public boolean isSkipped() {
        // --no-phaseIII is the same as:
        // --no-gene-scaffolding --no-named-complexes --no-protein-families --no-orthology
        return (hasOption(NO_P3_LONG_OPT) || (hasOption(NO_GS_LONG_OPT)
                && hasOption(NO_NC_LONG_OPT) && hasOption(NO_PF_LONG_OPT)
                && hasOption(PHASE3_NO_ORTHOLOGY_LONG_OPTION)));
    }
public boolean isSkipped ( ) { return ( hasOption ( NO_P3_LONG_OPT ) || ( hasOption ( NO_GS_LONG_OPT ) && hasOption ( NO_NC_LONG_OPT ) && hasOption ( NO_PF_LONG_OPT ) && hasOption ( PHASE3_NO_ORTHOLOGY_LONG_OPTION ) ) ) ; }
Determine whether phase III will be skipped (such as with the --no-phaseIII
command line option).

@return