public class BasicDomainSimilarityCalculator extends java.lang.Object implements DomainSimilarityCalculator
DomainSimilarityCalculator.Detailedness, DomainSimilarityCalculator.GoAnnotationOutput
Constructor and Description |
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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) |
Modifier and Type | Method and Description |
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java.util.SortedSet<DomainSimilarity> |
calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator,
java.util.List<GenomeWideCombinableDomains> cdc_list,
boolean ignore_domains_without_combinations_in_any_genome,
boolean ignore_domains_specific_to_one_genome) |
boolean |
isCalcSimilarityScore() |
public BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score, boolean verbose)
public BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score)
public java.util.SortedSet<DomainSimilarity> calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, java.util.List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)
calculateSimilarities
in interface DomainSimilarityCalculator
public boolean isCalcSimilarityScore()