- if ( gwcd_list.get( i ).getSize() > 0 ) {
- SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
- out_dir,
- per_genome_domain_promiscuity_statistics_writer,
- gwcd_list.get( i ),
- i,
- dc_sort_order );
- if ( output_binary_domain_combinationsfor_graph_analysis ) {
- SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
- out_dir,
- gwcd_list.get( i ),
- i,
- dc_sort_order );
+ if ( !DA_ANALYSIS ) {
+ gwcd_list.add( BasicGenomeWideCombinableDomains
+ .createInstance( protein_list,
+ ignore_combination_with_same,
+ new BasicSpecies( input_file_properties[ i ][ 1 ] ),
+ domain_id_to_go_ids_map,
+ dc_type,
+ protein_length_stats_by_dc,
+ domain_number_stats_by_dc ) );
+ if ( gwcd_list.get( i ).getSize() > 0 ) {
+ SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
+ out_dir,
+ per_genome_domain_promiscuity_statistics_writer,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ if ( output_binary_domain_combinationsfor_graph_analysis ) {
+ SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
+ out_dir,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ }
+ SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
+ SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
+ all_bin_domain_combinations_encountered );