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java.lang.Objectnct.networkblast.score.LogLikelihoodScoreModel<NodeType>
public class LogLikelihoodScoreModel<NodeType extends java.lang.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).
Constructor Summary | |
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LogLikelihoodScoreModel(double truthFactor,
double model,
double backgroundProbability)
Sets the truthFactor accordingly (ensures > 0) and initializes the graphMap object. |
Method Summary | |
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double |
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 |
scoreNode(NodeType node,
Graph<NodeType,java.lang.Double> g)
Given a node from graph, this function will return the score of the node. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public LogLikelihoodScoreModel(double truthFactor, double model, double backgroundProbability)
truthFactor
- factor used to consider the background truth distributionmodel
- Truth for the model (assumed between 0 and 1)Method Detail |
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public double scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
scoreEdge
in interface ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
srcNode
- node bewteen which it and destNode generates a scoredestNode
- node between which it and srcNode generates a scoregraph
- graph containing both srcNode and destNode
public double scoreNode(NodeType node, Graph<NodeType,java.lang.Double> g)
ScoreModel
scoreNode
in interface ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
node
- Node to score.g
- The graph that contains the node to score.
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