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layoutNetwork(PGraphView) - Method in class nct.visualization.cytoscape.dual.DualLayoutTask
Creates the layout of the network using the SpringEmbeddedLayouter.
layoutPass - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
LocalBlast - Class in nct.service.homology.blast
A Blast implementation of the HomologyModel interface that runs Blast locally.
LocalBlast(Properties, String, double) - Constructor for class nct.service.homology.blast.LocalBlast
Constructor.
LocalBlast(Properties, SynonymMapper, String, double) - Constructor for class nct.service.homology.blast.LocalBlast
Constructor.
logLevel - Static variable in class nct.networkblast.NetworkBlast
 
logLevelDefault - Static variable in class nct.networkblast.NetworkBlast
 
LogLikelihoodScoreModel<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast.score
This class implements the log likelihood edge scoring scheme described in the supplemental to Sharan, et al., 2005, Conserved patterns of protein interaction in multiple species, PNAS, 102(6).
LogLikelihoodScoreModel(double, double, double) - Constructor for class nct.networkblast.score.LogLikelihoodScoreModel
Sets the truthFactor accordingly (ensures > 0) and initializes the graphMap object.

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