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C

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
 
checkConstraint(int) - Method in class nct.networkblast.CompatColorCodingPathSearch
Checks if a given path contains at least one of the nodes in the constraint set.
checkConstraint(int) - Method in class nct.search.ColorCodingPathSearch
Checks if a given path contains at least one of the nodes in the constraint set.
clone() - Method in class nct.graph.BasicGraph
Returns a clone of this graph.
clone() - Method in interface nct.graph.Graph
Returns a clone of this object.
clone() - Method in class nct.networkblast.PathGraph
 
ColorCodingPathSearch<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.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.search.ColorCodingPathSearch
 
ColorCodingPathSearch(int, int) - Constructor for class nct.search.ColorCodingPathSearch
 
ColorCodingPathSearch(int, int, double) - Constructor for class nct.search.ColorCodingPathSearch
 
compareTo(Edge<NodeType, WeightType>) - Method in class nct.graph.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.BasicGraph
Returns the compareTo value of the score of this graph.
compareTo(WeightedNode<IDType, WeightType>) - Method in class nct.graph.BasicWeightedNode
 
compareTo(Graph<NodeType, WeightType>) - Method in interface nct.graph.Graph
Compares graph g to this graph.
compareTo(CompatibilityNode<NodeType, WeightType>) - Method in class nct.networkblast.CompatibilityNode
 
compareTo(Graph<NodeType, Double>) - Method in class nct.networkblast.PathGraph
 
CompatColorCodingPathSearch<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast
This class implements a color coding algorithm to search for pathways of size n in a given graph using a scoring object.
CompatColorCodingPathSearch(int) - Constructor for class nct.networkblast.CompatColorCodingPathSearch
 
CompatColorCodingPathSearch(int, int) - Constructor for class nct.networkblast.CompatColorCodingPathSearch
 
CompatColorCodingPathSearch(int, int, double) - Constructor for class nct.networkblast.CompatColorCodingPathSearch
 
CompatComplexSearch<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast
This class implements the SearchGraph interface.
CompatComplexSearch(int, int) - Constructor for class nct.networkblast.CompatComplexSearch
 
CompatComplexSearch(int, int, boolean, List<Graph<NodeType, Double>>) - Constructor for class nct.networkblast.CompatComplexSearch
 
compatFile - Variable in class nct.networkblast.NetworkBlast
 
CompatibilityGraph - Class in nct.networkblast
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>) - Constructor for class nct.networkblast.CompatibilityGraph
Constructor.
CompatibilityNode<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.networkblast
 
CompatibilityNode() - Constructor for class nct.networkblast.CompatibilityNode
 
CompatibilityScoreModel - Class in nct.networkblast
This interface will provide the scoring interface for all scoring algorithms to be used on a Graph object.
CompatibilityScoreModel(List<? extends Graph<String, Double>>, ScoreModel<String, Double>) - Constructor for class nct.networkblast.CompatibilityScoreModel
 
complexMaxSize - Static variable in class nct.networkblast.NetworkBlast
 
complexMinSeedSize - Static variable in class nct.networkblast.NetworkBlast
 
consistentSegmentation(NodeType, int) - Method in class nct.networkblast.CompatColorCodingPathSearch
Checks that the node is consistent with the segement indicated by the color combination (ie the number of bits).
consistentSegmentation(NodeType, int) - Method in class nct.search.ColorCodingPathSearch
Checks that the node is consistent with the segement indicated by the color combination (ie the number of bits).
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.
convert(CyNetwork, Monitor) - Static method in class nct.visualization.cytoscape.CytoscapeConverter
 
convert(Graph<String, Double>, String, Monitor) - Static method in class nct.visualization.cytoscape.CytoscapeConverter
Converts an NCT graph into a CyNetwork.
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.
createSeeds - Variable in class nct.networkblast.CompatComplexSearch
 
CytoscapeConverter - Class in nct.visualization.cytoscape
A utility class for converting an NCT graph into a CyNetwork.
CytoscapeConverter() - Constructor for class nct.visualization.cytoscape.CytoscapeConverter
 

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