Uses of Class
procope.data.complexes.ComplexSet

Packages that use ComplexSet
procope.data.complexes   
procope.data.petrinets   
procope.evaluation.comparison   
procope.evaluation.complexquality   
procope.evaluation.networkperformance   
procope.examples   
procope.methods.clustering   
procope.methods.scores   
procope.methods.scores.bootstrap   
procope.tools.userclasses   
 

Uses of ComplexSet in procope.data.complexes
 

Methods in procope.data.complexes that return ComplexSet
 ComplexSet ComplexSet.calculateSharedProteinsBootstrap(ProteinNetwork scores, float lambda)
          Calculates the complex set with added shared proteins using a given scores network.
 ComplexSet ComplexSet.calculateSharedProteinsPu(ProteinNetwork interactions, float a, float b)
          Calculates shared proteins with respect to a given interaction network as proposed by Pu et al., 2007 (Pubmed: 17370254).
 ComplexSet ComplexSet.copy()
          Creates a copy of this complex set
 ComplexSet ComplexSet.decompose(ProteinNetwork scores, float cutoff)
          Decomposes a complex set with respect to a given scores network.
 ComplexSet ComplexSet.randomizeByExchanging()
          Returns a randomized copy of the complex set.
 ComplexSet ComplexSet.randomizeByRemapping()
          Returns a randomized copy of the complex set.
static ComplexSet ComplexSetReader.readComplexes(File file)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(File file, String separator)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(InputStream input)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(InputStream input, String separator)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(String file)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(String file, String separator)
          Reads complexes from a given file.
 ComplexSet ComplexSet.removeComplexesByScore(ProteinNetwork scores, float cutoff)
          Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff.
 ComplexSet ComplexSet.removeComplexesByScore(ProteinNetwork scores, float cutoff, boolean ignoreMissing)
          Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff.
 ComplexSet ComplexSet.removeComplexesBySize(int cutoffSize, boolean below)
          Removes all complexes smaller or larger than a given threshold from the complex set.
 ComplexSet ComplexSet.removeSingletons()
          Removes singletons from the complex set.
 ComplexSet ComplexSet.restrictToProteins(Set<Integer> 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.
 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.
 

Methods in procope.data.complexes with parameters of type ComplexSet
static void ComplexSetWriter.writeComplexes(ComplexSet set, File outfile)
          Writes a complex set to a specified file.
static void ComplexSetWriter.writeComplexes(ComplexSet set, File outfile, String delimiter)
          Writes a complex set to a specified file.
static void ComplexSetWriter.writeComplexes(ComplexSet set, OutputStream outstream)
          Writes a complex set to an OutputStream.
static void ComplexSetWriter.writeComplexes(ComplexSet set, OutputStream outstream, String delimiter)
          Writes a complex set to an OutputStream.
static void ComplexSetWriter.writeComplexes(ComplexSet set, String outfile)
          Writes a complex set to a specified file.
static void ComplexSetWriter.writeComplexes(ComplexSet set, String outfile, String delimiter)
          Writes a complex set to a specified file.
static void ComplexSetWriter.writeXGMML(ComplexSet set, ProteinNetwork net, File outfile)
          Creates a Cytoscape-compatible XGMML file.
static void ComplexSetWriter.writeXGMML(ComplexSet set, ProteinNetwork net, OutputStream outstream)
          Creates a Cytoscape-compatible XGMML file, but writes to an output stream.
static void ComplexSetWriter.writeXGMML(ComplexSet set, ProteinNetwork net, String outfile)
          Creates a Cytoscape-compatible XGMML file.
 

Uses of ComplexSet in procope.data.petrinets
 

Methods in procope.data.petrinets with parameters of type ComplexSet
 void PetriNetCreator.addComplexSet(ComplexSet set, String name)
          Adds a ComplexSet which will be integrated into the Petri net.
 

Uses of ComplexSet in procope.evaluation.comparison
 

Methods in procope.evaluation.comparison that return ComplexSet
 ComplexSet ComplexMappings.getSetA()
          Returns the first complex set involved in this mapping set.
 ComplexSet ComplexMappings.getSetB()
          Returns the second complex set involved in this mapping set.
 

Methods in procope.evaluation.comparison with parameters of type ComplexSet
static BroheeSimilarity ComplexSetComparison.broheeComparison(ComplexSet candidate, ComplexSet reference)
          Calculate complex set similarity after
static int[][] ComplexSetComparison.complexSetsOverlap(ComplexSet setA, ComplexSet setB)
          Calculates the overlap matrix for two given complex sets.
static ComplexMappings ComplexSetComparison.mapComplexes(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
static ComplexMappings ComplexSetComparison.mapComplexesConsistently(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
static ComplexMappings ComplexSetComparison.mapComplexesExactly(ComplexSet setA, ComplexSet setB)
          Find complexes in two given complex sets which are identical
static ComplexMappings ComplexSetComparison.mapComplexesMultiple(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
 

Constructors in procope.evaluation.comparison with parameters of type ComplexSet
ComplexMappings(ComplexSet setA, ComplexSet setB, List<ComplexMapping> mappings)
          Creates a new set of complex mappings.
 

Uses of ComplexSet in procope.evaluation.complexquality
 

Methods in procope.evaluation.complexquality with parameters of type ComplexSet
 float Colocalization.getAverageColocalizationScore(ComplexSet complexes, boolean weighted, boolean ignoreMissing)
          Calculates the average colocalization score for a given complex set.
 float Colocalization.getAveragePPV(ComplexSet complexes, boolean weighted, boolean ignoreMissing)
          Calculates the average PPV for a given complex set.
 

Uses of ComplexSet in procope.evaluation.networkperformance
 

Methods in procope.evaluation.networkperformance with parameters of type ComplexSet
static float ComplexEnrichment.calculateComplexEnrichment(ProteinNetwork network, ComplexSet reference, int numrand, boolean useWeightedScores)
          Calculates the complex enrichment of a given network with respect to a given complex set.
static List<ROCCurve> ROC.calculateROCCurves(List<ProteinNetwork> scoreNetworks, ComplexSet reference, ComplexSet referenceForNegativeSet, LocalizationData locData, boolean restrictToNetworkProteins)
          Calculate the ROC curves for a given set of networks.
 

Uses of ComplexSet in procope.examples
 

Methods in procope.examples that return ComplexSet
 ComplexSet DummyClusterer.cluster(ProteinNetwork net)
           
 

Uses of ComplexSet in procope.methods.clustering
 

Methods in procope.methods.clustering that return ComplexSet
 ComplexSet MarkovClusterer.cluster(ProteinNetwork net)
          Perform MCL clustering.
 ComplexSet Clusterer.cluster(ProteinNetwork net)
          Calculates a clustering represented as ComplexSet from a given scores network.
 ComplexSet HierarchicalClusterer.cluster(ProteinNetwork net)
          Performs hierarchical agglomerative clustering on given similarity network.
 ComplexSet HierarchicalTreeNode.extractClustering(float threshold)
          Extracts a clustering from this tree by cutting it a given similarity threshold value.
 

Methods in procope.methods.clustering with parameters of type ComplexSet
static double MCLEfficiencyCalculator.calculateEfficiency(ProteinNetwork network, ComplexSet clustering)
          Calculate performance of the clustering using a given complex network.
 

Uses of ComplexSet in procope.methods.scores
 

Methods in procope.methods.scores with parameters of type ComplexSet
static float ComplexScoreCalculator.averageComplexSetScore(ProteinNetwork scoreNetwork, ComplexSet complexSet, boolean weighted)
          Calculates the average complex score of a given complex set.
static float ComplexScoreCalculator.averageComplexSetScore(ProteinNetwork scoreNetwork, ComplexSet complexSet, boolean weighted, boolean ignoreMissingScores)
          Calculates the average complex score of a given complex set.
static float ComplexScoreCalculator.averageComplexSetScore(ScoresCalculator scoreCalc, ComplexSet complexSet, boolean weighted)
          Calculates the average complex score of a given complex set.
static float ComplexScoreCalculator.averageComplexSetScore(ScoresCalculator scoreCalc, ComplexSet complexSet, boolean weighted, boolean ignoreMissingScores)
          Calculates the average complex score of a given complex set.
 

Uses of ComplexSet in procope.methods.scores.bootstrap
 

Methods in procope.methods.scores.bootstrap that return ComplexSet
 ComplexSet BootstrapClustering.getClustering()
          Returns the clustering.
 

Methods in procope.methods.scores.bootstrap that return types with arguments of type ComplexSet
static ArrayList<ComplexSet> Bootstrap.extractOptimalClusterings(ArrayList<BootstrapClusterings> clusteringLists, int optimalIndex)
          Extracts all clusterings at a given index of the clustering lists.
 

Method parameters in procope.methods.scores.bootstrap with type arguments of type ComplexSet
static ProteinNetwork Bootstrap.createBootstrapNetwork(Collection<ComplexSet> clusterings)
          Creates the bootstrap network for a given set of clusterings.
 

Constructors in procope.methods.scores.bootstrap with parameters of type ComplexSet
BootstrapClustering(ComplexSet set, String parameters, float efficiency)
          Create new bootstrap MCL clustering result.
 

Uses of ComplexSet in procope.tools.userclasses
 

Methods in procope.tools.userclasses that return ComplexSet
 ComplexSet DummyClusterer.cluster(ProteinNetwork net)
          Implementation of the Clusterer.cluster(ProteinNetwork) method.