Examples of OboFormatTag

org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

     *        the header frame
     */
    @SuppressWarnings("null")
    public void trHeaderFrame(@Nonnull Frame headerFrame) {
        for (String t : headerFrame.getTags()) {
            OboFormatTag tag = OBOFormatConstants.getTag(t);
            if (tag == OboFormatTag.TAG_ONTOLOGY) {
                // already processed
            } else if (tag == OboFormatTag.TAG_IMPORT) {
                // TODO
                // fac.getOWLImportsDeclaration(importedOntologyIRI);

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

     * @return the sets the
     */
    @Nonnull
    public Set<OWLAxiom> trTermFrameClauses(@Nonnull OWLClass cls,
            @Nonnull Collection<Clause> clauses, String t) {
        OboFormatTag tag = OBOFormatConstants.getTag(t);
        Set<OWLAxiom> axioms = new HashSet<>();
        if (tag == OboFormatTag.TAG_INTERSECTION_OF) {
            axioms.add(trIntersectionOf(cls, clauses));
        } else if (tag == OboFormatTag.TAG_UNION_OF) {
            axioms.add(trUnionOf(cls, clauses));

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

                        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
                    /*
                     * OWLAxiom ax = fac.getOWLSubAnnotationPropertyOfAxiom( p,
                     * trObjectProp((String)typedefFrame.getC), annotations);

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

             * new HashSet<>()); add(ax); // return
             * oboIdToIRI(xid); } } }
             */
            for (String tag : typedefFrame.getTags()) {
                Collection<Clause> clauses = typedefFrame.getClauses(tag);
                OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
                if (tagConstant == OboFormatTag.TAG_INTERSECTION_OF) {
                    OWLAxiom axiom = trRelationIntersectionOf(id, p, clauses);
                    if (axiom != null) {
                        add(axiom);
                    }

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

    @SuppressWarnings("null")
    protected OWLAxiom trTermClause(@Nonnull OWLClass cls, String tag,
            @Nonnull Clause clause) {
        Collection<QualifierValue> qvs = clause.getQualifierValues();
        Set<? extends OWLAnnotation> annotations = trAnnotations(clause);
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        // 5.2.2
        // The gci_relation qualifier translate cls to a class expression
        OWLClassExpression clsx = cls;
        String gciRel = getQVString("gci_relation", qvs);
        if (gciRel != null && !gciRel.isEmpty()) {

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

    protected OWLAxiom trTypedefClause(@Nonnull OWLObjectProperty p,
            String tag, @Nonnull Clause clause) {
        OWLAxiom ax = null;
        Object v = clause.getValue();
        Set<OWLAnnotation> annotations = trAnnotations(clause);
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        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());

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

        Set<OWLAnnotation> annotations = trAnnotations(clause);
        if (clause.getValue() == null) {
            LOG.error("Problem: {}", clause);
        }
        OWLAxiom ax = null;
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        // System.out.println("CLAUSE: "+clause+" // TAG="+_tag);
        if (tagConstant == OboFormatTag.TAG_NAME) {
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag),
                    sub, trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_DEF) {

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

        }
        Clause cl = new Clause(t);
        if (parseDeprecatedSynonym(t, cl)) {
            return cl;
        }
        OboFormatTag tag = OBOFormatConstants.getTag(t);
        if (tag == null) {
            error("Could not find tag for: " + t);
        }
        if (tag == OboFormatTag.TAG_IS_ANONYMOUS) {
            parseBoolean(cl);

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

        stream.advance(i + 1);
        parseWs();
        parseZeroOrMoreWs();
        // Memory optimization
        // re-use the tag string
        OboFormatTag formatTag = OBOFormatConstants.getTag(tag);
        if (formatTag != null) {
            tag = formatTag.getTag();
        }
        return mapDeprecatedTag(tag);
    }

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Examples of org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

        }
    }


    protected void parseIdLine(@Nonnull Frame f) {
        String t = getParseTag();
        OboFormatTag tag = OBOFormatConstants.getTag(t);
        if (tag != OboFormatTag.TAG_ID) {
            error("Expected id tag as first line in frame, but was: " + tag);
        }
        Clause cl = new Clause(t);
        f.addClause(cl);

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