- calculateMetricFromScratch() - Method in class penalties.defined.AntiDominatePenalty
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- calculateMetricFromScratch() - Method in class penalties.defined.GraphletG4Penalty
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- calculateMetricFromScratch() - Method in class penalties.defined.PredictionConfidencePenalty
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- calculateMetricFromScratch() - Method in class penalties.defined.TFSparsityPenalty
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- calculateMetricFromScratch() - Method in interface penalties.PenaltyFunction
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Calculates the metric from the current subnetwork/ranking
- clear() - Method in class network.node.Node
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Resets this node completely for all networks, removing all links
- clear() - Method in class schedulers.NetworkSA
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Completely clears all the resources registered by the procedure.
- clearNetwork(Network) - Method in class network.node.Node
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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
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Clears all assigned penalties and coefficients.
- commit() - Method in class fitnessfunctions.PartitionFitnessFunction
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Commits the changes made by the modifier to all subnetworks.
- commit() - Method in class network.link.LinkProperties
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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
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Make the last mutation permanent
- commit() - Method in class network.modifiers.PredictionModifierOpt
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Implements the commit method of this interface.
- commit() - Method in class network.Network
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Commits network by making all temporary modifications permanent.
- compare(Link, Link) - Method in class network.link.comparator.LinkNameComparator
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Overrides compare.
- compare(Link, Link) - Method in class network.link.comparator.LinkRankComparator
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Overrides compare.
- createNode(String) - Static method in class network.node.Node
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Method responsible for creating a node.
- CurrentSettings - Class in settings
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CurrentSettings is a collection class of all the global settings used in Netter.
- CurrentSettings(File) - Constructor for class settings.CurrentSettings
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Constructs a new settings objects from a paramater file.