 6 | import java.awt.*; 7 | import java.util.List; 8 | 9 | 10 | /** 11 | * @param - anything 12 | */ 13 | public interface ObjectDropTarget { 14 | 15 | JComponent getComponent(); 16 | 17 | boolean dropObjects(List owlObjects, Point pt, int type); 18 | 19 | OWLModelManager getOWLModelManager(); 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/util/ProgressView.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.util; 2 | 3 | import org.semanticweb.owlapi.model.IRI; 4 | 5 | import javax.swing.*; 6 | 7 | /** 8 | * Matthew Horridge 9 | * Stanford Center for Biomedical Informatics Research 10 | * 11 May 16 11 | */ 12 | public interface ProgressView { 13 | 14 | void setMessage(String message); 15 | 16 | void setSubMessage(String subMessage); 17 | 18 | void clearSubMessage(); 19 | 20 | JComponent asJComponent(); 21 | 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/test/resources/ontologies/VersionedOntology-functional.owl: -------------------------------------------------------------------------------- 1 | Prefix(rdf:=) 2 | Prefix(xsd:=) 3 | Prefix(skos:=) 4 | Prefix(xml:=) 5 | Prefix(rdfs:=) 6 | Prefix(owl:=) 7 | 8 | 9 | Ontology( 10 | 11 | ) 12 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/update/PluginDocumentParseException.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.update; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 18/11/15 7 | */ 8 | public class PluginDocumentParseException extends Exception { 9 | 10 | public PluginDocumentParseException(String message) { 11 | super(message); 12 | } 13 | 14 | public PluginDocumentParseException(String message, Throwable cause) { 15 | super(message, cause); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/hierarchy/HasFilter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.hierarchy; 2 | 3 | import java.util.function.Predicate; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 16/11/15 9 | */ 10 | public interface HasFilter { 11 | 12 | void setFilter(Predicate filter); 13 | 14 | void clearFilter(); 15 | 16 | /** 17 | * Gets the filter. 18 | * @return The filter. Not null. 19 | */ 20 | Predicate getFilter(); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/NullDeprecatedObjectChecker.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public class NullDeprecatedObjectChecker implements DeprecatedObjectChecker { 12 | 13 | public boolean isDeprecated(OWLEntity entity) { 14 | return false; 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/test/resources/logback-test.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | %d{HH:mm:ss.SSS} [%thread] %-5level %logger{0} %msg%n 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/UIConstants.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Mar 23, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface UIConstants { 19 | 20 | public static final int COMPONENT_PADDING = 4; 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/annotation/AnnotationValueProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.annotation; 2 | 3 | import org.semanticweb.owlapi.model.OWLAnnotationValue; 4 | import org.semanticweb.owlapi.model.OWLDataFactory; 5 | 6 | import java.util.Optional; 7 | 8 | /** 9 | * Matthew Horridge 10 | * Stanford Center for Biomedical Informatics Research 11 | * 29/01/16 12 | */ 13 | public interface AnnotationValueProvider { 14 | 15 | Optional getAnnotationValue(OWLDataFactory dataFactory); 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/InputVerificationStatusChangedListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: Mar 14, 2008

15 | */ 16 | public interface InputVerificationStatusChangedListener { 17 | 18 | void verifiedStatusChanged(boolean newState); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/plugin/DefaultPluginActivator.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.plugin; 2 | 3 | import org.osgi.framework.BundleActivator; 4 | import org.osgi.framework.BundleContext; 5 | 6 | public class DefaultPluginActivator implements BundleActivator { 7 | 8 | public void start(BundleContext arg0) throws Exception { 9 | // TODO Auto-generated method stub 10 | 11 | } 12 | 13 | public void stop(BundleContext arg0) throws Exception { 14 | // TODO Auto-generated method stub 15 | 16 | } 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/update/PluginRegistry.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.update; 2 | 3 | import java.util.List; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | /** 11 | * Author: drummond
12 | * http://www.cs.man.ac.uk/~drummond/

13 | 14 | * The University Of Manchester
15 | * Bio Health Informatics Group
16 | * Date: Nov 6, 2008

17 | */ 18 | public interface PluginRegistry { 19 | 20 | List getAvailablePlugins(); 21 | 22 | void reload(); 23 | } 24 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/OWLIconProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | import org.semanticweb.owlapi.model.OWLObject; 4 | 5 | import javax.swing.*; 6 | 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * The University Of Manchester
11 | * Medical Informatics Group
12 | * Date: Apr 2, 2006

13 | 14 | * matthew.horridge@cs.man.ac.uk
15 | * www.cs.man.ac.uk/~horridgm

16 | */ 17 | public interface OWLIconProvider { 18 | 19 | public Icon getIcon(OWLObject object); 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/find/AbstractSearchResultsRow.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.find; 2 | 3 | import javax.swing.table.TableCellRenderer; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 20/09/2012 10 | */ 11 | public abstract class AbstractSearchResultsRow { 12 | 13 | public abstract Object getValueAtColumnIndex(int columnIndex); 14 | 15 | public abstract TableCellRenderer getRendererAtColumnIndex(int columnIndex); 16 | 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/transfer/OWLObjectDragSource.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.transfer; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: 15-Jun-2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface OWLObjectDragSource { 19 | 20 | public void setDragOriginater(boolean b); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/progress/BackgroundTaskListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.progress; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: May 8, 2009

15 | */ 16 | public interface BackgroundTaskListener { 17 | 18 | void startTask(BackgroundTask task); 19 | 20 | void endTask(BackgroundTask task); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/FreshAxiomLocationStrategy.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import org.protege.editor.owl.model.HasActiveOntology; 4 | import org.semanticweb.owlapi.model.OWLAxiom; 5 | import org.semanticweb.owlapi.model.OWLOntology; 6 | 7 | /** 8 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 9 | */ 10 | public interface FreshAxiomLocationStrategy { 11 | 12 | OWLOntology getFreshAxiomLocation(OWLAxiom axiom, HasActiveOntology hasActiveOntology); 13 | } 14 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/table/ProgrammaticEditEvent.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.table; 2 | 3 | import java.util.EventObject; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 29-Sep-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public class ProgrammaticEditEvent extends EventObject { 16 | 17 | public ProgrammaticEditEvent(Object source) { 18 | super(source); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/list/MListItem.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.list; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 24-Feb-2007

14 | */ 15 | public interface MListItem { 16 | 17 | boolean isEditable(); 18 | 19 | void handleEdit(); 20 | 21 | boolean isDeleteable(); 22 | 23 | boolean handleDelete(); 24 | 25 | String getTooltip(); 26 | 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/SelectionProviderListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Mar 21, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface SelectionProviderListener { 19 | 20 | public void selectionChanged(SelectionProvider source); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/OWLUIActionStrategy.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.action; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: Apr 24, 2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface OWLUIActionStrategy { 16 | 17 | public boolean canPerform(OWLEntity owlEntity); 18 | 19 | 20 | public void performAction(); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/OWLEntityRendererListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 30-Aug-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface OWLEntityRendererListener { 16 | 17 | void renderingChanged(OWLEntity entity, OWLModelManagerEntityRenderer renderer); 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/event/OWLModelManagerListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.event; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Apr 19, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface OWLModelManagerListener { 19 | 20 | public void handleChange(OWLModelManagerChangeEvent event); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/tabbedpane/NullTabCloseHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.tabbedpane; 2 | 3 | import javax.swing.*; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 08/03/15 9 | */ 10 | public class NullTabCloseHandler implements TabCloseHandler { 11 | 12 | @Override 13 | public boolean shouldCloseTab(int tabIndex, JTabbedPane tabbedPane) { 14 | return false; 15 | } 16 | 17 | @Override 18 | public void handleCloseTab(int tabIndex, JTabbedPane tabbedPane) { 19 | 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/SWRLRulesFrame.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | import org.semanticweb.owlapi.model.OWLOntology; 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 06-Jul-2007

11 | */ 12 | public class SWRLRulesFrame extends AbstractOWLFrame { 13 | 14 | public SWRLRulesFrame(OWLEditorKit editorKit) { 15 | addSection(new SWRLRulesFrameSection(editorKit, this)); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/EntityActionIcon.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | import java.awt.*; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 9 Aug 16 9 | */ 10 | public interface EntityActionIcon { 11 | 12 | static final BasicStroke ACTION_STROKE = new BasicStroke(2); 13 | 14 | static void setupAlpha(Component c, Graphics2D g2) { 15 | if(!c.isEnabled()) { 16 | g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.5f)); 17 | } 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/entity/AutoIDGenerator.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.entity; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | /** 11 | * Author: drummond
12 | * http://www.cs.man.ac.uk/~drummond/

13 | 14 | * The University Of Manchester
15 | * Bio Health Informatics Group
16 | * Date: Jul 25, 2008

17 | */ 18 | public interface AutoIDGenerator { 19 | 20 | String getNextID(Class type) throws AutoIDException; 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/selection/OWLSelectionModelListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.selection; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Mar 21, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface OWLSelectionModelListener { 19 | 20 | public void selectionChanged() throws Exception; 21 | } 22 | 23 | 24 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/ProtegeOWLReasonerFactoryAdapter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * The University Of Manchester
8 | * Bio-Health Informatics Group
9 | * Date: 16-Apr-2007

10 | */ 11 | 12 | /** 13 | * This is here so that developers won't get confused by my constant refactoring. 14 | * 15 | * @deprecated Use AbstractProtegeOWLReasonerInfo instead. 16 | */ 17 | public abstract class ProtegeOWLReasonerFactoryAdapter extends AbstractProtegeOWLReasonerInfo { 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/repository/TONESRepository.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.repository; 2 | 3 | import java.net.URI; 4 | /* 5 | * Copyright (C) 2008, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 13 | * 18-Oct-2008

14 | */ 15 | public class TONESRepository extends ManchesterRepository { 16 | 17 | 18 | public TONESRepository() { 19 | super("TONES", URI.create("http://owl.cs.manchester.ac.uk/repository")); 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/action/start/AltStartupAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.action.start; 2 | 3 | import org.protege.editor.core.plugin.ProtegePluginInstance; 4 | 5 | import javax.swing.*; 6 | 7 | public abstract class AltStartupAction extends AbstractAction implements ProtegePluginInstance { 8 | private static final long serialVersionUID = -8693527745746711830L; 9 | private JFrame parent; 10 | 11 | 12 | public JFrame getParent() { 13 | return parent; 14 | } 15 | public void setParent(JFrame parent) { 16 | this.parent = parent; 17 | } 18 | 19 | 20 | 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/OWLEntityDisplayProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | import javax.swing.*; 6 | 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * The University Of Manchester
11 | * Medical Informatics Group
12 | * Date: 25-May-2006

13 | 14 | * matthew.horridge@cs.man.ac.uk
15 | * www.cs.man.ac.uk/~horridgm

16 | */ 17 | public interface OWLEntityDisplayProvider { 18 | 19 | boolean canDisplay(OWLEntity owlEntity); 20 | 21 | JComponent getDisplayComponent(); 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/OntologyVisibilityManagerListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: Apr 20, 2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface OntologyVisibilityManagerListener { 19 | 20 | public void ontologyVisibilityChanged(OntologyVisibilityManager source); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/ontology/wizard/move/MoveAxiomsKitPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.ontology.wizard.move; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | /* 5 | * Copyright (C) 2008, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 13 | * 11-Sep-2008

14 | */ 15 | public interface MoveAxiomsKitPlugin extends ProtegePlugin { 16 | 17 | public static final String ID = "moveaxiomskit"; 18 | 19 | 20 | 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewBarIcon.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.view; 2 | 3 | import javax.swing.*; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 28 Nov 2016 9 | */ 10 | public abstract class ViewBarIcon implements Icon { 11 | 12 | private static final int WIDTH = 12; 13 | 14 | private static final int HEIGHT = 12; 15 | 16 | @Override 17 | public int getIconWidth() { 18 | return WIDTH; 19 | } 20 | 21 | @Override 22 | public int getIconHeight() { 23 | return HEIGHT; 24 | } 25 | } 26 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/OntologyRepositoryFactoryPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | /* 5 | * Copyright (C) 2008, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 13 | * 18-Oct-2008

14 | */ 15 | public interface OntologyRepositoryFactoryPlugin extends ProtegePlugin { 16 | 17 | public static final String EXTENSION_POINT_ID = "OntologyRepositoryFactory"; 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/InferredAxiomsFrame.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | import org.semanticweb.owlapi.model.OWLOntology; 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Bio-Health Informatics Group
10 | * Date: 14-Oct-2007

11 | */ 12 | public class InferredAxiomsFrame extends AbstractOWLFrame { 13 | 14 | public InferredAxiomsFrame(OWLEditorKit owlEditorKit) { 15 | addSection(new InferredAxiomsFrameSection(owlEditorKit, this)); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/entity/LabelDescriptor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.entity; 2 | 3 | import org.semanticweb.owlapi.model.IRI; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | /** 11 | * Author: drummond
12 | * http://www.cs.man.ac.uk/~drummond/

13 | 14 | * The University Of Manchester
15 | * Bio Health Informatics Group
16 | * Date: Jul 28, 2008

17 | */ 18 | public interface LabelDescriptor { 19 | 20 | String getLanguage(); 21 | 22 | // @@TODO should be getAnnotationProperty() ? 23 | IRI getIRI(); 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/user/UserPreferences.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.user; 2 | 3 | import org.protege.editor.core.prefs.Preferences; 4 | import org.protege.editor.core.prefs.PreferencesManager; 5 | 6 | /** 7 | * Matthew Horridge 8 | * Stanford Center for Biomedical Informatics Research 9 | * 23/11/15 10 | * 11 | * Preferences for the user. For example, user name, ORCID etc. 12 | */ 13 | public class UserPreferences { 14 | 15 | public static Preferences get() { 16 | return PreferencesManager.getInstance().getApplicationPreferences("org.protege.user"); 17 | } 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/OWLAnnotationsFrame.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | import org.semanticweb.owlapi.model.OWLAnnotationSubject; 5 | 6 | 7 | /** 8 | * Author: Matthew Horridge
9 | * The University Of Manchester
10 | * Bio-Health Informatics Group
11 | * Date: 26-Jan-2007

12 | */ 13 | public class OWLAnnotationsFrame extends AbstractOWLFrame { 14 | 15 | public OWLAnnotationsFrame(OWLEditorKit man) { 16 | addSection(new OWLAnnotationFrameSection(man, this)); 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/workspace/views/ViewNodePanel.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.workspace.views; 2 | 3 | import org.protege.editor.core.ui.workspace.WorkspaceViewsTab; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 26-Sep-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public class ViewNodePanel { 16 | 17 | public ViewNodePanel(WorkspaceViewsTab workspaceViewsTab) { 18 | // Need to apply the defaul views 19 | 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/selection/OWLSelectionModelAdapter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.selection; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: 19-Sep-2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public class OWLSelectionModelAdapter implements OWLSelectionModelListener { 19 | 20 | public void selectionChanged() throws Exception { 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/AxiomListFrame.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | import org.semanticweb.owlapi.model.OWLAxiom; 5 | 6 | import java.util.Set; 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * The University Of Manchester
11 | * Bio-Health Informatics Group
12 | * Date: 19-Dec-2007

13 | */ 14 | public class AxiomListFrame extends AbstractOWLFrame> { 15 | 16 | public AxiomListFrame(OWLEditorKit owlEditorKit) { 17 | addSection(new AxiomListFrameSection(owlEditorKit, this)); 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/etc/owleditor-readme.html: -------------------------------------------------------------------------------- 1 | 2 | 3 |

OWL Editor

4 |

5 | This is one of the core Protégé plugins and is responsible for 6 | creating the core owl editing environment. 7 |

8 | 9 |

Version info

10 | 11 |

v4.2.0 Update Build 276 - 8 Jun, 2012

12 | 13 |
    14 |
  • Fixed a problem in the rename multiple entities refactor menu.
    • 15 |
16 | 17 |

v4.2.0 Release Build 276 - 22, May, 2012

18 | 19 | See 20 | the 21 | Protégé 4.2 beta release notes. 22 | 23 | 24 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/OWLEntityColorProviderPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 19-Jul-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface OWLEntityColorProviderPlugin extends ProtegePlugin { 16 | 17 | public static final String ID = "ui_renderer_entitycolorprovider"; 18 | } 19 | 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/layout/PageLayoutState.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.layout; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 07/11/2011 8 | *

9 | * Describes the layout state of a page - whether it is valid or invalid. 10 | *

11 | */ 12 | public enum PageLayoutState { 13 | 14 | /** 15 | * Represents a valid layout state of a page. 16 | */ 17 | VALID, 18 | 19 | /** 20 | * Represents an invalid layout state of a page. 21 | */ 22 | INVALID 23 | } 24 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/VerifiedInputEditor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: Mar 14, 2008

15 | */ 16 | public interface VerifiedInputEditor { 17 | 18 | void addStatusChangedListener(InputVerificationStatusChangedListener listener); 19 | 20 | void removeStatusChangedListener(InputVerificationStatusChangedListener listener); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/FindAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.action; 2 | 3 | import java.awt.event.ActionEvent; 4 | 5 | /** 6 | * Matthew Horridge 7 | * Stanford Center for Biomedical Informatics Research 8 | * 01/04/15 9 | */ 10 | public class FindAction extends ProtegeOWLAction { 11 | 12 | @Override 13 | public void initialise() throws Exception { 14 | 15 | } 16 | 17 | @Override 18 | public void dispose() throws Exception { 19 | 20 | } 21 | 22 | @Override 23 | public void actionPerformed(ActionEvent e) { 24 | getOWLWorkspace().showSearchDialog(); 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/plugin/RendererPluginLoader.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.plugin; 2 | 3 | import org.eclipse.core.runtime.IExtension; 4 | import org.protege.editor.core.plugin.AbstractPluginLoader; 5 | import org.protege.editor.owl.ProtegeOWL; 6 | 7 | public class RendererPluginLoader extends AbstractPluginLoader { 8 | 9 | public RendererPluginLoader() { 10 | super(ProtegeOWL.ID, RendererPlugin.RENDERER_PLUGIN_ID); 11 | } 12 | 13 | @Override 14 | protected RendererPlugin createInstance(IExtension extension) { 15 | return new RendererPlugin(extension); 16 | } 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/resources/InconsistentOntologyHelp.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Your ontology is inconsistent which means that the OWL reasoner will 4 | no longer be able to provide any useful information about the 5 | ontology. 6 |

7 | You have several options at this point: 8 |

    9 |
  • Click the Explain button to try the Protege explanation facility.
    • 10 |
  • If you think you know what the problem is, click 11 | Cancel to fix the 12 | ontology yourself.
    • 13 |
  • Some reasoners come with command line tools that will provide 14 | complete explanations for inconsistent ontologies.
    • 15 |
16 |

17 | 18 | 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/editorkit/plugin/EditorKitHookPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.editorkit.plugin; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | /** 11 | * Author: drummond
12 | * http://www.cs.man.ac.uk/~drummond/

13 | 14 | * The University Of Manchester
15 | * Bio Health Informatics Group
16 | * Date: Oct 15, 2008

17 | */ 18 | public interface EditorKitHookPlugin extends ProtegePlugin { 19 | 20 | public static final String EXTENSION_POINT_ID = "EditorKitHook"; 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/wizard/WizardPanelNotFoundException.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.wizard; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | public class WizardPanelNotFoundException extends RuntimeException { 10 | 11 | /** 12 | * 13 | */ 14 | private static final long serialVersionUID = -967700880863172861L; 15 | private Object id; 16 | 17 | public WizardPanelNotFoundException(Object id) { 18 | super(); 19 | this.id = id; 20 | } 21 | 22 | 23 | public String getMessage() { 24 | return id.toString(); 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchMetadataImportManager.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import java.util.ArrayList; 4 | import java.util.List; 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * Stanford University
9 | * Bio-Medical Informatics Research Group
10 | * Date: 03/10/2012 11 | */ 12 | public class SearchMetadataImportManager { 13 | 14 | public List getImporters() { 15 | List importers = new ArrayList<>(); 16 | importers.add(new DefaultSearchMetadataImporter()); 17 | return importers; 18 | } 19 | 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/NullLinkFactory.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.protege.editor.owl.ui.renderer.layout.Link; 4 | import org.semanticweb.owlapi.model.OWLObject; 5 | 6 | import java.util.Collections; 7 | import java.util.List; 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * Stanford University
12 | * Bio-Medical Informatics Research Group
13 | * Date: 01/10/2012 14 | */ 15 | public class NullLinkFactory implements LinkFactory { 16 | 17 | public List getLinks(OWLObject object) { 18 | return Collections.emptyList(); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/AbstractHierarchyViewComponent.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.view; 2 | 3 | import org.protege.editor.owl.model.hierarchy.HierarchyProvider; 4 | import org.protege.editor.owl.ui.tree.ObjectTree; 5 | 6 | /** 7 | * Created by @ssz on 07.01.2021. 8 | */ 9 | public abstract class AbstractHierarchyViewComponent 10 | extends AbstractOWLSelectionViewComponent implements Findable, Deleteable { 11 | 12 | protected abstract ObjectTree getTree(); 13 | 14 | protected abstract HierarchyProvider getHierarchyProvider(); 15 | 16 | protected abstract void transmitSelection(); 17 | } 18 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/TextFieldSearchHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | 3 | import javax.swing.*; 4 | import java.util.Optional; 5 | 6 | /** 7 | * Matthew Horridge 8 | * Stanford Center for Biomedical Informatics Research 9 | * 4 Aug 16 10 | */ 11 | public interface TextFieldSearchHandler { 12 | 13 | /** 14 | * Handle a request to perform a search with reference to a specific text field. 15 | * @param textField the originator of the request. 16 | * @return The search result to be entered into the text field. 17 | */ 18 | Optional handleSearch(JTextField textField); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/AnnotationContainer.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.semanticweb.owlapi.model.OWLAnnotation; 4 | 5 | import java.util.Set; 6 | /* 7 | * Copyright (C) 2007, University of Manchester 8 | * 9 | * 10 | */ 11 | 12 | /** 13 | * Author: drummond
14 | * http://www.cs.man.ac.uk/~drummond/

15 | 16 | * The University Of Manchester
17 | * Bio Health Informatics Group
18 | * Date: Jun 8, 2009

19 | * 20 | */ 21 | 22 | @Deprecated // todo: unused -> delete 23 | public interface AnnotationContainer { 24 | 25 | Set getAnnotations(); 26 | 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/RefreshableComponent.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 29-Nov-2007

14 | * 15 | * A marker interface for components that can regenerate 16 | * the view that they display. 17 | */ 18 | public interface RefreshableComponent { 19 | 20 | /** 21 | * Clears the data displayed by the component and 22 | * reloads data. 23 | */ 24 | void refreshComponent(); 25 | } 26 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/OWLFrameListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 19-Jan-2007

14 | */ 15 | public interface OWLFrameListener { 16 | 17 | /** 18 | * Gets called when the frame content has 19 | * been changed. Usually because a row has 20 | * been added or removed. 21 | * @throws Exception 22 | */ 23 | void frameContentChanged() throws Exception; 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/util/Recommendation.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.util; 2 | 3 | /** 4 | * Matthew Horridge 5 | * Stanford Center for Biomedical Informatics Research 6 | * 16 Sep 16 7 | * 8 | * A flag for whether something (e.g. an edit to an ontology) is recommended or not. 9 | */ 10 | public enum Recommendation { 11 | 12 | RECOMMENDED("Recommended"), 13 | NOT_RECOMMENDED("Not recommended"); 14 | 15 | private String printName; 16 | 17 | Recommendation(String printName) { 18 | this.printName = printName; 19 | } 20 | 21 | public String getPrintName() { 22 | return printName; 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/preferences/node/PreferenceNode.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.preferences.node; 2 | 3 | import javax.swing.*; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 08-Jun-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface PreferenceNode { 16 | 17 | public String getLabel(); 18 | 19 | 20 | public V getValue(); 21 | 22 | 23 | public void setValue(V object); 24 | 25 | 26 | public JComponent getComponent(); 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/inference/DefaultOWLReasonerExceptionHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.inference; 2 | 3 | import org.semanticweb.owlapi.model.OWLRuntimeException; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
13 | * The University Of Manchester
14 | * Bio-Health Informatics Group
15 | * Date: 26-Nov-2007

16 | */ 17 | public class DefaultOWLReasonerExceptionHandler implements OWLReasonerExceptionHandler { 18 | 19 | 20 | public void handle(Throwable t) { 21 | throw new OWLRuntimeException(t); 22 | } 23 | } 24 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/ontology/wizard/move/MoveType.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.ontology.wizard.move; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * Stanford University
6 | * Bio-Medical Informatics Research Group
7 | * Date: 24/09/2012 8 | */ 9 | public enum MoveType { 10 | 11 | COPY("copied"), 12 | 13 | MOVE("moved"), 14 | 15 | DELETE("deleted"); 16 | 17 | 18 | private String completedName; 19 | 20 | private MoveType(String completedName) { 21 | this.completedName = completedName; 22 | } 23 | 24 | public String getCompletedName() { 25 | return completedName; 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/DefinedClassChecker.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.semanticweb.owlapi.model.OWLClass; 4 | 5 | import javax.annotation.Nonnull; 6 | 7 | /** 8 | * Matthew Horridge 9 | * Stanford Center for Biomedical Informatics Research 10 | * 13 Sep 16 11 | */ 12 | public interface DefinedClassChecker { 13 | 14 | /** 15 | * Determines whether the specified class is a defined class. 16 | * @param cls The class. 17 | * @return true if the specified class is a defined class, otherwise false. 18 | */ 19 | boolean isDefinedClass(@Nonnull OWLClass cls); 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/OntologyRepositoryFactory.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core; 2 | 3 | import org.protege.editor.core.plugin.ProtegePluginInstance; 4 | /* 5 | * Copyright (C) 2008, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | 11 | /** 12 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 13 | * 18-Oct-2008

14 | */ 15 | public abstract class OntologyRepositoryFactory implements ProtegePluginInstance { 16 | 17 | /** 18 | * Creates the repository. 19 | * @return An ontology repository. 20 | */ 21 | public abstract OntologyRepository createRepository(); 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/io/IOListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.io; 2 | 3 | 4 | /** 5 | * Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 6 | * 16-Sep-2008

7 | * 8 | * A listener that is informed of load and save events on an 9 | * OWLModel. 10 | */ 11 | public abstract class IOListener { 12 | 13 | public abstract void beforeSave(IOListenerEvent event); 14 | 15 | public abstract void afterSave(IOListenerEvent event); 16 | 17 | public abstract void beforeLoad(IOListenerEvent event); 18 | 19 | public abstract void afterLoad(IOListenerEvent event); 20 | 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/action/ProtegeDynamicAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.action; 2 | 3 | import javax.swing.*; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 17-Sep-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public abstract class ProtegeDynamicAction extends ProtegeAction { 16 | 17 | /** 18 | * 19 | */ 20 | private static final long serialVersionUID = -8038803274995974199L; 21 | 22 | public abstract void rebuildChildMenuItems(JMenu thisMenuItem); 23 | } 24 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/library/CatalogEntryManagerLoader.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.library; 2 | 3 | import org.eclipse.core.runtime.IExtension; 4 | import org.protege.editor.core.plugin.AbstractPluginLoader; 5 | import org.protege.editor.owl.ProtegeOWL; 6 | 7 | public class CatalogEntryManagerLoader extends AbstractPluginLoader { 8 | 9 | public CatalogEntryManagerLoader() { 10 | super(ProtegeOWL.ID, CatalogEntryManagerPlugin.ID); 11 | } 12 | 13 | @Override 14 | protected CatalogEntryManagerPlugin createInstance(IExtension extension) { 15 | return new CatalogEntryManagerPlugin(extension); 16 | } 17 | 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/namespace/NamespaceManagerListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.namespace; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: 19-Jun-2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public interface NamespaceManagerListener { 19 | 20 | public void mappingAdded(String prefix, String namespace); 21 | 22 | 23 | public void mappingRemoved(String prefix, String namespace); 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/hierarchy/creation/TabIndentedHierachyTextPane.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.hierarchy.creation; 2 | 3 | import javax.swing.*; 4 | import java.awt.*; 5 | 6 | 7 | /** 8 | * Author: Matthew Horridge
9 | * The University Of Manchester
10 | * Medical Informatics Group
11 | * Date: 17-Jul-2006

12 | 13 | * matthew.horridge@cs.man.ac.uk
14 | * www.cs.man.ac.uk/~horridgm

15 | */ 16 | public class TabIndentedHierachyTextPane extends JTextArea { 17 | 18 | public TabIndentedHierachyTextPane() { 19 | setTabSize(4); 20 | setFont(new Font("monospaced", Font.PLAIN, 14)); 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/NullDataPropertySatisfiabilityChecker.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.semanticweb.owlapi.model.OWLDataProperty; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public class NullDataPropertySatisfiabilityChecker implements DataPropertySatisfiabilityChecker { 12 | 13 | public static final boolean DEFAULT_SATISFIABLE_VALUE = true; 14 | 15 | public boolean isSatisfiable(OWLDataProperty property) { 16 | return DEFAULT_SATISFIABLE_VALUE; 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/OpenRequestHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | 3 | import org.protege.editor.core.ui.workspace.Workspace; 4 | /* 5 | * Copyright (C) 2007, University of Manchester 6 | * 7 | * 8 | */ 9 | 10 | /** 11 | * Author: drummond
12 | * http://www.cs.man.ac.uk/~drummond/

13 | 14 | * The University Of Manchester
15 | * Bio Health Informatics Group
16 | * Date: Sep 22, 2008

17 | */ 18 | public interface OpenRequestHandler { 19 | 20 | Workspace getCurrentWorkspace(); 21 | 22 | void openInNewWorkspace() throws Exception; 23 | 24 | void openInCurrentWorkspace() throws Exception; 25 | } 26 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/IOListenerManager.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntologyID; 4 | 5 | import java.net.URI; 6 | 7 | /** 8 | * Matthew Horridge 9 | * Stanford Center for Biomedical Informatics Research 10 | * 17 May 16 11 | */ 12 | public interface IOListenerManager { 13 | 14 | void fireBeforeLoadEvent(OWLOntologyID ontologyID, URI documentURI); 15 | 16 | void fireAfterLoadEvent(OWLOntologyID ontologyID, URI documentURI); 17 | 18 | void fireBeforeSaveEvent(OWLOntologyID ontologyID, URI documentURI); 19 | 20 | void fireAfterSaveEvent(OWLOntologyID ontologyID, URI documentURI); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/annotation/EntityCreationMetadataPreferences.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.annotation; 2 | 3 | import org.protege.editor.core.prefs.Preferences; 4 | import org.protege.editor.core.prefs.PreferencesManager; 5 | 6 | /** 7 | * Matthew Horridge 8 | * Stanford Center for Biomedical Informatics Research 9 | * 27/01/16 10 | */ 11 | public class EntityCreationMetadataPreferences { 12 | 13 | private EntityCreationMetadataPreferences() { 14 | } 15 | 16 | public static Preferences get() { 17 | return PreferencesManager.getInstance().getApplicationPreferences(EntityCreationMetadataPreferences.class); 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/EntityBasedSearchMDImporter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | import java.util.Set; 6 | 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * Stanford University
11 | * Bio-Medical Informatics Research Group
12 | * Date: 03/10/2012 13 | */ 14 | public abstract class EntityBasedSearchMDImporter { 15 | 16 | public abstract boolean isImporterFor(Set categories); 17 | 18 | public abstract void generateSearchMetadataFor(OWLEntity entity, String entityRendering, SearchMetadataImportContext context, SearchMetadataDB db); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/DeprecatedObjectChecker.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public interface DeprecatedObjectChecker { 12 | 13 | /** 14 | * Determines whether or not the specified entity is deprecated. 15 | * @param entity The entity. 16 | * @return true if the entity is deprecated, otherwise false. 17 | */ 18 | boolean isDeprecated(OWLEntity entity); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/context/NullObjectPropertySatisfiabilityChecker.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.context; 2 | 3 | import org.semanticweb.owlapi.model.OWLObjectProperty; 4 | 5 | /** 6 | * Author: Matthew Horridge
7 | * Stanford University
8 | * Bio-Medical Informatics Research Group
9 | * Date: 01/10/2012 10 | */ 11 | public class NullObjectPropertySatisfiabilityChecker implements ObjectPropertySatisfiabilityChecker { 12 | 13 | public static final boolean DEFAULT_SATISFIABLE_VALUE = true; 14 | 15 | public boolean isSatisfiable(OWLObjectProperty property) { 16 | return DEFAULT_SATISFIABLE_VALUE; 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewActionPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.view; 2 | 3 | import org.protege.editor.core.ui.action.ToolBarActionPlugin; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: Mar 28, 2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | 15 | * A ViewActionPlugin is a ToolBarActionPlugin that 16 | * appears on a specific type of View. 17 | */ 18 | public interface ViewActionPlugin extends ToolBarActionPlugin { 19 | 20 | public View getView(); 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/OWLEditorKitOntologyShortFormProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | import org.semanticweb.owlapi.util.OntologyIRIShortFormProvider; 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * Stanford University
9 | * Bio-Medical Informatics Research Group
10 | * Date: 28/09/2012 11 | */ 12 | public class OWLEditorKitOntologyShortFormProvider extends OntologyIRIShortFormProvider { 13 | 14 | private OWLEditorKit editorKit; 15 | 16 | public OWLEditorKitOntologyShortFormProvider(OWLEditorKit editorKit) { 17 | this.editorKit = editorKit; 18 | } 19 | 20 | 21 | } 22 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/DefaultTopologicallySortedImportsClosureProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | import java.util.List; 6 | 7 | /** 8 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 9 | */ 10 | public class DefaultTopologicallySortedImportsClosureProvider implements TopologicallySortedImportsClosureProvider { 11 | @Override 12 | public List getTopologicallySortedImportsClosure(OWLOntology ontology) { 13 | return ontology.getOWLOntologyManager().getSortedImportsClosure(ontology); 14 | } 15 | } 16 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/OntologyBasedSearchMDImporter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | import java.util.Set; 6 | 7 | 8 | /** 9 | * Author: Matthew Horridge
10 | * Stanford University
11 | * Bio-Medical Informatics Research Group
12 | * Date: 03/10/2012 13 | */ 14 | public abstract class OntologyBasedSearchMDImporter extends SearchMDImporter { 15 | 16 | public abstract boolean isImporterFor(Set categories); 17 | 18 | public abstract void generateSearchMetadata(OWLOntology ontology, SearchMetadataImportContext context, SearchMetadataDB db); 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.view; 2 | 3 | import org.protege.editor.core.ui.action.ProtegeAction; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: Mar 29, 2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public abstract class ViewAction extends ProtegeAction { 16 | 17 | private View view; 18 | 19 | 20 | public View getView() { 21 | return view; 22 | } 23 | 24 | 25 | public void setView(View view) { 26 | this.view = view; 27 | } 28 | } 29 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/MissingImportHandler.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntologyIRIMapper; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 31-Aug-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | 15 | * The missing import handler is called by the system as a last resort if 16 | * it cannot obtain a physical URI of an ontology (and hence cannot load 17 | * the ontology). 18 | */ 19 | public interface MissingImportHandler extends OWLOntologyIRIMapper { 20 | 21 | } 22 | -------------------------------------------------------------------------------- /protege-launcher/src/main/java/org/protege/osgi/framework/Server.java: -------------------------------------------------------------------------------- 1 | package org.protege.osgi.framework; 2 | 3 | import org.osgi.framework.BundleException; 4 | 5 | import java.io.File; 6 | import java.io.IOException; 7 | 8 | public class Server { 9 | 10 | /** 11 | * @param args 12 | * @throws IOException 13 | * @throws BundleException 14 | * @throws ClassNotFoundException 15 | * @throws IllegalAccessException 16 | * @throws InstantiationException 17 | */ 18 | public static void main(String[] args) throws Exception { 19 | Launcher.setArguments(args); 20 | new Launcher(new File("server.xml")).start(true); 21 | System.exit(0); 22 | } 23 | 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/OWLEditorKitHook.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import org.protege.editor.core.editorkit.plugin.EditorKitHook; 4 | import org.protege.editor.owl.OWLEditorKit; 5 | /* 6 | * Copyright (C) 2007, University of Manchester 7 | * 8 | * 9 | */ 10 | 11 | /** 12 | * Author: drummond
13 | * http://www.cs.man.ac.uk/~drummond/

14 | 15 | * The University Of Manchester
16 | * Bio Health Informatics Group
17 | * Date: Oct 15, 2008

18 | */ 19 | public abstract class OWLEditorKitHook extends EditorKitHook { 20 | 21 | protected OWLEditorKit getEditorKit() { 22 | return (OWLEditorKit)super.getEditorKit(); 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/annotation/EntityCreationMetadataProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.annotation; 2 | 3 | import org.semanticweb.owlapi.model.OWLDataFactory; 4 | import org.semanticweb.owlapi.model.OWLEntity; 5 | import org.semanticweb.owlapi.model.OWLOntology; 6 | import org.semanticweb.owlapi.model.OWLOntologyChange; 7 | 8 | import java.util.List; 9 | 10 | /** 11 | * Matthew Horridge 12 | * Stanford Center for Biomedical Informatics Research 13 | * 20/11/15 14 | */ 15 | public interface EntityCreationMetadataProvider { 16 | 17 | List getEntityCreationMetadataChanges(OWLEntity entity, OWLOntology targetOntology, OWLDataFactory df); 18 | 19 | } 20 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/axiom/ActiveOntologyLocationStrategy.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.axiom; 2 | 3 | import org.protege.editor.owl.model.HasActiveOntology; 4 | import org.semanticweb.owlapi.model.OWLAxiom; 5 | import org.semanticweb.owlapi.model.OWLOntology; 6 | 7 | /** 8 | * @author Matthew Horridge, Stanford University, Bio-Medical Informatics Research Group, Date: 27/05/2014 9 | */ 10 | public class ActiveOntologyLocationStrategy implements FreshAxiomLocationStrategy { 11 | 12 | @Override 13 | public OWLOntology getFreshAxiomLocation(OWLAxiom axiom, HasActiveOntology hasActiveOntology) { 14 | return hasActiveOntology.getActiveOntology(); 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/history/UndoManagerListener.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.history; 2 | 3 | /** 4 | * Author: Matthew Horridge
5 | * The University Of Manchester
6 | * Medical Informatics Group
7 | * Date: 20-May-2006

8 | 9 | * matthew.horridge@cs.man.ac.uk
10 | * www.cs.man.ac.uk/~horridgm

11 | */ 12 | public interface UndoManagerListener { 13 | 14 | /** 15 | * Called when the state of the undo manager has changed. 16 | * This usually indicates that the availability of undo or 17 | * redo has changed. 18 | * 19 | * @param source 20 | */ 21 | public void stateChanged(HistoryManager source); 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/util/TimestampFormatter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.util; 2 | 3 | import org.semanticweb.owlapi.model.OWLDataFactory; 4 | import org.semanticweb.owlapi.model.OWLLiteral; 5 | import org.semanticweb.owlapi.vocab.OWL2Datatype; 6 | 7 | import java.util.Date; 8 | 9 | /** 10 | * Matthew Horridge 11 | * Stanford Center for Biomedical Informatics Research 12 | * 27/01/16 13 | */ 14 | public class TimestampFormatter implements DateFormatter { 15 | 16 | @Override 17 | public OWLLiteral formatDate(Date date, OWLDataFactory dataFactory) { 18 | return dataFactory.getOWLLiteral(Long.toString(date.getTime()), OWL2Datatype.XSD_LONG); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/frame/OWLFrameObject.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.frame; 2 | 3 | import org.protege.editor.owl.ui.editor.OWLObjectEditor; 4 | import org.semanticweb.owlapi.model.OWLObject; 5 | 6 | import java.util.List; 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Bio-Health Informatics Group
13 | * Date: 25-Jan-2007

14 | */ 15 | public interface OWLFrameObject { 16 | 17 | OWLObjectEditor getEditor(); 18 | 19 | boolean checkEditorResults(OWLObjectEditor editor); 20 | 21 | boolean canAcceptDrop(List objects); 22 | 23 | boolean dropObjects(List objects); 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ModelManager.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | 9 | import javax.annotation.Nullable; 10 | 11 | /** 12 | * Author: Matthew Horridge
13 | * The University Of Manchester
14 | * Medical Informatics Group
15 | * Date: Mar 16, 2006

16 | 17 | * matthew.horridge@cs.man.ac.uk
18 | * www.cs.man.ac.uk/~horridgm

19 | */ 20 | public interface ModelManager extends Disposable { 21 | 22 | boolean isDirty(); 23 | 24 | void put(Object key, T object); 25 | 26 | @Nullable 27 | T get(Object key); 28 | } 29 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/refactor/ontology/OntologyTargetResolver.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.refactor.ontology; 2 | 3 | import org.semanticweb.owlapi.model.OWLEntity; 4 | import org.semanticweb.owlapi.model.OWLOntology; 5 | 6 | import java.util.Set; 7 | /* 8 | * Copyright (C) 2007, University of Manchester 9 | * 10 | * 11 | */ 12 | 13 | /** 14 | * Author: drummond
15 | * http://www.cs.man.ac.uk/~drummond/

16 | 17 | * The University Of Manchester
18 | * Bio Health Informatics Group
19 | * Date: Aug 21, 2008

20 | */ 21 | public interface OntologyTargetResolver { 22 | 23 | Set resolve(OWLEntity entity, Set ontologies); 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/clsdescriptioneditor/OWLClassAxiomEditor.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.clsdescriptioneditor; 2 | 3 | import org.protege.editor.owl.OWLEditorKit; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 06-Oct-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public class OWLClassAxiomEditor extends ExpressionEditor { 16 | 17 | public OWLClassAxiomEditor(OWLEditorKit owlEditorKit) { 18 | super(owlEditorKit, owlEditorKit.getModelManager().getOWLExpressionCheckerFactory().getClassAxiomChecker()); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/resources/PrecomputePreferencesHelp.txt: -------------------------------------------------------------------------------- 1 | It is generally recommended that users don't touch this panel. The 2 | default setting is to allow plugins to configure what precomputation 3 | tasks (e.g. classification, realization,...) should be done when a 4 | reasoner is initialized. The panel below allows you to override the 5 | decisions of the plugins by either requiring additional initialization 6 | steps or by preventing initialization. Requiring extra precomputation 7 | may slow the time it takes to initialize a reasoner with no performance 8 | advantage. Disallowing precomputation may improve the performance 9 | of reasoner initialization but may slow the performance of the plugins 10 | that requested that precomputation. -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/view/DisposableAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.view; 2 | 3 | import javax.swing.*; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 25-May-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public abstract class DisposableAction extends AbstractAction { 16 | 17 | protected DisposableAction(String name, Icon icon) { 18 | super(name, icon); 19 | } 20 | 21 | /** 22 | * This method should be overridden and used to detach listeners etc. 23 | */ 24 | public abstract void dispose(); 25 | } 26 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/refactor/AnnotationDeleter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.refactor; 2 | 3 | import org.semanticweb.owlapi.model.OWLOntology; 4 | 5 | import java.util.HashSet; 6 | import java.util.Set; 7 | 8 | 9 | /** 10 | * Author: Matthew Horridge
11 | * The University Of Manchester
12 | * Medical Informatics Group
13 | * Date: 08-Jul-2006

14 | 15 | * matthew.horridge@cs.man.ac.uk
16 | * www.cs.man.ac.uk/~horridgm

17 | */ 18 | public class AnnotationDeleter { 19 | 20 | private Set ontologies; 21 | 22 | 23 | public AnnotationDeleter(Set ontologies) { 24 | this.ontologies = new HashSet<>(); 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/metrics/ClassCountMetric.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.metrics; 2 | 3 | /* 4 | * Copyright (C) 2007, University of Manchester 5 | * 6 | * 7 | */ 8 | 9 | 10 | /** 11 | * Author: Matthew Horridge
12 | * The University Of Manchester
13 | * Bio-Health Informatics Group
14 | * Date: 20-Feb-2007

15 | */ 16 | @Deprecated // todo: unused -> delete 17 | public class ClassCountMetric extends AbstractIntegerMetric { 18 | 19 | public ClassCountMetric() { 20 | super("Named Classes"); 21 | } 22 | 23 | 24 | protected int getIntMetric() { 25 | return getOWLModelManager().getActiveOntology().getClassesInSignature().size(); 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/entity/AutoIDException.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.entity; 2 | /* 3 | * Copyright (C) 2007, University of Manchester 4 | * 5 | * 6 | */ 7 | 8 | /** 9 | * Author: drummond
10 | * http://www.cs.man.ac.uk/~drummond/

11 | 12 | * The University Of Manchester
13 | * Bio Health Informatics Group
14 | * Date: Jul 25, 2008

15 | */ 16 | public class AutoIDException extends Exception{ 17 | 18 | private static final long serialVersionUID = 7843272693263950056L; 19 | 20 | public AutoIDException(String s) { 21 | super(s); 22 | } 23 | 24 | public AutoIDException(String message, Throwable t) { 25 | super(message, t); 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/search/SearchMetadataDB.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model.search; 2 | 3 | import java.util.ArrayList; 4 | import java.util.Collections; 5 | import java.util.List; 6 | 7 | /** 8 | * Author: Matthew Horridge
9 | * Stanford University
10 | * Bio-Medical Informatics Research Group
11 | * Date: 03/10/2012 12 | */ 13 | public class SearchMetadataDB { 14 | 15 | private List results = new ArrayList<>(); 16 | 17 | public void addResult(SearchMetadata searchMetadata) { 18 | results.add(searchMetadata); 19 | } 20 | 21 | public List getResults() { 22 | return Collections.unmodifiableList(results); 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/metrics/IndividualCountMetric.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.metrics; 2 | 3 | /* 4 | * Copyright (C) 2007, University of Manchester 5 | * 6 | * 7 | */ 8 | 9 | 10 | /** 11 | * Author: Matthew Horridge
12 | * The University Of Manchester
13 | * Bio-Health Informatics Group
14 | * Date: 20-Feb-2007

15 | */ 16 | @Deprecated // todo: unused -> delete 17 | public class IndividualCountMetric extends AbstractIntegerMetric { 18 | 19 | public IndividualCountMetric() { 20 | super("Individuals"); 21 | } 22 | 23 | 24 | protected int getIntMetric() { 25 | return getOWLModelManager().getActiveOntology().getIndividualsInSignature().size(); 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/renderer/menu/ConfigureRenderer.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.renderer.menu; 2 | 3 | import org.protege.editor.core.ui.preferences.PreferencesDialogPanel; 4 | import org.protege.editor.owl.ui.action.ProtegeOWLAction; 5 | 6 | import java.awt.event.ActionEvent; 7 | 8 | public class ConfigureRenderer extends ProtegeOWLAction { 9 | private static final long serialVersionUID = -6789172694929034645L; 10 | 11 | public void initialise() throws Exception { 12 | 13 | } 14 | 15 | public void dispose() throws Exception { 16 | 17 | } 18 | 19 | public void actionPerformed(ActionEvent e) { 20 | PreferencesDialogPanel.showPreferencesDialog("Renderer", getOWLEditorKit()); 21 | } 22 | 23 | } 24 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesPanelPlugin.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.preferences; 2 | 3 | import org.protege.editor.core.plugin.ProtegePlugin; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: 08-Jun-2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface PreferencesPanelPlugin extends ProtegePlugin { 16 | 17 | /** 18 | * Gets the label. This label is typically used in user interfaces 19 | * @return A String that represents the label. 20 | */ 21 | public String getLabel(); 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/inference/ExplainInconsistentOntologyAction.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.inference; 2 | 3 | import org.protege.editor.owl.ui.action.ProtegeOWLAction; 4 | import org.protege.editor.owl.ui.explanation.io.InconsistentOntologyManager; 5 | 6 | import java.awt.event.ActionEvent; 7 | 8 | public class ExplainInconsistentOntologyAction extends ProtegeOWLAction { 9 | private static final long serialVersionUID = -3932851787552935976L; 10 | 11 | public void initialise() throws Exception { 12 | 13 | } 14 | 15 | public void actionPerformed(ActionEvent e) { 16 | InconsistentOntologyManager.get(getOWLModelManager()).explain(); 17 | } 18 | 19 | public void dispose() throws Exception { 20 | 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/ui/metrics/ObjectPropertyCount.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.ui.metrics; 2 | 3 | /* 4 | * Copyright (C) 2007, University of Manchester 5 | * 6 | * 7 | */ 8 | 9 | 10 | /** 11 | * Author: Matthew Horridge
12 | * The University Of Manchester
13 | * Bio-Health Informatics Group
14 | * Date: 20-Feb-2007

15 | */ 16 | @Deprecated // todo: unused -> delete 17 | public class ObjectPropertyCount extends AbstractIntegerMetric { 18 | 19 | public ObjectPropertyCount() { 20 | super("Object properties"); 21 | } 22 | 23 | 24 | protected int getIntMetric() { 25 | return getOWLModelManager().getActiveOntology().getObjectPropertiesInSignature().size(); 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /protege-editor-core/src/main/java/org/protege/editor/core/ui/util/SelectionProvider.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.core.ui.util; 2 | 3 | import java.util.List; 4 | 5 | 6 | /** 7 | * Author: Matthew Horridge
8 | * The University Of Manchester
9 | * Medical Informatics Group
10 | * Date: Mar 21, 2006

11 | 12 | * matthew.horridge@cs.man.ac.uk
13 | * www.cs.man.ac.uk/~horridgm

14 | */ 15 | public interface SelectionProvider { 16 | 17 | public List getSelection(); 18 | 19 | 20 | // Add listener 21 | public void addSelectionProviderListener(SelectionProviderListener listener); 22 | 23 | 24 | // Remove listener 25 | public void removeSelectionProviderListener(SelectionProviderListener listener); 26 | 27 | 28 | } 29 | -------------------------------------------------------------------------------- /protege-editor-owl/src/main/java/org/protege/editor/owl/model/OntologyFileFilter.java: -------------------------------------------------------------------------------- 1 | package org.protege.editor.owl.model; 2 | 3 | import java.io.File; 4 | import java.io.FileFilter; 5 | 6 | 7 | /** 8 | * Author: Matthew Horridge
9 | * The University Of Manchester
10 | * Medical Informatics Group
11 | * Date: 23-Aug-2006

12 | 13 | * matthew.horridge@cs.man.ac.uk
14 | * www.cs.man.ac.uk/~horridgm

15 | 16 | * A file filter that accepts probable ontology files. 17 | */ 18 | public class OntologyFileFilter implements FileFilter { 19 | 20 | public boolean accept(File pathname) { 21 | String name = pathname.getName(); 22 | return name.endsWith(".owl") | name.endsWith(".rdf") | name.endsWith(".xml"); 23 | } 24 | } 25 | --------------------------------------------------------------------------------