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

S

score - Variable in class nct.graph.BasicGraph
The score of the graph.
scoreEdge(CompatibilityNode<String, Double>, CompatibilityNode<String, Double>, Graph<CompatibilityNode<String, Double>, Double>) - Method in class nct.networkblast.CompatibilityScoreModel
Given a sourceNode and destNode from a graph, this method will return the score of the edge.
scoreEdge(NodeType, NodeType, Graph<NodeType, Double>) - Method in class nct.score.LogLikelihoodScoreModel
For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
scoreEdge(NodeType, NodeType, Graph<NodeType, WeightType>) - Method in interface nct.score.ScoreModel
Given a sourceNode and destNode from a graph, this method will return the score of the edge.
scoreEdge(NodeType, NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleEdgeScoreModel
For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
scoreEdge(NodeType, NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleNodeScoreModel
For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
scoreEdge(NodeType, NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleScoreModel
For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model.
scoreGraph(Graph<CompatibilityNode<String, Double>, Double>) - Method in class nct.networkblast.CompatibilityScoreModel
 
scoreGraph(Graph<NodeType, Double>) - Method in class nct.score.LogLikelihoodScoreModel
 
scoreGraph(Graph<NodeType, WeightType>) - Method in interface nct.score.ScoreModel
 
scoreGraph(Graph<NodeType, Double>) - Method in class nct.score.SimpleEdgeScoreModel
 
scoreGraph(Graph<NodeType, Double>) - Method in class nct.score.SimpleNodeScoreModel
 
scoreGraph(Graph<NodeType, Double>) - Method in class nct.score.SimpleScoreModel
 
scoreModel - Variable in class nct.networkblast.CompatibilityGraph
 
ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Interface in nct.score
This interface will provide the scoring interface for all scoring algorithms to be used on a Graph object.
scoreNode(CompatibilityNode<String, Double>, Graph<CompatibilityNode<String, Double>, Double>) - Method in class nct.networkblast.CompatibilityScoreModel
Given a node from graph, this function will return the score of the node.
scoreNode(NodeType, Graph<NodeType, Double>) - Method in class nct.score.LogLikelihoodScoreModel
 
scoreNode(NodeType, Graph<NodeType, WeightType>) - Method in interface nct.score.ScoreModel
Given a node from graph, this function will return the score of the node.
scoreNode(NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleEdgeScoreModel
 
scoreNode(NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleNodeScoreModel
 
scoreNode(NodeType, Graph<NodeType, Double>) - Method in class nct.score.SimpleScoreModel
 
scoreObj - Variable in class nct.networkblast.CompatComplexSearch
 
searchGraph(Graph<NodeType, Double>, ScoreModel<NodeType, Double>) - Method in class nct.networkblast.CompatColorCodingPathSearch
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.
searchGraph(Graph<NodeType, Double>, ScoreModel<NodeType, Double>) - Method in class nct.networkblast.CompatComplexSearch
 
searchGraph(Graph<NodeType, Double>, ScoreModel<NodeType, Double>) - Method in class nct.search.ColorCodingPathSearch
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.
searchGraph(Graph<NodeType, Double>, ScoreModel<NodeType, Double>) - Method in class nct.search.NewComplexSearch
Search the graph for a complex between minSeedSize and maxComplexSize nodes in size.
SearchGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Interface in nct.search
This interface will provide an interface for all searching algorithms to be used on a Graph object.
searchGraph(Graph<NodeType, WeightType>, ScoreModel<NodeType, WeightType>) - Method in interface nct.search.SearchGraph
This method will be used to call a search algorithm on the given graph object.
seeds - Variable in class nct.networkblast.CompatComplexSearch
 
seedSize - Variable in class nct.networkblast.CompatComplexSearch
 
SequenceDatabase - Interface in nct.service.sequences
An interface describing a way to query a sequence database for sequence and existence information.
SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Interface in nct.graph
An interface that describes accessing a sequence database associated with the graph.
sequenceMap - Variable in class nct.service.sequences.DIPSequenceDatabase
 
setBeginNodes(Set<NodeType>) - Method in class nct.networkblast.CompatColorCodingPathSearch
This methods defines a set of nodes from which one must BEGIN every path.
setBeginNodes(Set<NodeType>) - Method in class nct.search.ColorCodingPathSearch
This methods defines a set of nodes from which one must BEGIN every path.
setConstraint(Set<NodeType>, int, int) - Method in class nct.networkblast.CompatColorCodingPathSearch
Sets a constraint on a path such that the path must contain a node (or nodes) in the specified constraint set.
setConstraint(Set<NodeType>, int, int) - Method in class nct.search.ColorCodingPathSearch
Sets a constraint on a path such that the path must contain a node (or nodes) in the specified constraint set.
setDBLocation(String) - Method in class nct.graph.BlastGraph
Sets the location of the database.
setDBLocation(String) - Method in class nct.graph.FastaGraph
Sets the location of the database.
setDBLocation(String) - Method in interface nct.graph.SequenceGraph
Sets the location of the database.
setDBLocation(String) - Method in class nct.networkblast.InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
setDBName(String) - Method in class nct.graph.BlastGraph
Sets the name of the database.
setDBName(String) - Method in class nct.graph.FastaGraph
Sets the name of the database.
setDBName(String) - Method in interface nct.graph.SequenceGraph
Sets the name of the database.
setDBName(String) - Method in class nct.networkblast.InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
setDBType(int) - Method in class nct.graph.BlastGraph
Sets the type of the database.
setDBType(int) - Method in class nct.graph.FastaGraph
Sets the type of the database.
setDBType(int) - Method in interface nct.graph.SequenceGraph
Sets the type of the database.
setDBType(int) - Method in class nct.networkblast.InteractionGraph
Dummy method needed to implement the SequenceGraph interface.
setDescription(String) - Method in class nct.graph.BasicEdge
 
setDescription(String) - Method in interface nct.graph.Edge
 
setDocumentLocator(Locator) - Method in class nct.xml.XMLSaxEventDistributor
 
setEdgeDescription(NodeType, NodeType, String) - Method in class nct.graph.BasicGraph
Sets the description for the specified edge.
setEdgeDescription(NodeType, NodeType, String) - Method in interface nct.graph.Graph
Sets a description for the edge implied by the two specified nodes.
setEdgeDescription(NodeType, NodeType, String) - Method in class nct.networkblast.PathGraph
 
setEdgeWeight(NodeType, NodeType, WeightType) - Method in class nct.graph.BasicGraph
Sets the edge weight of an existing edge.
setEdgeWeight(NodeType, NodeType, WeightType) - Method in interface nct.graph.Graph
 
setEdgeWeight(NodeType, NodeType, Double) - Method in class nct.networkblast.PathGraph
 
setEndNodes(Set<NodeType>) - Method in class nct.networkblast.CompatColorCodingPathSearch
This methods defines a set of nodes from which one must END every path.
setEndNodes(Set<NodeType>) - Method in class nct.search.ColorCodingPathSearch
This methods defines a set of nodes from which one must END every path.
setGraphView(GraphView) - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
setMonitor(Monitor) - Method in class nct.search.ColorCodingPathSearch
 
setMonitor(Monitor) - Method in class nct.search.NewComplexSearch
 
setMonitor(Monitor) - Method in interface nct.visualization.cytoscape.Monitorable
 
setPercentCompleted(int) - Method in class nct.visualization.cytoscape.Monitor
 
setScore(WeightType) - Method in class nct.graph.BasicGraph
Sets the score of the graph.
setScore(WeightType) - Method in interface nct.graph.Graph
Sets the score of the graph.
setScore(Double) - Method in class nct.networkblast.PathGraph
 
setSeeds(List<Graph<NodeType, Double>>) - Method in class nct.networkblast.CompatComplexSearch
 
setSeeds(List<Graph<NodeType, Double>>) - Method in class nct.search.NewComplexSearch
 
setSegments(Map<NodeType, Integer>, Map<NodeType, Integer>) - Method in class nct.networkblast.CompatColorCodingPathSearch
Sets the segments used for producing ordered paths.
setSegments(Map<NodeType, Integer>, Map<NodeType, Integer>) - Method in class nct.search.ColorCodingPathSearch
Sets the segments used for producing ordered paths.
setupAntiCollisionSprings() - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
setupForLayoutPass() - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
Called at the beginning of each layoutPass iteration.
setUpLogging(Level) - Static method in class nct.networkblast.NetworkBlast
Initializes the logger object according to user's wishes.
setupNodeDistanceSprings() - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
sifFile - Variable in class nct.service.homology.SIFHomologyReader
The file that contains the blast output to be parsed.
SIFFileName - Variable in class nct.service.interactions.SIFInteractionNetwork
The SIF file name used to build the interaction network.
SIFHomologyReader - Class in nct.service.homology
A class that implements the HomologyModel interface by reading a SIF file that contains nodes from two separate graphs.
SIFHomologyReader(String) - Constructor for class nct.service.homology.SIFHomologyReader
Constructor.
SIFInteractionNetwork - Class in nct.service.interactions
An implementation of the InteractionNetwork that updates a graph based on the information in a SIF file.
SIFInteractionNetwork(String) - Constructor for class nct.service.interactions.SIFInteractionNetwork
 
SIFParser - Class in nct.parsers
A simple class that provides a method of parse a SIF file.
SIFParser() - Constructor for class nct.parsers.SIFParser
 
SIFWriter<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.output
 
SIFWriter(Graph<NodeType, WeightType>, String) - Constructor for class nct.output.SIFWriter
 
SILENT - Static variable in class nct.networkblast.NetworkBlast
 
SimpleEdgeScoreModel<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.score
This class implements a simple score model that basically just returns the weight associated with a particular object
SimpleEdgeScoreModel() - Constructor for class nct.score.SimpleEdgeScoreModel
 
simpleMoveNode(SpringEmbeddedLayouter.PartialDerivatives) - Method in class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
SimpleNodeScoreModel<NodeType extends WeightedNode<?,java.lang.Double>> - Class in nct.score
This class implements a simple score model that basically just returns the weight associated with a particular object
SimpleNodeScoreModel() - Constructor for class nct.score.SimpleNodeScoreModel
 
SimpleScoreModel<NodeType extends WeightedNode<?,java.lang.Double>> - Class in nct.score
This class implements a simple score model that basically just returns the weight associated with a particular object
SimpleScoreModel() - Constructor for class nct.score.SimpleScoreModel
 
simulationsDefault - Static variable in class nct.networkblast.NetworkBlast
 
skippedEntity(String) - Method in class nct.xml.XMLSaxEventDistributor
 
SortFilter<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.filter
This filter sorts the given solutions from best score (most positive) to worst.
SortFilter(boolean) - Constructor for class nct.filter.SortFilter
SortFilter constructor.
sourceNode - Variable in class nct.graph.BasicEdge
The source node of the edge.
splitNetwork(CyNetwork) - Method in class nct.visualization.cytoscape.dual.DualLayoutTask
Separates the network nodes into their constituent parts and creates the homology edges between them.
SpringEmbeddedLayouter - Class in nct.visualization.cytoscape.dual
A modified implementation of Kamada and Kawai's spring embedded layout algorithm.
SpringEmbeddedLayouter(GraphView, HashMap, NodePairSet) - Constructor for class nct.visualization.cytoscape.dual.SpringEmbeddedLayouter
 
startDocument() - Method in class nct.service.interactions.DIPInteractionNetwork
Basic SAX event handler.
startDocument() - Method in class nct.service.synonyms.DIPSynonyms
Standard SAX event handler.
startDocument() - Method in class nct.xml.XMLSaxEventDistributor
 
startElement(String, String, String, Attributes) - Method in class nct.service.interactions.DIPInteractionNetwork
Basic SAX event handler.
startElement(String, String, String, Attributes) - Method in class nct.service.synonyms.DIPSynonyms
Standard SAX event handler.
startElement(String, String, String, Attributes) - Method in class nct.xml.XMLSaxEventDistributor
 
startPrefixMapping(String, String) - Method in class nct.xml.XMLSaxEventDistributor
 
synMap - Variable in class nct.service.synonyms.DIPSynonyms
Maps the dip file id to a synonym.
SynonymMapper - Interface in nct.service.synonyms
An interface that describes methods for transforming an identifier into a synonym of a particular type.
synonyms - Variable in class nct.service.homology.BiojavaLocalBlast
Used for mapping various ids to types of synonyms
synonyms - Variable in class nct.service.homology.LocalBlast
Used for mapping various ids to types of synonyms
synonyms - Variable in class nct.service.sequences.DIPSequenceDatabase
 

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