final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
true,
- calc_similarity_scores );
+ calc_similarity_scores,
+ true );
final SortedSet<DomainSimilarity> similarities = calc
.calculateSimilarities( pw_calc,
genome_pair,