Package org.biojava.ontology

Examples of org.biojava.ontology.Synonym

230
231
232
233
234
235
236
237
238
239
240
241
242
243
        sb.append("\nis_obsolete: true");
      }
      for (Object synonym : term.getSynonyms()) {
        sb.append("\nsynonym: ");
        if (synonym instanceof Synonym) {
          Synonym s = (Synonym) synonym;
          StringTools.append(sb, "\"", s.getName(), "\" [");
          if (s.getCategory() != null) {
            sb.append(s.getCategory());
          }
          sb.append(']');
        } else {
          sb.append(synonym);
        }
View Full Code Here
395
396
397
398
399
400
401
402
403
404
405
    public Synonym[] getSynonyms() {
      Object synonyms[] = term.getSynonyms();
      if ((synonyms == null) || (synonyms.length == 0)) {
        return new Synonym[0];
      }
      Synonym syn[] = new Synonym[synonyms.length];
      for (int i = 0; i < synonyms.length; i++) {
        syn[i] = (Synonym) synonyms[i];
      }
      return syn;
    }
View Full Code Here
218
219
220
221
222
223
224
225
226
227
228
         */
        if (value.length() == 0)
          throw new ParseException("Tag found with no value "+ line);

        if ( isSynonym(name)){
          Synonym synonym = parseSynonym(name,value);
          triggerNewSynonym(synonym);
        } else {
          //System.out.println("new key:" + name + " " + value);
          triggerNewKey(name,value);
        }
View Full Code Here
294
295
296
297
298
299
300
301
302
303
304
305
306
307
      } else
        throw new ParseException("Expected dbxref list,"
            + " instead found " + token +   line );
    }

    Synonym synonym = new Synonym();
    synonym.setScope(scope);
    synonym.setCategory(catID);
    synonym.setName(p.str);
    //System.out.println("SYNONYM: " + p.str +" " + synonym.getCategory() + " " + synonym.getScope());

    Map<String,Object>[] refs = getDbxrefList(value,defIndex + 1, value.length());
   
    // set the refs in the synonym
View Full Code Here
229
230
231
232
233
234
235
236
237
238
239
240
241
242
        sb.append("\nis_obsolete: true");
      }
      for (Object synonym : term.getSynonyms()) {
        sb.append("\nsynonym: ");
        if (synonym instanceof Synonym) {
          Synonym s = (Synonym) synonym;
          StringTools.append(sb, "\"", s.getName(), "\" [");
          if (s.getCategory() != null) {
            sb.append(s.getCategory());
          }
          sb.append(']');
        } else {
          sb.append(synonym);
        }
View Full Code Here
398
399
400
401
402
403
404
405
406
407
408
    public Synonym[] getSynonyms() {
      Object synonyms[] = term.getSynonyms();
      if ((synonyms == null) || (synonyms.length == 0)) {
        return new Synonym[0];
      }
      Synonym syn[] = new Synonym[synonyms.length];
      for (int i = 0; i < synonyms.length; i++) {
        syn[i] = (Synonym) synonyms[i];
      }
      return syn;
    }
View Full Code Here
228
229
230
231
232
233
234
235
236
237
238
239
240
241
        sb.append("\nis_obsolete: true");
      }
      for (Object synonym : term.getSynonyms()) {
        sb.append("\nsynonym: ");
        if (synonym instanceof Synonym) {
          Synonym s = (Synonym) synonym;
          StringTools.append(sb, "\"", s.getName(), "\" [");
          if (s.getCategory() != null) {
            sb.append(s.getCategory());
          }
          sb.append(']');
        } else {
          sb.append(synonym);
        }
View Full Code Here
397
398
399
400
401
402
403
404
405
406
407
    public Synonym[] getSynonyms() {
      Object synonyms[] = term.getSynonyms();
      if ((synonyms == null) || (synonyms.length == 0)) {
        return new Synonym[0];
      }
      Synonym syn[] = new Synonym[synonyms.length];
      for (int i = 0; i < synonyms.length; i++) {
        syn[i] = (Synonym) synonyms[i];
      }
      return syn;
    }
View Full Code Here
TOP

Related Classes of org.biojava.ontology.Synonym

  • org.biojava.ontology.obo.OboFileParser
  • org.sbml.jsbml.SBO$Term
    • 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.