org.forester.surfacing
Class BasicDomainSimilarityCalculator

java.lang.Object
  extended by 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