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C

calculate(Graph<String, Double>, List<? extends DistanceGraph<String, Double>>, String[], String[]) - Method in class nct.networkblast.graph.compatibility.AdditiveCompatibilityCalculator
The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.
calculate(Graph<String, Double>, List<? extends DistanceGraph<String, Double>>, String[], String[]) - Method in interface nct.networkblast.graph.compatibility.CompatibilityCalculator
The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.
calculateNodeDistances(List, GraphPerspective) - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
calculatePartials(SpringEmbeddedLayouter.PartialDerivatives, List, SpringEmbeddedLayouter.PotentialEnergy, boolean) - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
If partials_list is given, adjust all partials (bidirectional) for the current location of the given partials and return the new furthest node's partials.
characters(char[], int, int) - Method in class nct.service.interactions.DIPInteractionNetwork
Basic SAX event handler.
characters(char[], int, int) - Method in class nct.service.synonyms.DIPSynonyms
Standard SAX event handler.
characters(char[], int, int) - Method in class nct.xml.XMLSaxEventDistributor
 
clone() - Method in class nct.graph.basic.BasicGraph
Returns a clone of this graph.
clone() - Method in interface nct.graph.Graph
Returns a clone of this object.
ColorCodingPathSearch<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast.search
This class implements a color coding algorithm to search for pathways of size n in a given graph using a scoring object.
ColorCodingPathSearch(int) - Constructor for class nct.networkblast.search.ColorCodingPathSearch
 
ColorCodingPathSearch(int, int) - Constructor for class nct.networkblast.search.ColorCodingPathSearch
 
ColorCodingPathSearch(int, int, double) - Constructor for class nct.networkblast.search.ColorCodingPathSearch
 
compareTo(Edge<NodeType, WeightType>) - Method in class nct.graph.basic.BasicEdge
First compares whether the source and target nodes are the same and if so assumes the edge is the same.
compareTo(Graph<NodeType, WeightType>) - Method in class nct.graph.basic.BasicGraph
Returns the compareTo value of the score of this graph.
compareTo(WeightedNode<IDType, WeightType>) - Method in class nct.graph.basic.BasicWeightedNode
 
compareTo(Graph<NodeType, WeightType>) - Method in interface nct.graph.Graph
Compares graph g to this graph.
compatCalc - Variable in class nct.networkblast.graph.CompatibilityGraph
 
compatFile - Variable in class nct.networkblast.NetworkBlast
 
CompatibilityCalculator - Interface in nct.networkblast.graph.compatibility
Provides an interface for alternative methods of determining which potential compatibility nodes should be included in the compatibility graph and how the edge scores between the nodes are calculated.
CompatibilityGraph - Class in nct.networkblast.graph
This class creates a compatibility graph based on the homology of proteins between two species and the interaction graphs for the given species.
CompatibilityGraph(KPartiteGraph<String, Double, ? extends DistanceGraph<String, Double>>, List<? extends DistanceGraph<String, Double>>, ScoreModel<String, Double>, CompatibilityCalculator) - Constructor for class nct.networkblast.graph.CompatibilityGraph
Constructor.
complexMaxSize - Static variable in class nct.networkblast.NetworkBlast
 
complexMinSeedSize - Static variable in class nct.networkblast.NetworkBlast
 
contains(String) - Method in class nct.service.sequences.DIPSequenceDatabase
Determines whether or not the specified id points to a sequence in the database.
contains(String) - Method in interface nct.service.sequences.SequenceDatabase
Determines whether or not the specified id points to a sequence in the database.
contains(Node, Node) - Method in class nct.visualization.cytoscape.dual.NodePairSet
 
content - Variable in class nct.output.ZIPSIFWriter
The content to be written.
create(Graph<String, Double>, String, String, String, String) - Static method in class nct.visualization.cytoscape.dual.DualLayout
Creates a dual layout PNG graphic of the specified graph.

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