code: @Override
      public List<Option> getCommandLineOptions() {
          List<Option> ret = super.getCommandLineOptions();
  
          String help;
  
          help = EXPAND_PROTEIN_FAMILIES_HELP;
          ret.add(new Option(null, EXPAND_PF_LONG_OPT, false, help));
  
          help = EXPAND_NAMED_COMPLEXES_HELP;
          ret.add(new Option(null, EXPAND_NC_LONG_OPT, false, help));
  
          help = NO_PROTEIN_FAMILIES_HELP;
          ret.add(new Option(null, NO_PF_LONG_OPT, false, help));
  
          help = NO_NAMED_COMPLEXES_HELP;
          ret.add(new Option(null, NO_NC_LONG_OPT, false, help));
  
          help = NO_GENE_SCAFFOLDING_HELP;
          ret.add(new Option(null, NO_GS_LONG_OPT, false, help));
  
          help = NO_ORTHOLOGY_HELP;
          ret.add(new Option(null, PHASE3_NO_ORTHOLOGY_LONG_OPTION, false, help));
  
          help = NO_PHASE_THREE;
          ret.add(new Option(null, NO_P3_LONG_OPT, false, help));
  
          return ret;
      }
docs: {@inheritDoc}