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N

nct.filter - package nct.filter
 
nct.graph - package nct.graph
 
nct.graph.basic - package nct.graph.basic
 
nct.graph.util - package nct.graph.util
 
nct.networkblast - package nct.networkblast
 
nct.networkblast.filter - package nct.networkblast.filter
 
nct.networkblast.graph - package nct.networkblast.graph
 
nct.networkblast.graph.compatibility - package nct.networkblast.graph.compatibility
 
nct.networkblast.score - package nct.networkblast.score
 
nct.networkblast.search - package nct.networkblast.search
 
nct.output - package nct.output
 
nct.parsers - package nct.parsers
 
nct.service.homology - package nct.service.homology
 
nct.service.homology.blast - package nct.service.homology.blast
 
nct.service.homology.sif - package nct.service.homology.sif
 
nct.service.interactions - package nct.service.interactions
 
nct.service.sequences - package nct.service.sequences
 
nct.service.synonyms - package nct.service.synonyms
 
nct.visualization.cytoscape.dual - package nct.visualization.cytoscape.dual
 
nct.xml - package nct.xml
 
NetworkBlast - Class in nct.networkblast
The main program (NetworkBlast.java) will create all the objects needed to run the NetworkBlast algorithm.
NetworkBlast(String[]) - Constructor for class nct.networkblast.NetworkBlast
This is the main class that initializes and executes everything.
NewComplexSearch<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast.search
This class implements the SearchGraph interface.
NewComplexSearch(int, int) - Constructor for class nct.networkblast.search.NewComplexSearch
Sets the max and min sizes for complexes.
NewComplexSearch(int, int, boolean, List<Graph<NodeType, Double>>) - Constructor for class nct.networkblast.search.NewComplexSearch
 
node2Index - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
node2Species - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeCount - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeDistanceRestLengthConstant - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeDistanceSpringRestLengths - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeDistanceSpringScalars - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeDistanceSpringStrengths - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeDistanceStrengthConstant - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
nodeId - Variable in class nct.service.interactions.DIPInteractionNetwork
 
nodeOrganismMap - Variable in class nct.service.interactions.DIPInteractionNetwork
 
NodePairSet - Class in nct.visualization.cytoscape.dual
This class keeps track of a set of unordered pairs of nodes
NodePairSet() - Constructor for class nct.visualization.cytoscape.dual.NodePairSet
 
normalize - Variable in class nct.service.homology.blast.LocalBlast
Whether or not to normalize e-values based on database size.
notationDecl(String, String, String) - Method in class nct.xml.XMLSaxEventDistributor
 
numberOfEdges() - Method in class nct.graph.basic.BasicGraph
Returns the number of edges in the graph.
numberOfEdges() - Method in interface nct.graph.Graph
Returns the number of edges in the graph.
numberOfNodes() - Method in class nct.graph.basic.BasicGraph
Returns the number of nodes in the graph.
numberOfNodes() - Method in interface nct.graph.Graph
Returns the number of nodes in the graph.
numEdges - Variable in class nct.graph.basic.BasicGraph
The number of edges in the graph.
numLayoutPasses - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
numSimulations - Variable in class nct.networkblast.NetworkBlast
 

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