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

            } 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(
                        getOwlOntology(), ontAnn);
                apply(addAnn);
            } else {

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     *        the annotations
     */
    protected void addOntologyAnnotation(@Nonnull OWLAnnotationProperty ap,
            @Nonnull OWLAnnotationValue v,
            @Nonnull Set<OWLAnnotation> annotations) {
        OWLAnnotation ontAnn = fac.getOWLAnnotation(ap, v, annotations);
        AddOntologyAnnotation addAnn = new AddOntologyAnnotation(
                getOwlOntology(), ontAnn);
        apply(addAnn);
    }

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            chain.add(trObjectProp(v));
            ax = fac.getOWLSubPropertyChainOfAxiom(chain, p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_HOLDS_OVER_CHAIN
                || tagConstant == OboFormatTag.TAG_EQUIVALENT_TO_CHAIN) {
            if (tagConstant == OboFormatTag.TAG_EQUIVALENT_TO_CHAIN) {
                OWLAnnotation ann = fac.getOWLAnnotation(
                        trAnnotationProp(IRI_PROP_ISREVERSIBLEPROPERTYCHAIN),
                        trLiteral("true"));
                annotations.add(ann);
                // isReversiblePropertyChain
            }

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            Object[] values = clause.getValues().toArray();
            String synType;
            if (values.length > 1) {
                synType = values[1].toString();
                if (values.length > 2) {
                    OWLAnnotation ann = fac
                            .getOWLAnnotation(
                                    trTagToAnnotationProp(OboFormatTag.TAG_HAS_SYNONYM_TYPE
                                            .getTag()),
                                    trAnnotationProp(values[2].toString())
                                            .getIRI());
                    annotations.add(ann);
                }
            } else {
                LOG.warn(
                        "Assume 'RELATED'for missing scope in synonym clause: {}",
                        clause);
                // we make allowances for obof1.0, where the synonym scope is
                // optional
                synType = OboFormatTag.TAG_RELATED.getTag();
            }
            ax = fac.getOWLAnnotationAssertionAxiom(trSynonymType(synType),
                    sub, trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_XREF) {
            Xref xref = (Xref) clause.getValue();
            String xrefAnnotation = xref.getAnnotation();
            if (xrefAnnotation != null) {
                OWLAnnotation owlAnnotation = fac.getOWLAnnotation(
                        fac.getRDFSLabel(), fac.getOWLLiteral(xrefAnnotation));
                annotations.add(owlAnnotation);
            }
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag),
                    sub, trLiteral(clause.getValue()), annotations);

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        Collection<Xref> xrefs = clause.getXrefs();
        for (Xref x : xrefs) {
            if (x.getIdref() != null && !x.getIdref().isEmpty()) {
                OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_XREF
                        .getTag());
                OWLAnnotation ann = fac.getOWLAnnotation(ap, trLiteral(x));
                anns.add(ann);
            }
        }
        Collection<QualifierValue> qvs = clause.getQualifierValues();
        for (QualifierValue qv : qvs) {
            String qTag = qv.getQualifier();
            if (SKIPPED_QUALIFIERS.contains(qTag)) {
                continue;
            }
            OWLAnnotationProperty ap = trTagToAnnotationProp(qTag);
            OWLAnnotation ann = fac.getOWLAnnotation(ap,
                    trLiteral(qv.getValue()));
            anns.add(ann);
        }
    }

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        String sep = COMMA.keyword();
        Set<OWLAnnotation> annos = new HashSet<>();
        while (COMMA.matches(sep)) {
            potentialKeywords.clear();
            Set<OWLAnnotation> annotations = parseAnnotations();
            OWLAnnotation anno = parseAnnotation();
            anno = anno.getAnnotatedAnnotation(annotations);
            annos.add(anno);
            sep = peekToken();
            if (COMMA.matches(sep)) {
                consumeToken();
            }

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    @Nonnull
    protected OWLAnnotation parseAnnotation() {
        OWLAnnotationProperty annoProp = parseAnnotationProperty();
        String obj = peekToken();
        OWLAnnotation anno = null;
        if (isIndividualName(obj) || isClassName(obj)
                || isObjectPropertyName(obj) || isDataPropertyName(obj)) {
            consumeToken();
            OWLAnnotationValue value;
            if (obj.startsWith("_:")) {

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        throw new Error("Missing return statement in function");
    }


    final public void Ontology() throws ParseException, OWLParserException,
            UnloadableImportException {
        OWLAnnotation anno;
        OWLAxiom ax;
        OWLImportsDeclaration decl;
        int count = 0;
        IRI versionIRI = null;
        jj_consume_token(ONTOLOGY);

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    final public OWLAnnotation Annotation() throws ParseException {
        OWLAnnotationProperty prop;
        OWLAnnotationValue val;
        Set<OWLAnnotation> annos = null;
        OWLAnnotation anno = null;
        jj_consume_token(ANNOTATION);
        annos = new HashSet<OWLAnnotation>();
        jj_consume_token(OPENPAR);
        label_14: while (true) {
            switch (jj_ntk == -1 ? jj_ntk_f() : jj_ntk) {

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        throw new Error("Missing return statement in function");
    }


    final public Set<OWLAnnotation> AxiomAnnotationSet() throws ParseException {
        Set<OWLAnnotation> annos = null;
        OWLAnnotation anno;
        label_15: while (true) {
            switch (jj_ntk == -1 ? jj_ntk_f() : jj_ntk) {
                case ANNOTATION: {
                    ;
                    break;

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