- output_binary_domain_combinationsfor_graph_analysis,
- all_bin_domain_combinations_gained_fitch,
- all_bin_domain_combinations_lost_fitch,
- dc_type,
- protein_length_stats_by_dc,
- domain_number_stats_by_dc,
- domain_length_stats_by_domain,
- tax_code_to_id_map,
- write_to_nexus,
- use_last_in_fitch_parsimony,
- perform_dc_fich );
- // Listing of all domain combinations gained is only done if only one input tree is used.
+ output_binary_domain_combinationsfor_graph_analysis,
+ all_bin_domain_combinations_gained_fitch,
+ all_bin_domain_combinations_lost_fitch,
+ dc_type,
+ protein_length_stats_by_dc,
+ domain_number_stats_by_dc,
+ domain_length_stats_by_domain,
+ tax_code_to_id_map,
+ write_to_nexus,
+ use_last_in_fitch_parsimony,
+ perform_dc_fich );
+ // Listing of all domain combinations gained is only done if only one input tree is used.