nct.networkblast.graph.compatibility
Class AdditiveCompatibilityCalculator

java.lang.Object
  extended by nct.networkblast.graph.compatibility.AdditiveCompatibilityCalculator
All Implemented Interfaces:
CompatibilityCalculator

public class AdditiveCompatibilityCalculator
extends java.lang.Object
implements CompatibilityCalculator

This class creates the compatibility edge score by summing the edge weights of the interaction edges that comprise the compatibility node.


Field Summary
protected  boolean allowZero
           
protected  double orthologyThreshold
           
protected  ScoreModel<java.lang.String,java.lang.Double> scoreModel
           
 
Constructor Summary
AdditiveCompatibilityCalculator(double orthologyThreshold, ScoreModel<java.lang.String,java.lang.Double> scoreModel)
           
AdditiveCompatibilityCalculator(double orthologyThreshold, ScoreModel<java.lang.String,java.lang.Double> scoreModel, boolean allowZero)
           
 
Method Summary
 boolean calculate(Graph<java.lang.String,java.lang.Double> compatGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> partitionGraphs, java.lang.String[] nodeBase, java.lang.String[] nodeBranch)
          The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

orthologyThreshold

protected double orthologyThreshold

scoreModel

protected ScoreModel<java.lang.String,java.lang.Double> scoreModel

allowZero

protected boolean allowZero
Constructor Detail

AdditiveCompatibilityCalculator

public AdditiveCompatibilityCalculator(double orthologyThreshold,
                                       ScoreModel<java.lang.String,java.lang.Double> scoreModel,
                                       boolean allowZero)
Parameters:
orthologyThreshold - The orthology threshold for determining if a compatibility edge weight is sufficient for inclusion.
scoreModel - The ScoreModel used to calculate edge weights.
allowZero - Whether or not edges of 0 distance (i.e. potential compat nodes where a constituent node is the same for both potential compat nodes).

AdditiveCompatibilityCalculator

public AdditiveCompatibilityCalculator(double orthologyThreshold,
                                       ScoreModel<java.lang.String,java.lang.Double> scoreModel)
Parameters:
orthologyThreshold - The orthology threshold for determining if a compatibility edge weight is sufficient for inclusion.
scoreModel - The ScoreModel used to calculate edge weights.
Method Detail

calculate

public boolean calculate(Graph<java.lang.String,java.lang.Double> compatGraph,
                         java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> partitionGraphs,
                         java.lang.String[] nodeBase,
                         java.lang.String[] nodeBranch)
The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.

Specified by:
calculate in interface CompatibilityCalculator
Parameters:
compatGraph - The compatibility graph that appropriate compatibility nodes and edges are added to.
partitionGraphs - Possibly used to
nodeBase - An array of nodes from the respective partition graphs that form a potential compatibility node.
nodeBranch - An array of nodes from the respective partition graphs that form a potential compatibility node.