Package org.forester.surfacing
Class BasicDomainSimilarityCalculator
- java.lang.Object
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- org.forester.surfacing.BasicDomainSimilarityCalculator
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- All Implemented Interfaces:
DomainSimilarityCalculator
public class BasicDomainSimilarityCalculator extends java.lang.Object implements DomainSimilarityCalculator
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.forester.surfacing.DomainSimilarityCalculator
DomainSimilarityCalculator.Detailedness, DomainSimilarityCalculator.GoAnnotationOutput
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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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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()
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Constructor Detail
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BasicDomainSimilarityCalculator
public BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score, boolean verbose)
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BasicDomainSimilarityCalculator
public BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score)
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Method Detail
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calculateSimilarities
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)
- Specified by:
calculateSimilarities
in interfaceDomainSimilarityCalculator
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isCalcSimilarityScore
public boolean isCalcSimilarityScore()
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