@Override
 protected AlignmentAnalyzerParametersImpl parseParameters() throws UserError, IOException {
   AlignmentAnalyzerParametersImpl params = super.parseParameters();
   params.setMaxNumberOfStates(getParameterAsInt(PARAMETER_KEY_MAX_STATE_SPACE));
   params.setTimeoutMili(getParameterAsInt(PARAMETER_KEY_TIMEOUT));
   return params;
 }