nct.networkblast
Class HomologyGraph
java.lang.Object
nct.graph.BasicGraph<NodeType,WeightType>
nct.graph.BasicKPartiteGraph<java.lang.String,java.lang.Double,SequenceGraph<java.lang.String,java.lang.Double>>
nct.networkblast.HomologyGraph
- All Implemented Interfaces:
- java.lang.Cloneable, java.lang.Comparable<Graph<java.lang.String,java.lang.Double>>, Graph<java.lang.String,java.lang.Double>, KPartiteGraph<java.lang.String,java.lang.Double,SequenceGraph<java.lang.String,java.lang.Double>>
public class HomologyGraph
- extends BasicKPartiteGraph<java.lang.String,java.lang.Double,SequenceGraph<java.lang.String,java.lang.Double>>
This class creates a K-partite graph based on the homology
of proteins between two or more species.
Method Summary |
boolean |
addGraph(SequenceGraph<java.lang.String,java.lang.Double> sg)
Adds the nodes of the specified graph to this graph and adds the graph as a
partition. |
Methods inherited from class nct.graph.BasicGraph |
addEdge, 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 |
Methods inherited from interface nct.graph.Graph |
addEdge, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString |
homModel
protected HomologyModel homModel
exThresh
protected double exThresh
HomologyGraph
public HomologyGraph(HomologyModel homModel,
double exThresh)
- Parameters:
homModel
- The homology model used to generate the edges in the graph.exThresh
- The expectation threshold. Expectation values above this
threshold will not be added to the graph.
HomologyGraph
public HomologyGraph(HomologyModel homModel,
double exThresh,
java.util.Collection<SequenceGraph<java.lang.String,java.lang.Double>> graphs)
- Parameters:
homModel
- The homology model used to generate the edges in the graph.exThresh
- The expectation threshold. Expectation values above this
threshold will not be added to the graph.graphs
- A collection of graphs to be added to this graph.
addGraph
public boolean addGraph(SequenceGraph<java.lang.String,java.lang.Double> sg)
- Adds the nodes of the specified graph to this graph and adds the graph as a
partition.
- Parameters:
sg
- The SequenceGraph to be added to this graph.
- Returns:
- Returns true if we're able to add the graph as a partition and we successfully
add at least one node to the graph.