Examples of org.semanticweb.owlapi.model.OWLAnnotation

org.semanticweb.owlapi.model.OWLAnnotation
Annotations are used in the various types of annotation axioms, which bind annotations to their subjects (i.e. axioms or declarations).
An annotation is equal to another annotation if both objects have equal annotation URIs and have equal annotation values. @author Matthew Horridge, The University Of Manchester, Bio-HealthInformatics Group @since 2.0.0

    @Nonnull
    private OWLAnnotationAssertionAxiom convertToAnnotation(
            @Nonnull OWLNamedIndividual ind,
            @Nonnull OWLDataPropertyAssertionAxiom ax) {
        OWLDataFactory df = getDataFactory();
        OWLAnnotation anno = df.getOWLAnnotation(
                df.getOWLAnnotationProperty(ax.getProperty()
                        .asOWLDataProperty().getIRI()), ax.getObject());
        return df.getOWLAnnotationAssertionAxiom(ind.getIRI(), anno);
    }

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        if (xrefs != null) {
            StringTokenizer tokenizer = new StringTokenizer(xrefs, ",");
            while (tokenizer.hasMoreTokens()) {
                String xrefValue = tokenizer.nextToken();
                assert xrefValue != null;
                OWLAnnotation xrefAnnotation = getConsumer().parseXRef(
                        xrefValue);
                annotations.add(xrefAnnotation);
            }
        }
        return annotations;

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    public LegacyEntityAnnotationElementHandler(OWLXMLParserHandler handler) {
        super(handler);
    }


    protected OWLAxiom createAxiom() throws OWLXMLParserException {
        OWLAnnotation anno = annotation;
        annotation = null;
        entity = null;
        return getOWLDataFactory().getOWLAnnotationAssertionAxiom(anno.getProperty(), entity.getIRI(), anno.getValue());
    }

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          OWLAxiom removeax = factory.getOWLAnnotationAssertionAxiom(
              (OWLAnnotationSubject) annind, ann);
          manager.applyChange(new RemoveAxiom(ontology, removeax));
        }
        String[] array = (String[]) urisandvals.get(keys[i]);
        OWLAnnotation newann = factory.getOWLAnnotation(factory
            .getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL
                .getIRI()), factory.getOWLStringLiteral(
            array[0], "en"));
        OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(
            annind.getIRI(), newann);

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      OWLAnnotationSubject annsub = annind.getIRI();
      OWLAxiom removeax = factory.getOWLAnnotationAssertionAxiom(annsub,
          ann);
      manager.applyChange(new RemoveAxiom(ontology, removeax));
    }
    OWLAnnotation newann = factory.getOWLAnnotation(
        factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL
            .getIRI()), factory.getOWLStringLiteral(value, "en"));
    OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(annind.getIRI(),
        newann);
    manager.applyChange(new AddAxiom(ontology, ax));

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    for (OWLAnnotation ann : anns) {
      OWLAnnotationSubject annsub = ent.getIRI();
      OWLAxiom removeax = factory.getOWLAnnotationAssertionAxiom(annsub, ann);
      manager.applyChange(new RemoveAxiom(ontology, removeax));
    }
    OWLAnnotation newann = factory.getOWLAnnotation(
        factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), factory.getOWLStringLiteral(value, "en"));
    OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(ent.getIRI(), newann);
    manager.applyChange(new AddAxiom(ontology, ax));
//    SBMLreactionCollector.logfilewriter.println("RDF label for " + ent.toString() + ": "
//        + value);

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        OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
        OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
        OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
        OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
        OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
        OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
        OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
        OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
        OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
        OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls); // Classe

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        OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
        OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
        OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
        OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
        OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
        OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
        OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
        OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
        OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
        OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls); // Classe

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                annoAnnos = parseAnnotationList();
            }
            else {
                annoAnnos = Collections.emptySet();
            }
            OWLAnnotation anno = parseAnnotation();
            if (anno != null) {
                anno = anno.getAnnotatedAnnotation(annoAnnos);
                annos.add(anno);
            }
            sep = peekToken();
            if (sep.equals(",")) {
                consumeToken();

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    private OWLAnnotation parseAnnotation() throws ParserException {
        OWLAnnotationProperty annoProp = parseAnnotationProperty();
        String obj = peekToken();
        OWLAnnotation anno = null;
        if (isIndividualName(obj) || isClassName(obj) || isObjectPropertyName(obj) || isDataPropertyName(obj)) {
            consumeToken();
            OWLAnnotationValue value;
            if(obj.startsWith("_:")) {
                value = dataFactory.getOWLAnonymousIndividual(obj);

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