Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Frame

17
18
19
20
21
22
23
24
25
26
27
28
29
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());
        Iterator<Xref> iterator = xrefs.iterator();
        Xref xref1 = iterator.next();
View Full Code Here
205
206
207
208
209
210
211
212
213
214
215
    public void write(@Nonnull OBODoc doc, @Nonnull BufferedWriter writer,
            NameProvider nameProvider) throws IOException {
        if (isCheckStructure) {
            doc.check();
        }
        Frame headerFrame = doc.getHeaderFrame();
        writeHeader(headerFrame, writer, nameProvider);
        List<Frame> termFrames = new ArrayList<>();
        termFrames.addAll(doc.getTermFrames());
        Collections.sort(termFrames, FramesComparator.INSTANCE);
        List<Frame> typeDefFrames = new ArrayList<>();
View Full Code Here
56
57
58
59
60
61
62
63
64
65
66
        for (Frame f : fl2) {
            fm2.put(f.getId(), f);
        }
        for (Frame f1 : fl1) {
            if (fm2.containsKey(f1.getId())) {
                Frame f2 = fm2.get(f1.getId());
                if (isCheckFrame) {
                    // we only need to do this once
                    diffs.addAll(getDiffs(ftype, f1, f2));
                }
            } else {
View Full Code Here
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
         * @param oboDoc
         *        the obo doc
         */
        public OBODocNameProvider(@Nonnull OBODoc oboDoc) {
            this.oboDoc = oboDoc;
            Frame headerFrame = oboDoc.getHeaderFrame();
            if (headerFrame != null) {
                defaultOboNamespace = headerFrame.getTagValue(
                        OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class);
            } else {
                defaultOboNamespace = null;
            }
        }
View Full Code Here
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
        @Nullable
        @Override
        public String getName(String id) {
            String name = null;
            Frame frame = oboDoc.getTermFrame(id);
            if (frame == null) {
                frame = oboDoc.getTypedefFrame(id);
            }
            if (frame != null) {
                Clause cl = frame.getClause(OboFormatTag.TAG_NAME);
                if (cl != null) {
                    name = cl.getValue(String.class);
                }
            }
            return name;
View Full Code Here
TOP

Related Classes of org.obolibrary.oboformat.model.Frame

  • org.obolibrary.obo2owl.BFOROXrefTest
  • org.obolibrary.obo2owl.CommentRemarkConversionTest
  • org.obolibrary.obo2owl.DanglingOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRestrictionOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRoundTripTest
  • org.obolibrary.obo2owl.EquivalentToTest
  • org.obolibrary.obo2owl.GCIQualifierTest
  • org.obolibrary.obo2owl.IDsTest
  • org.obolibrary.obo2owl.LogicalDefinitionPropertyViewTest
  • org.obolibrary.obo2owl.ObsoleteTermTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.