public class PairwiseGenomeComparator {
private List<DistanceMatrix> _domain_distance_scores_means;
- private List<DistanceMatrix> _shared_domains_based_distances;
private List<DistanceMatrix> _shared_binary_combinations_based_distances;
+ private List<DistanceMatrix> _shared_domains_based_distances;
public PairwiseGenomeComparator() {
init();
return _shared_domains_based_distances;
}
- private void init() {
- _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
- _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
- _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
- }
-
public void performPairwiseComparisons( final StringBuilder html_desc,
final boolean sort_by_species_count_first,
final Detailedness detailedness,
final boolean ignore_domains_without_combs_in_all_spec,
final boolean ignore_domains_specific_to_one_species,
final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
- final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final DomainSimilarity.DomainSimilarityScoring scoring,
final Map<String, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
}
}
+ private void init() {
+ _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
+ _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
+ _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
+ }
+
static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
String[] all_domain_ids_array;
final SortedSet<String> all_domain_ids = new TreeSet<String>();