org.forester.surfacing.BasicDomainSimilarityCalculator

public class BasicDomainSimilarityCalculator extends Object implements DomainSimilarityCalculator

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.surfacing.DomainSimilarityCalculator
DomainSimilarityCalculator.Detailedness, DomainSimilarityCalculator.GoAnnotationOutput
Constructor Summary

Constructors

Constructor

Description

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score)

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score, boolean verbose)
Method Summary

Modifier and Type

Method

Description

SortedSet<DomainSimilarity>

calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)

boolean

isCalcSimilarityScore()

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Class BasicDomainSimilarityCalculator

Nested Class Summary