- TFSparsityPenalty - Class in penalties.defined
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TFSparsityPenalty implements the the cost function penalizing a large amount of nodes in the network with atleast one outgoing link.
- TFSparsityPenalty(Object) - Constructor for class penalties.defined.TFSparsityPenalty
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Constructs a new TFSparsityPenalty, the arguments are specified as an String[] passed as an object for classloading.
- toFile() - Method in class loggers.ManualLogger
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- toString() - Method in class network.link.Link
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The String reprensentation of this class.
- toString() - Method in class network.node.Node
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Overrides to String method, simple prints the name of node
- TranscriptionFactorExtractor - Class in extractors
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TranscriptionFactorExtractor is a class responsible for calculating and keeping track of the 'Regulatory gene function' metric associated with a network.
- TranscriptionFactorExtractor() - Constructor for class extractors.TranscriptionFactorExtractor
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Constructs a Transcriptionfactor with no network set.
- TranscriptionFactorExtractor(Network) - Constructor for class extractors.TranscriptionFactorExtractor
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Constructs a Transcriptionfactor with an associated network and already calculates the metric from scratch.