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A

add(Graph<NodeType, WeightType>, String) - Method in class nct.output.ZIPSIFWriter
Adds graph to zip archive.
add(Node, Node) - Method in class nct.visualization.cytoscape.dual.NodePairSet
 
addEdge(NodeType, NodeType, WeightType) - Method in class nct.graph.basic.BasicGraph
Adds an edge to the graph.
addEdge(NodeType, NodeType, WeightType, String) - Method in class nct.graph.basic.BasicGraph
Adds an edge to the graph.
addEdge(NodeType, NodeType, WeightType) - Method in class nct.graph.basic.BasicKPartiteGraph
Adds an edge to the graph.
addEdge(NodeType, NodeType, WeightType) - Method in interface nct.graph.Graph
Adds an edge to the graph.
addEdge(NodeType, NodeType, WeightType, String) - Method in interface nct.graph.Graph
Adds an edge to the graph.
addGraph(SequenceGraph<String, Double>) - Method in class nct.networkblast.graph.HomologyGraph
Adds the nodes of the specified graph to this graph and adds the graph as a partition.
addHandler(HandlerType) - Method in class nct.xml.XMLSaxEventDistributor
 
addId(String, String, String) - Method in class nct.service.synonyms.DIPSynonyms
Adds an id to the synonym database for a specific type.
AdditiveCompatibilityCalculator - Class in nct.networkblast.graph.compatibility
This class creates the compatibility edge score by summing the edge weights of the interaction edges that comprise the compatibility node.
AdditiveCompatibilityCalculator(double, ScoreModel<String, Double>, boolean) - Constructor for class nct.networkblast.graph.compatibility.AdditiveCompatibilityCalculator
 
AdditiveCompatibilityCalculator(double, ScoreModel<String, Double>) - Constructor for class nct.networkblast.graph.compatibility.AdditiveCompatibilityCalculator
 
addNode(NodeType) - Method in class nct.graph.basic.BasicGraph
Adds a node to the graph.
addNode(NodeType) - Method in class nct.graph.basic.BasicKPartiteGraph
This method overrides the BasicGraph implementation of addNode and always returns false because it is impossible to add a node to a k-paritite graph without also specifying the partition.
addNode(NodeType, PartitionType) - Method in class nct.graph.basic.BasicKPartiteGraph
Adds a node to the graph.
addNode(NodeType) - Method in interface nct.graph.Graph
Adds a node to the graph.
addNode(NodeType, PartitionType) - Method in interface nct.graph.KPartiteGraph
Adds a node to a specific partition in the graph.
addValue(String, String, String) - Method in class nct.service.synonyms.DIPSynonyms
Adds a value to the synonym database for a specific type.
allowZero - Variable in class nct.networkblast.graph.compatibility.AdditiveCompatibilityCalculator
 
anticollisionSpringScalars - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
anticollisionSpringStrength - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
assumeGraphFinished - Variable in class nct.graph.basic.BasicGraph
Used to indicate whether the graph has been updated (ie node or edge added) since the last time a value based on the graph (eg numEdges) was calculated.
averageIterationsPerNode - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 

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