GoOboParser.java 文件源码

/**
 * Parse OBO file into {@link HpoOntology} object.
 *
 * @return {@link HpoOntology} from parsing OBO file.
 * @throws IOException In case of problems with file I/O.
 */
@SuppressWarnings("unchecked")
public GoOntology parse() throws IOException {
  final OboImmutableOntologyLoader<GoTerm, GoTermRelation> loader =
      new OboImmutableOntologyLoader<>(oboFile, debug);
  final GoOboFactory factory = new GoOboFactory();
  final ImmutableOntology<GoTerm, GoTermRelation> o = loader.load(factory);

  // Convert ImmutableOntology into GoOntology. The casts here are ugly and require the
  // @SuppressWarnings above but this saves us one factory layer of indirection.
  return new GoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(),
      (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(),
      o.getNonObsoleteTermIds(), o.getObsoleteTermIds(),
      (ImmutableMap<TermId, GoTerm>) o.getTermMap(),
      (ImmutableMap<Integer, GoTermRelation>) o.getRelationMap());
}