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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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