org.semanticweb.owlapi.model

Interface OWLOntologyManager

All Superinterfaces:

HasAddAxiom, HasAddAxioms, HasApplyChange, HasApplyChanges, HasContainsOntology, HasDataFactory, HasGetOntologies, HasGetOntologyById, HasOntologyChangeListeners, HasOntologyLoaderConfiguration, HasOntologyLoaderConfigurationProvider, HasRemoveAxiom, HasRemoveAxioms, OWLOntologySetProvider, Serializable

All Known Implementing Classes:

OWLOntologyManagerImpl

public interface OWLOntologyManager
extends OWLOntologySetProvider, HasDataFactory, HasGetOntologyById, HasApplyChanges, HasApplyChange, HasAddAxioms, HasAddAxiom, HasRemoveAxioms, HasRemoveAxiom, HasContainsOntology, HasOntologyChangeListeners, HasOntologyLoaderConfigurationProvider, HasOntologyLoaderConfiguration, Serializable

An OWLOntologyManager manages a set of ontologies. It is the main point for creating, loading and accessing ontologies.
An OWLOntologyManager also manages the mapping betweem an ontology and its ontology document.

Since:

2.0.0

Author:

Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group

Method Summary

Modifier and Type	Method and Description
void	addImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener)
void	addIRIMapper(OWLOntologyIRIMapper mapper) Deprecated. use getIRIMappers().add() instead
void	addMissingImportListener(MissingImportListener listener) In the case where silent missing imports handling is enabled, a listener can be attached via this method so that there is a mechanism that allows clients to be informed of the reason when an import cannot be loaded.
void	addOntologyChangeListener(OWLOntologyChangeListener listener, OWLOntologyChangeBroadcastStrategy strategy) Adds an ontology change listener, which listens to ontology changes.
void	addOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener) Adds an ontology change progress listener.
void	addOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener)
void	addOntologyLoaderListener(OWLOntologyLoaderListener listener) Adds an ontology loaded listener to this manager.
void	addOntologyStorer(OWLStorerFactory storer) Deprecated. use getOntologyStorers().add() instead
void	clearIRIMappers() Deprecated. use getIRIMappers().clear() instead
void	clearOntologyStorers() Deprecated. use getOntologyStorers().clear() instead
boolean	contains(IRI ontologyIRI) Determines if there is an ontology with the specified IRI, and no version IRI, that is managed by this manager
boolean	contains(OWLOntology ontology)
boolean	contains(OWLOntologyID id) Determines if there is an ontology with the specified id that is managed by this manager
boolean	containsVersion(IRI ontologyVersionIRI) Determines if there is an ontology with the specified version IRI, that is managed by this manager.
OWLOntology	copyOntology(OWLOntology toCopy, OntologyCopy settings) Copy an ontology from another manager to this one.
OWLOntology	createOntology() Creates a new (empty) ontology that does not have an ontology IRI (and therefore does not have a version IRI).
OWLOntology	createOntology(IRI ontologyIRI) Creates a new (empty) ontology that has the specified ontology IRI (and no version IRI).
OWLOntology	createOntology(IRI ontologyIRI, Set<OWLOntology> ontologies) Creates a new ontology that has the specified ontology IRI and is initialised to contain the axioms that are contained in the specified ontologies.
OWLOntology	createOntology(IRI ontologyIRI, Set<OWLOntology> ontologies, boolean copyLogicalAxiomsOnly) Creates a new ontology that has the specified ontology IRI and is initialised to contain the axioms that are contained in the specified ontologies.
OWLOntology	createOntology(OWLOntologyID ontologyID) Creates a new (empty) ontology that has the specified ontology ID.
OWLOntology	createOntology(Set<OWLAxiom> axioms) Creates a new ontology that is initialised to contain specific axioms.
OWLOntology	createOntology(Set<OWLAxiom> axioms, IRI ontologyIRI) Creates a new ontology that has the specified ontology IRI and is initialised to contain specific axioms.
Set<OWLOntology>	getDirectImports(OWLOntology ontology) Gets the set of loaded ontologies that the specified ontology is related to via the directlyImports relation as defined in Section 3.4 of the OWL 2 Structural specification
OWLOntology	getImportedOntology(OWLImportsDeclaration declaration) Given an imports declaration, obtains the ontology that this import has been resolved to.
Set<OWLOntology>	getImports(OWLOntology ontology) Gets the set of ontologies that are in the transitive closure of the directly imports relation.
Set<OWLOntology>	getImportsClosure(OWLOntology ontology) Gets the imports closure for the specified ontology.
PriorityCollection<OWLOntologyIRIMapper>	getIRIMappers()
Set<OWLOntology>	getOntologies(OWLAxiom axiom) Gets the ontologies that are managed by this manager that contain the specified axiom.
OWLOntology	getOntology(IRI ontologyIRI) Gets a previously loaded/created ontology that has the specified ontology IRI and no version IRI.
OWLOntology	getOntology(OWLOntologyID ontologyID) Gets a previously loaded/created ontology that has the specified ontology ID
IRI	getOntologyDocumentIRI(OWLOntology ontology) Gets the document IRI for a given ontology.
PriorityCollection<OWLOntologyFactory>	getOntologyFactories()
OWLDocumentFormat	getOntologyFormat(OWLOntology ontology) Gets the ontology format for the specified ontology.
Set<OWLOntologyID>	getOntologyIDsByVersion(IRI ontologyVersionIRI) Gets a set of OWLOntologyIDs representing ontologies that are managed by this manager.
PriorityCollection<OWLParserFactory>	getOntologyParsers()
PriorityCollection<OWLStorerFactory>	getOntologyStorers()
List<OWLOntology>	getSortedImportsClosure(OWLOntology ontology) Gets the topologically ordered imports closure.
Set<OWLOntology>	getVersions(IRI ontology) Gets the versions (if any) of the ontology that have the specified IRI
OWLOntology	loadOntology(IRI ontologyIRI) Loads an ontology that is assumed to have the specified ontologyIRI as its IRI or version IRI.
OWLOntology	loadOntologyFromOntologyDocument(File file) Loads an ontology from an ontology document contained in a local file.
OWLOntology	loadOntologyFromOntologyDocument(InputStream inputStream) Loads an ontology from an ontology document obtained from an input stream.
OWLOntology	loadOntologyFromOntologyDocument(IRI documentIRI) Loads an ontology from an ontology document specified by an IRI.
OWLOntology	loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource) A convenience method that load an ontology from an input source.
OWLOntology	loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource, OWLOntologyLoaderConfiguration config) A convenience method that load an ontology from an input source with specified configuration.
void	makeLoadImportRequest(OWLImportsDeclaration declaration) Requests that the manager loads an imported ontology that is described by an imports statement.
void	makeLoadImportRequest(OWLImportsDeclaration declaration, OWLOntologyLoaderConfiguration configuration) Requests that the manager loads an imported ontology that is described by an imports statement.
void	removeImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener)
void	removeIRIMapper(OWLOntologyIRIMapper mapper) Deprecated. use getIRIMappers().remove() instead
void	removeMissingImportListener(MissingImportListener listener) Removes a previously added missing import listener.
void	removeOntology(OWLOntology ontology) Attempts to remove an ontology.
void	removeOntology(OWLOntologyID ontologyID) Attempts to remove an ontology.
void	removeOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener) Removes a previously added ontology change listener.
void	removeOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener)
void	removeOntologyLoaderListener(OWLOntologyLoaderListener listener) Removes a previously added ontology loaded listener.
void	removeOntologyStorer(OWLStorerFactory storer) Deprecated. use getOntologyStorers().remove() instead
void	saveOntology(OWLOntology ontology) Saves the specified ontology.
void	saveOntology(OWLOntology ontology, IRI documentIRI) Saves the specified ontology, using the specified document IRI to determine where/how the ontology should be saved.
void	saveOntology(OWLOntology ontology, OutputStream outputStream) Saves the specified ontology, to the specified output stream
void	saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat) Saves the specified ontology in the specified ontology format to its document URI.
void	saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, IRI documentIRI) Saves the specified ontology to the specified document IRI in the specified ontology format.
void	saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, OutputStream outputStream) Saves the specified ontology to the specified output stream in the specified ontology format.
void	saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, OWLOntologyDocumentTarget documentTarget) Saves the specified ontology to the specified output target in the specified ontology format.
void	saveOntology(OWLOntology ontology, OWLOntologyDocumentTarget documentTarget) Saves the specified ontology to the specified OWLOntologyDocumentTarget.
void	setDefaultChangeBroadcastStrategy(OWLOntologyChangeBroadcastStrategy strategy) Sets the default strategy that is used to broadcast ontology changes.
void	setIRIMappers(Set<OWLOntologyIRIMapper> mappers) Set the collection of IRI mappers.
void	setOntologyDocumentIRI(OWLOntology ontology, IRI documentIRI) Overrides the current document IRI for a given ontology.
void	setOntologyFactories(Set<OWLOntologyFactory> factories) Set the collection of ontology factories.
void	setOntologyFormat(OWLOntology ontology, OWLDocumentFormat ontologyFormat) Sets the format for the specified ontology.
void	setOntologyParsers(Set<OWLParserFactory> parsers) Set the collection of parsers.
void	setOntologyStorers(Set<OWLStorerFactory> storers) Set the list of ontology storers.

Methods inherited from interface org.semanticweb.owlapi.model.HasGetOntologies

getOntologies

Methods inherited from interface org.semanticweb.owlapi.model.HasDataFactory

getOWLDataFactory

Methods inherited from interface org.semanticweb.owlapi.model.HasApplyChanges

applyChanges

Methods inherited from interface org.semanticweb.owlapi.model.HasApplyChange

applyChange

Methods inherited from interface org.semanticweb.owlapi.model.HasAddAxioms

addAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasAddAxiom

addAxiom

Methods inherited from interface org.semanticweb.owlapi.model.HasRemoveAxioms

removeAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasRemoveAxiom

removeAxiom

Methods inherited from interface org.semanticweb.owlapi.model.HasOntologyChangeListeners

addOntologyChangeListener, removeOntologyChangeListener

Methods inherited from interface org.semanticweb.owlapi.model.HasOntologyLoaderConfigurationProvider

setOntologyLoaderConfigurationProvider

Methods inherited from interface org.semanticweb.owlapi.model.HasOntologyLoaderConfiguration

getOntologyLoaderConfiguration, setOntologyLoaderConfiguration

Method Detail

getOntologies

@Nonnull
Set<OWLOntology> getOntologies(@Nonnull
                                        OWLAxiom axiom)

Gets the ontologies that are managed by this manager that contain the specified axiom.

Parameters:

axiom - The axioms

Returns:

The set of ontologies such that for each ontology, O the specified axiom is contained in O.

getVersions

@Nonnull
Set<OWLOntology> getVersions(@Nonnull
                                      IRI ontology)

Gets the versions (if any) of the ontology that have the specified IRI

Parameters:

ontology - The ontology IRI

Returns:

The set of ontologies that have the specified ontology IRI.

contains

boolean contains(@Nonnull
                 OWLOntology ontology)

Parameters:

ontology - ontology to check

Returns:

true if the ontology is contained

contains

boolean contains(@Nonnull
                 IRI ontologyIRI)

Determines if there is an ontology with the specified IRI, and no version IRI, that is managed by this manager

Parameters:

ontologyIRI - The IRI of the ontology to test for (the version IRI is assumed to be null)

Returns:

true if there is an ontology with the specified IRI, and no version IRI, that is managed by this manager, otherwise false.

contains

boolean contains(@Nonnull
                 OWLOntologyID id)

Determines if there is an ontology with the specified id that is managed by this manager

Specified by:

contains in interface HasContainsOntology

Parameters:

id - The id of the ontology to test for

Returns:

true if there is an ontology with the specified id that is managed by this manager, otherwise false.

containsVersion

boolean containsVersion(@Nonnull
                        IRI ontologyVersionIRI)

Determines if there is an ontology with the specified version IRI, that is managed by this manager.

Parameters:

ontologyVersionIRI - The version IRI of the ontology to test for (the ontology IRI may be anything)

Returns:

true if there is an ontology with the specified version IRI, that is managed by this manager, otherwise false.

getOntologyIDsByVersion

@Nonnull
Set<OWLOntologyID> getOntologyIDsByVersion(@Nonnull
                                                    IRI ontologyVersionIRI)

Gets a set of OWLOntologyIDs representing ontologies that are managed by this manager.

Parameters:

ontologyVersionIRI - The version IRI to match against all of the known ontologies.

Returns:

A set of OWLOntologyIDs where the version matches the given version or the empty set if none match.

getOntology

@Nullable
OWLOntology getOntology(@Nonnull
                                  IRI ontologyIRI)

Gets a previously loaded/created ontology that has the specified ontology IRI and no version IRI.

Parameters:

ontologyIRI - The IRI of the ontology to be retrieved.

Returns:

The ontology that has the specified IRI and no version IRI, or null if this manager does not manage an ontology with the specified IRI and no version IRI.

getOntology

@Nullable
OWLOntology getOntology(@Nonnull
                                  OWLOntologyID ontologyID)

Gets a previously loaded/created ontology that has the specified ontology ID

Specified by:

getOntology in interface HasGetOntologyById

Parameters:

ontologyID - The ID of the ontology to retrieve

Returns:

The ontology that has the specified ID, or null if this manager does not manage an ontology with the specified ontology ID.

getImportedOntology

@Nullable
OWLOntology getImportedOntology(@Nonnull
                                          OWLImportsDeclaration declaration)

Given an imports declaration, obtains the ontology that this import has been resolved to.

Parameters:

declaration - The declaration that points to the imported ontology.

Returns:

The ontology that the imports declaration resolves to, or null if the imports declaration could not be resolved to an ontology, because the ontology was not loaded or has been removed from this manager

getDirectImports

@Nonnull
Set<OWLOntology> getDirectImports(@Nonnull
                                           OWLOntology ontology)

Gets the set of loaded ontologies that the specified ontology is related to via the directlyImports relation as defined in Section 3.4 of the OWL 2 Structural specification

Parameters:

ontology - The ontology whose direct imports are to be retrieved.

Returns:

The set of loaded ontologies that the specified ontology is related to via the directlyImports relation. If the ontology is not managed by this manager then the empty set will be returned.

getImports

@Nonnull
Set<OWLOntology> getImports(@Nonnull
                                     OWLOntology ontology)

Gets the set of ontologies that are in the transitive closure of the directly imports relation.

Parameters:

ontology - The ontology whose imports are to be retrieved.

Returns:

A set of OWLOntologyies that are in the transitive closure of the directly imports relation of this ontology. If, for what ever reason, an imported ontology could not be loaded, then it will not be contained in the returned set of ontologies. If the ontology is not managed by this manager then the empty set will be returned.

getImportsClosure

@Nonnull
Set<OWLOntology> getImportsClosure(@Nonnull
                                            OWLOntology ontology)

Gets the imports closure for the specified ontology.

Parameters:

ontology - The ontology whose imports closure is to be retrieved.

Returns:

A Set of ontologies that contains the imports closure for the specified ontology. This set will also include the specified ontology. Example: if A imports B and B imports C, then calling this method with A will return the set consisting of A, B and C. If, for what ever reason, an imported ontology could not be loaded, then it will not be contained in the returned set of ontologies. If the ontology is not managed by this manager then the empty set will be returned.

getSortedImportsClosure

@Nonnull
List<OWLOntology> getSortedImportsClosure(@Nonnull
                                                   OWLOntology ontology)

Gets the topologically ordered imports closure.

Parameters:

ontology - The ontology whose imports closure is to be determined.

Returns:

A list that represents a topological ordering of the imports closure. The first element in the list will be the specified ontology. If the ontology is not managed by this manager then an empty list will be returned.

createOntology

@Nonnull
OWLOntology createOntology()
                             throws OWLOntologyCreationException

Creates a new (empty) ontology that does not have an ontology IRI (and therefore does not have a version IRI). A document IRI will automatically be generated.

Returns:

The newly created ontology

Throws:

OWLOntologyCreationException - if there was a problem creating the ontology

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    Set<OWLAxiom> axioms)
                             throws OWLOntologyCreationException

Creates a new ontology that is initialised to contain specific axioms. The ontology will not have an IRI. The document IRI of the created ontology will be auto-generated.

Parameters:

axioms - The axioms that should be copied into the new ontology

Returns:

An ontology without an IRI that contains all of the specified axioms

Throws:

OWLOntologyCreationException - if there was a problem creating the new ontology.

OWLOntologyChangeException - if there was a problem copying the axioms.

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    Set<OWLAxiom> axioms,
                                    @Nonnull
                                    IRI ontologyIRI)
                             throws OWLOntologyCreationException

Creates a new ontology that has the specified ontology IRI and is initialised to contain specific axioms.

Parameters:

ontologyIRI - The IRI of the new ontology.
The ontology document IRI of the created ontology will be set to the value returned by any installed OWLOntologyIRIMappers. If no mappers are installed or the ontology IRI was not mapped to a document IRI by any of the installed mappers, then the ontology document IRI will be set to the value of ontologyIRI.

axioms - The axioms that should be copied into the new ontology

Returns:

An ontology that has the specified IRI and contains all of the specified axioms

Throws:

OWLOntologyCreationException - if there was a problem creating the new ontology, if the new ontology already exists in this manager.

OWLOntologyChangeException - if there was a problem copying the axioms.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI.

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    IRI ontologyIRI)
                             throws OWLOntologyCreationException

Creates a new (empty) ontology that has the specified ontology IRI (and no version IRI).
The ontology document IRI of the created ontology will be set to the value returned by any installed OWLOntologyIRIMappers. If no mappers are installed or the ontology IRI was not mapped to a document IRI by any of the installed mappers, then the ontology document IRI will be set to the value of ontologyIRI.

Parameters:

ontologyIRI - The IRI of the ontology to be created. The ontology IRI will be mapped to a document IRI in order to determine the type of ontology factory that will be used to create the ontology. If this mapping is null then a default (in memory) implementation of the ontology will most likely be created.

Returns:

The newly created ontology, or if an ontology with the specified IRI already exists then this existing ontology will be returned.

Throws:

OWLOntologyCreationException - If the ontology could not be created.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no version IRI).

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    OWLOntologyID ontologyID)
                             throws OWLOntologyCreationException

Creates a new (empty) ontology that has the specified ontology ID.

Parameters:

ontologyID - The ID of the ontology to be created.
The ontology document IRI of the created ontology will be set to the value returned by any installed OWLOntologyIRIMappers. If no mappers are installed or the ontology IRI was not mapped to a document IRI by any of the installed mappers, then the ontology document IRI will be set to the value of ontologyIRI.

Returns:

The newly created ontology, or if an ontology with the specified IRI already exists then this existing ontology will be returned.

Throws:

OWLOntologyCreationException - If the ontology could not be created.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyID (and no version IRI).

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyID is mapped to a ontology document IRI for which there already exists a mapping in this manager.

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    IRI ontologyIRI,
                                    @Nonnull
                                    Set<OWLOntology> ontologies,
                                    boolean copyLogicalAxiomsOnly)
                             throws OWLOntologyCreationException

Creates a new ontology that has the specified ontology IRI and is initialised to contain the axioms that are contained in the specified ontologies. Note that the specified ontologies need not be managed by this manager.
The ontology document IRI of the created ontology will be set to the value returned by any installed OWLOntologyIRIMappers. If no mappers are installed or the ontology IRI was not mapped to a document IRI by any of the installed mappers, then the ontology document IRI will be set to the value of ontologyIRI.

Parameters:

ontologyIRI - The IRI of the new ontology.

ontologies - The ontologies whose axioms should be copied into the new ontology

copyLogicalAxiomsOnly - If set to true only logical axioms are copied into the new ontology. If set to false then all axioms (including annotation axioms) are copied into the new ontology.

Returns:

An ontology that has the specified IRI and contains all of the axioms that are contained in the specified ontologies possibly minus all non-logical axioms

Throws:

OWLOntologyCreationException - if there was a problem creating the new ontology, if the new ontology already exists in this manager.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no ontology version IRI).

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

createOntology

@Nonnull
OWLOntology createOntology(@Nonnull
                                    IRI ontologyIRI,
                                    @Nonnull
                                    Set<OWLOntology> ontologies)
                             throws OWLOntologyCreationException

Creates a new ontology that has the specified ontology IRI and is initialised to contain the axioms that are contained in the specified ontologies. Note that the specified ontologies need not be managed by this manager.
The ontology document IRI of the created ontology will be set to the value returned by any installed OWLOntologyIRIMappers. If no mappers are installed or the ontology IRI was not mapped to a document IRI by any of the installed mappers, then the ontology document IRI will be set to the value of ontologyIRI.

Parameters:

ontologyIRI - The IRI of the new ontology.

ontologies - The ontologies whose axioms should be copied into the new ontology

Returns:

An ontology that has the specified IRI and contains all of the axioms that are contained in the specified ontologies

Throws:

OWLOntologyCreationException - if there was a problem creating the new ontology, if the new ontology already exists in this manager.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no version IRI).

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

copyOntology

@Nonnull
OWLOntology copyOntology(@Nonnull
                                  OWLOntology toCopy,
                                  @Nonnull
                                  OntologyCopy settings)
                           throws OWLOntologyCreationException

Copy an ontology from another manager to this one. The returned OWLOntology will return this manager when getOWLOntologyManager() is invoked. The copy mode is defined by the OntologyCopy parameter: SHALLOW for simply creating a new ontology containing the same axioms and same id, DEEP for copying actoss format and document IRI, MOVE to remove the ontology from its previous manager.

Parameters:

toCopy - ontology to copy

settings - settings for the copy

Returns:

copied ontology. This is the same object as toCopy only for MOVE copies

Throws:

OWLOntologyCreationException - if this manager cannot add the new ontology

loadOntology

@Nonnull
OWLOntology loadOntology(@Nonnull
                                  IRI ontologyIRI)
                           throws OWLOntologyCreationException

Loads an ontology that is assumed to have the specified ontologyIRI as its IRI or version IRI.
The ontology IRI will be mapped to an ontology document IRI. The mapping will be determined using one of the loaded OWLOntologyIRIMapper objects. By default, if no custom OWLOntologyIRIMappers have been registered using the getIRIMappers() PriorityCollection PriorityCollection.add(Serializable...) method, or no mapping can be found, the ontology document IRI is taken to be the specified ontology IRI.

Parameters:

ontologyIRI - The IRI that identifies the ontology. It is expected that the ontology will also have this IRI (although the OWL API will tolerated situations where this is not the case).

Returns:

The OWLOntology representation of the ontology that was loaded.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (where the ontology doesn't have a version IRI).

OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

loadOntologyFromOntologyDocument

@Nonnull
OWLOntology loadOntologyFromOntologyDocument(@Nonnull
                                                      IRI documentIRI)
                                               throws OWLOntologyCreationException

Loads an ontology from an ontology document specified by an IRI. In contrast the the loadOntology(IRI) method, no mapping is performed on the specified IRI.

Parameters:

documentIRI - The ontology document IRI where the ontology will be loaded from.

Returns:

The ontology that was loaded.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyDocumentAlreadyExistsException - if the specified documentIRI is already the document IRI for a loaded ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology whose ontology IRI and version IRI is the same as the ontology IRI and version IRI of the ontology contained in the document pointed to by documentIRI.

loadOntologyFromOntologyDocument

@Nonnull
OWLOntology loadOntologyFromOntologyDocument(@Nonnull
                                                      File file)
                                               throws OWLOntologyCreationException

Loads an ontology from an ontology document contained in a local file. The loaded ontology will be assigned a document IRI that corresponds to the file IRI.

Parameters:

file - The file that contains a representation of an ontology

Returns:

The ontology that was parsed from the file.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology could not be parsed.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyDocumentAlreadyExistsException - if the IRI of the specified file is already the document IRI for a loaded ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology whose ontology IRI and version IRI is the same as the ontology IRI and version IRI of the ontology contained in the document pointed to by documentIRI.

loadOntologyFromOntologyDocument

@Nonnull
OWLOntology loadOntologyFromOntologyDocument(@Nonnull
                                                      InputStream inputStream)
                                               throws OWLOntologyCreationException

Loads an ontology from an ontology document obtained from an input stream. The loaded ontology will be assigned an auto-generated document IRI with "inputstream" as its scheme.

Parameters:

inputStream - The input stream that can be used to obtain a representation of an ontology

Returns:

The ontology that was parsed from the input stream.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology could not be parsed.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology whose ontology IRI and version IRI is the same as the ontology IRI and version IRI of the ontology obtained from parsing the content of the input stream.

loadOntologyFromOntologyDocument

@Nonnull
OWLOntology loadOntologyFromOntologyDocument(@Nonnull
                                                      OWLOntologyDocumentSource documentSource)
                                               throws OWLOntologyCreationException

A convenience method that load an ontology from an input source.

Parameters:

documentSource - The input source that describes where the ontology should be loaded from.

Returns:

The ontology that was loaded.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyDocumentAlreadyExistsException - if the document IRI of the input source is already the document IRI for a loaded ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology whose ontology IRI and version IRI is the same as the ontology IRI and version IRI of the ontology contained in the document represented by the input source.

loadOntologyFromOntologyDocument

@Nonnull
OWLOntology loadOntologyFromOntologyDocument(@Nonnull
                                                      OWLOntologyDocumentSource documentSource,
                                                      @Nonnull
                                                      OWLOntologyLoaderConfiguration config)
                                               throws OWLOntologyCreationException

A convenience method that load an ontology from an input source with specified configuration.

Parameters:

documentSource - The input source that describes where the ontology should be loaded from.

config - the configuration to use

Returns:

The ontology that was loaded.

Throws:

OWLOntologyCreationException - If there was a problem in creating and loading the ontology.

UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.

UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.

OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.

OWLOntologyDocumentAlreadyExistsException - if the document IRI of the input source is already the document IRI for a loaded ontology.

OWLOntologyAlreadyExistsException - if the manager already contains an ontology whose ontology IRI and version IRI is the same as the ontology IRI and version IRI of the ontology contained in the document represented by the input source.

removeOntology

void removeOntology(@Nonnull
                    OWLOntology ontology)

Attempts to remove an ontology. The ontology which is identified by the specified IRI is removed regardless of whether it is referenced by other ontologies via imports statements.

Parameters:

ontology - The ontology to be removed. If this manager does not manage the ontology then nothing happens.

removeOntology

void removeOntology(@Nonnull
                    OWLOntologyID ontologyID)

Attempts to remove an ontology. The ontology which is identified by the specified IRI is removed regardless of whether it is referenced by other ontologies via imports statements.

Parameters:

ontologyID - The ontology to be removed. If this manager does not manage the ontology then nothing happens.

getOntologyDocumentIRI

@Nonnull
IRI getOntologyDocumentIRI(@Nonnull
                                    OWLOntology ontology)

Gets the document IRI for a given ontology. This will either be the document IRI from where the ontology was obtained from during loading, or the document IRI which was specified (via a mapper) when the (empty) ontology was created. Note that this may not correspond to the first document IRI found in the list of mappings from ontology IRI to document IRI. The reason for this is that it might not have been possible to load the ontology from the first document IRI found in the mapping table.

Parameters:

ontology - The ontology whose document IRI is to be obtained.

Returns:

The document IRI of the ontology.

Throws:

UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

setOntologyDocumentIRI

void setOntologyDocumentIRI(@Nonnull
                            OWLOntology ontology,
                            @Nonnull
                            IRI documentIRI)

Overrides the current document IRI for a given ontology. This method does not alter the IRI mappers which are installed, but alters the actual document IRI of an ontology that has already been loaded.

Parameters:

ontology - The ontology that has already been loaded.

documentIRI - The new ontology document IRI

Throws:

UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

getOntologyFormat

@Nullable
OWLDocumentFormat getOntologyFormat(@Nonnull
                                              OWLOntology ontology)

Gets the ontology format for the specified ontology.

Parameters:

ontology - The ontology whose format it to be obtained.

Returns:

The format of the ontology.

setOntologyFormat

void setOntologyFormat(@Nonnull
                       OWLOntology ontology,
                       @Nonnull
                       OWLDocumentFormat ontologyFormat)

Sets the format for the specified ontology.

Parameters:

ontology - The ontology whose format is to be set.

ontologyFormat - The format for the specified ontology.

Throws:

UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology)
           throws OWLOntologyStorageException

Saves the specified ontology. The ontology will be saved to the location that it was loaded from, or if it was created programmatically, it will be saved to the location specified by an ontology IRI mapper at creation time. The ontology will be saved in the same format which it was loaded from, or the default ontology format if the ontology was created programmatically.

Parameters:

ontology - The ontology to be saved.

Throws:

OWLOntologyStorageException - An exception will be thrown if there is a problem with saving the ontology, or the ontology can't be saved in the format it was loaded from.

UnknownOWLOntologyException - if this manager does not manage the specified ontology

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  IRI documentIRI)
           throws OWLOntologyStorageException

Saves the specified ontology, using the specified document IRI to determine where/how the ontology should be saved.

Parameters:

ontology - The ontology to be saved.

documentIRI - The document IRI where the ontology should be saved to

Throws:

OWLOntologyStorageException - If the ontology cannot be saved

UnknownOWLOntologyException - if the specified ontology is not managed by this manager.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OutputStream outputStream)
           throws OWLOntologyStorageException

Saves the specified ontology, to the specified output stream

Parameters:

ontology - The ontology to be saved.

outputStream - The output stream where the ontology will be saved to

Throws:

OWLOntologyStorageException - If there was a problem saving this ontology to the specified output stream

UnknownOWLOntologyException - if this manager does not manage the specified ontology.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OWLDocumentFormat ontologyFormat)
           throws OWLOntologyStorageException

Saves the specified ontology in the specified ontology format to its document URI.

Parameters:

ontology - The ontology to be saved.

ontologyFormat - The format in which the ontology should be saved.

Throws:

OWLOntologyStorageException - If the ontology cannot be saved.

UnknownOWLOntologyException - if the specified ontology is not managed by this manager

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  IRI documentIRI)
           throws OWLOntologyStorageException

Saves the specified ontology to the specified document IRI in the specified ontology format.

Parameters:

ontology - The ontology to be saved

ontologyFormat - The format in which to save the ontology

documentIRI - The document IRI where the ontology should be saved to

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

UnknownOWLOntologyException - if the specified ontology is not managed by the manager.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  OutputStream outputStream)
           throws OWLOntologyStorageException

Saves the specified ontology to the specified output stream in the specified ontology format.

Parameters:

ontology - The ontology to be saved

ontologyFormat - The format in which to save the ontology

outputStream - The output stream where the ontology will be saved to.

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

UnknownOWLOntologyException - if the specified ontology is not managed by the manager.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OWLOntologyDocumentTarget documentTarget)
           throws OWLOntologyStorageException

Saves the specified ontology to the specified OWLOntologyDocumentTarget.

Parameters:

ontology - The ontology to be saved.

documentTarget - The output target where the ontology will be saved to.

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

UnknownOWLOntologyException - if the specified ontology is not managed by this manager.

saveOntology

void saveOntology(@Nonnull
                  OWLOntology ontology,
                  @Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  OWLOntologyDocumentTarget documentTarget)
           throws OWLOntologyStorageException

Saves the specified ontology to the specified output target in the specified ontology format.

Parameters:

ontology - The ontology to be saved.

ontologyFormat - The output format in which to save the ontology

documentTarget - The output target where the ontology will be saved to

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

addIRIMapper

@Deprecated
void addIRIMapper(@Nonnull
                              OWLOntologyIRIMapper mapper)

Deprecated. use getIRIMappers().add() instead

Add an IRI mapper to the manager

Parameters:

mapper - the mapper to add

removeIRIMapper

@Deprecated
void removeIRIMapper(@Nonnull
                                 OWLOntologyIRIMapper mapper)

Deprecated. use getIRIMappers().remove() instead

Remove an IRI mapper from the manager

Parameters:

mapper - the mapper to remove

clearIRIMappers

@Deprecated
void clearIRIMappers()

Deprecated. use getIRIMappers().clear() instead

Clear the manager mappers

addOntologyStorer

@Deprecated
void addOntologyStorer(@Nonnull
                                   OWLStorerFactory storer)

Deprecated. use getOntologyStorers().add() instead

Add astorer to the manager

Parameters:

storer - the storer to add

removeOntologyStorer

@Deprecated
void removeOntologyStorer(@Nonnull
                                      OWLStorerFactory storer)

Deprecated. use getOntologyStorers().remove() instead

Remove a storer from the manager

Parameters:

storer - the storer to remove

clearOntologyStorers

@Deprecated
void clearOntologyStorers()

Deprecated. use getOntologyStorers().clear() instead

Clear the manager storers

setIRIMappers

void setIRIMappers(Set<OWLOntologyIRIMapper> mappers)

Set the collection of IRI mappers. It is used by Guice injection, but can be used manually as well to replace the existing mappers with new ones. The mappers are used to obtain ontology document IRIs for ontology IRIs. If their type is annotated with a HasPriority type, this will be used to decide the order they are used. Otherwise, the order in which the collection is iterated will determine the order in which the mappers are used.

Parameters:

mappers - the mappers to be injected

getIRIMappers

@Nonnull
PriorityCollection<OWLOntologyIRIMapper> getIRIMappers()

Returns:

the collection of IRI mappers. This allows for iteration and modification of the list.

setOntologyParsers

void setOntologyParsers(Set<OWLParserFactory> parsers)

Set the collection of parsers. It is used by Guice injection, but can be used manually as well to replace the existing parsers with new ones. If their type is annotated with a HasPriority type, this will be used to decide the order they are used. Otherwise, the order in which the collection is iterated will determine the order in which the parsers are used.

Parameters:

parsers - the factories to be injected

getOntologyParsers

@Nonnull
PriorityCollection<OWLParserFactory> getOntologyParsers()

Returns:

the collection of parsers. This allows for iteration and modification of the list.

setOntologyFactories

void setOntologyFactories(Set<OWLOntologyFactory> factories)

Set the collection of ontology factories. It is used by Guice injection, but can be used manually as well to replace the existing factories with new ones. If their type is annotated with a HasPriority type, this will be used to decide the order they are used. Otherwise, the order in which the collection is iterated will determine the order in which the parsers are used.

Parameters:

factories - the factories to be injected

getOntologyFactories

@Nonnull
PriorityCollection<OWLOntologyFactory> getOntologyFactories()

Returns:

the collection of ontology factories. This allows for iteration and modification of the list.

setOntologyStorers

void setOntologyStorers(@Nonnull
                        Set<OWLStorerFactory> storers)

Set the list of ontology storers. If their type is annotated with a HasPriority type, this will be used to decide the order they are used. Otherwise, the order in which the collection is iterated will determine the order in which the storers are used.

Parameters:

storers - The storers to be used

getOntologyStorers

@Nonnull
PriorityCollection<OWLStorerFactory> getOntologyStorers()

Returns:

the collection of storers. This allows for iteration and modification of the list.

addOntologyChangeListener

void addOntologyChangeListener(@Nonnull
                               OWLOntologyChangeListener listener,
                               @Nonnull
                               OWLOntologyChangeBroadcastStrategy strategy)

Adds an ontology change listener, which listens to ontology changes. An ontology change broadcast strategy must be specified, which determines the changes that are broadcast to the listener.

Parameters:

listener - The listener to be added.

strategy - The strategy that should be used for broadcasting changes to the listener.

addImpendingOntologyChangeListener

void addImpendingOntologyChangeListener(@Nonnull
                                        ImpendingOWLOntologyChangeListener listener)

Parameters:

listener - the listener to add

removeImpendingOntologyChangeListener

void removeImpendingOntologyChangeListener(@Nonnull
                                           ImpendingOWLOntologyChangeListener listener)

Parameters:

listener - the listener to remove

addOntologyChangesVetoedListener

void addOntologyChangesVetoedListener(@Nonnull
                                      OWLOntologyChangesVetoedListener listener)

Parameters:

listener - the listener to add

removeOntologyChangesVetoedListener

void removeOntologyChangesVetoedListener(@Nonnull
                                         OWLOntologyChangesVetoedListener listener)

Parameters:

listener - the listener to remove

setDefaultChangeBroadcastStrategy

void setDefaultChangeBroadcastStrategy(@Nonnull
                                       OWLOntologyChangeBroadcastStrategy strategy)

Sets the default strategy that is used to broadcast ontology changes.

Parameters:

strategy - The strategy to be used for broadcasting changes. This strategy will override any previously set broadcast strategy.

See Also:

DefaultChangeBroadcastStrategy, EDTChangeBroadcastStrategy

makeLoadImportRequest

void makeLoadImportRequest(@Nonnull
                           OWLImportsDeclaration declaration)

Requests that the manager loads an imported ontology that is described by an imports statement. This method is generally used by parsers and other kinds of loaders. For simply loading an ontology, use the loadOntologyXXX methods. The method respects the list of ignored imports in the specified configuration. In other words, if this methods is called for an ignored import as specified by the configuration object then the import won't be loaded. The ontology loader configuration used is the default one for this manager.

Parameters:

declaration - The declaration that describes the import to be loaded.

Throws:

UnloadableImportException - if there was a problem creating and loading the import and silent missing imports handling is not turned on. If silent missing import handling is turned on then this exception will not be thrown.

makeLoadImportRequest

void makeLoadImportRequest(@Nonnull
                           OWLImportsDeclaration declaration,
                           @Nonnull
                           OWLOntologyLoaderConfiguration configuration)

Requests that the manager loads an imported ontology that is described by an imports statement. This method is generally used by parsers and other kinds of loaders. For simply loading an ontology, use the loadOntologyXXX methods. The method respects the list of ignored imports in the specified configuration. In other words, if this methods is called for an ignored import as specified by the configuration object then the import won't be loaded.

Parameters:

declaration - The declaration that describes the import to be loaded.

configuration - The configuration object that passes arguments to the mechanism used for loading.

Throws:

UnloadableImportException - if there was a problem creating and loading the import and silent missing imports handling is not turned on. If silent missing import handling is turned on then this exception will not be thrown.

addMissingImportListener

void addMissingImportListener(@Nonnull
                              MissingImportListener listener)

In the case where silent missing imports handling is enabled, a listener can be attached via this method so that there is a mechanism that allows clients to be informed of the reason when an import cannot be loaded.

Parameters:

listener - The listener to be added.

removeMissingImportListener

void removeMissingImportListener(@Nonnull
                                 MissingImportListener listener)

Removes a previously added missing import listener.

Parameters:

listener - The listener to be removed.

addOntologyLoaderListener

void addOntologyLoaderListener(@Nonnull
                               OWLOntologyLoaderListener listener)

Adds an ontology loaded listener to this manager.

Parameters:

listener - The listener to be added.

removeOntologyLoaderListener

void removeOntologyLoaderListener(@Nonnull
                                  OWLOntologyLoaderListener listener)

Removes a previously added ontology loaded listener.

Parameters:

listener - The listener to be removed.

addOntologyChangeProgessListener

void addOntologyChangeProgessListener(@Nonnull
                                      OWLOntologyChangeProgressListener listener)

Adds an ontology change progress listener.

Parameters:

listener - The listener to be added.

removeOntologyChangeProgessListener

void removeOntologyChangeProgessListener(@Nonnull
                                         OWLOntologyChangeProgressListener listener)

Removes a previously added ontology change listener.

Parameters:

listener - The listener to be removed.