Uses of Class
data.networks.ProteinNetwork

Packages that use ProteinNetwork
data.complexes   
data.networks   
data.petrinets   
data.purifications   
evaluation.comparison   
evaluation.networkperformance   
methods.clustering   
methods.interologs   
methods.interologs.blast   
methods.scores   
methods.scores.bootstrap   
tools.namemapping   
userinterface.gui   
zplayground   
 

Uses of ProteinNetwork in data.complexes
 

Methods in data.complexes that return ProteinNetwork
 ProteinNetwork ComplexSet.getComplexInducedNetwork()
          Creates a network which contains a fully connected subgraph for each complex.
 ProteinNetwork Complex.getMinimalSpanningTree(ProteinNetwork scores)
          Returns the minimal spanning tree of this complex as a network object.
 

Methods in data.complexes with parameters of type ProteinNetwork
 ComplexSet ComplexSet.decompose(ProteinNetwork scores, float cutoff)
          Decomposes a complex set with respect to a given scores network.
 ProteinNetwork Complex.getMinimalSpanningTree(ProteinNetwork scores)
          Returns the minimal spanning tree of this complex as a network object.
 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.
 

Uses of ProteinNetwork in data.networks
 

Methods in data.networks that return ProteinNetwork
 ProteinNetwork ProteinNetwork.combineWith(ProteinNetwork other, CombinationRules rules)
          Combines two network using a given combination rules.
 ProteinNetwork ProteinNetwork.copy()
          Create a copy of the network.
static ProteinNetwork NetworkGenerator.generateNetwork(ScoresCalculator calculator)
          Generate a network from a given scores calculator.
static ProteinNetwork NetworkGenerator.generateNetwork(ScoresCalculator calculator, float cutOff)
          Generate a network from a given scores calculator.
static ProteinNetwork NetworkGenerator.generateRandomNetwork(int nodes, int edges)
          Generates a random network with the given number of nodes and edges.
static ProteinNetwork NetworkGenerator.generateRandomNetwork(int nodes, int edges, Random random)
          Generates a random network with the given number of nodes and edges.
 ProteinNetwork ProteinNetwork.getCutOffNetwork(float cutOff)
          Returns a network containing only edges with a weight greater or equal than a given cutoff value.
 ProteinNetwork ProteinNetwork.getCutOffNetwork(float cutOff, boolean cutBelow)
          Returns a network containing only edges with a weight above or below a given cutoff value.
 ProteinNetwork ProteinNetwork.getFilteredNetwork(BooleanExpression statement)
          Filters the network using a given boolean expression.
 ProteinNetwork CombinationRules.getMapping()
          Returns the mapping network of this rules set.
 ProteinNetwork ProteinNetwork.randomizeByRewiring()
          Randomizes a network by rewiring.
 ProteinNetwork ProteinNetwork.randomizeByRewiring(int rewirings)
          Randomizes a network by rewiring.
static ProteinNetwork NetworkReader.readNetwork(File file)
          Reads an undirected network from a given file.
static ProteinNetwork NetworkReader.readNetwork(File file, boolean directed)
          Reads a network from a given file.
static ProteinNetwork NetworkReader.readNetwork(File file, boolean directed, String organism1, String organism2)
          Reads a network from a given file.
static ProteinNetwork NetworkReader.readNetwork(InputStream input)
          Reads an undirected network from a given InputStream.
static ProteinNetwork NetworkReader.readNetwork(InputStream input, boolean directed)
          Reads a network from a given InputStream.
static ProteinNetwork NetworkReader.readNetwork(InputStream input, boolean directed, String organism1, String organism2)
          Reads a network from a given InputStream.
static ProteinNetwork NetworkReader.readNetwork(String file)
          Reads an undirected network from a given file.
static ProteinNetwork NetworkReader.readNetwork(String file, boolean directed)
          Reads a network from a given file.
static ProteinNetwork NetworkReader.readNetwork(String file, boolean directed, String organism1, String organism2)
          Reads a network from a given file.
 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.
 ProteinNetwork ProteinNetwork.restrictToProteins(Set<Integer> proteinIDs, 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.
 ProteinNetwork ProteinNetwork.undirectedCopy()
          Create an explicitly undirected copy of the network.
 

Methods in data.networks with parameters of type ProteinNetwork
 ProteinNetwork ProteinNetwork.combineWith(ProteinNetwork other, CombinationRules rules)
          Combines two network using a given combination rules.
 boolean ProteinNetwork.equalScores(ProteinNetwork compare)
          Checks whether two networks are equal regardings their edge weights
 void CombinationRules.setMapping(ProteinNetwork mapping)
          Sets a mapping, mapped nodes will be merged into single nodes in the resulting network.
static void NetworkWriter.writeNetwork(ProteinNetwork network, File outfile)
          Writes a network to a specified file.
static void NetworkWriter.writeNetwork(ProteinNetwork network, File outfile, String separator)
          Writes a network to a specified file.
static void NetworkWriter.writeNetwork(ProteinNetwork network, OutputStream outstream)
          Writes a network to a specified outputstream.
static void NetworkWriter.writeNetwork(ProteinNetwork network, OutputStream outstream, String separator)
          Writes a network to a specified outputstream.
static void NetworkWriter.writeNetwork(ProteinNetwork network, String outfile)
          Writes a network to a specified file.
static void NetworkWriter.writeNetwork(ProteinNetwork network, String outfile, String separator)
          Writes a network to a specified file.
static void NetworkWriter.writeXGMML(ProteinNetwork network, File outfile)
          Creates a Cytoscape-compatible XGMML file.
static void NetworkWriter.writeXGMML(ProteinNetwork network, OutputStream outstream)
          Creates a Cytoscape-compatible XGMML file, but writes to an output stream.
static void NetworkWriter.writeXGMML(ProteinNetwork network, String outfile)
          Creates a Cytoscape-compatible XGMML file.
 

Uses of ProteinNetwork in data.petrinets
 

Methods in data.petrinets with parameters of type ProteinNetwork
 void PetriNetCreator.addInteractionNetwork(ProteinNetwork net, String name, boolean insertScores)
          Adds a ProteinNetwork which will be integrated into the Petri net.
 

Uses of ProteinNetwork in data.purifications
 

Methods in data.purifications that return ProteinNetwork
 ProteinNetwork PurificationData.getBaitPreyInteractions()
          Calculates a directed network containing all bait-prey interactions.
 

Uses of ProteinNetwork in evaluation.comparison
 

Methods in evaluation.comparison with parameters of type ProteinNetwork
static List<Point> NetworkComparison.weightsOverlap(ProteinNetwork scores1, ProteinNetwork scores2, boolean excludeZeros)
          Compares the weights of all edges of two networks.
 

Uses of ProteinNetwork in evaluation.networkperformance
 

Methods in evaluation.networkperformance with parameters of type ProteinNetwork
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.
 

Method parameters in evaluation.networkperformance with type arguments of type ProteinNetwork
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 ProteinNetwork in methods.clustering
 

Methods in methods.clustering with parameters of type ProteinNetwork
static double MCLPerfomanceCalculator.calculatePerformance(ProteinNetwork network, ComplexSet clustering)
          Calculate performance of the clustering using a given complex network.
 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.
static HierarchicalTreeNode HierarchicalClusteringTrees.clusterSimilarities(ProteinNetwork net, HierarchicalLinkage linkage)
          Performs agglomerative hierarchical clustering on a given network using a given linkage method.
static HierarchicalTreeNode HierarchicalClusteringTrees.clusterSimilarities(ProteinNetwork net, HierarchicalLinkage linkage, Set<Integer> proteins)
          Performs agglomerative hierarchical clustering on a given network using a given linkage method.
 

Uses of ProteinNetwork in methods.interologs
 

Methods in methods.interologs that return ProteinNetwork
static ProteinNetwork InterologsCalculator.calculateInterologs(ProteinNetwork toTransfer, ProteinNetwork mapping, InterologScorer scorer)
          Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits).
 

Methods in methods.interologs with parameters of type ProteinNetwork
static ProteinNetwork InterologsCalculator.calculateInterologs(ProteinNetwork toTransfer, ProteinNetwork mapping, InterologScorer scorer)
          Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits).
 

Uses of ProteinNetwork in methods.interologs.blast
 

Methods in methods.interologs.blast that return ProteinNetwork
 ProteinNetwork BlastHits.getBidirectionalBestHits(BlastHits backward, BlastBBHConstraints constraints)
          Calculate bidirectional best hits (BBHs).
 

Uses of ProteinNetwork in methods.scores
 

Methods in methods.scores with parameters of type ProteinNetwork
static float ComplexScoreCalculator.averageComplexScore(ProteinNetwork scoreNetwork, Complex complex)
          Calculates the score of a complex using a given scores network.
static float ComplexScoreCalculator.averageComplexScore(ProteinNetwork scoreNetwork, Complex complex, boolean ignoreMissingScores)
          Calculates the score of a complex using a given scores network.
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.
 

Uses of ProteinNetwork in methods.scores.bootstrap
 

Methods in methods.scores.bootstrap that return ProteinNetwork
static ProteinNetwork Bootstrap.createBootstrapNetwork(Collection<ComplexSet> clusterings)
          Creates the bootstrap network for a given set of clusterings.
 

Methods in methods.scores.bootstrap with parameters of type ProteinNetwork
static ComplexSet Bootstrap.calculateOptimalSharedProteinsSet(ComplexSet complexes, ProteinNetwork scores, float lambda)
          Calculates the complex set with added shared proteins using a given scores network.
static BootstrapMCLClusterings Bootstrap.clusterForSample(ProteinNetwork scores, ArrayList<Float> inflationCoefficients)
          Performs MCL clustering of a given scores network with a set of inflation coefficient.
static BootstrapMCLClusterings Bootstrap.clusterForSample(ProteinNetwork scores, Float... inflationCoefficients)
          Performs MCL clustering of a given scores network with a set of inflation coefficient.
 

Uses of ProteinNetwork in tools.namemapping
 

Methods in tools.namemapping with parameters of type ProteinNetwork
 void Synonyms.addMappingNetwork(ProteinNetwork mappings)
          Adds all mappings induced by the edges of a given directed network to the synonyms list.
static void ProteinManager.addNameMappings(ProteinNetwork mappings)
          Add a list of name mappings to the protein manager.
 

Uses of ProteinNetwork in userinterface.gui
 

Fields in userinterface.gui declared as ProteinNetwork
 ProteinNetwork NameMapping.mapNet
           
 

Methods in userinterface.gui that return ProteinNetwork
 ProteinNetwork GUIMain.getNetwork(int index)
           
 

Methods in userinterface.gui with parameters of type ProteinNetwork
 void GUIMain.addNetwork(ProteinNetwork network, String name)
           
 

Constructors in userinterface.gui with parameters of type ProteinNetwork
NameMapping(ProteinNetwork mapNet, String label)
           
NetworkQuery(GUIMain parent, ProteinNetwork network, String name)
           
 

Uses of ProteinNetwork in zplayground
 

Methods in zplayground with parameters of type ProteinNetwork
 ComplexSet DummyClusterer.cluster(ProteinNetwork net)
           
static void Sandbox.debugOutputNet(ProteinNetwork net)