org.forester.surfacing
public interface DomainSimilarity extends java.lang.Comparable<DomainSimilarity>
Modifier and Type | Interface and Description |
---|---|
static class |
DomainSimilarity.DomainSimilarityScoring |
static class |
DomainSimilarity.DomainSimilaritySortField |
Modifier and Type | Method and Description |
---|---|
java.util.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
|
java.util.SortedSet<Species> |
getSpecies() |
java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> |
getSpeciesData()
This should return a map, which maps species names to
SpeciesSpecificDomainSimilariyData
|
double |
getStandardDeviationOfSimilarityScore() |
java.lang.StringBuffer |
toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option) |
java.util.SortedSet<DomainId> getCombinableDomainIds(Species species_of_combinable_domain)
DomainId getDomainId()
int getMaximalDifference()
int getMaximalDifferenceInCounts()
double getMaximalSimilarityScore()
double getMeanSimilarityScore()
double getMinimalSimilarityScore()
int getN()
java.util.SortedSet<Species> getSpecies()
java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> getSpeciesData()
double getStandardDeviationOfSimilarityScore()
java.lang.StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)