Uses of Interface
procope.data.ProteinSet

Packages that use ProteinSet
procope.data.complexes   
procope.data.networks   
procope.data.purifications   
procope.evaluation.complexquality.go   
procope.examples   
procope.methods.scores   
 

Uses of ProteinSet in procope.data.complexes
 

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

Methods in procope.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 procope.data.networks
 

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

Methods in procope.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 procope.data.purifications
 

Classes in procope.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 procope.evaluation.complexquality.go
 

Classes in procope.evaluation.complexquality.go that implement ProteinSet
 class FunctionalSimilarities
          This class is extended by classes which calculate a semantic similarity score of two given proteins based on GO information.
 class FunctionalSimilaritiesSchlicker
          Implements the calculation of functional similarites between proteins as described in
 class GOAnnotations
          Represents a set of gene-product to GO-term annotations which are normally read from a file.
 

Uses of ProteinSet in procope.examples
 

Classes in procope.examples that implement ProteinSet
 class DummyScores
           
 

Uses of ProteinSet in procope.methods.scores
 

Classes in procope.methods.scores that implement ProteinSet
 class DiceCoefficients
          Provides an efficient implementation of "Dice coefficients", a protein protein affinity measure derived from purification datasets according to
 class HartCalculator
          Calculates protein-protein interaction scores from purification data according to
 class PECalculator
          Calculates Purification Enrichment scores according to
 class ScoresCalculator
          Extended by all classes which calculate interaction scores between proteins based on experimental or other data.
 class SocioAffinityCalculator
          Calculates socio affinity scores according to