public MetabolismNetwork(MetabolismProperties ps) {
   props = ps;
   logger = props.getLogger("MetabolismNetwork");
   entries = new Vector<MetabolicEntry>();
   locations = new TreeSet<String>();
   reactions = new TreeMap<String, Rxn>();
   orfSets = new TreeMap<String, LogicalORFTree>();
   totalORFs = new TreeSet<String>();
 }
  public void loadNetwork() throws IOException {
    logger.log(Level.INFO, "Loading metabolism network...");

    File file = props.getNetworkFile();
    Mapper<String, MetabolicEntry> entryMapper = new MetabolicEntry.MetabolicMapper();
    Parser<MetabolicEntry> parser = new Parser<MetabolicEntry>(file, entryMapper);

    while (parser.hasNext()) {
      MetabolicEntry entry = parser.next();
      entries.add(entry);

      Rxn rxn =
          new Rxn(
              props,
              entry.getReaction(),
              entry.getAbbreviation(),
              entry.getReactionName(),
              entry.getORF());
      reactions.put(entry.getAbbreviation(), rxn);

      locations.add(rxn.getLocation());

      LogicalORFTree lot = new LogicalORFTree(entry.getORF());
      ORFSet os = new ORFSet(entry.getORF());

      totalORFs.addAll(os.getORFs());
      orfSets.put(entry.getAbbreviation(), lot);
    }

    logger.log(Level.FINE, String.format("Loaded %d entries.", entries.size()));

    abbrevs = new MetabolismAbbreviations(props);
    abbrevs.loadAbbreviations();

    logger.log(Level.FINEST, "Loaded abbrevations.");
  }