org.forester.surfacing
Interface DomainSimilarity

All Superinterfaces:
Comparable<DomainSimilarity>
All Known Implementing Classes:
PrintableDomainSimilarity

public interface DomainSimilarity
extends Comparable<DomainSimilarity>


Nested Class Summary
static class DomainSimilarity.DomainSimilarityScoring
           
static class DomainSimilarity.DomainSimilaritySortField
           
 
Method Summary
 SortedSet<DomainId> getCombinableDomainIds(Species species_of_combinable_domain)
           
 DomainId getDomainId()
           
 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.
 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
 double getMaximalSimilarityScore()
           
 double getMeanSimilarityScore()
           
 double getMinimalSimilarityScore()
           
 int getN()
          This should return the number of pairwise distances used to calculate this similarity score
 SortedSet<Species> getSpecies()
           
 SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> getSpeciesData()
          This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData
 double getStandardDeviationOfSimilarityScore()
           
 StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)
           
 
Methods inherited from interface java.lang.Comparable
compareTo
 

Method Detail

getCombinableDomainIds

SortedSet<DomainId> getCombinableDomainIds(Species species_of_combinable_domain)

getDomainId

DomainId getDomainId()

getMaximalDifference

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

Returns:

getMaximalDifferenceInCounts

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

double getMaximalSimilarityScore()

getMeanSimilarityScore

double getMeanSimilarityScore()

getMinimalSimilarityScore

double getMinimalSimilarityScore()

getN

int getN()
This should return the number of pairwise distances used to calculate this similarity score

Returns:
the number of pairwise distances

getSpecies

SortedSet<Species> getSpecies()

getSpeciesData

SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> getSpeciesData()
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData

Returns:
SortedMap

getStandardDeviationOfSimilarityScore

double getStandardDeviationOfSimilarityScore()

toStringBuffer

StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)