Uses of Interface
nct.graph.Graph

Packages that use Graph
nct.filter   
nct.graph   
nct.graph.util   
nct.networkblast   
nct.output   
nct.score   
nct.search   
nct.service.interactions   
nct.visualization.cytoscape   
nct.visualization.cytoscape.dual   
 

Uses of Graph in nct.filter
 

Methods in nct.filter that return types with arguments of type Graph
 java.util.List<Graph<NodeType,WeightType>> DuplicateThresholdFilter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          Given the solutions, this filter compares the nodes contained in each graph, calculates the percentage of identical nodes, and throws out any solutions that have a percent identity greater than or equal to the specified threshold.
 java.util.List<Graph<NodeType,WeightType>> Filter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          This provides the basic foundation for filtering.
 java.util.List<Graph<NodeType,WeightType>> SortFilter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          Given a List of Graphs, it sorts the graphs based on the comparable implementation of the graph.
 java.util.List<Graph<java.lang.String,java.lang.Double>> UniqueCompatNodeFilter.filter(java.util.List<Graph<java.lang.String,java.lang.Double>> solutions)
           
 

Method parameters in nct.filter with type arguments of type Graph
 java.util.List<Graph<NodeType,WeightType>> DuplicateThresholdFilter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          Given the solutions, this filter compares the nodes contained in each graph, calculates the percentage of identical nodes, and throws out any solutions that have a percent identity greater than or equal to the specified threshold.
 java.util.List<Graph<NodeType,WeightType>> Filter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          This provides the basic foundation for filtering.
 java.util.List<Graph<NodeType,WeightType>> SortFilter.filter(java.util.List<Graph<NodeType,WeightType>> solutions)
          Given a List of Graphs, it sorts the graphs based on the comparable implementation of the graph.
 java.util.List<Graph<java.lang.String,java.lang.Double>> UniqueCompatNodeFilter.filter(java.util.List<Graph<java.lang.String,java.lang.Double>> solutions)
           
 

Uses of Graph in nct.graph
 

Subinterfaces of Graph in nct.graph
 interface DistanceGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          This interface describes a method that returns the distance between two nodes.
 interface KPartiteGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>,PartitionType extends Comparable<? super PartitionType>>
          A generic interface to a K-partite graph.
 interface SequenceGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An interface that describes accessing a sequence database associated with the graph.
 

Classes in nct.graph that implement Graph
 class BasicDistanceGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicGraph that calculates the minimum distance between nodes.
 class BasicGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          A generic implementation of the Graph interface.
 class BasicKPartiteGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>,PartitionType extends Comparable<? super PartitionType>>
          A generic implementation of the KPartiteGraph interface.
 class BlastGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicDistanceGraph that implements SequenceGraph and contains a pointer to a Blast database.
 class FastaGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicDistanceGraph that implements the SequenceGraph interface and contains a (pointer to a) fasta database.
 

Methods in nct.graph with parameters of type Graph
 int BasicGraph.compareTo(Graph<NodeType,WeightType> g)
          Returns the compareTo value of the score of this graph.
 int Graph.compareTo(Graph<NodeType,WeightType> g)
          Compares graph g to this graph.
 

Constructors in nct.graph with parameters of type Graph
BasicDistanceGraph(Graph<NodeType,WeightType> g)
          Copy Constructor.
BasicGraph(Graph<NodeType,WeightType> g)
          Copy Constructor.
 

Uses of Graph in nct.graph.util
 

Methods in nct.graph.util with parameters of type Graph
 void DegreePreservingRandomizer.randomize(Graph<NodeType,WeightType> g)
          The method that performs the randomization.
 void GraphRandomizer.randomize(Graph<NodeType,WeightType> g)
          The method used to randomize the graph.
 void EdgeWeightShuffle.randomize(Graph<NodeType,WeightType> g)
          Basic Fisher-Yates edge weight shuffle.
 

Uses of Graph in nct.networkblast
 

Classes in nct.networkblast that implement Graph
 class CompatibilityGraph
          This class creates a compatibility graph based on the homology of proteins between two species and the interaction graphs for the given species.
 class HomologyGraph
          This class creates a K-partite graph based on the homology of proteins between two or more species.
 class InteractionGraph
          An implementation of a SequenceGraph that is specified by a SIF file.
 class PathGraph<NodeType extends Comparable<? super NodeType>>
           
 

Fields in nct.networkblast declared as Graph
protected  Graph<NodeType,java.lang.Double> CompatComplexSearch.graph
           
 

Fields in nct.networkblast with type parameters of type Graph
protected  java.util.List<Graph<NodeType,WeightType>> CompatibilityNode.graphList
           
protected  java.util.List<Graph<NodeType,java.lang.Double>> CompatComplexSearch.seeds
           
 

Methods in nct.networkblast that return Graph
 Graph<NodeType,WeightType> CompatibilityNode.getGraph(NodeType n)
           
 

Methods in nct.networkblast that return types with arguments of type Graph
 java.util.List<Graph<NodeType,java.lang.Double>> CompatComplexSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
           
 java.util.List<Graph<NodeType,java.lang.Double>> CompatColorCodingPathSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          This function searches for pathways in the given graph of size pathSize using scoreObj and the color coding algorithm described by Scott, et al, 2005, Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks, Lecture Notes in Computer Science, vol 3500.
 

Methods in nct.networkblast with parameters of type Graph
 boolean CompatibilityNode.add(Graph<NodeType,WeightType> g, NodeType n)
           
 int PathGraph.compareTo(Graph<NodeType,java.lang.Double> g)
           
protected static void TestSearch.doSearch(int min, int max, Graph<WeightedNode<java.lang.Integer,java.lang.Double>,java.lang.Double> graph, SimpleScoreModel<WeightedNode<java.lang.Integer,java.lang.Double>> model)
           
 int CompatibilityNode.getIndex(Graph<NodeType,WeightType> g)
           
 NodeType CompatibilityNode.getNode(Graph<NodeType,WeightType> g)
           
 double CompatibilityScoreModel.scoreEdge(CompatibilityNode<java.lang.String,java.lang.Double> srcNode, CompatibilityNode<java.lang.String,java.lang.Double> destNode, Graph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double> g)
          Given a sourceNode and destNode from a graph, this method will return the score of the edge.
 double CompatibilityScoreModel.scoreGraph(Graph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double> g)
           
 double CompatibilityScoreModel.scoreNode(CompatibilityNode<java.lang.String,java.lang.Double> node, Graph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double> g)
          Given a node from graph, this function will return the score of the node.
 java.util.List<Graph<NodeType,java.lang.Double>> CompatComplexSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
           
 java.util.List<Graph<NodeType,java.lang.Double>> CompatColorCodingPathSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          This function searches for pathways in the given graph of size pathSize using scoreObj and the color coding algorithm described by Scott, et al, 2005, Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks, Lecture Notes in Computer Science, vol 3500.
 

Method parameters in nct.networkblast with type arguments of type Graph
 void CompatComplexSearch.setSeeds(java.util.List<Graph<NodeType,java.lang.Double>> newSeeds)
           
 

Constructor parameters in nct.networkblast with type arguments of type Graph
CompatComplexSearch(int seedSize, int maxComplexSize, boolean createSeeds, java.util.List<Graph<NodeType,java.lang.Double>> seeds)
           
CompatibilityScoreModel(java.util.List<? extends Graph<java.lang.String,java.lang.Double>> cg, ScoreModel<java.lang.String,java.lang.Double> logScore)
           
 

Uses of Graph in nct.output
 

Methods in nct.output with parameters of type Graph
 void ZIPSIFWriter.add(Graph<NodeType,WeightType> graph, java.lang.String name)
          Adds graph to zip archive.
static
<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
java.lang.String
SIFWriter.getSIFString(Graph<NodeType,WeightType> g)
           
 

Constructors in nct.output with parameters of type Graph
SIFWriter(Graph<NodeType,WeightType> g, java.lang.String name)
           
 

Uses of Graph in nct.score
 

Methods in nct.score with parameters of type Graph
 double SimpleNodeScoreModel.scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
          For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
 double SimpleEdgeScoreModel.scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
          For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
 double SimpleScoreModel.scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
          For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
 double LogLikelihoodScoreModel.scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
          For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
 double ScoreModel.scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,WeightType> g)
          Given a sourceNode and destNode from a graph, this method will return the score of the edge.
 double SimpleNodeScoreModel.scoreGraph(Graph<NodeType,java.lang.Double> g)
           
 double SimpleEdgeScoreModel.scoreGraph(Graph<NodeType,java.lang.Double> g)
           
 double SimpleScoreModel.scoreGraph(Graph<NodeType,java.lang.Double> graph)
           
 double LogLikelihoodScoreModel.scoreGraph(Graph<NodeType,java.lang.Double> g)
           
 double ScoreModel.scoreGraph(Graph<NodeType,WeightType> g)
           
 double SimpleNodeScoreModel.scoreNode(NodeType node, Graph<NodeType,java.lang.Double> graph)
           
 double SimpleEdgeScoreModel.scoreNode(NodeType node, Graph<NodeType,java.lang.Double> graph)
           
 double SimpleScoreModel.scoreNode(NodeType node, Graph<NodeType,java.lang.Double> graph)
           
 double LogLikelihoodScoreModel.scoreNode(NodeType node, Graph<NodeType,java.lang.Double> g)
           
 double ScoreModel.scoreNode(NodeType node, Graph<NodeType,WeightType> g)
          Given a node from graph, this function will return the score of the node.
 

Uses of Graph in nct.search
 

Methods in nct.search that return types with arguments of type Graph
 java.util.List<Graph<NodeType,java.lang.Double>> NewComplexSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          Search the graph for a complex between minSeedSize and maxComplexSize nodes in size.
 java.util.List<Graph<NodeType,java.lang.Double>> ColorCodingPathSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          This function searches for pathways in the given graph of size pathSize using scoreObj and the color coding algorithm described by Scott, et al, 2005, Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks, Lecture Notes in Computer Science, vol 3500.
 java.util.List<Graph<NodeType,WeightType>> SearchGraph.searchGraph(Graph<NodeType,WeightType> graph, ScoreModel<NodeType,WeightType> scoreObj)
          This method will be used to call a search algorithm on the given graph object.
 

Methods in nct.search with parameters of type Graph
 java.util.List<Graph<NodeType,java.lang.Double>> NewComplexSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          Search the graph for a complex between minSeedSize and maxComplexSize nodes in size.
 java.util.List<Graph<NodeType,java.lang.Double>> ColorCodingPathSearch.searchGraph(Graph<NodeType,java.lang.Double> graph, ScoreModel<NodeType,java.lang.Double> scoreObj)
          This function searches for pathways in the given graph of size pathSize using scoreObj and the color coding algorithm described by Scott, et al, 2005, Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks, Lecture Notes in Computer Science, vol 3500.
 java.util.List<Graph<NodeType,WeightType>> SearchGraph.searchGraph(Graph<NodeType,WeightType> graph, ScoreModel<NodeType,WeightType> scoreObj)
          This method will be used to call a search algorithm on the given graph object.
 

Method parameters in nct.search with type arguments of type Graph
 void NewComplexSearch.setSeeds(java.util.List<Graph<NodeType,java.lang.Double>> seeds)
           
 

Constructor parameters in nct.search with type arguments of type Graph
NewComplexSearch(int minSize, int maxSize, boolean create, java.util.List<Graph<NodeType,java.lang.Double>> seeds)
           
 

Uses of Graph in nct.service.interactions
 

Fields in nct.service.interactions declared as Graph
protected  Graph<java.lang.String,java.lang.Double> DIPInteractionNetwork.graph
           
 

Methods in nct.service.interactions with parameters of type Graph
 void InteractionNetwork.updateGraph(Graph<NodeType,WeightType> graph)
          Updates the given graph with whatever values are created from the interaction network.
 void SIFInteractionNetwork.updateGraph(Graph<java.lang.String,java.lang.Double> graph)
           
 void DIPInteractionNetwork.updateGraph(Graph<java.lang.String,java.lang.Double> graph)
          Updates the specified graph with the relevant nodes and edges contained in the XIN file and for the organism specified in the constructor.
 

Uses of Graph in nct.visualization.cytoscape
 

Methods in nct.visualization.cytoscape that return Graph
static Graph<java.lang.String,java.lang.Double> CytoscapeConverter.convert(cytoscape.CyNetwork network, Monitor monitor)
           
 

Methods in nct.visualization.cytoscape with parameters of type Graph
static cytoscape.CyNetwork CytoscapeConverter.convert(Graph<java.lang.String,java.lang.Double> nctGraph, java.lang.String title, Monitor monitor)
          Converts an NCT graph into a CyNetwork.
 

Uses of Graph in nct.visualization.cytoscape.dual
 

Methods in nct.visualization.cytoscape.dual with parameters of type Graph
static void DualLayout.create(Graph<java.lang.String,java.lang.Double> graph, java.lang.String style, java.lang.String outFile, java.lang.String outThumbFile, java.lang.String vizmapFileLoc)
          Creates a dual layout PNG graphic of the specified graph.