- Link - Class in network.link
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Link is the class representing a directed link between a transcription factor or regulatory gene and a target node.
- Link(Node, Node, LinkProperties) - Constructor for class network.link.Link
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Constructs a new link with associated LinkProperties
- LinkNameComparator - Class in network.link.comparator
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LinkNameComparator is a Comparator for Links to sort based on node names.
- LinkNameComparator() - Constructor for class network.link.comparator.LinkNameComparator
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- LinkProperties - Class in network.link
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LinkProperties is the class representing all additional properties a Link can have besides the defining properties: target and source node.
- LinkProperties(boolean, int) - Constructor for class network.link.LinkProperties
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Constructs a LinkProperties with a certain position in the ranking and indicates if this is a true positive link
- LinkRankComparator - Class in network.link.comparator
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LinkRankComparator is a Comparator for Links to sort based on the ranking.
- LinkRankComparator() - Constructor for class network.link.comparator.LinkRankComparator
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- loadedClasses - Variable in class main.DynamicLoader
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Set used to keep track of which classes were already loaded
- loadPenaltyOrLogger(String, boolean, String[]) - Method in class main.DynamicLoader
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Static method responsible for loading and instantiating a new instance of a penalty (or logger).
- log(NetworkSA) - Method in class loggers.ManualLogger
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- LoggerOrPenaltyDefinition - Class in settings
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LoggerOrPenaltyDefinition defines a penalty or logger as a class and associated content/settings
- LoggerOrPenaltyDefinition(String, String[]) - Constructor for class settings.LoggerOrPenaltyDefinition
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Constructs a LoggerOrPenaltyDefinition.
- loggers - package loggers
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A group of classes responsible for logging metrics or penalty evolutions over time during a single re-ranking process
- loggers.defined - package loggers.defined
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Predefined loggers.