/** * @param e entity * @param ontology the ontology to use * @return the annotation assertion axioms about this entity in the provided ontology */ public static Stream<OWLAnnotationAssertionAxiom> getAnnotationAssertionAxioms( OWLAnnotationSubject e, OWLOntology ontology) { return ontology.annotationAssertionAxioms(e); }
/** * @param e entity * @param ontology the ontology to use * @return the annotation assertion axioms about this entity in the provided ontology */ public static Stream<OWLAnnotationAssertionAxiom> getAnnotationAssertionAxioms( OWLAnnotationSubject e, OWLOntology ontology) { return ontology.annotationAssertionAxioms(e); }
@Override public Stream<OWLAnnotationAssertionAxiom> annotationAssertionAxioms( OWLAnnotationSubject entity) { return withReadLock(() -> delegate.annotationAssertionAxioms(entity)); }
/** * Writes of the annotation for the specified entity. * * @param entity The entity * @param alreadyWrittenAxioms already written axioms, to be updated with the newly written * axioms */ protected void writeAnnotations(OWLEntity entity, Set<OWLAxiom> alreadyWrittenAxioms) { ont.annotationAssertionAxioms(entity.getIRI()).sorted().filter(alreadyWrittenAxioms::add) .forEach(this::acceptAndReturn); }
@Override public Stream<OWLAnnotationAssertionAxiom> annotationAssertionAxioms( OWLAnnotationSubject entity) { return withReadLock(() -> delegate.annotationAssertionAxioms(entity)); }
@Override public Stream<OWLAnnotationAssertionAxiom> annotationAssertionAxioms( OWLAnnotationSubject entity) { return withReadLock(() -> delegate.annotationAssertionAxioms(entity)); }
/** * Writes of the annotation for the specified entity. * * @param entity The entity * @param alreadyWrittenAxioms already written axioms, to be updated with the newly written * axioms */ protected void writeAnnotations(OWLEntity entity, Set<OWLAxiom> alreadyWrittenAxioms) { ont.annotationAssertionAxioms(entity.getIRI()).sorted().filter(alreadyWrittenAxioms::add) .forEach(this::acceptAndReturn); }
/** * Writes of the annotation for the specified entity. * * @param entity The entity * @param alreadyWrittenAxioms already written axioms, to be updated with the newly written * axioms */ protected void writeAnnotations(OWLEntity entity, Set<OWLAxiom> alreadyWrittenAxioms) { ont.annotationAssertionAxioms(entity.getIRI()).sorted().filter(alreadyWrittenAxioms::add) .forEach(this::acceptAndReturn); }
private void processIfAnonymous(OWLIndividual ind, @Nullable OWLAxiom root) { if (!currentIndividuals.contains(ind)) { currentIndividuals.add(ind); if (ind.isAnonymous()) { ont.axioms(ind).sorted().filter(ax -> root == null || !root.equals(ax)) .forEach(ax -> ax.accept(this)); ont.annotationAssertionAxioms(ind.asOWLAnonymousIndividual()).sorted() .forEach(ax -> ax.accept(this)); } currentIndividuals.remove(ind); } }
private void processIfAnonymous(OWLIndividual ind) { if (!currentIndividuals.contains(ind)) { currentIndividuals.add(ind); if (ind.isAnonymous()) { ont.axioms(ind).sorted().forEach(ax -> ax.accept(this)); ont.annotationAssertionAxioms(ind.asOWLAnonymousIndividual()).sorted() .forEach(ax -> ax.accept(this)); } currentIndividuals.remove(ind); } }
private void processIfAnonymous(OWLIndividual ind) { if (!currentIndividuals.contains(ind)) { currentIndividuals.add(ind); if (ind.isAnonymous()) { ont.axioms(ind).sorted().forEach(ax -> ax.accept(this)); ont.annotationAssertionAxioms(ind.asOWLAnonymousIndividual()).sorted() .forEach(ax -> ax.accept(this)); } currentIndividuals.remove(ind); } }
private void generateChanges(OWLEntity entity) { checkNotNull(entity, "entity cannot be null"); for (OWLOntology ont : ontologies) { ont.referencingAxioms(entity).forEach(ax -> changes.add(new RemoveAxiom(ont, ax))); ont.annotationAssertionAxioms(entity.getIRI()) .forEach(ax -> changes.add(new RemoveAxiom(ont, ax))); } }
private void generateChanges(OWLEntity entity) { checkNotNull(entity, "entity cannot be null"); for (OWLOntology ont : ontologies) { ont.referencingAxioms(entity).forEach(ax -> changes.add(new RemoveAxiom(ont, ax))); ont.annotationAssertionAxioms(entity.getIRI()) .forEach(ax -> changes.add(new RemoveAxiom(ont, ax))); } }
protected void writeEntity(OWLEntity entity, Set<OWLAxiom> alreadyWrittenAxioms) { writeEntity2(entity, "", asList(getUnsortedAxiomsForEntity(entity).sorted()), asList(ont.annotationAssertionAxioms(entity.getIRI()).sorted()), alreadyWrittenAxioms); }
private boolean isMetadataTag(OWLAnnotationProperty p) { final IRI metadataTagIRI = IRI .create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, OboFormatTag.TAG_IS_METADATA_TAG .getTag()); return owlOntology.annotationAssertionAxioms(p.getIRI()) .anyMatch(ax -> metadataTagIRI.equals(ax.getProperty() .getIRI())); }
private boolean isMetadataTag(OWLAnnotationProperty p) { final IRI metadataTagIRI = IRI .create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, OboFormatTag.TAG_IS_METADATA_TAG .getTag()); return owlOntology.annotationAssertionAxioms(p.getIRI()) .anyMatch(ax -> metadataTagIRI.equals(ax.getProperty() .getIRI())); }
private boolean isMetadataTag(OWLAnnotationProperty p) { final IRI metadataTagIRI = IRI .create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, OboFormatTag.TAG_IS_METADATA_TAG .getTag()); return owlOntology.annotationAssertionAxioms(p.getIRI()) .anyMatch(ax -> metadataTagIRI.equals(ax.getProperty() .getIRI())); }
protected void renderIRI(IRI iri) { beginObject(); createGraph(ontology.annotationAssertionAxioms(iri)); render(new RDFResourceIRI(iri), true); renderAnonRoots(); endObject(); }
protected void renderIRI(IRI iri) { beginObject(); createGraph(ontology.annotationAssertionAxioms(iri)); render(new RDFResourceIRI(iri), true); renderAnonRoots(); endObject(); }
protected void renderIRI(IRI iri) { beginObject(); createGraph(ontology.annotationAssertionAxioms(iri)); render(new RDFResourceIRI(iri), true); renderAnonRoots(); endObject(); }