Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.OBODoc

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                newLineCount);
    }

    @Test
    public void testWriteOpaqueIdsAsComments() throws Exception {
        OBODoc oboDoc = parseOBOFile("opaque_ids_test.obo");
        String oboString = renderOboToString(oboDoc);
        String[] lines = oboString.split("\n");
        boolean ok = false;
        for (String line : lines) {
            // System.out.println("LINE: "+line);
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            sb.append(line);
            sb.append('\n');
        }
        reader.close();
        String input = sb.toString();
        OBODoc obodoc = parseOboToString(input);
        String written = renderOboToString(obodoc);
        assertEquals(input, written);
    }
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@SuppressWarnings("javadoc")
public class CAROTest extends OboFormatTestBasics {

    @Test
    public void testParseCARO() {
        OBODoc obodoc = parseOBOFile("caro.obo");
        assertTrue(obodoc.getTermFrames().size() > 2);
        Frame cc = obodoc.getTermFrame("CARO:0000014");
        assert cc != null;
        assertEquals("cell component", cc.getTagValue(OboFormatTag.TAG_NAME));
        assertEquals("Anatomical structure that is a direct part of the cell.",
                cc.getTagValue(OboFormatTag.TAG_DEF));
        Clause dc = cc.getClause(OboFormatTag.TAG_DEF);
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@SuppressWarnings("javadoc")
public class ChebiXRefTest extends OboFormatTestBasics {

    @Test
    public void testExpand() {
        OBODoc obodoc = parseOBOFile("chebi_problematic_xref.obo");
        assertNotNull(obodoc);
    }
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@SuppressWarnings({ "javadoc", "null" })
public class TagTest extends OboFormatTestBasics {

    @Test
    public void testParseOBOFile() {
        OBODoc obodoc = parseOBOFile("tag_test.obo");
        assertEquals(4, obodoc.getTermFrames().size());
        assertEquals(1, obodoc.getTypedefFrames().size());
        Frame frame = obodoc.getTermFrame("X:1");
        assertNotNull(frame);
        assertEquals("x1", frame.getTagValue(OboFormatTag.TAG_NAME));
    }
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        assertEquals("x1", frame.getTagValue(OboFormatTag.TAG_NAME));
    }

    @Test
    public void testParseOBOFile2() {
        OBODoc obodoc = parseOBOFile("testqvs.obo");
        assertEquals(4, obodoc.getTermFrames().size());
        assertEquals(1, obodoc.getTypedefFrames().size());
    }
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        assertEquals(1, obodoc.getTypedefFrames().size());
    }

    @Test
    public void testParseOBODoc() {
        OBODoc obodoc = parseOBODoc("[Term]\nid: x\nname: foo\n\n\n[Term]\nid: y\nname: y");
        assertEquals(2, obodoc.getTermFrames().size());
        Frame frame = obodoc.getTermFrame("x");
        assertEquals("foo", frame.getTagValue(OboFormatTag.TAG_NAME));
    }
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        assertEquals("foo", frame.getTagValue(OboFormatTag.TAG_NAME));
    }

    @Test
    public void testParseFrames() {
        OBODoc obodoc = parseFrames("[Term]\nid: x\nname: foo");
        assertEquals(1, obodoc.getTermFrames().size());
        Frame frame = obodoc.getTermFrames().iterator().next();
        assertEquals("foo", frame.getTagValue(OboFormatTag.TAG_NAME));
    }
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    private static OBODoc parseFrames(@Nonnull String s) {
        StringReader sr = new StringReader(s);
        OBOFormatParser p = new OBOFormatParser();
        BufferedReader br = new BufferedReader(sr);
        p.setReader(br);
        OBODoc obodoc = new OBODoc();
        p.parseTermFrame(obodoc);
        return obodoc;
    }
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    private static OBODoc parseOBODoc(@Nonnull String s) {
        StringReader sr = new StringReader(s);
        OBOFormatParser p = new OBOFormatParser();
        BufferedReader br = new BufferedReader(sr);
        p.setReader(br);
        OBODoc obodoc = new OBODoc();
        p.parseOBODoc(obodoc);
        return obodoc;
    }
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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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