private ArrayList<SequencePart> parseDomainParts(List<String> lines, 
      String type) {
    ArrayList<SequencePart> ret = new ArrayList<SequencePart>();
    for (String line : lines) {
      String fromStr = line.substring(15, 20).trim();
      String toStr = line.substring(21, 27).trim();
      if (fromStr.contains("?") || toStr.contains("?")) {
        continue;
      }
      if (fromStr.startsWith("<") || fromStr.startsWith(">")) {
        fromStr = fromStr.substring(1);
      }
      if (toStr.startsWith("<") || toStr.startsWith(">")) {
        toStr = toStr.substring(1);
      }
      // -1  because the data file indexes letters in strings starting with 1
      int from = Integer.parseInt(fromStr) - 1; 
      int to = Integer.parseInt(toStr) - 1;
      ret.add(new SequencePart(from, to, type));
    }
    return ret;
  }