Uses of Class
data.complexes.ComplexSet

Packages that use ComplexSet
data.complexes   
data.petrinets   
evaluation.comparison   
evaluation.complexquality   
evaluation.networkperformance   
methods.clustering   
methods.scores   
methods.scores.bootstrap   
userinterface.gui   
zplayground   
 

Uses of ComplexSet in data.complexes
 

Methods in data.complexes that return ComplexSet
 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 organism)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(File file, String organism, 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 organism)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(InputStream input, String organism, 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 organism)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(String file, String organism, 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 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.
 

Uses of ComplexSet in data.petrinets
 

Methods in 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 evaluation.comparison
 

Methods in 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 evaluation.comparison with parameters of type ComplexSet
static BroheeSimilarity ComplexSetComparison.broheeComparison(ComplexSet candidate, ComplexSet reference)
          Calculate complex set similarity after Brohée, S. & van Helden, J.
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 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 evaluation.complexquality
 

Methods in 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 evaluation.networkperformance
 

Methods in evaluation.networkperformance with parameters of type ComplexSet
static float ComplexEnrichment.calculateComplexEnrichment(ProteinNetwork network, ComplexSet reference, 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)
          Calculate the ROC curves for a given set of networks.
 

Uses of ComplexSet in methods.clustering
 

Methods in methods.clustering that return ComplexSet
 ComplexSet HierarchicalClusterer.cluster(ProteinNetwork net)
          Performs hierarchical agglomerative clustering on given similarity network.
 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 HierarchicalTreeNode.extractClustering(float threshold)
          Extracts a clustering from this tree by cutting it a given similarity threshold value.
 

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

Uses of ComplexSet in methods.scores
 

Methods in 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 methods.scores.bootstrap
 

Methods in methods.scores.bootstrap that return ComplexSet
static ComplexSet Bootstrap.calculateOptimalSharedProteinsSet(ComplexSet complexes, ProteinNetwork scores, float lambda)
          Calculates the complex set with added shared proteins using a given scores network.
 ComplexSet BootstrapMCLClustering.getClustering()
          Returns the clustering.
 

Methods in methods.scores.bootstrap that return types with arguments of type ComplexSet
static ArrayList<ComplexSet> Bootstrap.extractClusteringsWithOptimalInflation(ArrayList<BootstrapMCLClusterings> clusteringLists, float optimalInflation)
          Extracts clusterings created with a given inflation coefficient (should be the optimal one) from a set of clusterings.
 

Methods in methods.scores.bootstrap with parameters of type ComplexSet
static ComplexSet Bootstrap.calculateOptimalSharedProteinsSet(ComplexSet complexes, ProteinNetwork scores, float lambda)
          Calculates the complex set with added shared proteins using a given scores network.
 

Method parameters in 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 methods.scores.bootstrap with parameters of type ComplexSet
BootstrapMCLClustering(ComplexSet set, float inflation, float efficiency)
          Create new bootstrap MCL clustering result.
 

Uses of ComplexSet in userinterface.gui
 

Methods in userinterface.gui with parameters of type ComplexSet
 void GUIMain.addComplexSet(ComplexSet set, String name)
           
 

Constructors in userinterface.gui with parameters of type ComplexSet
GUIComplexScorer(ComplexSet complexSet, Colocalization coloc, boolean PPV, Frame parent, String title)
           
GUIComplexScorer(ComplexSet complexSet, GUIMain parent, String title)
           
GUIComplexScorer(ComplexSet complexSet, ScoresCalculator scoresCalc, Frame parent, String title)
           
ShowComplexes(GUIMain parent, ComplexSet set, String name, GUIComplexScorer scorer)
           
 

Uses of ComplexSet in zplayground
 

Methods in zplayground that return ComplexSet
 ComplexSet DummyClusterer.cluster(ProteinNetwork net)
           
static ComplexSet PESandbox.loadClusters(String tabfile, String graphfile)