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