Package org.semanticweb.owlapi.model

Examples of org.semanticweb.owlapi.model.OWLAnnotationProperty

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    private static Set<OWLAnnotationProperty> getProperties(
            @Nonnull OWLDataFactory factory, @Nonnull OboFormatTag... tags) {
        Set<OWLAnnotationProperty> set = new HashSet<>();
        for (OboFormatTag tag : tags) {
            IRI iri = OWLAPIObo2Owl.trTagToIRI(tag.getTag());
            OWLAnnotationProperty property = factory
                    .getOWLAnnotationProperty(iri);
            set.add(property);
        }
        return set;
    }
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            @Nonnull OWLOntologyManager manager)
            throws AnnotationCardinalityException {
        Set<OWLAnnotation> annotations = ontology.getAnnotations();
        Map<OWLAnnotationProperty, Set<OWLAnnotation>> groupedAnnotations = new HashMap<>();
        for (OWLAnnotation annotation : annotations) {
            OWLAnnotationProperty current = annotation.getProperty();
            if (properties.contains(current)) {
                Set<OWLAnnotation> set = groupedAnnotations.get(current);
                if (set == null) {
                    groupedAnnotations.put(current,
                            Collections.singleton(annotation));
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            throws AnnotationCardinalityException {
        Set<OWLAnnotationAssertionAxiom> axioms = ontology
                .getAnnotationAssertionAxioms(owlClass.getIRI());
        Map<OWLAnnotationProperty, Set<OWLAnnotationAssertionAxiom>> groupedAxioms = new HashMap<>();
        for (OWLAnnotationAssertionAxiom axiom : axioms) {
            OWLAnnotationProperty current = axiom.getProperty();
            if (properties.contains(current)) {
                Set<OWLAnnotationAssertionAxiom> set = groupedAxioms
                        .get(current);
                if (set == null) {
                    groupedAxioms.put(current, Collections.singleton(axiom));
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                // fac.getOWLImportsDeclaration(importedOntologyIRI);
                // manager.applyChange(new AddImport(baseOnt,
                // manager.getOWLDataFactory()
                // .getOWLImportsDeclaration(importedIRI)));
            } else if (tag == OboFormatTag.TAG_SUBSETDEF) {
                OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t);
                /*
                 * OWLClass cls = clsToDeclar.get(t); if(cls == null){ cls =
                 * trClass(trTagToIRI(t).toString());
                 * add(fac.getOWLDeclarationAxiom(cls)); clsToDeclar.put(t,
                 * cls); }
                 */
                for (Clause clause : headerFrame.getClauses(t)) {
                    OWLAnnotationProperty childAnnotProp = trAnnotationProp(clause
                            .getValue(String.class));
                    Set<OWLAnnotation> annotations = trAnnotations(clause);
                    add(fac.getOWLSubAnnotationPropertyOfAxiom(childAnnotProp,
                            parentAnnotProp, annotations));
                    // OWLIndividual indv= trIndividual(
                    // clause.getValue().toString() );
                    // add (fac.getOWLClassAssertionAxiom(cls, indv) );
                    OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_COMMENT
                            .getTag());
                    add(fac.getOWLAnnotationAssertionAxiom(ap,
                            childAnnotProp.getIRI(),
                            trLiteral(clause.getValue2())));
                }
            } else if (tag == OboFormatTag.TAG_SYNONYMTYPEDEF) {
                OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t);
                for (Clause clause : headerFrame.getClauses(t)) {
                    Object[] values = clause.getValues().toArray();
                    OWLAnnotationProperty childAnnotProp = trAnnotationProp(values[0]
                            .toString());
                    IRI childIRI = childAnnotProp.getIRI();
                    Set<OWLAnnotation> annotations = trAnnotations(clause);
                    add(fac.getOWLSubAnnotationPropertyOfAxiom(childAnnotProp,
                            parentAnnotProp, annotations));
                    OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_NAME
                            .getTag());
                    add(fac.getOWLAnnotationAssertionAxiom(ap, childIRI,
                            trLiteral(values[1])));
                    if (values.length > 2 && !values[2].toString().isEmpty()) {
                        ap = trTagToAnnotationProp(OboFormatTag.TAG_SCOPE
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            if (v == null) {
                // 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(
                        getOwlOntology(), ontAnn);
                apply(addAnn);
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            @Nonnull Frame typedefFrame) {
        Object tagValue = typedefFrame
                .getTagValue(OboFormatTag.TAG_IS_METADATA_TAG);
        if (Boolean.TRUE.equals(tagValue)) {
            String id = typedefFrame.getId();
            OWLAnnotationProperty p = trAnnotationProp(id);
            add(fac.getOWLDeclarationAxiom(p));
            // handle xrefs also for meta data tags
            String xid = translateShorthandIdToExpandedId(id);
            if (!id.equals(xid)) {
                OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(
                        trTagToAnnotationProp("shorthand"), p.getIRI(),
                        trLiteral(id), new HashSet<OWLAnnotation>());
                add(ax);
            }
            typedefToAnnotationProperty.put(p.getIRI().toString(), p);
            for (String tag : typedefFrame.getTags()) {
                OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
                if (tagConstant == OboFormatTag.TAG_IS_A) {
                    // todo - subAnnotationProperty
                    /*
 
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            ax = fac.getOWLSubClassOfAxiom(clsx,
                    trClass((String) clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RELATIONSHIP) {
            // TODO
            IRI relId = oboIdToIRI((String) clause.getValue());
            OWLAnnotationProperty prop = typedefToAnnotationProperty.get(relId
                    .toString());
            if (prop != null) {
                ax = fac.getOWLAnnotationAssertionAxiom(prop, cls.getIRI(),
                        oboIdToIRI((String) clause.getValue2()), annotations);
            } else {
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        if (tagConstant == OboFormatTag.TAG_IS_A) {
            ax = fac.getOWLSubObjectPropertyOfAxiom(p,
                    trObjectProp((String) v), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RELATIONSHIP) {
            IRI relId = oboIdToIRI((String) clause.getValue());
            OWLAnnotationProperty metaProp = typedefToAnnotationProperty
                    .get(relId.toString());
            if (metaProp != null) {
                ax = fac.getOWLAnnotationAssertionAxiom(metaProp, p.getIRI(),
                        oboIdToIRI((String) clause.getValue2()), annotations);
            } else {
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    protected void trAnnotations(@Nonnull Clause clause,
            @Nonnull Set<OWLAnnotation> anns) {
        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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     * @return the oWL annotation property
     */
    @Nonnull
    protected OWLAnnotationProperty trTagToAnnotationProp(@Nonnull String tag) {
        IRI iri = trTagToIRI(tag);
        OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
        if (!apToDeclare.contains(ap)) {
            apToDeclare.add(ap);
            add(fac.getOWLDeclarationAxiom(ap));
            Obo2OWLVocabulary vocab = Obo2OWLConstants.getVocabularyObj(tag);
            if (vocab != null) {
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Related Classes of org.semanticweb.owlapi.model.OWLAnnotationProperty

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  • edu.stanford.bmir.protege.web.client.ui.ontology.metadata.AnnotationsGrid$GetAnnotationsHandler
  • edu.stanford.bmir.protege.web.server.frame.PropertyValueComparator
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