A B C D E F G H I L M N P R S T U V W X

C

calculateComplexEnrichment(ProteinNetwork, ComplexSet, int, boolean) - Static method in class procope.evaluation.networkperformance.ComplexEnrichment

Calculates the complex enrichment of a given network with respect to a given complex set.

calculateEfficiency(ProteinNetwork, ComplexSet) - Static method in class procope.methods.clustering.MCLEfficiencyCalculator

Calculate performance of the clustering using a given complex network.

calculateInterologs(ProteinNetwork, ProteinNetwork, InterologScorer) - Static method in class procope.methods.interologs.InterologsCalculator

Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits).

calculateJaccardIndex(Complex) - Method in class procope.data.complexes.Complex

Calculates the Jaccard index as a measure of similarity between two complexes.

calculateOverlap(Complex) - Method in class procope.data.complexes.Complex

Calculates the number of overlapping proteins with another complex.

calculateROCCurves(List<ProteinNetwork>, ComplexSet, ComplexSet, LocalizationData, boolean) - Static method in class procope.evaluation.networkperformance.ROC

Calculate the ROC curves for a given set of networks.

calculateSharedProteinsBootstrap(ProteinNetwork, float) - Method in class procope.data.complexes.ComplexSet

Calculates the complex set with added shared proteins using a given scores network.

calculateSharedProteinsPu(ProteinNetwork, float, float) - Method in class procope.data.complexes.ComplexSet

Calculates shared proteins with respect to a given interaction network as proposed by Pu et al., 2007 (Pubmed: 17370254).

calculateSimilarity(String, String) - Method in interface procope.evaluation.complexquality.go.TermSimilarities

Calculates the similarity of two given GO terms.

calculateSimilarity(String, String) - Method in class procope.evaluation.complexquality.go.TermSimilaritiesSchlicker

Calculates the similarity of two given GO terms.

CALCULATORSFILE - Static variable in class procope.tools.Tools

caseSensitive - Static variable in class procope.tools.namemapping.ProteinManager

Should protein identifiers be handled case-sensitive? This value can be changed using ProteinManager.setCaseSensitivity(boolean)

ChartTools - Class in procope.tools

Contains static methods to handle JFreeChart chart objects.

ChartTools() - Constructor for class procope.tools.ChartTools

children - Variable in class procope.methods.clustering.HierarchicalTreeNode

List of children for this tree node.

clearAnnotations() - Static method in class procope.tools.namemapping.ProteinManager

Deletes all protein annotations.

clearNameMappings() - Static method in class procope.tools.namemapping.ProteinManager

Removes all existing name mappings from the protein manager.

close() - Method in class procope.data.petrinets.PetriNetCreator

Closes the output stream this creator is writing to.

close() - Method in class procope.data.XGMMLWriter

Closes the writer and the underlying stream

cluster(ProteinNetwork) - Method in class procope.examples.DummyClusterer

cluster(ProteinNetwork) - Method in interface procope.methods.clustering.Clusterer

Calculates a clustering represented as ComplexSet from a given scores network.

cluster(ProteinNetwork) - Method in class procope.methods.clustering.HierarchicalClusterer

Performs hierarchical agglomerative clustering on given similarity network.

cluster(ProteinNetwork) - Method in class procope.methods.clustering.MarkovClusterer

Perform MCL clustering.

cluster(ProteinNetwork) - Method in class procope.tools.userclasses.DummyClusterer

Implementation of the Clusterer.cluster(ProteinNetwork) method.

Clusterer - Interface in procope.methods.clustering

Common interface implemented by clustering methods which take a ProteinNetwork as input and return a set of clusters calculated on that similarity network.

CLUSTERERSFILE - Static variable in class procope.tools.Tools

clusterSimilarities(ProteinNetwork, HierarchicalLinkage) - Static method in class procope.methods.clustering.HierarchicalClusteringTrees

Performs agglomerative hierarchical clustering on a given network using a given linkage method.

clusterSimilarities(ProteinNetwork, HierarchicalLinkage, Set<Integer>) - Static method in class procope.methods.clustering.HierarchicalClusteringTrees

Performs agglomerative hierarchical clustering on a given network using a given linkage method.

Colocalization - Class in procope.evaluation.complexquality

Implements measures for the degree of colocalization of proteins contained in a predicted protein complex.

Colocalization(LocalizationData) - Constructor for class procope.evaluation.complexquality.Colocalization

Creates a new colocalization score calculator.

CombinationRules - Class in procope.data.networks

A set of combination rules defines how the combination of two networks is accomplished.

CombinationRules(CombinationRules.CombinationType) - Constructor for class procope.data.networks.CombinationRules

Creates a combination rule object using the given CombinationRules.CombinationType

CombinationRules.CombinationType - Enum in procope.data.networks

Defines how the nodes of both source networks are combined into a new set of nodes

CombinationRules.WeightMergePolicy - Enum in procope.data.networks

Defines how the weights of identical edges are combined for the resulting network

combineWith(ProteinNetwork, CombinationRules) - Method in class procope.data.networks.ProteinNetwork

Combines two network using a given combination rules.

CommonAncestors - Class in procope.evaluation.complexquality.go

Calculates and holds common ancestors for a given GO network.

CommonAncestors(GONetwork) - Constructor for class procope.evaluation.complexquality.go.CommonAncestors

Creates common ancestors object for a given GO network.

compareTo(NetworkEdge) - Method in class procope.data.networks.NetworkEdge

Compare this network edge with another.

compareTo(BlastHit) - Method in class procope.methods.interologs.blast.BlastHit

Orders the hits by their hit ID.

Complex - Class in procope.data.complexes

Represents a complex of proteins.

Complex(Collection<Integer>) - Constructor for class procope.data.complexes.Complex

Intializes the complex with a given list of proteins.

Complex(Integer...) - Constructor for class procope.data.complexes.Complex

Intializes the complex with a given integer array provided as a c onvenient parameter list.

Complex() - Constructor for class procope.data.complexes.Complex

Creates an empty complex.

ComplexEnrichment - Class in procope.evaluation.networkperformance

Contains one static method to calculate the complex enrichment score of a network with respect to a complex set.

ComplexEnrichment() - Constructor for class procope.evaluation.networkperformance.ComplexEnrichment

complexesOverlap(Complex, Complex) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculate the number of proteins which overlap between two given complexes.

ComplexMapping - Class in procope.evaluation.comparison

Represents a mapping between two complexes.

ComplexMapping(int, int, int) - Constructor for class procope.evaluation.comparison.ComplexMapping

Creates a new complex mapping.

ComplexMappings - Class in procope.evaluation.comparison

Represents a list of mappings between complexes of two complex sets.

ComplexMappings(ComplexSet, ComplexSet, List<ComplexMapping>) - Constructor for class procope.evaluation.comparison.ComplexMappings

Creates a new set of complex mappings.

ComplexScoreCalculator - Class in procope.methods.scores

Contains static methods to calculate scores of complexes using a given scores network.

ComplexSet - Class in procope.data.complexes

A complex set is a list of complexes.

ComplexSet() - Constructor for class procope.data.complexes.ComplexSet

Creates an empty complex set

ComplexSet(Collection<? extends Collection<Integer>>) - Constructor for class procope.data.complexes.ComplexSet

Creates a complex set from a given list of lists of internal IDs.

ComplexSetComparison - Class in procope.evaluation.comparison

This class contains static methods for the comparison of two complex sets.

ComplexSetReader - Class in procope.data.complexes

This class contains static methods to read complexes from files or streams.

complexSetsOverlap(ComplexSet, ComplexSet) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculates the overlap matrix for two given complex sets.

ComplexSetWriter - Class in procope.data.complexes

This class contains static methods to write complex sets to files or streams.

ComplexSetWriter() - Constructor for class procope.data.complexes.ComplexSetWriter

CONFIGFILE - Static variable in class procope.tools.Tools

CONFIGPATH - Static variable in class procope.tools.Tools

contains(int) - Method in class procope.data.complexes.Complex

Checks whether a given protein is contained in this complex.

contains(Complex) - Method in class procope.data.complexes.ComplexSet

Checks if a specified complex is contained in this set.

convertToToPNet(String, String, String) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToToPNet(String, String, String, boolean) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToToPNet(File, File, File) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToToPNet(File, File, File, boolean) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToToPNet(InputStream, OutputStream, OutputStream) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToToPNet(InputStream, OutputStream, OutputStream, boolean) - Static method in class procope.data.petrinets.ToPNetGenerator

Converts a given Petri net to ToPNet places and transitions

convertToXGMML(String, String) - Static method in class procope.data.petrinets.XGMMLGenerator

Converts the given Petri net file to the XGMML format.

convertToXGMML(File, File) - Static method in class procope.data.petrinets.XGMMLGenerator

Converts the given Petri net file to the XGMML format.

convertToXGMML(InputStream, OutputStream) - Static method in class procope.data.petrinets.XGMMLGenerator

Converts a Petri net coming from an input stream to the XGMML format written to an output stream.

copy() - Method in class procope.data.complexes.Complex

Creates a copy of this complex

copy() - Method in class procope.data.complexes.ComplexSet

Creates a copy of this complex set

copy() - Method in class procope.data.networks.ProteinNetwork

Create a copy of the network.

CorrelationCoefficient - Interface in procope.tools.math

Interface implemented by classes which calculate correlation coefficients of a list of pairs of data points.

createBootstrapNetwork(Collection<ComplexSet>) - Static method in class procope.methods.scores.bootstrap.Bootstrap

Creates the bootstrap network for a given set of clusterings.

createPetriNet() - Method in class procope.data.petrinets.PetriNetCreator

Creates the Petri net and writes it to the output specified in the constructor.