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Packages that use Graph | |
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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 |
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Methods in nct.filter that return types with arguments of type Graph | |
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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)
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Method parameters in nct.filter with type arguments of type Graph | |
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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)
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Uses of Graph in nct.graph |
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Subinterfaces of Graph in nct.graph | |
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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. |
Methods in nct.graph with parameters of type Graph | |
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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 | |
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BasicDistanceGraph(Graph<NodeType,WeightType> g)
Copy Constructor. |
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BasicGraph(Graph<NodeType,WeightType> g)
Copy Constructor. |
Uses of Graph in nct.graph.util |
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Methods in nct.graph.util with parameters of type Graph | |
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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 |
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Classes in nct.networkblast that implement Graph | |
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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 | |
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protected Graph<NodeType,java.lang.Double> |
CompatComplexSearch.graph
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Fields in nct.networkblast with type parameters of type Graph | |
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protected java.util.List<Graph<NodeType,WeightType>> |
CompatibilityNode.graphList
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protected java.util.List<Graph<NodeType,java.lang.Double>> |
CompatComplexSearch.seeds
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Methods in nct.networkblast that return Graph | |
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Graph<NodeType,WeightType> |
CompatibilityNode.getGraph(NodeType n)
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Methods in nct.networkblast that return types with arguments of type Graph | |
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java.util.List<Graph<NodeType,java.lang.Double>> |
CompatComplexSearch.searchGraph(Graph<NodeType,java.lang.Double> graph,
ScoreModel<NodeType,java.lang.Double> scoreObj)
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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 | |
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boolean |
CompatibilityNode.add(Graph<NodeType,WeightType> g,
NodeType n)
|
int |
PathGraph.compareTo(Graph<NodeType,java.lang.Double> g)
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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)
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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)
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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 | |
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void |
CompatComplexSearch.setSeeds(java.util.List<Graph<NodeType,java.lang.Double>> newSeeds)
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Constructor parameters in nct.networkblast with type arguments of type Graph | |
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CompatComplexSearch(int seedSize,
int maxComplexSize,
boolean createSeeds,
java.util.List<Graph<NodeType,java.lang.Double>> seeds)
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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 |
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Methods in nct.output with parameters of type Graph | ||
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void |
ZIPSIFWriter.add(Graph<NodeType,WeightType> graph,
java.lang.String name)
Adds graph to zip archive. |
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static
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SIFWriter.getSIFString(Graph<NodeType,WeightType> g)
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Constructors in nct.output with parameters of type Graph | |
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SIFWriter(Graph<NodeType,WeightType> g,
java.lang.String name)
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Uses of Graph in nct.score |
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Methods in nct.score with parameters of type Graph | |
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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)
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double |
LogLikelihoodScoreModel.scoreGraph(Graph<NodeType,java.lang.Double> g)
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double |
ScoreModel.scoreGraph(Graph<NodeType,WeightType> g)
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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)
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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 |
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Methods in nct.search that return types with arguments of type Graph | |
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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 | |
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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 | |
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void |
NewComplexSearch.setSeeds(java.util.List<Graph<NodeType,java.lang.Double>> seeds)
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Constructor parameters in nct.search with type arguments of type Graph | |
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NewComplexSearch(int minSize,
int maxSize,
boolean create,
java.util.List<Graph<NodeType,java.lang.Double>> seeds)
|
Uses of Graph in nct.service.interactions |
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Fields in nct.service.interactions declared as Graph | |
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protected Graph<java.lang.String,java.lang.Double> |
DIPInteractionNetwork.graph
|
Methods in nct.service.interactions with parameters of type Graph | |
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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 |
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Methods in nct.visualization.cytoscape that return Graph | |
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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 | |
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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 |
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Methods in nct.visualization.cytoscape.dual with parameters of type Graph | |
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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. |
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