Class DomainSimilarity

  • All Implemented Interfaces:
    java.lang.Comparable<DomainSimilarity>

    public class DomainSimilarity
    extends java.lang.Object
    implements java.lang.Comparable<DomainSimilarity>
    • Field Detail

      • SPECIES_SEPARATOR

        public static final java.lang.String SPECIES_SEPARATOR
        See Also:
        Constant Field Values
    • Constructor Detail

      • DomainSimilarity

        public DomainSimilarity​(CombinableDomains combinable_domains,
                                double min,
                                double max,
                                double mean,
                                double median,
                                double sd,
                                int n,
                                int max_difference_in_counts,
                                int max_difference,
                                java.util.SortedMap<Species,​org.forester.surfacing.SpeciesSpecificDcData> species_data,
                                boolean sort_by_species_count_first,
                                boolean treat_as_binary_comparison)
      • DomainSimilarity

        public DomainSimilarity​(CombinableDomains combinable_domains,
                                int max_difference_in_counts,
                                int max_difference,
                                java.util.SortedMap<Species,​org.forester.surfacing.SpeciesSpecificDcData> species_data,
                                boolean sort_by_species_count_first,
                                boolean treat_as_binary_comparison)
    • Method Detail

      • getCombinableDomainIds

        public java.util.SortedSet<java.lang.String> getCombinableDomainIds​(Species species_of_combinable_domain)
      • getDomainId

        public java.lang.String getDomainId()
      • getMaximalDifference

        public int getMaximalDifference()
        For pairwise similarities, this should return the "difference"; for example the difference in counts for copy number based features (the same as getMaximalDifferenceInCounts(), or the number of actually different domain combinations. For pairwise similarities, this should return the difference, while for comparisons of more than two domains, this should return the maximal difference
      • getMaximalDifferenceInCounts

        public int getMaximalDifferenceInCounts()
        For pairwise similarities, this should return the difference in counts, while for comparisons of more than two domains, this should return the maximal difference in counts
        Returns:
        the (maximal) difference in counts
      • getMaximalSimilarityScore

        public double getMaximalSimilarityScore()
      • getMeanSimilarityScore

        public double getMeanSimilarityScore()
      • getMinimalSimilarityScore

        public double getMinimalSimilarityScore()
      • getN

        public int getN()
        This should return the number of pairwise distances used to calculate this similarity score
        Returns:
        the number of pairwise distances
      • getSpecies

        public java.util.SortedSet<Species> getSpecies()
      • getSpeciesCustomOrder

        public java.util.List<Species> getSpeciesCustomOrder()
      • getSpeciesData

        public java.util.SortedMap<Species,​org.forester.surfacing.SpeciesSpecificDcData> getSpeciesData()
        This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData
        Returns:
        SortedMap
      • getStandardDeviationOfSimilarityScore

        public double getStandardDeviationOfSimilarityScore()
      • setSpeciesOrder

        public void setSpeciesOrder​(java.util.List<Species> species_order)
      • toStringBuffer

        public java.lang.StringBuffer toStringBuffer​(DomainSimilarity.PRINT_OPTION print_option,
                                                     java.util.Map<java.lang.String,​java.lang.Integer> tax_code_to_id_map,
                                                     Phylogeny phy)