- getAccepted() - Method in class loggers.defined.AcceptanceLogger
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- getAcceptedList() - Method in class loggers.defined.AcceptanceLogger
-
- getAmountOfTF() - Method in class extractors.TranscriptionFactorExtractor
-
Returns the amount of nodes with at least one outgoing edge in the network.
- getAnnealingMultiplier() - Method in class settings.CurrentSettings
-
- getBetter() - Method in class loggers.defined.AcceptanceLogger
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- getBetterList() - Method in class loggers.defined.AcceptanceLogger
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- getBiDirectionalLinks(Network) - Method in class network.node.Node
-
Returns list of nodes connected by a birectional link in a given network context
- getChance() - Method in class loggers.defined.AcceptanceLogger
-
- getChunckIncrease() - Method in class settings.CurrentSettings
-
- getChuncks() - Method in class network.NetworkFileBackedWrapper
-
- getChuncks() - Method in class settings.CurrentSettings
-
- getClassName() - Method in class settings.LoggerOrPenaltyDefinition
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- getCoef() - Method in class penalties.defined.AntiDominatePenalty
-
- getCoef() - Method in class penalties.defined.GraphletG4Penalty
-
- getCoef() - Method in class penalties.defined.PredictionConfidencePenalty
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- getCoef() - Method in class penalties.defined.TFSparsityPenalty
-
- getCoef() - Method in interface penalties.PenaltyFunction
-
Gets the relative weight for this penalty
- getCoefs() - Method in class network.NetworkFileBackedWrapper
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- getContent() - Method in class settings.LoggerOrPenaltyDefinition
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- getCoolingMultiplier() - Method in class schedulers.NetworkSA
-
- getCurrentSet() - Method in class network.link.LinkProperties
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- getCurrentSettings() - Method in class main.Netter
-
Getter for the current settings
- getCutoff() - Method in class network.NetworkFileBackedWrapper
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- getCutoff() - Method in class network.postprocessing.RerankingResult
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- getCutoff() - Method in class settings.CurrentSettings
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- getDetailedFitness() - Method in class fitnessfunctions.PartitionFitnessFunction
-
Returns the list of pairs consisting of the penalty name and its current fitness score.
- getDeterminationZone() - Method in class settings.CurrentSettings
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- getDominatorPercentage() - Method in class extractors.DominatingExtractor
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Returns the current anti-dominating metric associated with the network state.
- getEndTemperature() - Method in class settings.CurrentSettings
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- getEnsemble() - Method in class schedulers.NetworkSA
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- getFileName() - Method in class network.NetworkFileBackedWrapper
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- getFitness() - Method in class fitnessfunctions.PartitionFitnessFunction
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Returns the calculated fitness score of the network ranking.
- getFitness() - Method in class schedulers.NetworkSA
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- getFitnessFunction() - Method in class network.modifiers.PredictionModifierOpt
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- getFreezingTemperature() - Method in class schedulers.NetworkSA
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- getFrequency() - Method in class extractors.GraphletCounterExtractor
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Returns the relative graphlet frequencies associated with the network
- getGranularity() - Method in class loggers.defined.AcceptanceLogger
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- getGraphletCounts() - Method in class extractors.GraphletCounterExtractor
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Returns the graphlet counts associated with the network
- getIncomingLinks(Network) - Method in class network.node.Node
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Returns list of nodes connected by an incoming link in a given network context
- getIterations() - Method in class loggers.ManualLogger
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Getter which return frequency of logging
- getIterations() - Method in class wrappers.EnsembleSA
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- getIterationsSoFar() - Method in class loggers.ManualLogger
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Getter which return frequency of logging
- getIterationsSoFar() - Method in class schedulers.NetworkSA
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- getLastAction() - Method in class schedulers.NetworkSA
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- getLastChance() - Method in class schedulers.NetworkSA
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- getLinkCount() - Method in class network.Network
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Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
- getLinkProperties() - Method in class network.link.Link
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Getter for the properties
- getLinks() - Method in class network.Network
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- getLogFile() - Method in class loggers.ManualLogger
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Getter which returns the log filename
- getLogged() - Method in class loggers.defined.AcceptanceLogger
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- getLoggers() - Method in class settings.CurrentSettings
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- getLowerBoundSet() - Method in class network.link.LinkProperties
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- getMaxIterations() - Method in class schedulers.NetworkSA
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- getMaxIterations() - Method in class settings.CurrentSettings
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- getMetric() - Method in class penalties.defined.AntiDominatePenalty
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- getMetric() - Method in class penalties.defined.GraphletG4Penalty
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- getMetric() - Method in class penalties.defined.PredictionConfidencePenalty
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- getMetric() - Method in class penalties.defined.TFSparsityPenalty
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- getMetric() - Method in interface penalties.PenaltyFunction
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Returns the current penalty metric (unmapped to the cost)
- getModified() - Method in class network.modifiers.PredictionModifierOpt
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- getModifier() - Method in class schedulers.NetworkSA
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- getModifyEachTurn() - Method in class network.modifiers.PredictionModifierOpt
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- getModifyEachTurn() - Method in class settings.CurrentSettings
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- getMoveEachTurn() - Method in class network.modifiers.PredictionModifierOpt
-
- getMoveEachTurn() - Method in class settings.CurrentSettings
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- getName() - Method in class fitnessfunctions.PenaltyPair
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Getter for the penalty name
- getName() - Method in class network.Network
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Getter for network name
- getName() - Method in class network.node.Node
-
Getter for name of node
- getNetwork() - Method in class extractors.DominatingExtractor
-
Returns the network associated with this extractor.
- getNetwork() - Method in class extractors.GraphletCounterExtractor
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Returns the network associated with this extractor.
- getNetwork() - Method in class extractors.TranscriptionFactorExtractor
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Returns the network associated with this extractor.
- getNetwork() - Method in interface network.modifiers.NetworkModifier
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Return the current network/ranking the modifier is working on
- getNetwork() - Method in class network.modifiers.PredictionModifierOpt
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- getNetwork() - Method in class network.NetworkFileBackedWrapper
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- getNetwork() - Method in class schedulers.NetworkSA
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- getNetworkCoefMap() - Method in class network.NetworkPartition
-
- getNetworks() - Method in class network.NetworkPartition
-
- getNextName() - Static method in class network.NetworkNameGenerator
-
Request a new name for a network
- getNode(String) - Static method in class network.node.NodeCollection
-
Returns the node identified by a certain name.
- getNodeCount() - Method in class network.Network
-
Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
- getNodes() - Method in class network.Network
-
- getNodeSize() - Method in class extractors.TranscriptionFactorExtractor
-
Returns the amount of nodes in the network.
- getNonCommitalAdded() - Method in class network.Network
-
- getNonCommittalDeleted() - Method in class network.Network
-
- getOriginalFile() - Method in class network.postprocessing.RerankingResult
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- getOriginalPredictionRank() - Method in class network.link.LinkProperties
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- getOutGoingLinks(Network) - Method in class network.node.Node
-
Returns list of nodes connected by an outgoing link in a given network context
- getOutputDir() - Method in class settings.CurrentSettings
-
- getOutputDirString() - Method in class settings.CurrentSettings
-
- getOutputFileName() - Method in class network.NetworkFileBackedWrapper
-
- getOutputSuffix() - Method in class settings.CurrentSettings
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- getPartition() - Method in class network.NetworkFileBackedWrapper
-
- getPartitions() - Method in class network.NetworkPartition
-
- getPenalties() - Method in class settings.CurrentSettings
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- getPenaltyName() - Method in class penalties.defined.AntiDominatePenalty
-
- getPenaltyName() - Method in class penalties.defined.GraphletG4Penalty
-
- getPenaltyName() - Method in class penalties.defined.PredictionConfidencePenalty
-
- getPenaltyName() - Method in class penalties.defined.TFSparsityPenalty
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- getPenaltyName() - Method in interface penalties.PenaltyFunction
-
The penalty name, used for logging functionality
- getPenaltyScore() - Method in class penalties.defined.AntiDominatePenalty
-
- getPenaltyScore() - Method in class penalties.defined.GraphletG4Penalty
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- getPenaltyScore() - Method in class penalties.defined.PredictionConfidencePenalty
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- getPenaltyScore() - Method in class penalties.defined.TFSparsityPenalty
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- getPenaltyScore() - Method in interface penalties.PenaltyFunction
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Returns the current penalty score (metric mapped on cost function)
- getPrediction() - Method in class network.NetworkPartition
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- getPredictionRank() - Method in class network.link.LinkProperties
-
- getPreds() - Method in class settings.CurrentSettings
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- getPreviousLowerBound() - Method in class network.link.LinkProperties
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- getPreviousPredictionRank() - Method in class network.link.LinkProperties
-
- getPreviousSet() - Method in class network.link.LinkProperties
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- getPreviousUpperBound() - Method in class network.link.LinkProperties
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- getProgress() - Method in class main.Netter
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Reports back on the progress of the optimization process in %.
- getReverted() - Method in class loggers.defined.AcceptanceLogger
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- getRevertedList() - Method in class loggers.defined.AcceptanceLogger
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- getScore() - Method in class fitnessfunctions.PenaltyPair
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Getter for the fitness score
- getStartTemperature() - Method in class settings.CurrentSettings
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- getT0() - Method in class schedulers.NetworkSA
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- getTarget() - Method in class network.link.Link
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Getter for target node
- getTemperatureAllowedDeviation() - Method in class settings.CurrentSettings
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- getTemperatureTargetGoal() - Method in class settings.CurrentSettings
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- getTempIterationCheck() - Method in class loggers.defined.AcceptanceLogger
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- getTempTargetGoal() - Method in class loggers.defined.AcceptanceLogger
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- getTempTargetGoalAllowedDeviation() - Method in class loggers.defined.AcceptanceLogger
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- getTestDir() - Method in class settings.CurrentSettings
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- getTf() - Method in class network.link.Link
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Getter for source node/transcription factor
- getThreadPool() - Method in class wrappers.EnsembleSA
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- getTotalIterations() - Method in class settings.CurrentSettings
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- getUnidirectedLinks(Network) - Method in class network.node.Node
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Returns list of nodes connected by any type of link in a given network context
- getUpperBoundSet() - Method in class network.link.LinkProperties
-
- getWorkersAvailable() - Method in class settings.CurrentSettings
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- getWorkersInProgress() - Method in class wrappers.EnsembleSA
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- getWrapper() - Method in class schedulers.NetworkSA
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- GraphletCounterExtractor - Class in extractors
-
GraphletCounterExtractor is a class responsible for calculating and keeping track of all graplet counts associated with a network.
- GraphletCounterExtractor(Network) - Constructor for class extractors.GraphletCounterExtractor
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- GraphletCounterExtractor() - Constructor for class extractors.GraphletCounterExtractor
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- GraphletG4Penalty - Class in penalties.defined
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GraphletG4Penalty penalty implements the cost function encouraging the appareance of G4 graphlets in the subnetworks
It is a (sub)network based penalty and supports incremental updates.
- GraphletG4Penalty(Object) - Constructor for class penalties.defined.GraphletG4Penalty
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Constructs a new GraphletG4Penalty, the arguments are specified as an String[] passed as an object for classloading.