A B C D E F G H I K L M N O P Q R S T U V W X Z

G

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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