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Packages that use ScoreModel | |
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nct.networkblast.graph | |
nct.networkblast.graph.compatibility | |
nct.networkblast.score | |
nct.networkblast.search |
Uses of ScoreModel in nct.networkblast.graph |
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Fields in nct.networkblast.graph declared as ScoreModel | |
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protected ScoreModel<java.lang.String,java.lang.Double> |
CompatibilityGraph.scoreModel
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Constructors in nct.networkblast.graph with parameters of type ScoreModel | |
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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,
CompatibilityCalculator compatCalc)
Constructor. |
Uses of ScoreModel in nct.networkblast.graph.compatibility |
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Fields in nct.networkblast.graph.compatibility declared as ScoreModel | |
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protected ScoreModel<java.lang.String,java.lang.Double> |
AdditiveCompatibilityCalculator.scoreModel
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Constructors in nct.networkblast.graph.compatibility with parameters of type ScoreModel | |
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AdditiveCompatibilityCalculator(double orthologyThreshold,
ScoreModel<java.lang.String,java.lang.Double> scoreModel)
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AdditiveCompatibilityCalculator(double orthologyThreshold,
ScoreModel<java.lang.String,java.lang.Double> scoreModel,
boolean allowZero)
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Uses of ScoreModel in nct.networkblast.score |
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Classes in nct.networkblast.score that implement ScoreModel | |
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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 |
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.networkblast.search |
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Methods in nct.networkblast.search with parameters of type ScoreModel | |
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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>> |
GreedyComplexSearch.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. |
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