edu.stanford.smi.protegex.owl.jena
Class JenaOWLModel

java.lang.Object
  edu.stanford.smi.protege.model.DefaultKnowledgeBase
      edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel
          edu.stanford.smi.protegex.owl.jena.JenaOWLModel

All Implemented Interfaces:

edu.stanford.smi.protege.util.Disposable, edu.stanford.smi.protege.model.KnowledgeBase, NamespaceManagerListener, OntModelProvider, OWLModel, OWLTestManager, ProtegeKnowledgeBase

public class JenaOWLModel

extends AbstractOWLModel

implements OntModelProvider

An OWLModel that can be synchronized with a Jena OntModel.

Author:

Holger Knublauch

Field Summary

static String	COPYRIGHT
static String	DEFAULT_PREFIX
static boolean	inUI
static String	TEMPLATE_FILE_NAME
private TripleStoreModel	tripleStoreModel
static String	WRITER_PROTEGE
static String	WRITER_SETTINGS_PROPERTY

Fields inherited from class edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel

ANONYMOUS_BASE, DEFAULT_ANNOTATION_PROPERTY_NAME, DEFAULT_CLASS_NAME, DEFAULT_DATATYPE_PROPERTY_NAME, DEFAULT_INDIVIDUAL_NAME, DEFAULT_OBJECT_PROPERTY_NAME, DEFAULT_PROPERTY_NAME, DEFAULT_TODO_PREFIX, DEFAULT_USED_LANGUAGES

Fields inherited from class edu.stanford.smi.protege.model.DefaultKnowledgeBase

Fields inherited from interface edu.stanford.smi.protegex.owl.jena.OntModelProvider

OWL_DL, OWL_FULL, OWL_LITE

Fields inherited from interface edu.stanford.smi.protege.model.KnowledgeBase

MAXIMUM_CARDINALITY_UNBOUNDED, UNLIMITED_MATCHES

Constructor Summary

protected

JenaOWLModel(edu.stanford.smi.protege.model.KnowledgeBaseFactory factory, NamespaceManager namespaceManager)

Method Summary

private void	closeRDFLists()
void	defaultNamespaceChanged(String oldValue, String newValue)
com.hp.hpl.jena.ontology.OntModel	getOntModel() Gets an OntModel which represents the current state.
com.hp.hpl.jena.ontology.OntModel	getOWLDLOntModel() Gets or prepares an OntModel which is guaranteed to be in OWL DL, for classification and other reasoning tasks.
String	getOWLFilePath() Gets the currently assigned file name for the top-level file of this OWLModel.
int	getOWLSpecies() Gets the OWL Species of the current main OntModel.
RDFResource	getRDFResource(com.hp.hpl.jena.rdf.model.Resource resource)
com.hp.hpl.jena.ontology.OntModel	getReasonerOntModel(String classifierURL) Gets an OntModel that is connected to a (DIG) reasoner.
TripleStoreModel	getTripleStoreModel()
WriterSettings	getWriterSettings()
void	initOWLFrameFactoryInvocationHandler()
private void	initPrefixes(NamespaceManager nsm, com.hp.hpl.jena.shared.PrefixMapping mapping)
void	initPrefixes(com.hp.hpl.jena.ontology.OntModel ontModel)
void	load(InputStream is, String language)
void	load(Reader reader, String language)
void	load(URI uri, String language)
void	load(URI uri, String language, Collection errors)
void	namespaceChanged(String prefix, String oldValue, String newValue)
void	prefixAdded(String prefix)
void	prefixChanged(String namespace, String oldPrefix, String newPrefix)
void	prefixRemoved(String prefix)
static void	save(File file, com.hp.hpl.jena.ontology.OntModel ontModel, String language, String namespace)
private static void	save(OutputStream outputStream, com.hp.hpl.jena.ontology.OntModel ontModel, String language, String namespace)
void	save(OutputStream os, String language, Collection errors) Deprecated. please use the version with the URIs or access the OntModel directly
void	save(OutputStream os, String language, Collection errors, com.hp.hpl.jena.ontology.OntModel ontModel) Deprecated. please use the version with the URIs or access the OntModel directly
void	save(URI fileURI) Saves the current OWLModel in the standard format.
void	save(URI fileURI, String language, Collection errors) Writes the base model of this into a given file.
void	save(URI fileURI, String language, Collection errors, com.hp.hpl.jena.ontology.OntModel ontModel)
static void	saveModel(OutputStream outputStream, com.hp.hpl.jena.rdf.model.Model model, String language, String namespace)
void	setProjectFileName(String filePath) Sets the name of the file in the associated Project.
void	setWriterSettings(WriterSettings writerSettings)

Methods inherited from class edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel

addClassListener, addModelListener, addOWLTest, addPropertyListener, addPropertyValueListener, addResourceListener, adjustSystemClasses, adjustThing, asRDFObject, asRDFSLiteral, asRDFSLiterals, copyFacetValuesIntoNamedClses, createAnnotationOWLDatatypeProperty, createAnnotationOWLObjectProperty, createCls, createDefaultOWLOntologyReally, createFrameStoreManager, createInstance, createNewResourceName, createOWLAllDifferent, createOWLAllValuesFrom, createOWLAllValuesFrom, createOWLAllValuesFrom, createOWLCardinality, createOWLCardinality, createOWLCardinality, createOWLComplementClass, createOWLComplementClass, createOWLDataRange, createOWLDataRange, createOWLDatatypeProperty, createOWLDatatypeProperty, createOWLDatatypeProperty, createOWLDatatypeProperty, createOWLEnumeratedClass, createOWLEnumeratedClass, createOWLHasValue, createOWLHasValue, createOWLIntersectionClass, createOWLIntersectionClass, createOWLMaxCardinality, createOWLMaxCardinality, createOWLMaxCardinality, createOWLMinCardinality, createOWLMinCardinality, createOWLMinCardinality, createOWLNamedClass, createOWLNamedClass, createOWLNamedClass, createOWLNamedSubclass, createOWLObjectProperty, createOWLObjectProperty, createOWLObjectProperty, createOWLOntology, createOWLOntology, createOWLSomeValuesFrom, createOWLSomeValuesFrom, createOWLSomeValuesFrom, createOWLUnionClass, createOWLUnionClass, createRDFExternalResource, createRDFList, createRDFList, createRDFProperty, createRDFSClassFromExpression, createRDFSDatatype, createRDFSLiteral, createRDFSLiteral, createRDFSLiteral, createRDFSLiteralOrString, createRDFSNamedClass, createRDFSNamedClass, createRDFSNamedClass, createRDFSNamedSubclass, createRDFUntypedResource, createSubclass, createSubclass, createSubproperty, createSystemFrames, createTriple, createUniqueNewFrameName, deleteAllFrames, deleteCls, endTransaction, ensureProtegeMetaOntologyImported, executeSPARQLQuery, getAllImports, getAnonymousRootCls, getBrowserText, getChangedInferredClasses, getCommonSuperclass, getDefaultLanguage, getDefaultOWLOntology, getDomainlessProperties, getFloatDatatypes, getFrameNameForURI, getInconsistentClasses, getIntegerDatatypes, getJenaModel, getLocalNameForResourceName, getLocalNameForURI, getMatchingResources, getNamespaceForResourceName, getNamespaceForURI, getNamespaceManager, getNextAnonymousResourceName, getOWLAllDifferentClass, getOWLAllDifferentClassCls, getOWLAllDifferents, getOWLAnnotationProperties, getOWLAnnotationPropertyClass, getOWLClassDisplay, getOWLClasses, getOWLClassParser, getOWLDataRangeClass, getOWLDatatypeProperty, getOWLDatatypePropertyClass, getOWLDatatypePropertyMetaClassCls, getOWLDeprecatedClassClass, getOWLDifferentFromProperty, getOWLDisjointWithProperty, getOWLDistinctMembersProperty, getOWLEquivalentClassProperty, getOWLEquivalentPropertyProperty, getOWLFrameStore, getOWLFunctionalPropertyClass, getOWLIndividual, getOWLIndividuals, getOWLIndividuals, getOWLIntersectionOfProperty, getOWLInverseFunctionalPropertyClass, getOWLInverseOfProperty, getOWLJavaFactory, getOWLNamedClass, getOWLNamedClassClass, getOWLNamedClassMetaClassCls, getOWLNothing, getOWLObjectProperty, getOWLObjectPropertyClass, getOWLObjectPropertyMetaClassCls, getOWLOneOfProperty, getOWLOntologies, getOWLOntologyByURI, getOWLOntologyClass, getOWLOntologyCls, getOWLOntologyProperties, getOWLProject, getOWLProperty, getOWLRestrictionMetaclasses, getOWLRestrictionsOnProperty, getOWLSameAsProperty, getOWLSystemResources, getOWLTests, getOWLThingClass, getOWLUnionOfProperty, getOWLValuesFromProperty, getOWLValueType, getOWLVersionInfoProperty, getPrefixForResourceName, getPropertyValueLiterals, getPropertyValueValidator, getProtegeAllowedParentProperty, getProtegeClassificationStatusProperty, getProtegeInferredSubclassesProperty, getProtegeInferredSuperclassesProperty, getProtegeReadOnlyProperty, getProtegeSubclassesDisjointProperty, getRDFExternalResource, getRDFExternalResourceClass, getRDFFirstProperty, getRDFIndividual, getRDFIndividuals, getRDFIndividuals, getRDFListClass, getRDFListCls, getRDFNil, getRDFProperties, getRDFProperty, getRDFPropertyClass, getRDFResource, getRDFResourceAs, getRDFResourceByBrowserText, getRDFResourceByNameOrBrowserText, getRDFResourceCount, getRDFResources, getRDFResources, getRDFResourcesWithPropertyValue, getRDFRestProperty, getRDFSClassCount, getRDFSClasses, getRDFSClassMetaClassCls, getRDFSCommentProperty, getRDFSDatatypeByName, getRDFSDatatypeByURI, getRDFSDatatypeClass, getRDFSDatatypeFactory, getRDFSDatatypeOfValue, getRDFSDatatypes, getRDFSDomainProperty, getRDFSIsDefinedByProperty, getRDFSLabelProperty, getRDFSNamedClass, getRDFSNamedClassClass, getRDFSRangeProperty, getRDFSSubClassOfProperty, getRDFSSubPropertyOfProperty, getRDFTypeProperty, getRDFUntypedResource, getRDFUntypedResourcesClass, getRDFXMLLiteralType, getRepositoryManager, getResourceNameForURI, getResourceNameMatches, getResourcesWithPrefix, getRootCls, getRootSlotMetaCls, getSearchSynonymProperties, getSystemAnnotationProperties, getTaskManager, getTodoAnnotationPrefix, getTodoAnnotationProperty, getUniqueFrameName, getURIForResourceName, getURIResolver, getUsedLanguages, getUserDefinedOWLDatatypeProperties, getUserDefinedOWLNamedClasses, getUserDefinedOWLObjectProperties, getUserDefinedOWLProperties, getUserDefinedRDFIndividuals, getUserDefinedRDFProperties, getUserDefinedRDFSNamedClasses, getValidNamespaceFrameName, getValidOWLFrameName, getValueLiterals, getValueTypeURI, getVisibleResources, getVisibleUserDefinedOWLProperties, getVisibleUserDefinedRDFProperties, getXSDanyURI, getXSDbase64Binary, getXSDboolean, getXSDbyte, getXSDdate, getXSDdateTime, getXSDdecimal, getXSDdouble, getXSDduration, getXSDfloat, getXSDint, getXSDinteger, getXSDlong, getXSDshort, getXSDstring, getXSDtime, initOWLFrameStore, isAnonymousResource, isAnonymousResourceName, isAutoRepairEnabled, isDefaultAnonymousType, isDefaultAnonymousType, isOWLSystemFrame, isOWLTestGroupEnabled, isProtegeMetaOntologyImported, isSlotMetaCls, isTrueInstance, isValidOWLFrameName, isValidOWLFrameName, isValidPropertyValue, isValidResourceName, listOWLAnonymousClasses, listOWLNamedClasses, listRDFProperties, listRDFSNamedClasses, listReferences, listSubjects, removeClassListener, removeModelListener, removeOWLTest, removePropertyListener, removePropertyValueListener, removeResourceListener, replacePrefixInInstances, resetJenaModel, setAutoRepairEnabled, setDirectType, setLoadDefaults, setNamespaceManager, setOWLClassDisplay, setOWLJavaFactory, setOWLProject, setOWLTestGroupEnabled, setProject, setPropertyValueValidator, setSearchSynonymProperties, setTaskManager, setURIResolver, updateProtegeMetaOntologyImported

Methods inherited from class edu.stanford.smi.protege.model.DefaultKnowledgeBase

addClsListener, addClsListener, addDirectSuperclass, addDirectSuperslot, addDirectTemplateSlot, addDirectType, addDirectTypes, addFacetListener, addFacetListener, addFrameListener, addFrameListener, addInstance, addInstanceListener, addInstanceListener, addJavaLoadPackage, addKnowledgeBaseListener, addOwnSlotValue, addSlotListener, addSlotListener, addTemplateFacetValue, addTemplateSlotValue, addTransactionListener, areValidOwnSlotValues, beginTransaction, changeFrameName, clearAllListeners, close, commitTransaction, containsFrame, createCls, createCls, createCls, createCls, createFacet, createFacet, createFacet, createFacet, createFrameFactory, createInstance, createInstance, createInstance, createInstance, createSimpleInstance, createSimpleInstance, createSimpleInstance, createSlot, createSlot, createSlot, createSlot, createSlot, createUniqueFrameName, deleteFacet, deleteFrame, deleteInstance, deleteSimpleInstance, deleteSlot, dispose, endTransaction, equals, flushCache, getAllowedClses, getAllowedParents, getAllowedValues, getAllowsMultipleValues, getAssociatedFacet, getAssociatedSlot, getBuildString, getClientInformation, getCls, getClsCount, getClses, getClsesWithMatchingBrowserText, getClsNameMatches, getCommandManager, getCurrentUsers, getDefaultClsMetaCls, getDefaultFacetMetaCls, getDefaultSlotMetaCls, getDefaultValues, getDirectBrowserSlotPattern, getDirectDomain, getDirectInstanceCount, getDirectInstances, getDirectlyOverriddenTemplateFacets, getDirectlyOverriddenTemplateSlots, getDirectOwnSlotValue, getDirectOwnSlotValues, getDirectOwnSlotValuesClosure, getDirectSubclassCount, getDirectSubclasses, getDirectSubslotCount, getDirectSubslots, getDirectSuperclassCount, getDirectSuperclasses, getDirectSuperslotCount, getDirectSuperslots, getDirectTemplateFacetValues, getDirectTemplateSlots, getDirectTemplateSlotValues, getDirectType, getDirectTypes, getDispatchEventsEnabled, getDisplaySlotNotSetString, getDisplaySlotPatternValueNotSetString, getDocumentation, getDomain, getEventsEnabled, getFacet, getFacetCheckingEnabled, getFacetCount, getFacets, getFrame, getFrame, getFrameCount, getFrameCounts, getFrameCreationTimestamp, getFrameCreator, getFrameFactory, getFrameLastModificationTimestamp, getFrameLastModifier, getFrameNameMatches, getFrameNamePrefix, getFrames, getFrameStoreManager, getFrameStores, getFramesWithMatchingDirectOwnSlotValue, getFramesWithValue, getGenerateEventsEnabled, getHeadFrameStore, getInheritedTemplateSlots, getInstance, getInstanceCount, getInstances, getInstances, getInvalidFrameNameDescription, getInvalidOwnSlotValuesText, getInvalidOwnSlotValueText, getInverseSlot, getKnowledgeBaseFactory, getMatchingFrames, getMatchingReferences, getMaximumCardinality, getMaximumCardinality2, getMaximumValue, getMinimumCardinality, getMinimumValue, getMissingTypeString, getName, getName, getNameSlot, getNextFrameNumber, getOverriddenTemplateFacets, getOverriddenTemplateSlots, getOwnFacets, getOwnFacetValues, getOwnSlotAllowsMultipleValues, getOwnSlotAndSubslotValues, getOwnSlotDefaultValues, getOwnSlotFacets, getOwnSlotFacetValues, getOwnSlots, getOwnSlotValue, getOwnSlotValueCount, getOwnSlotValues, getOwnSlotValueType, getProject, getReachableSimpleInstances, getReachableSimpleInstances, getReferences, getReferences, getReifedRelationFromSlot, getReifedRelationToSlot, getReifiedRelationCls, getRootClses, getRootClsMetaCls, getRootFacetMetaCls, getRootSlots, getSimpleInstance, getSimpleInstanceCount, getSlot, getSlotCount, getSlots, getSlotValueLastModificationTimestamp, getSlotValueLastModifier, getSubclasses, getSubslots, getSuperclasses, getSuperslots, getSystemFrames, getTemplateFacets, getTemplateFacetValue, getTemplateFacetValues, getTemplateSlotAllowedClses, getTemplateSlotAllowedParents, getTemplateSlotAllowedValues, getTemplateSlotAllowsMultipleValues, getTemplateSlotDefaultValues, getTemplateSlotDocumentation, getTemplateSlotMaximumCardinality, getTemplateSlotMaximumCardinality2, getTemplateSlotMaximumValue, getTemplateSlotMinimumCardinality, getTemplateSlotMinimumCardinality2, getTemplateSlotMinimumValue, getTemplateSlots, getTemplateSlotValue, getTemplateSlotValues, getTemplateSlotValueType, getTerminalFrameStore, getTypes, getUnreachableSimpleInstances, getUserName, getValueChecking, getValues, getValueType, getVersionString, hasChanged, hasDirectlyOverriddenTemplateFacet, hasDirectlyOverriddenTemplateSlot, hasDirectSuperclass, hasDirectSuperslot, hasDirectTemplateSlot, hasDirectType, hasInheritedTemplateSlot, hasOverriddenTemplateFacet, hasOverriddenTemplateSlot, hasOwnSlot, hasSlotValueAtSomeFrame, hasSuperclass, hasSuperslot, hasTemplateSlot, hasType, insertFrameStore, insertFrameStore, isAbstract, isAutoUpdatingFacetValues, isCallCachingEnabled, isClosed, isClsMetaCls, isDefaultClsMetaCls, isDefaultFacetMetaCls, isDefaultSlotMetaCls, isFacetMetaCls, isJournalingEnabled, isLoading, isMetaCls, isUndoEnabled, isValidFrameName, isValidOwnSlotValue, moveDirectOwnSlotValue, moveDirectSubclass, moveDirectSubclass, moveDirectSubslot, moveDirectSubslot, moveDirectTemplateSlot, moveDirectType, notifyVisibilityChanged, removeClsListener, removeClsListener, removeDirectSuperclass, removeDirectSuperslot, removeDirectTemplateFacetOverrides, removeDirectTemplateSlot, removeDirectType, removeDirectTypes, removeFacetListener, removeFacetListener, removeFrameListener, removeFrameListener, removeFrameStore, removeInstanceListener, removeInstanceListener, removeJavaLoadPackage, removeKnowledgeBaseListener, removeOwnSlotValue, removeSlotListener, removeSlotListener, removeTemplateFacetOverrides, removeTransactionListener, rollbackTransaction, setAbstract, setAllowedClses, setAllowedParents, setAllowedValues, setAllowsMultipleValues, setArgumentCheckingEnabled, setAssociatedFacet, setAssociatedSlot, setAutoUpdateFacetValues, setBuildString, setCallCachingEnabled, setChanged, setChangeMonitorEnabled, setCleanDispatchEnabled, setClientInformation, setDefaultClsMetaCls, setDefaultFacetMetaCls, setDefaultSlotMetaCls, setDefaultValues, setDirectBrowserSlot, setDirectBrowserSlotPattern, setDirectBrowserTextPattern, setDirectOwnSlotValue, setDirectOwnSlotValues, setDirectTemplateFacetValue, setDirectTemplateFacetValues, setDirectTemplateSlotValues, setDirectTypeOfSubclasses, setDirectTypeOfSubslots, setDirectTypes, setDispatchEventsEnabled, setDocumentation, setDocumentation, setEventDispatchEnabled, setEventsEnabled, setFacetCheckingEnabled, setFrameFactory, setFrameName, setFrameNamePrefix, setFrameNameValidator, setGenerateDeletingFrameEventsEnabled, setGenerateEventsEnabled, setInverseSlot, setJournalingEnabled, setLoading, setMaximumCardinality, setMaximumValue, setMinimumCardinality, setMinimumValue, setModificationRecordUpdatingEnabled, setName, setNextFrameNumber, setOwnSlotValue, setOwnSlotValues, setPollForEvents, setTemplateFacetValue, setTemplateFacetValues, setTemplateSlotAllowedClses, setTemplateSlotAllowedParents, setTemplateSlotAllowedValues, setTemplateSlotAllowsMultipleValues, setTemplateSlotDefaultValues, setTemplateSlotDocumentation, setTemplateSlotDocumentation, setTemplateSlotMaximumCardinality, setTemplateSlotMaximumValue, setTemplateSlotMinimumCardinality, setTemplateSlotMinimumValue, setTemplateSlotValue, setTemplateSlotValues, setTemplateSlotValueType, setTerminalFrameStore, setUndoEnabled, setUserName, setValueChecking, setValues, setValueType, setVersionString, startJournaling, stopJournaling, toString, toString, toString, toStringForFrame, toStringForObject

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.stanford.smi.protegex.owl.model.OWLModel

beginTransaction, endTransaction, getDispatchEventsEnabled, getGenerateEventsEnabled, setDispatchEventsEnabled, setGenerateEventsEnabled

Methods inherited from interface edu.stanford.smi.protegex.owl.model.ProtegeKnowledgeBase

addClsListener, addClsListener, addDirectSuperclass, addDirectSuperslot, addDirectTemplateSlot, addDirectType, addFacetListener, addFacetListener, addFrameListener, addFrameListener, addInstance, addInstanceListener, addInstanceListener, addKnowledgeBaseListener, addOwnSlotValue, addSlotListener, addSlotListener, addTemplateFacetValue, addTemplateSlotValue, areValidOwnSlotValues, clearAllListeners, containsFrame, createCls, createCls, createCls, createFacet, createFacet, createFacet, createInstance, createInstance, createInstance, createSimpleInstance, createSlot, createSlot, createSlot, createSlot, deleteFacet, deleteFrame, deleteInstance, deleteSlot, getAllowedClses, getAllowedParents, getAllowedValues, getAllowsMultipleValues, getAssociatedFacet, getAssociatedSlot, getCls, getClsCount, getClses, getClsNameMatches, getCommandManager, getCurrentUsers, getDefaultClsMetaCls, getDefaultFacetMetaCls, getDefaultSlotMetaCls, getDefaultValues, getDirectBrowserSlotPattern, getDirectDomain, getDirectInstanceCount, getDirectInstances, getDirectlyOverriddenTemplateFacets, getDirectlyOverriddenTemplateSlots, getDirectOwnSlotValue, getDirectOwnSlotValues, getDirectOwnSlotValuesClosure, getDirectSubclassCount, getDirectSubclasses, getDirectSubslotCount, getDirectSubslots, getDirectSuperclassCount, getDirectSuperclasses, getDirectSuperslotCount, getDirectSuperslots, getDirectTemplateFacetValues, getDirectTemplateSlots, getDirectTemplateSlotValues, getDirectType, getDirectTypes, getDocumentation, getDomain, getFacet, getFacetCount, getFacets, getFrame, getFrame, getFrameCount, getFrameCounts, getFrameCreationTimestamp, getFrameCreator, getFrameFactory, getFrameLastModificationTimestamp, getFrameLastModifier, getFrameNameMatches, getFrameNamePrefix, getFrames, getFrameStores, getFramesWithValue, getInstance, getInstanceCount, getInstances, getInstances, getInvalidFrameNameDescription, getInvalidOwnSlotValuesText, getInvalidOwnSlotValueText, getInverseSlot, getMatchingFrames, getMatchingReferences, getMaximumCardinality, getMaximumValue, getMinimumCardinality, getMinimumValue, getName, getName, getNameSlot, getNextFrameNumber, getOverriddenTemplateFacets, getOwnSlotAllowsMultipleValues, getOwnSlotAndSubslotValues, getOwnSlotDefaultValues, getOwnSlotFacets, getOwnSlotFacetValues, getOwnSlots, getOwnSlotValue, getOwnSlotValueCount, getOwnSlotValues, getOwnSlotValueType, getProject, getReachableSimpleInstances, getReferences, getRootClses, getRootClsMetaCls, getRootFacetMetaCls, getRootSlots, getSimpleInstanceCount, getSlot, getSlotCount, getSlots, getSlotValueLastModificationTimestamp, getSlotValueLastModifier, getSubclasses, getSubslots, getSuperclasses, getSuperslots, getSystemFrames, getTemplateFacets, getTemplateFacetValue, getTemplateFacetValues, getTemplateSlotAllowedClses, getTemplateSlotAllowedParents, getTemplateSlotAllowedValues, getTemplateSlotAllowsMultipleValues, getTemplateSlotDefaultValues, getTemplateSlotDocumentation, getTemplateSlotMaximumCardinality, getTemplateSlotMaximumValue, getTemplateSlotMinimumCardinality, getTemplateSlotMinimumValue, getTemplateSlots, getTemplateSlotValue, getTemplateSlotValues, getTemplateSlotValueType, getUnreachableSimpleInstances, getUserName, getValueChecking, getValues, getValueType, getVersionString, hasDirectlyOverriddenTemplateFacet, hasDirectlyOverriddenTemplateSlot, hasDirectSuperclass, hasDirectSuperslot, hasDirectTemplateSlot, hasDirectType, hasInheritedTemplateSlot, hasOverriddenTemplateFacet, hasOverriddenTemplateSlot, hasOwnSlot, hasSlotValueAtSomeFrame, hasSuperclass, hasSuperslot, hasTemplateSlot, hasType, insertFrameStore, insertFrameStore, isAbstract, isAutoUpdatingFacetValues, isCallCachingEnabled, isClsMetaCls, isDefaultClsMetaCls, isDefaultFacetMetaCls, isDefaultSlotMetaCls, isFacetMetaCls, isJournalingEnabled, isLoading, isMetaCls, isValidFrameName, isValidOwnSlotValue, moveDirectSubclass, moveDirectSubslot, moveDirectTemplateSlot, notifyVisibilityChanged, removeClsListener, removeClsListener, removeDirectSuperclass, removeDirectSuperslot, removeDirectTemplateSlot, removeDirectType, removeFacetListener, removeFacetListener, removeFrameListener, removeFrameListener, removeFrameStore, removeInstanceListener, removeInstanceListener, removeJavaLoadPackage, removeKnowledgeBaseListener, removeOwnSlotValue, removeSlotListener, removeSlotListener, removeTemplateFacetOverrides, setAbstract, setAllowedClses, setAllowedParents, setAllowedValues, setAllowsMultipleValues, setArgumentCheckingEnabled, setAssociatedFacet, setAssociatedSlot, setAutoUpdateFacetValues, setBuildString, setCallCachingEnabled, setChanged, setChangeMonitorEnabled, setCleanDispatchEnabled, setDefaultClsMetaCls, setDefaultFacetMetaCls, setDefaultSlotMetaCls, setDefaultValues, setDirectBrowserSlot, setDirectBrowserSlotPattern, setDirectOwnSlotValues, setDirectTypeOfSubclasses, setDirectTypeOfSubslots, setDirectTypes, setDocumentation, setDocumentation, setFacetCheckingEnabled, setFrameFactory, setFrameName, setFrameNamePrefix, setFrameNameValidator, setGenerateDeletingFrameEventsEnabled, setInverseSlot, setJournalingEnabled, setMaximumCardinality, setMaximumValue, setMinimumCardinality, setMinimumValue, setName, setNextFrameNumber, setOwnSlotValues, setPollForEvents, setTemplateFacetValue, setTemplateFacetValues, setTemplateSlotAllowedClses, setTemplateSlotAllowedParents, setTemplateSlotAllowedValues, setTemplateSlotAllowsMultipleValues, setTemplateSlotDefaultValues, setTemplateSlotDocumentation, setTemplateSlotDocumentation, setTemplateSlotMaximumCardinality, setTemplateSlotMaximumValue, setTemplateSlotMinimumCardinality, setTemplateSlotMinimumValue, setTemplateSlotValue, setTemplateSlotValues, setTemplateSlotValueType, setUndoEnabled, setUserName, setValueChecking, setValues, setValueType, setVersionString, startJournaling, stopJournaling

Methods inherited from interface edu.stanford.smi.protege.model.KnowledgeBase

addJavaLoadPackage, addTransactionListener, changeFrameName, createInstance, createUniqueFrameName, flushCache, getBuildString, getClientInformation, getClsesWithMatchingBrowserText, getEventsEnabled, getKnowledgeBaseFactory, getReifedRelationFromSlot, getReifedRelationToSlot, getReifiedRelationCls, getSimpleInstance, hasChanged, isClosed, moveDirectOwnSlotValue, moveDirectType, removeTransactionListener, setClientInformation, setEventsEnabled, setModificationRecordUpdatingEnabled

Methods inherited from interface edu.stanford.smi.protege.util.Disposable

dispose

Field Detail

COPYRIGHT

public static final String COPYRIGHT

See Also:

Constant Field Values

inUI

public static boolean inUI

tripleStoreModel

private TripleStoreModel tripleStoreModel

TEMPLATE_FILE_NAME

public static final String TEMPLATE_FILE_NAME

See Also:

Constant Field Values

DEFAULT_PREFIX

public static final String DEFAULT_PREFIX

See Also:

Constant Field Values

WRITER_SETTINGS_PROPERTY

public static final String WRITER_SETTINGS_PROPERTY

WRITER_PROTEGE

public static final String WRITER_PROTEGE

See Also:

Constant Field Values

Constructor Detail

JenaOWLModel

protected JenaOWLModel(edu.stanford.smi.protege.model.KnowledgeBaseFactory factory,
                       NamespaceManager namespaceManager)

Method Detail

closeRDFLists

private void closeRDFLists()

defaultNamespaceChanged

public void defaultNamespaceChanged(String oldValue,
                                    String newValue)

Specified by:

defaultNamespaceChanged in interface NamespaceManagerListener

Overrides:

defaultNamespaceChanged in class AbstractOWLModel

getRDFResource

public RDFResource getRDFResource(com.hp.hpl.jena.rdf.model.Resource resource)

getOntModel

public com.hp.hpl.jena.ontology.OntModel getOntModel()

Description copied from interface: OntModelProvider

Gets an OntModel which represents the current state.

Specified by:

getOntModel in interface OntModelProvider

Returns:

an OntModel

getOWLDLOntModel

public com.hp.hpl.jena.ontology.OntModel getOWLDLOntModel()

Description copied from interface: OntModelProvider

Gets or prepares an OntModel which is guaranteed to be in OWL DL, for classification and other reasoning tasks.

Specified by:

getOWLDLOntModel in interface OntModelProvider

Returns:

null if the OntModel cannot be reduced to OWL DL

getOWLFilePath

public String getOWLFilePath()

Gets the currently assigned file name for the top-level file of this OWLModel. Note that this only returns a meaningful value after the user has assigned a name (using save as...)

Returns:

the file name

getOWLSpecies

public int getOWLSpecies()

Description copied from interface: OntModelProvider

Gets the OWL Species of the current main OntModel.

Specified by:

getOWLSpecies in interface OntModelProvider

Returns:

one of the three OWL_xxx constants

getReasonerOntModel

public com.hp.hpl.jena.ontology.OntModel getReasonerOntModel(String classifierURL)

Description copied from interface: OntModelProvider

Gets an OntModel that is connected to a (DIG) reasoner.

Specified by:

getReasonerOntModel in interface OntModelProvider

Parameters:

classifierURL - the URL of the classifier (usually defined in the preferences)

Returns:

An OntModel that contains the classification result

getTripleStoreModel

public TripleStoreModel getTripleStoreModel()

Specified by:

getTripleStoreModel in interface OWLModel

getWriterSettings

public WriterSettings getWriterSettings()

initOWLFrameFactoryInvocationHandler

public void initOWLFrameFactoryInvocationHandler()

Specified by:

initOWLFrameFactoryInvocationHandler in class AbstractOWLModel

initPrefixes

public void initPrefixes(com.hp.hpl.jena.ontology.OntModel ontModel)

initPrefixes

private void initPrefixes(NamespaceManager nsm,
                          com.hp.hpl.jena.shared.PrefixMapping mapping)

load

public void load(URI uri,
                 String language)
          throws Exception

Throws:

Exception

load

public void load(InputStream is,
                 String language)
          throws Exception

Throws:

Exception

load

public void load(Reader reader,
                 String language)
          throws Exception

Throws:

Exception

load

public void load(URI uri,
                 String language,
                 Collection errors)

namespaceChanged

public void namespaceChanged(String prefix,
                             String oldValue,
                             String newValue)

Specified by:

namespaceChanged in interface NamespaceManagerListener

Overrides:

namespaceChanged in class AbstractOWLModel

prefixAdded

public void prefixAdded(String prefix)

Specified by:

prefixAdded in interface NamespaceManagerListener

Overrides:

prefixAdded in class AbstractOWLModel

prefixChanged

public void prefixChanged(String namespace,
                          String oldPrefix,
                          String newPrefix)

Specified by:

prefixChanged in interface NamespaceManagerListener

Overrides:

prefixChanged in class AbstractOWLModel

prefixRemoved

public void prefixRemoved(String prefix)

Specified by:

prefixRemoved in interface NamespaceManagerListener

Overrides:

prefixRemoved in class AbstractOWLModel

save

public void save(URI fileURI)
          throws Exception

Saves the current OWLModel in the standard format.

Parameters:

fileURI - the URI to write into

Throws:

Exception - if something went wrong

save

public void save(URI fileURI,
                 String language,
                 Collection errors)

Writes the base model of this into a given file.

Parameters:

fileURI - the URI of the target file

language - the Jena output language (typically FileUtils.langXMLAbbrev)

errors - an initially empty collection of errors

save

public void save(OutputStream os,
                 String language,
                 Collection errors)

Deprecated. please use the version with the URIs or access the OntModel directly

save

public void save(URI fileURI,
                 String language,
                 Collection errors,
                 com.hp.hpl.jena.ontology.OntModel ontModel)

save

public static void save(File file,
                        com.hp.hpl.jena.ontology.OntModel ontModel,
                        String language,
                        String namespace)
                 throws IOException

Throws:

IOException

save

public void save(OutputStream os,
                 String language,
                 Collection errors,
                 com.hp.hpl.jena.ontology.OntModel ontModel)

Deprecated. please use the version with the URIs or access the OntModel directly

save

private static void save(OutputStream outputStream,
                         com.hp.hpl.jena.ontology.OntModel ontModel,
                         String language,
                         String namespace)
                  throws IOException

Throws:

IOException

saveModel

public static void saveModel(OutputStream outputStream,
                             com.hp.hpl.jena.rdf.model.Model model,
                             String language,
                             String namespace)
                      throws IOException

Throws:

IOException

setProjectFileName

public void setProjectFileName(String filePath)

Sets the name of the file in the associated Project. This should be called before a newly created Project is saved.

Parameters:

filePath - the new (typically relative) path to the .owl file

See Also:

Project.save(java.util.Collection)

setWriterSettings

public void setWriterSettings(WriterSettings writerSettings)