Examples of org.semanticweb.owlapi.model.OWLAnnotationValue

org.semanticweb.owlapi.model.OWLAnnotationValue
A marker interface for annotation values, which can either be an IRI (URI), Literal or Anonymous Individual, with visitor methods. @see org.semanticweb.owlapi.model.IRI @see org.semanticweb.owlapi.model.OWLLiteral @see org.semanticweb.owlapi.model.OWLAnonymousIndividual @author Matthew Horridge, The University of Manchester, InformationManagement Group @since 3.0.0

    protected void postProcess(@Nonnull OWLOntology ontology) {
        IRI pIRI = null;
        for (OWLAnnotation ann : ontology.getAnnotations()) {
            if (Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation
                    .sameIRI(ann.getProperty())) {
                OWLAnnotationValue v = ann.getValue();
                if (v instanceof OWLLiteral) {
                    String rel = ((OWLLiteral) v).getLiteral();
                    pIRI = oboIdToIRI(rel);
                } else {
                    pIRI = (IRI) v;

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                // TODO: Throw Exceptions
                LOG.error("Cannot translate: {}", clause);
            } else if (values.size() == 2) {
                // property_value(Rel-ID Entity-ID Qualifiers)
                OWLAnnotationProperty prop = trAnnotationProp((String) v);
                OWLAnnotationValue value = trAnnotationProp(v2.toString())
                        .getIRI();
                OWLAnnotation ontAnn = fac.getOWLAnnotation(prop, value,
                        annotations);
                AddOntologyAnnotation addAnn = new AddOntologyAnnotation(
                        getOwlOntology(), ontAnn);
                apply(addAnn);
            } else if (values.size() == 3) {
                // property_value(Rel-ID Value XSD-Type Qualifiers)
                Iterator<Object> it = clause.getValues().iterator();
                it.next();
                it.next();
                String v3String = (String) it.next();
                IRI valueIRI;
                if (v3String.startsWith("xsd:")) {
                    valueIRI = IRI.create(Namespaces.XSD
                            + v3String.substring(4));
                } else {
                    valueIRI = IRI.create(v3String);
                }
                OWLAnnotationValue value = fac.getOWLLiteral((String) v2,
                        OWL2Datatype.getDatatype(valueIRI));
                OWLAnnotationProperty prop = trAnnotationProp((String) v);
                OWLAnnotation ontAnn = fac.getOWLAnnotation(prop, value,
                        annotations);
                AddOntologyAnnotation addAnn = new AddOntologyAnnotation(

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                    valueIRI = IRI.create(Namespaces.XSD
                            + v3String.substring(4));
                } else {
                    valueIRI = IRI.create(v3String);
                }
                OWLAnnotationValue value = fac.getOWLLiteral((String) v2,
                        OWL2Datatype.getDatatype(valueIRI));
                ax = fac.getOWLAnnotationAssertionAxiom(
                        trAnnotationProp((String) v), sub, value, annotations);
            } else {
                LOG.error("Cannot translate: {}", clause);

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        for (OWLAnnotation ann : getOWLOntology().getAnnotations()) {
            if (ann.getProperty()
                    .getIRI()
                    .equals(Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation
                            .getIRI())) {
                OWLAnnotationValue v = ann.getValue();
                if (v instanceof OWLLiteral) {
                    viewRel = ((OWLLiteral) v).getLiteral();
                } else {
                    viewRel = getIdentifier((IRI) v);
                }

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            Set<OWLAnnotation> unprocessedQualifiers = new HashSet<>(qualifiers);
            if (tag == OboFormatTag.TAG_DEF) {
                for (OWLAnnotation aan : qualifiers) {
                    String propId = owlObjectToTag(aan.getProperty());
                    if ("xref".equals(propId)) {
                        OWLAnnotationValue v = aan.getValue();
                        String xrefValue;
                        if (v instanceof IRI) {
                            xrefValue = v.toString();
                        } else {
                            xrefValue = ((OWLLiteral) v).getLiteral();
                        }
                        Xref xref = new Xref(xrefValue);
                        clause.addXref(xref);
                        unprocessedQualifiers.remove(aan);
                    }
                }
            } else if (tag == OboFormatTag.TAG_XREF) {
                Xref xref = new Xref(value);
                for (OWLAnnotation annotation : qualifiers) {
                    if (fac.getRDFSLabel().equals(annotation.getProperty())) {
                        OWLAnnotationValue owlAnnotationValue = annotation
                                .getValue();
                        if (owlAnnotationValue instanceof OWLLiteral) {
                            unprocessedQualifiers.remove(annotation);
                            String xrefAnnotation = ((OWLLiteral) owlAnnotationValue)
                                    .getLiteral();

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        String type = null;
        clause.setXrefs(new ArrayList<Xref>());
        for (OWLAnnotation aan : qualifiers) {
            String propId = owlObjectToTag(aan.getProperty());
            if (OboFormatTag.TAG_XREF.getTag().equals(propId)) {
                OWLAnnotationValue v = aan.getValue();
                String xrefValue;
                if (v instanceof IRI) {
                    xrefValue = v.toString();
                } else {
                    xrefValue = ((OWLLiteral) v).getLiteral();
                }
                Xref xref = new Xref(xrefValue);
                clause.addXref(xref);

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                String propId = getIdentifierFromObject(ax.getProperty()
                        .getIRI(), ont);
                // see BFOROXrefTest
                // 5.9.3. Special Rules for Relations
                if (propId.equals("shorthand")) {
                    OWLAnnotationValue value = ax.getValue();
                    if (value instanceof OWLLiteral) {
                        return ((OWLLiteral) value).getLiteral();
                    }
                    throw new UntranslatableAxiomException(
                            "Untranslatable axiom, expected literal value, but was: "

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        IRI getIRIByLabel(@Nonnull String label) {
            for (OWLOntology o : ontologies) {
                Set<OWLAnnotationAssertionAxiom> aas = o
                        .getAxioms(AxiomType.ANNOTATION_ASSERTION);
                for (OWLAnnotationAssertionAxiom aa : aas) {
                    OWLAnnotationValue v = aa.getValue();
                    OWLAnnotationProperty property = aa.getProperty();
                    if (isMatchingLabel(label, v, property)) {
                        OWLAnnotationSubject obj = aa.getSubject();
                        if (obj instanceof IRI) {
                            return (IRI) obj;

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        @Override
        public String getPrefixIRI(IRI iri) {
            for (OWLAnnotationAssertionAxiom annotation : ontology
                    .getAnnotationAssertionAxioms(iri)) {
                if (annotation.getProperty().isLabel()) {
                    OWLAnnotationValue value = annotation.getValue();
                    if (value instanceof OWLLiteral) {
                        return '<' + ((OWLLiteral) value).getLiteral() + '>';
                    }
                }
            }

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                    Set<OWLAnnotation> annotations = axiom.getAnnotations();
                    for (OWLAnnotation owlAnnotation : annotations) {
                        OWLAnnotationProperty property = owlAnnotation
                                .getProperty();
                        if (property.getIRI().equals(isInferredIRI)) {
                            OWLAnnotationValue value = owlAnnotation.getValue();
                            if (value instanceof OWLLiteral) {
                                OWLLiteral literal = (OWLLiteral) value;
                                assertEquals("true", literal.getLiteral());
                            } else {
                                fail("The value is not the expected type, expected OWLiteral but was: "
                                        + value.getClass().getName());
                            }
                            hasAnnotation = true;
                        }
                    }
                }

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