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calculateMetricFromScratch() - Method in class penalties.defined.AntiDominatePenalty
calculateMetricFromScratch() - Method in class penalties.defined.GraphletG4Penalty
calculateMetricFromScratch() - Method in class penalties.defined.PredictionConfidencePenalty
calculateMetricFromScratch() - Method in class penalties.defined.TFSparsityPenalty
calculateMetricFromScratch() - Method in interface penalties.PenaltyFunction
Calculates the metric from the current subnetwork/ranking
clear() - Method in class network.node.Node
Resets this node completely for all networks, removing all links
clear() - Method in class schedulers.NetworkSA
Completely clears all the resources registered by the procedure.
clearNetwork(Network) - Method in class network.node.Node
Removes all links of this node in a given network, use with caution as the network representation can become inconsistent.
clearNetworks() - Method in class fitnessfunctions.PartitionFitnessFunction
Clears all assigned penalties and coefficients.
commit() - Method in class fitnessfunctions.PartitionFitnessFunction
Commits the changes made by the modifier to all subnetworks.
commit() - Method in class
This method confirms the latest changes to this link and makes them permanent, such that a revert is no longer possible.
commit() - Method in interface network.modifiers.NetworkModifier
Make the last mutation permanent
commit() - Method in class network.modifiers.PredictionModifierOpt
Implements the commit method of this interface.
commit() - Method in class network.Network
Commits network by making all temporary modifications permanent.
compare(Link, Link) - Method in class
Overrides compare.
compare(Link, Link) - Method in class
Overrides compare.
createNode(String) - Static method in class network.node.Node
Method responsible for creating a node.
CurrentSettings - Class in settings
CurrentSettings is a collection class of all the global settings used in Netter.
CurrentSettings(File) - Constructor for class settings.CurrentSettings
Constructs a new settings objects from a paramater file.
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