Uses of Interface
data.ProteinSet

Packages that use ProteinSet
data.complexes   
data.networks   
data.purifications   
methods.scores   
methods.scores.go   
 

Uses of ProteinSet in data.complexes
 

Classes in data.complexes that implement ProteinSet
 class Complex
          Represents a complex of proteins.
 class ComplexSet
          A complex set is a list of complexes.
 

Methods in data.complexes with parameters of type ProteinSet
 ComplexSet ComplexSet.restrictToProteinSpace(ProteinSet proteins, boolean fullCoverage)
          Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins.
 

Uses of ProteinSet in data.networks
 

Classes in data.networks that implement ProteinSet
 class ProteinNetwork
          Represents a network of binary protein interactions.
 

Methods in data.networks with parameters of type ProteinSet
 ProteinNetwork ProteinNetwork.restrictToProteins(ProteinSet proteins, boolean fullCoverage)
          Returns a new network object which contains only those edges where one or both adjacent proteins are contained in a given set of proteins.
 

Uses of ProteinSet in data.purifications
 

Classes in data.purifications that implement ProteinSet
 class PurificationData
          A set of protein purification experiments where each experiment constists of a bait protein along with a list of prey proteins it purified.
 class PurificationExperiment
          Represents a single purification experiment having a bait protein and a list of prey proteins which were purified by that bait.
 

Uses of ProteinSet in methods.scores
 

Subinterfaces of ProteinSet in methods.scores
 interface ScoresCalculator
          Implemented by all classes which calculate interaction scores between proteins based on experimental or other data.
 

Classes in methods.scores that implement ProteinSet
 class HartCalculator
          Calculates protein-protein interaction scores from purification data according to Hart, G.
 class PECalculator
          Calculates Purification Enrichment scores according to Collins et al.
 class SocioAffinityCalculator
          Calculates socio affinity scores according to Gavin et al.
 

Uses of ProteinSet in methods.scores.go
 

Subinterfaces of ProteinSet in methods.scores.go
 interface FunctionalSimilarities
          This interface is implemented by classes which calculate a semantic similarity score of two given proteins based on GO information.
 

Classes in methods.scores.go that implement ProteinSet
 class FunctionalSimilaritiesSchlicker
          Implements the calculation of functional similarites between proteins as described in Schlicker, A.; Domingues, F.
 class GOAnnotations
          Represents a set of gene-product to GO-term annotations which are normally read from a file.