final boolean calc_similarity_scores,
final Phylogeny phy ) {
init();
- final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
if ( verbose ) {
System.out.println();
System.out.println( "Pairwise genome distances:" );
final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
jacknife_ratio,
generator );
- final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
for( int i = 0; i < number_of_genomes; ++i ) {
final String species_i = species[ i ].getSpeciesId();
shared_domains_based_distances.setIdentifier( i, species_i );