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getAllKCliques()
- Method in class nct.graph.
BasicKPartiteGraph
Returns a list of all k-cliques that exist in the graph.
getDBLocation()
- Method in class nct.graph.
BlastGraph
Returns the location of the Blast database used.
getDBLocation()
- Method in class nct.graph.
FastaGraph
Returns the location of the database used.
getDBLocation()
- Method in interface nct.graph.
SequenceGraph
Returns the location of the database used.
getDBLocation()
- Method in class nct.networkblast.
InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
getDBName()
- Method in class nct.graph.
BlastGraph
Returns the name of the Blast database used.
getDBName()
- Method in class nct.graph.
FastaGraph
Returns the name of the database used.
getDBName()
- Method in interface nct.graph.
SequenceGraph
Returns the name of the database used.
getDBName()
- Method in class nct.networkblast.
InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
getDBType()
- Method in class nct.graph.
BlastGraph
Returns an integer identifying the type of database as Blast.
getDBType()
- Method in class nct.graph.
FastaGraph
Returns an integer identifying the type of database as FASTA.
getDBType()
- Method in interface nct.graph.
SequenceGraph
Returns an integer identifying the type of database used.
getDBType()
- Method in class nct.networkblast.
InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
getDescription()
- Method in class nct.graph.
BasicEdge
getDescription()
- Method in interface nct.graph.
Edge
getDistance(NodeType, NodeType)
- Method in class nct.graph.
BasicDistanceGraph
Returns the minimum distance between the specified nodes.
getDistance(NodeType, NodeType)
- Method in interface nct.graph.
DistanceGraph
Returns the minimum distance between the specified nodes.
getEdge(NodeType, NodeType)
- Method in class nct.graph.
BasicGraph
Returns the specified edge.
getEdge(NodeType, NodeType)
- Method in interface nct.graph.
Graph
Returns a specific edge.
getEdge(NodeType, NodeType)
- Method in class nct.networkblast.
PathGraph
getEdgeDescription(NodeType, NodeType)
- Method in class nct.graph.
BasicGraph
Returns a description of the edge implied by the two specified nodes.
getEdgeDescription(NodeType, NodeType)
- Method in interface nct.graph.
Graph
Returns a description of the edge implied by the two specified nodes.
getEdgeDescription(NodeType, NodeType)
- Method in class nct.networkblast.
PathGraph
getEdgeList()
- Method in class nct.graph.
BasicGraph
getEdgeList()
- Method in interface nct.graph.
Graph
getEdgeList()
- Method in class nct.networkblast.
PathGraph
getEdges()
- Method in class nct.graph.
BasicGraph
Returns a list of all edges in the graph.
getEdges()
- Method in interface nct.graph.
Graph
Returns all edges in the graph.
getEdges()
- Method in class nct.networkblast.
PathGraph
getEdgeWeight(NodeType, NodeType)
- Method in class nct.graph.
BasicGraph
Returns the weight of the edge implied by the two specified nodes.
getEdgeWeight(NodeType, NodeType)
- Method in interface nct.graph.
Graph
Returns the weight of the edge implied by the two specified nodes.
getEdgeWeight(String, String)
- Method in class nct.networkblast.
InteractionGraph
Instead of returning null when an edge doesn't exist, it returns -1.
getEdgeWeight(NodeType, NodeType)
- Method in class nct.networkblast.
PathGraph
getGraph(NodeType)
- Method in class nct.networkblast.
CompatibilityNode
getGraphView()
- Method in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
getId()
- Method in class nct.graph.
BasicGraph
Returns the id of the graph, in this case the filename of the input file that specifies the graph.
getID()
- Method in class nct.graph.
BasicWeightedNode
getId()
- Method in interface nct.graph.
Graph
Returns the id of the graph.
getID()
- Method in interface nct.graph.
WeightedNode
getId()
- Method in class nct.networkblast.
PathGraph
getIdFromSynonym(String)
- Method in class nct.service.synonyms.
DIPSynonyms
Returns the unique id for the specified synonym.
getIdFromSynonym(String)
- Method in interface nct.service.synonyms.
SynonymMapper
Returns the unique id for the specified synonym.
getIndex(NodeType)
- Method in class nct.networkblast.
CompatibilityNode
getIndex(Graph<NodeType, WeightType>)
- Method in class nct.networkblast.
CompatibilityNode
getK()
- Method in class nct.graph.
BasicKPartiteGraph
This method returns the number of possible partitions.
getK()
- Method in interface nct.graph.
KPartiteGraph
Returns the number of possible partitions in the graph.
getMonitor()
- Method in class nct.search.
ColorCodingPathSearch
getMonitor()
- Method in class nct.search.
NewComplexSearch
getMonitor()
- Method in interface nct.visualization.cytoscape.
Monitorable
getNeighbors(NodeType)
- Method in class nct.graph.
BasicGraph
Returns a set all nodes adjacent to the specified node.
getNeighbors(NodeType)
- Method in interface nct.graph.
Graph
Returns a set all nodes adjacent to the specified node.
getNeighbors(NodeType)
- Method in class nct.networkblast.
PathGraph
getNode(Graph<NodeType, WeightType>)
- Method in class nct.networkblast.
CompatibilityNode
getNodes()
- Method in class nct.graph.
BasicGraph
Returns a set containing all nodes in the graph.
getNodes()
- Method in interface nct.graph.
Graph
Returns a set containing all nodes in the graph.
getNodes()
- Method in class nct.networkblast.
CompatibilityNode
getNodes()
- Method in class nct.networkblast.
PathGraph
getNodeViewIndex(NodeView)
- Method in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
getNumPartitions()
- Method in class nct.graph.
BasicKPartiteGraph
This method returns the number of existing partitions.
getNumPartitions()
- Method in interface nct.graph.
KPartiteGraph
Returns the number of partitions currently contained in the graph (not necessarily K if K partitions haven't yet been added).
getOrganism
- Variable in class nct.service.interactions.
DIPInteractionNetwork
getOuterMap()
- Method in class nct.visualization.cytoscape.dual.
NodePairSet
getPartitions()
- Method in class nct.graph.
BasicKPartiteGraph
Returns a list of the partitions currently contained in the graph (not necessarily K if K partitions haven't yet been added).
getPartitions()
- Method in interface nct.graph.
KPartiteGraph
Returns a list of the partitions currently contained in the graph (not necessarily K if K partitions haven't yet been added).
getPotentialSynonyms(String)
- Method in class nct.service.synonyms.
DIPSynonyms
Returns a list of matches to the input string which is treated as a regular expression pattern.
getPotentialSynonyms(String)
- Method in interface nct.service.synonyms.
SynonymMapper
This method will return a list of potential synonyms that match the input.
getScore()
- Method in class nct.graph.
BasicGraph
Returns the score of the graph.
getScore()
- Method in interface nct.graph.
Graph
Returns the score of the graph.
getScore()
- Method in class nct.networkblast.
PathGraph
getSequence(String)
- Method in class nct.service.sequences.
DIPSequenceDatabase
Returns the sequence associated with the specified id from the database.
getSequence(String)
- Method in interface nct.service.sequences.
SequenceDatabase
Returns the sequence associated with the specified id from the database.
getSIFString(Graph<NodeType, WeightType>)
- Static method in class nct.output.
SIFWriter
getSourceNode()
- Method in class nct.graph.
BasicEdge
getSourceNode()
- Method in interface nct.graph.
Edge
getSynonym(String, String)
- Method in class nct.service.synonyms.
DIPSynonyms
A shortcut method for calling:
String s = syns.getSynonymFromId(syns.getIdFromSynonym(synonym), type);
getSynonym(String, String)
- Method in interface nct.service.synonyms.
SynonymMapper
A shortcut method for calling:
String s = syns.getSynonymFromId(syns.getIdFromSynonym(synonym), type);
getSynonymFromId(String, String)
- Method in class nct.service.synonyms.
DIPSynonyms
Returns a synonym of a particular type for the specified id.
getSynonymFromId(String, String)
- Method in interface nct.service.synonyms.
SynonymMapper
Returns a synonym of a particular type for the specified id.
getTargetNode()
- Method in class nct.graph.
BasicEdge
getTargetNode()
- Method in interface nct.graph.
Edge
getValue
- Variable in class nct.service.interactions.
DIPInteractionNetwork
getWeight()
- Method in class nct.graph.
BasicEdge
getWeight()
- Method in class nct.graph.
BasicWeightedNode
getWeight()
- Method in interface nct.graph.
Edge
getWeight()
- Method in interface nct.graph.
WeightedNode
Graph
<
NodeType
extends java.lang.Comparable<? super
NodeType
>,
WeightType
extends java.lang.Comparable<? super
WeightType
>> - Interface in
nct.graph
A generic interface that defines an edge weighted, undirected graph.
graph
- Variable in class nct.networkblast.
CompatComplexSearch
graph
- Variable in class nct.service.interactions.
DIPInteractionNetwork
graphList
- Variable in class nct.networkblast.
CompatibilityNode
GraphRandomizer
<
NodeType
extends java.lang.Comparable<? super
NodeType
>,
WeightType
extends java.lang.Comparable<? super
WeightType
>> - Interface in
nct.graph.util
A randomization interface.
graphView
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
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