Uses of Interface
nct.score.ScoreModel

Packages that use ScoreModel
nct.networkblast   
nct.score   
nct.search   
 

Uses of ScoreModel in nct.networkblast
 

Classes in nct.networkblast that implement ScoreModel
 class CompatibilityScoreModel
          This interface will provide the scoring interface for all scoring algorithms to be used on a Graph object.
 

Fields in nct.networkblast declared as ScoreModel
protected  ScoreModel<java.lang.String,java.lang.Double> CompatibilityGraph.scoreModel
           
protected  ScoreModel<NodeType,java.lang.Double> CompatComplexSearch.scoreObj
           
 

Methods in nct.networkblast with parameters of type ScoreModel
 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.
 

Constructors in nct.networkblast with parameters of type ScoreModel
CompatibilityGraph(KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> homologyGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> interactionGraphs, ScoreModel<java.lang.String,java.lang.Double> scoreModel)
          Constructor.
CompatibilityScoreModel(java.util.List<? extends Graph<java.lang.String,java.lang.Double>> cg, ScoreModel<java.lang.String,java.lang.Double> logScore)
           
 

Uses of ScoreModel in nct.score
 

Classes in nct.score that implement ScoreModel
 class LogLikelihoodScoreModel<NodeType extends Comparable<? super NodeType>>
          This class implements the log likelihood edge scoring scheme described in the supplemental to Sharan, et al., 2005, Conserved patterns of protein interaction in multiple species, PNAS, 102(6).
 class SimpleEdgeScoreModel<NodeType extends Comparable<? super NodeType>>
          This class implements a simple score model that basically just returns the weight associated with a particular object
 class SimpleNodeScoreModel<NodeType extends WeightedNode<?,java.lang.Double>>
          This class implements a simple score model that basically just returns the weight associated with a particular object
 class SimpleScoreModel<NodeType extends WeightedNode<?,java.lang.Double>>
          This class implements a simple score model that basically just returns the weight associated with a particular object
 

Uses of ScoreModel in nct.search
 

Methods in nct.search with parameters of type ScoreModel
 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.