genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator