nct.networkblast
Class CompatibilityGraph

java.lang.Object
  extended by nct.graph.BasicGraph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double>
      extended by nct.networkblast.CompatibilityGraph
All Implemented Interfaces:
java.lang.Cloneable, java.lang.Comparable<Graph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double>>, Graph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double>

public class CompatibilityGraph
extends BasicGraph<CompatibilityNode<java.lang.String,java.lang.Double>,java.lang.Double>

This class creates a compatibility graph based on the homology of proteins between two species and the interaction graphs for the given species.


Field Summary
 boolean allowZero
           
protected  java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> edgeDescMap
           
protected  KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> homologyGraph
           
protected  java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> homologyMap
           
protected  java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> interactionGraphs
           
protected  ScoreModel<java.lang.String,java.lang.Double> scoreModel
           
 
Fields inherited from class nct.graph.BasicGraph
assumeGraphFinished, descMap, id, numEdges, score, weightMap
 
Constructor Summary
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.
 
Method Summary
 
Methods inherited from class nct.graph.BasicGraph
addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

homologyMap

protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> homologyMap

edgeDescMap

protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> edgeDescMap

interactionGraphs

protected java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> interactionGraphs

homologyGraph

protected KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> homologyGraph

scoreModel

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

allowZero

public boolean allowZero
Constructor Detail

CompatibilityGraph

public 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.

Parameters:
homologyGraph - A k-partite graph where edges represent homology relations between proteins and partitions represent species/organisms.
interactionGraphs -
scoreModel - The scoring model used to score the edges of the compat graph.