nct.networkblast.graph
Class CompatibilityGraph
java.lang.Object
nct.graph.basic.BasicGraph<java.lang.String,java.lang.Double>
nct.networkblast.graph.CompatibilityGraph
- All Implemented Interfaces:
- java.lang.Cloneable, java.lang.Comparable<Graph<java.lang.String,java.lang.Double>>, Graph<java.lang.String,java.lang.Double>
public class CompatibilityGraph
- extends BasicGraph<java.lang.String,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.
Methods inherited from class nct.graph.basic.BasicGraph |
addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, 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 |
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
compatCalc
protected CompatibilityCalculator compatCalc
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,
CompatibilityCalculator compatCalc)
- Constructor.
- Parameters:
homologyGraph
- A k-partite graph where edges represent homology relations between
proteins and partitions represent species/organisms.interactionGraphs
- scoreModel
- The ScoreModel used to score an edge in the graph.compatCalc
- The CompatibilityCalculator used to determine whether two possible compatibility
nodes should be added to the compatibility graph and if so, adds the nodes and edge.