Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.OBODoc

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@SuppressWarnings("javadoc")
public class DbXrefCommentsTest extends OboFormatTestBasics {

    @Test
    public void testDbXrefCommentsRoundtrip() throws Exception {
        OBODoc obodoc = parseOBOFile("db_xref_comments.obo");
        Frame frame = obodoc.getTermFrame("MOD:00516");
        assertNotNull(frame);
        Clause defClause = frame.getClause(OboFormatTag.TAG_DEF);
        assertNotNull(defClause);
        Collection<Xref> xrefs = defClause.getXrefs();
        assertEquals(2, xrefs.size());
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    @Nonnull
    protected OBODoc parseOBOFile(@Nonnull Reader fn, boolean allowEmptyFrames)
            throws IOException {
        OBOFormatParser p = new OBOFormatParser();
        OBODoc obodoc = p.parse(new BufferedReader(fn));
        assertNotNull("The obodoc should not be null", obodoc);
        if (obodoc.getTermFrames().isEmpty() && !allowEmptyFrames) {
            fail("Term frames should not be empty.");
        }
        return obodoc;
    }
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    @Nonnull
    protected static OBODoc parseOboToString(@Nonnull String oboString)
            throws IOException {
        OBOFormatParser p = new OBOFormatParser();
        BufferedReader reader = new BufferedReader(new StringReader(oboString));
        OBODoc parsedOboDoc = p.parse(reader);
        reader.close();
        return parsedOboDoc;
    }
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            @Nonnull Writer writer, OWLDocumentFormat format)
            throws OWLOntologyStorageException {
        try {
            OWLAPIOwl2Obo translator = new OWLAPIOwl2Obo(
                    ontology.getOWLOntologyManager());
            final OBODoc result = translator.convert(ontology);
            boolean hasImports = ontology.getImports().isEmpty() == false;
            NameProvider nameProvider;
            if (hasImports) {
                // if the ontology has imports
                // use it as secondary lookup for labels
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     *         the oBO format parser exception
     */
    public void write(BufferedReader reader, @Nonnull BufferedWriter writer)
            throws IOException {
        OBOFormatParser parser = new OBOFormatParser();
        OBODoc doc = parser.parse(reader);
        write(doc, writer);
    }
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        if (iri == null && source == null) {
            throw new IllegalArgumentException(
                    "iri and source annot both be null");
        }
        OBOFormatParser p = new OBOFormatParser();
        OBODoc obodoc = null;
        if (iri != null) {
            obodoc = p.parse(iri.toURI().toURL());
        } else {
            if (source.isReaderAvailable()) {
                obodoc = p.parse(new BufferedReader(source.getReader()));
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Related Classes of org.obolibrary.oboformat.model.OBODoc

  • org.obolibrary.macro.ManchesterSyntaxTool$AdvancedEntityChecker
  • org.obolibrary.obo2owl.BFOROXrefTest
  • org.obolibrary.obo2owl.CommentRemarkConversionTest
  • org.obolibrary.obo2owl.DanglingOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRestrictionOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRoundTripTest
  • org.obolibrary.obo2owl.DuplicateTagsTest
  • org.obolibrary.obo2owl.EquivalentToTest
  • org.obolibrary.obo2owl.GCIQualifierTest
  • org.obolibrary.obo2owl.IDsTest
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