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/* This file is part of the OWL API.
* The contents of this file are subject to the LGPL License, Version 3.0.
* Copyright 2014, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
* You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
package uk.ac.manchester.cs.owl.owlapi;
import static org.semanticweb.owlapi.model.parameters.Imports.*;
import static org.semanticweb.owlapi.util.CollectionFactory.createSet;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
import java.io.OutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.annotation.Nonnull;
import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationPropertyDomainAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationPropertyRangeAxiom;
import org.semanticweb.owlapi.model.OWLAnonymousIndividual;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAxiom;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEntityVisitor;
import org.semanticweb.owlapi.model.OWLImportsDeclaration;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLIndividualAxiom;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLNamedObjectVisitor;
import org.semanticweb.owlapi.model.OWLNamedObjectVisitorEx;
import org.semanticweb.owlapi.model.OWLObject;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectVisitor;
import org.semanticweb.owlapi.model.OWLObjectVisitorEx;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLPrimitive;
import org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom;
import org.semanticweb.owlapi.model.parameters.AxiomAnnotations;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.model.parameters.Navigation;
import org.semanticweb.owlapi.util.CollectionFactory;
import org.semanticweb.owlapi.util.OWLAxiomSearchFilter;
import org.semanticweb.owlapi.util.OWLObjectTypeIndexProvider;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import com.google.common.base.Optional;
import com.google.common.collect.Iterables;
/**
* @author Matthew Horridge, The University Of Manchester, Bio-Health
* Informatics Group
* @since 2.0.0
*/
public class OWLImmutableOntologyImpl extends OWLAxiomIndexImpl implements
OWLOntology, Serializable {
private static final long serialVersionUID = 40000L;
@Nonnull
protected OWLOntologyManager manager;
@Nonnull
protected OWLOntologyID ontologyID;
@Override
protected int index() {
return OWLObjectTypeIndexProvider.ONTOLOGY;
}
/**
* @param manager
* ontology manager
* @param ontologyID
* ontology id
*/
public OWLImmutableOntologyImpl(@Nonnull OWLOntologyManager manager,
@Nonnull OWLOntologyID ontologyID) {
this.manager = checkNotNull(manager, "manager cannot be null");
this.ontologyID = checkNotNull(ontologyID, "ontologyID cannot be null");
}
@SuppressWarnings("null")
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Ontology(");
sb.append(ontologyID);
sb.append(") [Axioms: ");
int axiomCount = ints.getAxiomCount();
sb.append(axiomCount);
sb.append(" Logical Axioms: ");
sb.append(ints.getLogicalAxiomCount());
sb.append("] First 20 axioms: {");
for (OWLAxiom ax : Iterables.limit(ints.getAxioms(), 20)) {
sb.append(ax).append(' ');
}
sb.append('}');
return sb.toString();
}
@Override
public OWLOntologyManager getOWLOntologyManager() {
return manager;
}
@SuppressWarnings("null")
@Override
public void setOWLOntologyManager(OWLOntologyManager manager) {
this.manager = manager;
}
@Override
public OWLOntologyID getOntologyID() {
return ontologyID;
}
@Override
public boolean isAnonymous() {
return ontologyID.isAnonymous();
}
@Override
protected int compareObjectOfSameType(OWLObject object) {
if (object == this) {
return 0;
}
OWLOntology other = (OWLOntology) object;
return ontologyID.compareTo(other.getOntologyID());
}
@Override
public boolean isEmpty() {
return ints.isEmpty();
}
@Override
public int getAxiomCount(AxiomType axiomType,
boolean includeImportsClosure) {
return getAxiomCount(axiomType,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public int getAxiomCount(boolean includeImportsClosure) {
return getAxiomCount(Imports.fromBoolean(includeImportsClosure));
}
@Override
public int getAxiomCount(AxiomType axiomType,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getAxiomCount(axiomType);
}
int result = 0;
for (OWLOntology ont : getImportsClosure()) {
result += ont.getAxiomCount(axiomType);
}
return result;
}
@Override
public boolean containsAxiom(@Nonnull OWLAxiom axiom) {
return Internals.contains(ints.getAxiomsByType(), axiom.getAxiomType(),
axiom);
}
@Override
public int getAxiomCount() {
return getAxiomCount(EXCLUDED);
}
@Override
public int getAxiomCount(Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.getAxiomCount();
}
int total = 0;
for (OWLOntology o : getImportsClosure()) {
total += o.getAxiomCount();
}
return total;
}
@Override
public Set getAxioms() {
return getAxioms(EXCLUDED);
}
@Override
public Set getAxioms(boolean b) {
return getAxioms(Imports.fromBoolean(b));
}
@Override
public Set getAxioms(Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return asSet(ints.getAxioms());
}
Set axioms = new HashSet<>();
for (OWLOntology o : getImportsClosure()) {
axioms.addAll(o.getAxioms());
}
return axioms;
}
@Nonnull
@Override
@SuppressWarnings("unchecked")
public Set getAxioms(AxiomType axiomType) {
return (Set) asSet(ints.getAxiomsByType().getValues(axiomType));
}
@Override
public Set getAxioms(AxiomType axiomType,
boolean includeImportsClosure) {
return getAxioms(axiomType, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxioms(AxiomType axiomType,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getAxioms(axiomType);
}
Set toReturn = createSet();
for (OWLOntology o : getImportsClosure()) {
toReturn.addAll(o.getAxioms(axiomType));
}
return toReturn;
}
@Nonnull
@Override
public Set getTBoxAxioms(Imports includeImportsClosure) {
Set toReturn = new HashSet<>();
for (AxiomType type : AxiomType.TBoxAxiomTypes) {
assert type != null;
toReturn.addAll(getAxioms(type, includeImportsClosure));
}
return toReturn;
}
@Nonnull
@Override
public Set getABoxAxioms(Imports includeImportsClosure) {
Set toReturn = new HashSet<>();
for (AxiomType type : AxiomType.ABoxAxiomTypes) {
assert type != null;
toReturn.addAll(getAxioms(type, includeImportsClosure));
}
return toReturn;
}
@Nonnull
@Override
public Set getRBoxAxioms(Imports includeImportsClosure) {
Set toReturn = new HashSet<>();
for (AxiomType type : AxiomType.RBoxAxiomTypes) {
assert type != null;
toReturn.addAll(getAxioms(type, includeImportsClosure));
}
return toReturn;
}
@Override
public int getAxiomCount(AxiomType axiomType) {
return ints.getAxiomCount(axiomType);
}
@Override
public Set getLogicalAxioms() {
return ints.getLogicalAxioms();
}
@Override
public Set getLogicalAxioms(Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.getLogicalAxioms();
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getLogicalAxioms(EXCLUDED));
}
return result;
}
@Override
public Set getLogicalAxioms(boolean includeImportsClosure) {
return getLogicalAxioms(Imports.fromBoolean(includeImportsClosure));
}
@Override
public int getLogicalAxiomCount() {
return ints.getLogicalAxiomCount();
}
@Override
public int getLogicalAxiomCount(boolean includeImportsClosure) {
return getLogicalAxiomCount(Imports.fromBoolean(includeImportsClosure));
}
@Override
public int getLogicalAxiomCount(Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.getLogicalAxiomCount();
}
int total = 0;
for (OWLOntology o : getImportsClosure()) {
total += o.getLogicalAxiomCount(EXCLUDED);
}
return total;
}
@Nonnull
@Override
public Set getAnnotations() {
return (Set) ints.getOntologyAnnotations(true);
}
@Override
public Set getGeneralClassAxioms() {
return ints.getGeneralClassAxioms();
}
@Override
public boolean containsAxiom(@Nonnull OWLAxiom axiom,
boolean includeImportsClosure) {
return containsAxiom(axiom, Imports.fromBoolean(includeImportsClosure),
AxiomAnnotations.CONSIDER_AXIOM_ANNOTATIONS);
}
@Override
public boolean containsAxiom(@Nonnull OWLAxiom axiom,
Imports includeImportsClosure, AxiomAnnotations ignoreAnnotations) {
if (includeImportsClosure == EXCLUDED) {
if (ignoreAnnotations == AxiomAnnotations.CONSIDER_AXIOM_ANNOTATIONS) {
return containsAxiom(axiom);
} else {
return containsAxiomIgnoreAnnotations(axiom);
}
}
for (OWLOntology ont : getImportsClosure()) {
if (ont.containsAxiom(axiom, EXCLUDED, ignoreAnnotations)) {
return true;
}
}
return false;
}
@Override
public boolean containsAxiomIgnoreAnnotations(@Nonnull OWLAxiom axiom) {
for (OWLAxiom ax : ints.getAxiomsByType().getValues(
axiom.getAxiomType())) {
if (ax.equalsIgnoreAnnotations(axiom)) {
return true;
}
}
return false;
}
@Override
public boolean containsAxiomIgnoreAnnotations(@Nonnull OWLAxiom axiom,
boolean importsIncluded) {
return containsAxiom(axiom, Imports.fromBoolean(importsIncluded),
AxiomAnnotations.IGNORE_AXIOM_ANNOTATIONS);
}
@Override
@Nonnull
public Set getAxiomsIgnoreAnnotations(@Nonnull OWLAxiom axiom) {
Set result = createSet();
if (containsAxiom(axiom)) {
result.add(axiom);
}
for (OWLAxiom ax : ints.getAxiomsByType().getValues(
axiom.getAxiomType())) {
if (ax.equalsIgnoreAnnotations(axiom)) {
result.add(ax);
}
}
return result;
}
@Override
public Set getAxiomsIgnoreAnnotations(@Nonnull OWLAxiom axiom,
boolean includeImportsClosure) {
return getAxiomsIgnoreAnnotations(axiom,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxiomsIgnoreAnnotations(@Nonnull OWLAxiom axiom,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getAxiomsIgnoreAnnotations(axiom);
}
Set result = createSet();
for (OWLOntology ont : getImportsClosure()) {
result.addAll(ont.getAxiomsIgnoreAnnotations(axiom, EXCLUDED));
}
return result;
}
@Override
public boolean containsClassInSignature(IRI owlClassIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsClassInSignature(owlClassIRI);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsClassInSignature(owlClassIRI, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean containsObjectPropertyInSignature(IRI owlObjectPropertyIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsObjectPropertyInSignature(owlObjectPropertyIRI);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsObjectPropertyInSignature(owlObjectPropertyIRI,
EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean containsDataPropertyInSignature(IRI owlDataPropertyIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsDataPropertyInSignature(owlDataPropertyIRI);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsDataPropertyInSignature(owlDataPropertyIRI, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean containsAnnotationPropertyInSignature(
IRI owlAnnotationPropertyIRI, Imports includeImportsClosure) {
OWLAnnotationProperty p = manager.getOWLDataFactory()
.getOWLAnnotationProperty(owlAnnotationPropertyIRI);
if (includeImportsClosure == INCLUDED) {
for (OWLOntology o : getImportsClosure()) {
if (o.containsAnnotationPropertyInSignature(
owlAnnotationPropertyIRI, EXCLUDED)) {
return true;
}
}
} else {
if (ints.containsAnnotationPropertyInSignature(owlAnnotationPropertyIRI)) {
return true;
}
}
return checkOntologyAnnotations(p);
}
private boolean checkOntologyAnnotations(
OWLAnnotationProperty owlAnnotationProperty) {
for (OWLAnnotation anno : ints.getOntologyAnnotations(false)) {
if (anno.getProperty().equals(owlAnnotationProperty)) {
return true;
}
}
return false;
}
@Override
public boolean containsIndividualInSignature(IRI owlIndividualIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsIndividualInSignature(owlIndividualIRI);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsIndividualInSignature(owlIndividualIRI, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean containsDatatypeInSignature(IRI owlDatatypeIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsDatatypeInSignature(owlDatatypeIRI);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsDatatypeInSignature(owlDatatypeIRI, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public Set getEntitiesInSignature(@Nonnull IRI entityIRI) {
return getEntitiesInSignature(entityIRI, EXCLUDED);
}
@Override
public Set getEntitiesInSignature(IRI iri,
Imports includeImportsClosure) {
Set result = createSet(6);
if (containsClassInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory().getOWLClass(iri));
}
if (containsObjectPropertyInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory().getOWLObjectProperty(iri));
}
if (containsDataPropertyInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory().getOWLDataProperty(iri));
}
if (containsIndividualInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory().getOWLNamedIndividual(iri));
}
if (containsDatatypeInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory().getOWLDatatype(iri));
}
if (containsAnnotationPropertyInSignature(iri, includeImportsClosure)) {
result.add(manager.getOWLDataFactory()
.getOWLAnnotationProperty(iri));
}
return result;
}
@Override
public Set getPunnedIRIs(Imports includeImportsClosure) {
Set punned = new HashSet<>();
Set test = new HashSet<>();
if (includeImportsClosure == INCLUDED) {
for (OWLOntology o : getImportsClosure()) {
for (OWLEntity e : o.getClassesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : o.getDataPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : o.getObjectPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : o
.getAnnotationPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : o.getDatatypesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : o.getIndividualsInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
}
if (punned.isEmpty()) {
return CollectionFactory. emptySet();
}
return punned;
}
for (OWLEntity e : getClassesInSignature(EXCLUDED)) {
punned.add(e.getIRI());
}
for (OWLEntity e : getDataPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : getObjectPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : getAnnotationPropertiesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : getDatatypesInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
for (OWLEntity e : getIndividualsInSignature(EXCLUDED)) {
if (test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
if (punned.isEmpty()) {
return CollectionFactory. emptySet();
}
return punned;
}
@Override
public boolean containsReference(@Nonnull OWLEntity entity,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsReference(entity);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsReference(entity, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean isDeclared(OWLEntity owlEntity) {
return ints.isDeclared(owlEntity);
}
@Override
public boolean
isDeclared(OWLEntity owlEntity, Imports includeImportsClosure) {
if (isDeclared(owlEntity)) {
return true;
}
if (includeImportsClosure == INCLUDED) {
for (OWLOntology ont : manager.getImportsClosure(this)) {
if (!ont.equals(this) && ont.isDeclared(owlEntity)) {
return true;
}
}
}
return false;
}
@Override
public boolean containsEntityInSignature(@Nonnull OWLEntity owlEntity) {
return containsEntityInSignature(owlEntity, EXCLUDED);
}
private final OWLEntityReferenceChecker entityReferenceChecker = new OWLEntityReferenceChecker();
@Override
public boolean containsEntityInSignature(@Nonnull OWLEntity owlEntity,
Imports includeImportsClosure) {
if (includeImportsClosure != INCLUDED) {
return entityReferenceChecker.containsReference(owlEntity);
}
for (OWLOntology o : getImportsClosure()) {
if (o.containsEntityInSignature(owlEntity, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public boolean containsEntityInSignature(IRI entityIRI,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
if (containsClassInSignature(entityIRI, EXCLUDED)) {
return true;
}
if (containsObjectPropertyInSignature(entityIRI, EXCLUDED)) {
return true;
}
if (containsDataPropertyInSignature(entityIRI, EXCLUDED)) {
return true;
}
if (containsIndividualInSignature(entityIRI, EXCLUDED)) {
return true;
}
if (containsDatatypeInSignature(entityIRI, EXCLUDED)) {
return true;
}
if (containsAnnotationPropertyInSignature(entityIRI, EXCLUDED)) {
return true;
}
return false;
}
for (OWLOntology ont : getImportsClosure()) {
if (ont.containsEntityInSignature(entityIRI, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public Set getSignature() {
// We might want to cache this for performance reasons,
// but I'm not sure right now.
Set entities = createSet();
entities.addAll(getClassesInSignature());
entities.addAll(getObjectPropertiesInSignature());
entities.addAll(getDataPropertiesInSignature());
entities.addAll(getIndividualsInSignature());
entities.addAll(getDatatypesInSignature());
entities.addAll(getAnnotationPropertiesInSignature(EXCLUDED));
return entities;
}
@Override
public Set getSignature(Imports includeImportsClosure) {
Set entities = getSignature();
if (includeImportsClosure == INCLUDED) {
for (OWLOntology ont : getImportsClosure()) {
entities.addAll(ont.getSignature(EXCLUDED));
}
}
return entities;
}
@Nonnull
private static Set asSet(Iterable i) {
List list = new ArrayList<>();
Iterables.addAll(list, i);
return CollectionFactory
.getCopyOnRequestSetFromImmutableCollection(list);
}
@Override
public Set getAnonymousIndividuals() {
return asSet(ints.get(OWLAnonymousIndividual.class, OWLAxiom.class)
.get().keySet());
}
@Override
public Set getClassesInSignature() {
return asSet(ints.get(OWLClass.class, OWLAxiom.class).get().keySet());
}
@Override
public Set getDataPropertiesInSignature() {
return asSet(ints.get(OWLDataProperty.class, OWLAxiom.class).get()
.keySet());
}
@Override
public Set getObjectPropertiesInSignature() {
return asSet(ints.get(OWLObjectProperty.class, OWLAxiom.class).get()
.keySet());
}
@Override
public Set getIndividualsInSignature() {
return asSet(ints.get(OWLNamedIndividual.class, OWLAxiom.class).get()
.keySet());
}
@Override
public Set getDatatypesInSignature() {
return asSet(ints.get(OWLDatatype.class, OWLAxiom.class).get().keySet());
}
@Override
public Set getClassesInSignature(Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getClassesInSignature();
}
Set results = createSet();
for (OWLOntology ont : getImportsClosure()) {
results.addAll(ont.getClassesInSignature());
}
return results;
}
@Override
public Set getObjectPropertiesInSignature(
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getObjectPropertiesInSignature();
}
Set results = createSet();
for (OWLOntology ont : getImportsClosure()) {
results.addAll(ont.getObjectPropertiesInSignature());
}
return results;
}
@Override
public Set getDataPropertiesInSignature(
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getDataPropertiesInSignature();
}
Set results = createSet();
for (OWLOntology ont : getImportsClosure()) {
results.addAll(ont.getDataPropertiesInSignature());
}
return results;
}
@Override
public Set getIndividualsInSignature(
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getIndividualsInSignature();
}
Set results = createSet();
for (OWLOntology ont : getImportsClosure()) {
results.addAll(ont.getIndividualsInSignature());
}
return results;
}
@Override
public Set getReferencedAnonymousIndividuals(
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return asSet(ints.get(OWLAnonymousIndividual.class, OWLAxiom.class)
.get().keySet());
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getReferencedAnonymousIndividuals(EXCLUDED));
}
return result;
}
@Override
public Set getDatatypesInSignature(
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getDatatypesInSignature();
}
Set results = createSet();
for (OWLOntology ont : getImportsClosure()) {
results.addAll(ont.getDatatypesInSignature());
}
return results;
}
@Override
public Set getAnnotationPropertiesInSignature(
Imports includeImportsClosure) {
Set props = createSet();
if (includeImportsClosure == EXCLUDED) {
Iterables.addAll(
props,
ints.get(OWLAnnotationProperty.class, OWLAxiom.class,
Navigation.IN_SUB_POSITION).get().keySet());
for (OWLAnnotation anno : ints.getOntologyAnnotations(false)) {
props.add(anno.getProperty());
}
} else {
for (OWLOntology ont : getImportsClosure()) {
props.addAll(ont.getAnnotationPropertiesInSignature(EXCLUDED));
}
}
return props;
}
@Nonnull
@Override
public Set getImportsDeclarations() {
return (Set) ints.getImportsDeclarations(true);
}
@Override
public Set getDirectImportsDocuments() {
Set result = createSet();
for (OWLImportsDeclaration importsDeclaration : ints
.getImportsDeclarations(false)) {
result.add(importsDeclaration.getIRI());
}
return result;
}
@Override
public Set getImports() {
return manager.getImports(this);
}
@Override
public Set getDirectImports() {
return manager.getDirectImports(this);
}
@Override
public Set getImportsClosure() {
return getOWLOntologyManager().getImportsClosure(this);
}
// Add/Remove axiom mechanism. Each axiom gets visited by a visitor, which
// adds the axiom
// to the appropriate index.
@Override
public void accept(@Nonnull OWLObjectVisitor visitor) {
visitor.visit(this);
}
@Override
public void accept(@Nonnull OWLNamedObjectVisitor visitor) {
visitor.visit(this);
}
@Override
public O accept(OWLNamedObjectVisitorEx visitor) {
return visitor.visit(this);
}
@Override
public O accept(@Nonnull OWLObjectVisitorEx visitor) {
return visitor.visit(this);
}
// Utility methods for getting/setting various values in maps and sets
@Override
public boolean equals(Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof OWLOntology)) {
return false;
}
OWLOntology other = (OWLOntology) obj;
return ontologyID.equals(other.getOntologyID());
}
@Override
public int hashCode() {
return ontologyID.hashCode();
}
private class OWLEntityReferenceChecker implements OWLEntityVisitor,
Serializable {
OWLEntityReferenceChecker() {}
private static final long serialVersionUID = 40000L;
private boolean ref;
public boolean containsReference(@Nonnull OWLEntity entity) {
ref = false;
entity.accept(this);
return ref;
}
@Override
public void visit(@Nonnull OWLClass cls) {
ref = OWLImmutableOntologyImpl.this.ints
.containsClassInSignature(cls);
}
@Override
public void visit(@Nonnull OWLDatatype datatype) {
ref = OWLImmutableOntologyImpl.this.ints
.containsDatatypeInSignature(datatype);
}
@Override
public void visit(@Nonnull OWLNamedIndividual individual) {
ref = OWLImmutableOntologyImpl.this.ints
.containsIndividualInSignature(individual);
}
@Override
public void visit(@Nonnull OWLDataProperty property) {
ref = OWLImmutableOntologyImpl.this.ints
.containsDataPropertyInSignature(property);
}
@Override
public void visit(@Nonnull OWLObjectProperty property) {
ref = OWLImmutableOntologyImpl.this.ints
.containsObjectPropertyInSignature(property);
}
@Override
public void visit(@Nonnull OWLAnnotationProperty property) {
ref = OWLImmutableOntologyImpl.this.ints
.containsAnnotationPropertyInSignature(property);
}
}
@Override
public Set getAxioms(OWLClass cls,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return asSet(ints.get(OWLClass.class, OWLClassAxiom.class).get()
.getValues(cls));
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(cls, EXCLUDED));
}
return result;
}
@Override
public Set
getAxioms(OWLObjectPropertyExpression property,
Imports includeImportsClosure) {
Set result = createSet(50);
if (includeImportsClosure == EXCLUDED) {
result.addAll(getAsymmetricObjectPropertyAxioms(property));
result.addAll(getReflexiveObjectPropertyAxioms(property));
result.addAll(getSymmetricObjectPropertyAxioms(property));
result.addAll(getIrreflexiveObjectPropertyAxioms(property));
result.addAll(getTransitiveObjectPropertyAxioms(property));
result.addAll(getInverseFunctionalObjectPropertyAxioms(property));
result.addAll(getFunctionalObjectPropertyAxioms(property));
result.addAll(getInverseObjectPropertyAxioms(property));
result.addAll(getObjectPropertyDomainAxioms(property));
result.addAll(getEquivalentObjectPropertiesAxioms(property));
result.addAll(getDisjointObjectPropertiesAxioms(property));
result.addAll(getObjectPropertyRangeAxioms(property));
result.addAll(getObjectSubPropertyAxiomsForSubProperty(property));
} else {
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(property, EXCLUDED));
}
}
return result;
}
@Override
public Set getAxioms(OWLAnnotationProperty property,
Imports includeImportsClosure) {
Set result = createSet();
if (includeImportsClosure == EXCLUDED) {
for (OWLSubAnnotationPropertyOfAxiom ax : getAxioms(AxiomType.SUB_ANNOTATION_PROPERTY_OF)) {
if (ax.getSubProperty().equals(property)) {
result.add(ax);
}
}
for (OWLAnnotationPropertyRangeAxiom ax : getAxioms(AxiomType.ANNOTATION_PROPERTY_RANGE)) {
if (ax.getProperty().equals(property)) {
result.add(ax);
}
}
for (OWLAnnotationPropertyDomainAxiom ax : getAxioms(AxiomType.ANNOTATION_PROPERTY_DOMAIN)) {
if (ax.getProperty().equals(property)) {
result.add(ax);
}
}
} else {
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(property, EXCLUDED));
}
}
return result;
}
@Override
public Set getAxioms(OWLDataProperty property,
Imports includeImportsClosure) {
Set result = createSet();
if (includeImportsClosure == EXCLUDED) {
result.addAll(getDataPropertyDomainAxioms(property));
result.addAll(getEquivalentDataPropertiesAxioms(property));
result.addAll(getDisjointDataPropertiesAxioms(property));
result.addAll(getDataPropertyRangeAxioms(property));
result.addAll(getFunctionalDataPropertyAxioms(property));
result.addAll(getDataSubPropertyAxiomsForSubProperty(property));
} else {
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(property, EXCLUDED));
}
}
return result;
}
@Override
public Set getAxioms(OWLIndividual individual,
Imports includeImportsClosure) {
Set result = createSet();
if (includeImportsClosure == EXCLUDED) {
result.addAll(getClassAssertionAxioms(individual));
result.addAll(getObjectPropertyAssertionAxioms(individual));
result.addAll(getDataPropertyAssertionAxioms(individual));
result.addAll(getNegativeObjectPropertyAssertionAxioms(individual));
result.addAll(getNegativeDataPropertyAssertionAxioms(individual));
result.addAll(getSameIndividualAxioms(individual));
result.addAll(getDifferentIndividualAxioms(individual));
} else {
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(individual, EXCLUDED));
}
}
return result;
}
@Override
public Set getAxioms(OWLDatatype datatype,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return getDatatypeDefinitions(datatype);
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(datatype, EXCLUDED));
}
return result;
}
@Override
public Set getReferencingAxioms(OWLPrimitive owlEntity) {
return getReferencingAxioms(owlEntity, EXCLUDED);
}
@Override
public Set getReferencingAxioms(OWLPrimitive owlEntity,
boolean includeImports) {
return getReferencingAxioms(owlEntity,
Imports.fromBoolean(includeImports));
}
@Override
public Set getReferencingAxioms(OWLPrimitive owlEntity,
Imports includeImportsClosure) {
if (owlEntity instanceof OWLEntity) {
if (includeImportsClosure == EXCLUDED) {
return asSet(ints.getReferencingAxioms((OWLEntity) owlEntity));
}
Set result = createSet();
for (OWLOntology ont : getImportsClosure()) {
result.addAll(ont.getReferencingAxioms(owlEntity, EXCLUDED));
}
return result;
} else if (owlEntity instanceof OWLAnonymousIndividual) {
return asSet(ints.get(OWLAnonymousIndividual.class, OWLAxiom.class)
.get().getValues((OWLAnonymousIndividual) owlEntity));
} else if (owlEntity instanceof IRI) {
Set axioms = new HashSet<>();
// axioms referring entities with this IRI, data property assertions
// with IRI as subject, annotations with IRI as subject or object.
Set entities = getEntitiesInSignature((IRI) owlEntity,
includeImportsClosure);
for (OWLEntity e : entities) {
assert e != null;
axioms.addAll(getReferencingAxioms(e, includeImportsClosure));
}
for (OWLDataPropertyAssertionAxiom ax : getAxioms(AxiomType.DATA_PROPERTY_ASSERTION)) {
if (ax.getObject().getDatatype().getIRI()
.equals(OWL2Datatype.XSD_ANY_URI.getIRI())) {
if (ax.getObject().getLiteral()
.equals(owlEntity.toString())) {
axioms.add(ax);
}
}
}
for (OWLAnnotationAssertionAxiom ax : getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
if (ax.getSubject().equals(owlEntity)) {
axioms.add(ax);
} else if (ax.getValue().asLiteral().isPresent()) {
Optional lit = ax.getValue().asLiteral();
if (lit.get().getDatatype().getIRI()
.equals(OWL2Datatype.XSD_ANY_URI.getIRI())) {
if (lit.get().getLiteral().equals(owlEntity.toString())) {
axioms.add(ax);
}
}
}
}
return axioms;
} else if (owlEntity instanceof OWLLiteral) {
Set axioms = new HashSet<>();
for (OWLDataPropertyAssertionAxiom ax : getAxioms(AxiomType.DATA_PROPERTY_ASSERTION)) {
if (ax.getObject().getDatatype().getIRI()
.equals(OWL2Datatype.XSD_ANY_URI.getIRI())) {
if (ax.getObject().equals(owlEntity)) {
axioms.add(ax);
}
}
}
for (OWLAnnotationAssertionAxiom ax : getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
if (owlEntity.equals(ax.getValue().asLiteral().orNull())) {
axioms.add(ax);
}
}
return axioms;
}
return CollectionFactory.emptySet();
}
// OWLAxiomIndex
@SuppressWarnings("null")
@Override
public Set getAxioms(@Nonnull Class type,
@Nonnull OWLObject entity, Imports includeImports,
Navigation forSubPosition) {
if (includeImports == EXCLUDED) {
return getAxioms(type, entity.getClass(), entity, EXCLUDED,
forSubPosition);
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(type, entity, EXCLUDED, forSubPosition));
}
return result;
}
@Override
@SuppressWarnings("unchecked")
public Set getAxioms(@Nonnull Class type,
@Nonnull Class explicitClass,
@Nonnull OWLObject entity, @Nonnull Imports includeImports,
@Nonnull Navigation forSubPosition) {
if (includeImports == EXCLUDED) {
Optional> optional = ints.get(
(Class) explicitClass, type, forSubPosition);
if (optional.isPresent()) {
return asSet(optional.get().getValues(entity));
}
Set toReturn = new HashSet<>();
for (A ax : getAxioms(AxiomType.getTypeForClass(type))) {
if (ax.getSignature().contains(entity)) {
toReturn.add(ax);
}
}
return toReturn;
}
Set result = createSet();
for (OWLOntology o : getImportsClosure()) {
result.addAll(o.getAxioms(type, entity, EXCLUDED, forSubPosition));
}
return result;
}
@Nonnull
@SuppressWarnings("unchecked")
@Override
public Collection filterAxioms(
@Nonnull OWLAxiomSearchFilter filter, @Nonnull Object key,
Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return (Collection) ints.filterAxioms(filter, key);
}
// iterating over the import closure; using a set because there might be
// duplicate axioms
Set toReturn = new HashSet<>();
for (OWLOntology o : getImportsClosure()) {
toReturn.addAll((Collection) o.filterAxioms(filter, key,
EXCLUDED));
}
return toReturn;
}
@Override
public boolean contains(@Nonnull OWLAxiomSearchFilter filter,
@Nonnull Object key, Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.contains(filter, key);
}
for (OWLOntology o : getImportsClosure()) {
if (o.contains(filter, key, EXCLUDED)) {
return true;
}
}
return false;
}
@Override
public Set getAxioms(OWLClass cls) {
return getAxioms(cls, false);
}
@Override
public Set getAxioms(
OWLObjectPropertyExpression property) {
return getAxioms(property, EXCLUDED);
}
@Override
public Set getAxioms(OWLDataProperty property) {
return getAxioms(property, EXCLUDED);
}
@Override
public Set getAxioms(OWLIndividual individual) {
return getAxioms(individual, EXCLUDED);
}
@Override
public Set getAxioms(OWLAnnotationProperty property) {
return getAxioms(property, EXCLUDED);
}
@Override
public Set getAxioms(OWLDatatype datatype) {
return getAxioms(datatype, EXCLUDED);
}
@Override
public Set getAxioms(OWLClass cls,
boolean includeImportsClosure) {
return getAxioms(cls, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set
getAxioms(OWLObjectPropertyExpression property,
boolean includeImportsClosure) {
return getAxioms(property, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxioms(OWLDataProperty property,
boolean includeImportsClosure) {
return getAxioms(property, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxioms(OWLIndividual individual,
boolean includeImportsClosure) {
return getAxioms(individual, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxioms(OWLAnnotationProperty property,
boolean includeImportsClosure) {
return getAxioms(property, Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getAxioms(OWLDatatype datatype,
boolean includeImportsClosure) {
return getAxioms(datatype, Imports.fromBoolean(includeImportsClosure));
}
@Override
public void saveOntology() throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this);
}
@Override
public void saveOntology(IRI documentIRI)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, documentIRI);
}
@Override
public void saveOntology(OutputStream outputStream)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, outputStream);
}
@Override
public void saveOntology(OWLDocumentFormat ontologyFormat)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, ontologyFormat);
}
@Override
public void saveOntology(OWLDocumentFormat ontologyFormat, IRI documentIRI)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, ontologyFormat, documentIRI);
}
@Override
public void saveOntology(OWLDocumentFormat ontologyFormat,
OutputStream outputStream) throws OWLOntologyStorageException {
getOWLOntologyManager()
.saveOntology(this, ontologyFormat, outputStream);
}
@Override
public void saveOntology(OWLOntologyDocumentTarget documentTarget)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, documentTarget);
}
@Override
public void saveOntology(OWLDocumentFormat ontologyFormat,
OWLOntologyDocumentTarget documentTarget)
throws OWLOntologyStorageException {
getOWLOntologyManager().saveOntology(this, ontologyFormat,
documentTarget);
}
@Override
public boolean containsDatatypeInSignature(IRI owlDatatypeIRI) {
return containsDatatypeInSignature(owlDatatypeIRI, EXCLUDED);
}
@Override
public boolean containsEntityInSignature(IRI entityIRI) {
return containsEntityInSignature(entityIRI, EXCLUDED);
}
@Override
public boolean containsClassInSignature(IRI owlClassIRI) {
return containsClassInSignature(owlClassIRI, EXCLUDED);
}
@Override
public boolean containsObjectPropertyInSignature(IRI owlObjectPropertyIRI) {
return containsObjectPropertyInSignature(owlObjectPropertyIRI, EXCLUDED);
}
@Override
public boolean containsDataPropertyInSignature(IRI owlDataPropertyIRI) {
return containsDataPropertyInSignature(owlDataPropertyIRI, EXCLUDED);
}
@Override
public boolean containsAnnotationPropertyInSignature(
IRI owlAnnotationPropertyIRI) {
return containsAnnotationPropertyInSignature(owlAnnotationPropertyIRI,
EXCLUDED);
}
@Override
public boolean containsIndividualInSignature(IRI owlIndividualIRI) {
return containsIndividualInSignature(owlIndividualIRI, EXCLUDED);
}
@Override
public boolean containsReference(OWLEntity entity) {
return containsReference(entity, EXCLUDED);
}
@Override
public Set getClassesInSignature(boolean includeImportsClosure) {
return getClassesInSignature(Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getObjectPropertiesInSignature(
boolean includeImportsClosure) {
return getObjectPropertiesInSignature(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public Set getDataPropertiesInSignature(
boolean includeImportsClosure) {
return getDataPropertiesInSignature(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public Set getIndividualsInSignature(
boolean includeImportsClosure) {
return getIndividualsInSignature(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public Set getReferencedAnonymousIndividuals(
boolean includeImportsClosure) {
return getReferencedAnonymousIndividuals(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public Set getDatatypesInSignature(
boolean includeImportsClosure) {
return getDatatypesInSignature(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public Set getAnnotationPropertiesInSignature(
boolean includeImportsClosure) {
return getAnnotationPropertiesInSignature(Imports
.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsEntityInSignature(OWLEntity owlEntity,
boolean includeImportsClosure) {
return containsEntityInSignature(owlEntity,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsEntityInSignature(IRI entityIRI,
boolean includeImportsClosure) {
return containsEntityInSignature(entityIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsClassInSignature(IRI owlClassIRI,
boolean includeImportsClosure) {
return containsClassInSignature(owlClassIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsObjectPropertyInSignature(IRI owlObjectPropertyIRI,
boolean includeImportsClosure) {
return containsObjectPropertyInSignature(owlObjectPropertyIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsDataPropertyInSignature(IRI owlDataPropertyIRI,
boolean includeImportsClosure) {
return containsDataPropertyInSignature(owlDataPropertyIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsAnnotationPropertyInSignature(
IRI owlAnnotationPropertyIRI, boolean includeImportsClosure) {
return containsAnnotationPropertyInSignature(owlAnnotationPropertyIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsDatatypeInSignature(IRI owlDatatypeIRI,
boolean includeImportsClosure) {
return containsDatatypeInSignature(owlDatatypeIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsIndividualInSignature(IRI owlIndividualIRI,
boolean includeImportsClosure) {
return containsIndividualInSignature(owlIndividualIRI,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public Set getEntitiesInSignature(IRI iri,
boolean includeImportsClosure) {
return getEntitiesInSignature(iri,
Imports.fromBoolean(includeImportsClosure));
}
@Override
public boolean containsReference(OWLEntity entity,
boolean includeImportsClosure) {
return containsReference(entity,
Imports.fromBoolean(includeImportsClosure));
}
}
