Package org.obolibrary.oboformat.parser

Examples of org.obolibrary.oboformat.parser.XrefExpander$Rule

142
143
144
145
146
147
148
149
150
151
152
            String segment = currTextSegment.toString();
            List<Rule> parentMatches = getMatches().peek();
            int len = parentMatches.size();
            for ( int i = 0; i < len; ++i )
            {
                Rule r = parentMatches.get( i );
                if ( r instanceof TextSegmentHandler )
                {
                    TextSegmentHandler h = (TextSegmentHandler) r;
                    try
                    {
View Full Code Here
43
44
45
46
47
48
49
50
51
52
53
    {

        @Override
        protected void configure()
        {
            forPattern( "bar" ).addRule( new Rule()
            {

                @Override
                public void body( String namespace, String name, String text )
                    throws Exception
View Full Code Here
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
            Log log = getDigester().getLogger();
            boolean debug = log.isDebugEnabled();
            for ( int i = 0; i < rules.size(); i++ )
            {
                int j = ( rules.size() - i ) - 1;
                Rule rule = rules.get( j );
                if ( debug )
                {
                    log.debug( "  Fire end() for " + rule );
                }
                try
                {
                    rule.end( namespaceURI, name );
                }
                catch ( Exception e )
                {
                    throw getDigester().createSAXException( e );
                }
View Full Code Here
14
15
16
17
18
19
20
21
22
23
24
25
public class XrefExpanderTest extends OboFormatTestBasics {

    @Test
    public void testExpand() {
        OBODoc obodoc = parseOBOFile("treat_xrefs_test.obo");
        XrefExpander x = new XrefExpander(obodoc);
        x.expandXrefs();
        OBODoc tdoc = obodoc.getImportedOBODocs().iterator().next();
        assertTrue(!tdoc.getTermFrames().isEmpty());
        Frame termFrame = tdoc.getTermFrame("ZFA:0001689");
        assert termFrame != null;
        assertEquals(2, termFrame.getClauses(OboFormatTag.TAG_INTERSECTION_OF)
View Full Code Here
35
36
37
38
39
40
41
42
43
44
45
46
    }

    @Test
    public void testExpandIntoSeparateBridges() {
        OBODoc obodoc = parseOBOFile("treat_xrefs_test.obo");
        XrefExpander x = new XrefExpander(obodoc, "bridge");
        x.expandXrefs();
        int n = 0;
        for (OBODoc tdoc : obodoc.getImportedOBODocs()) {
            Frame hf = tdoc.getHeaderFrame();
            if (hf == null) {
                continue;
View Full Code Here
126
127
128
129
130
131
132
133
134
135
   */
  public String graph() throws Exception {
    StringBuffer text = new StringBuffer();
   
    text.append("digraph M5Tree {\n");
    Rule temp = (Rule)m_ruleSet.elementAt(0);
    temp.topOfTree().graph(text);
    text.append("}\n");
    return text.toString();
  }
View Full Code Here
TOP

Related Classes of org.obolibrary.oboformat.parser.XrefExpander$Rule

  • br.com.caelum.vraptor.asm.Label
  • com.alibaba.citrus.asm.Label
  • com.bbn.openmap.omGraphics.DrawingAttributes
  • com.facebook.presto.jdbc.internal.joda.time.Chronology
  • com.googlecode.aviator.asm.Label
  • com.stimulus.archiva.domain.fields.EmailFieldValue
  • dk.brics.automaton.RegExp
  • dk.brics.automaton.RunAutomaton
  • oracle.toplink.libraries.asm.Label
  • org.antlr.runtime.tree.Tree
    • 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.