org.forester.surfacing
Class BasicDomainSimilarityCalculator

java.lang.Object
  org.forester.surfacing.BasicDomainSimilarityCalculator

All Implemented Interfaces:

DomainSimilarityCalculator

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

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

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BasicDomainSimilarityCalculator

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

Method Detail

calculateSimilarities

public 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)

Specified by:

calculateSimilarities in interface DomainSimilarityCalculator