|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |