Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Frame.addClause()

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                String fillerId = getIdentifier(filler);
                if (fillerId == null) {
                    error(ax, true);
                    return;
                }
                f.addClause(createRelationshipClauseWithCardinality(
                        cardinality, fillerId, qvs, ax));
            } else if (sup instanceof OWLQuantifiedObjectRestriction) {
                // OWLObjectSomeValuesFrom
                // OWLObjectAllValuesFrom
                OWLQuantifiedObjectRestriction r = (OWLQuantifiedObjectRestriction) sup;
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                String fillerId = getIdentifier(filler);
                if (fillerId == null) {
                    error(ax, true);
                    return;
                }
                f.addClause(createRelationshipClauseWithRestrictions(r,
                        fillerId, qvs, ax));
            } else if (sup instanceof OWLObjectIntersectionOf) {
                OWLObjectIntersectionOf i = (OWLObjectIntersectionOf) sup;
                List<Clause> clauses = new ArrayList<>();
                for (OWLClassExpression operand : i.getOperands()) {
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                    error(ax, true);
                    return;
                }
                clauses = normalizeRelationshipClauses(clauses);
                for (Clause clause : clauses) {
                    f.addClause(clause);
                }
            } else {
                error(ax, true);
                return;
            }
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        Frame shf = src.getHeaderFrame();
        String ontId = shf.getTagValue(OboFormatTag.TAG_ONTOLOGY, String.class);
        String tgtOntId = ontId + "/xref_expansions";
        targetOBODoc = new OBODoc();
        Frame thf = new Frame(FrameType.HEADER);
        thf.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, tgtOntId));
        targetOBODoc.setHeaderFrame(thf);
        sourceOBODoc.addImportedOBODoc(targetOBODoc);
        setUp();
    }
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            }
            if (targetBase != null) {
                // create a new bridge ontology for every expansion macro
                OBODoc tgt = new OBODoc();
                Frame thf = new Frame(FrameType.HEADER);
                thf.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, targetBase
                        + "-" + idSpace.toLowerCase()));
                tgt.setHeaderFrame(thf);
                targetDocMap.put(idSpace, tgt);
                sourceOBODoc.addImportedOBODoc(tgt);
                if (relation != null) {
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        oboDocSource.setHeaderFrame(new Frame(FrameType.HEADER));
        oboDocSource.addDefaultOntologyHeader("caro");
        // add source frame that contains at least one new line
        Frame sourceFrame = new Frame(FrameType.TERM);
        sourceFrame.setId("CARO:0000049");
        sourceFrame
                .addClause(new Clause(
                        OboFormatTag.TAG_DEF,
                        "Sequential hermaphroditic organism that produces\ngametes first of the male sex, and then later of the\nfemale sex."));
        oboDocSource.addTermFrame(sourceFrame);
        // convert to OWL and retrieve def
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    @Nonnull
    private static OBODoc createPVDoc() {
        OBODoc oboDoc = new OBODoc();
        Frame headerFrame = new Frame(FrameType.HEADER);
        headerFrame
                .addClause(new Clause(OboFormatTag.TAG_FORMAT_VERSION, "1.2"));
        headerFrame.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, "test"));
        addPropertyValue(headerFrame, "http://purl.org/dc/elements/1.1/title",
                "Ontology for Biomedical Investigation", "xsd:string");
        addPropertyValue(headerFrame, "defaultLanguage", "en", "xsd:string");
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    private static OBODoc createPVDoc() {
        OBODoc oboDoc = new OBODoc();
        Frame headerFrame = new Frame(FrameType.HEADER);
        headerFrame
                .addClause(new Clause(OboFormatTag.TAG_FORMAT_VERSION, "1.2"));
        headerFrame.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, "test"));
        addPropertyValue(headerFrame, "http://purl.org/dc/elements/1.1/title",
                "Ontology for Biomedical Investigation", "xsd:string");
        addPropertyValue(headerFrame, "defaultLanguage", "en", "xsd:string");
        oboDoc.setHeaderFrame(headerFrame);
        return oboDoc;
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    public void testIDs() throws OWLOntologyCreationException {
        OBODoc doc = new OBODoc();
        Frame header = new Frame(FrameType.HEADER);
        Clause c = new Clause(OboFormatTag.TAG_ONTOLOGY.getTag());
        c.setValue("test");
        header.addClause(c);
        doc.setHeaderFrame(header);
        OWLAPIObo2Owl obo2owl = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
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    @Test
    public void writeCurlyBracesInComments() throws Exception {
        OBODoc doc = new OBODoc();
        Frame h = new Frame(FrameType.HEADER);
        h.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, "test"));
        doc.setHeaderFrame(h);
        Frame t = new Frame(FrameType.TERM);
        String id = "TEST:0001";
        t.setId(id);
        t.addClause(new Clause(OboFormatTag.TAG_ID, id));
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