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D

dbLocation - Variable in class nct.graph.BlastGraph
This string is the location of the database files.
dbName - Variable in class nct.graph.BlastGraph
This string is the name of the database files.
DEFAULT_ANTICOLLISION_SPRING_SCALARS - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_ANTICOLLISION_SPRING_STRENGTH - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_AVERAGE_ITERATIONS_PER_NODE - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_DISCONNECTED_NODE_DISTANCE_SPRING_REST_LENGTH - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_DISCONNECTED_NODE_DISTANCE_SPRING_STRENGTH - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_EPSILON - Static variable in class nct.networkblast.CompatColorCodingPathSearch
The default epsilon value.
DEFAULT_EPSILON - Static variable in class nct.search.ColorCodingPathSearch
The default epsilon value.
DEFAULT_NODE_DISTANCE_REST_LENGTH_CONSTANT - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_NODE_DISTANCE_SPRING_SCALARS - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_NODE_DISTANCE_STRENGTH_CONSTANT - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DEFAULT_NUM_LAYOUT_PASSES - Static variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
defaultPathSize - Static variable in class nct.networkblast.NetworkBlast
 
degreeOfNode(NodeType) - Method in class nct.graph.BasicGraph
Returns the degree (number of neighbors) of the node.
degreeOfNode(NodeType) - Method in interface nct.graph.Graph
Returns the degree (number of neighbors) of the node.
degreeOfNode(NodeType) - Method in class nct.networkblast.PathGraph
 
DegreePreservingRandomizer<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph.util
This class shuffles the edges in a graph while preserving the degree of each node in the class and only swapping edges with "similar" edge weights.
DegreePreservingRandomizer(Random, boolean) - Constructor for class nct.graph.util.DegreePreservingRandomizer
 
descMap - Variable in class nct.graph.BasicGraph
A mapping of nodes to nodes to edge descriptions.
description - Variable in class nct.graph.BasicEdge
The edge description.
DIPInteractionNetwork - Class in nct.service.interactions
Implements the InteractionNetwork interface by reading a DIP XIN (xml) file.
DIPInteractionNetwork(String) - Constructor for class nct.service.interactions.DIPInteractionNetwork
A SAX event handler that extracts graph information (nodes and edges) for a specific organism from a specified DIP XIN database file http://dip.doe-mbi.ucla.edu.
DIPSequenceDatabase - Class in nct.service.sequences
An implementation of the SequenceDatabase interface that is constructed from a DIP fasta file.
DIPSequenceDatabase(String, SynonymMapper) - Constructor for class nct.service.sequences.DIPSequenceDatabase
 
DIPSynonyms - Class in nct.service.synonyms
Implements a SynonymMapper based on a DIP XIN file.
DIPSynonyms() - Constructor for class nct.service.synonyms.DIPSynonyms
Initializes the content handler.
disconnectedNodeDistanceSpringRestLength - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
disconnectedNodeDistanceSpringStrength - Variable in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
DistanceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Interface in nct.graph
This interface describes a method that returns the distance between two nodes.
distMap - Variable in class nct.graph.BasicDistanceGraph
A mapping of node to node to distance.
doctypeRegEx - Static variable in class nct.service.homology.BlastXMLFileFilterInputStream
The string defining the regular expression used to identify the DOCTYPE tags in the Blast ouptput.
doLayout() - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
doSearch(int, int, Graph<WeightedNode<Integer, Double>, Double>, SimpleScoreModel<WeightedNode<Integer, Double>>) - Static method in class nct.networkblast.TestSearch
 
DualLayout - Class in nct.visualization.cytoscape.dual
Constructs several Cytoscape objects based on an input Graph and renders the graph in Dual Layout mode.
DualLayout() - Constructor for class nct.visualization.cytoscape.dual.DualLayout
 
DualLayoutTask - Class in nct.visualization.cytoscape.dual
The Thread that does the actual DualLayout calculations.
DualLayoutTask(CyNetwork) - Constructor for class nct.visualization.cytoscape.dual.DualLayoutTask
 
DUMMY - Static variable in interface nct.graph.SequenceGraph
A dummy (non-existant) database type.
dupeThreshold - Variable in class nct.networkblast.NetworkBlast
 
dupeThresholdDefault - Static variable in class nct.networkblast.NetworkBlast
 
DuplicateThresholdFilter<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.filter
This class will throw out any solutions with a certain percentage of duplicate nodes.
DuplicateThresholdFilter(double) - Constructor for class nct.filter.DuplicateThresholdFilter
Sets the threshold according to the given value.

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