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