ignore_combination_with_same_domain,
species,
null,
- DomainCombinationType.BASIC );
+ DomainCombinationType.BASIC,
+ null,
+ null );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
final boolean ignore_combination_with_same_domain,
final Species species,
final DomainCombinationType dc_type ) {
- return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type );
+ return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type, null, null );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
final boolean ignore_combination_with_same_domain,
final Species species,
final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
- final DomainCombinationType dc_type ) {
+ final DomainCombinationType dc_type,
+ final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
+ final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
final BasicGenomeWideCombinableDomains instance = new BasicGenomeWideCombinableDomains( species, dc_type );
final Map<DomainId, Integer> domain_counts = new HashMap<DomainId, Integer>();
final Map<DomainId, Integer> domain_protein_counts = new HashMap<DomainId, Integer>();
if ( ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) && ( closest != null ) ) {
domain_combination.addCombinableDomain( closest.getDomainId() );
}
+ if ( protein_length_stats_by_dc != null ) {
+ final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
+ for( final BinaryDomainCombination dc : dcs ) {
+ final String dc_str = dc.toString();
+ if ( !protein_length_stats_by_dc.containsKey( dc_str ) ) {
+ protein_length_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
+ }
+ protein_length_stats_by_dc.get( dc_str ).addValue( protein.getLength() );
+ }
+ }
+ if ( domain_number_stats_by_dc != null ) {
+ final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
+ for( final BinaryDomainCombination dc : dcs ) {
+ final String dc_str = dc.toString();
+ if ( !domain_number_stats_by_dc.containsKey( dc_str ) ) {
+ domain_number_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
+ }
+ domain_number_stats_by_dc.get( dc_str ).addValue( protein.getNumberOfProteinDomains() );
+ }
+ }
+ //
}
}
}