nct.networkblast
Class CompatComplexSearch<NodeType extends java.lang.Comparable<? super NodeType>>
java.lang.Object
nct.networkblast.CompatComplexSearch<NodeType>
- All Implemented Interfaces:
- SearchGraph<NodeType,java.lang.Double>
public class CompatComplexSearch<NodeType extends java.lang.Comparable<? super NodeType>>
- extends java.lang.Object
- implements SearchGraph<NodeType,java.lang.Double>
This class implements the SearchGraph interface. It implements the
greedy search algorithm described in the supplemental material of
Sharan, et al. 2005. "Conserved patterns of protein interaction in
mulitple species." PNAS, 102(6),1974-1979.
Complexes are defined as branched or unbranched pathways invovling
seedSize or more nodes.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
seedSize
protected int seedSize
maxComplexSize
protected int maxComplexSize
createSeeds
protected boolean createSeeds
seeds
protected java.util.List<Graph<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>> seeds
graph
protected Graph<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double> graph
scoreObj
protected ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double> scoreObj
CompatComplexSearch
public CompatComplexSearch(int seedSize,
int maxComplexSize)
CompatComplexSearch
public CompatComplexSearch(int seedSize,
int maxComplexSize,
boolean createSeeds,
java.util.List<Graph<NodeType,java.lang.Double>> seeds)
searchGraph
public java.util.List<Graph<NodeType,java.lang.Double>> searchGraph(Graph<NodeType,java.lang.Double> graph,
ScoreModel<NodeType,java.lang.Double> scoreObj)
- Description copied from interface:
SearchGraph
- This method will be used to call a search algorithm on the given graph
object.
- Specified by:
searchGraph
in interface SearchGraph<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
- Parameters:
graph
- The Graph object to searchscoreObj
- The ScoreModel object to use to score pathways in the graph
- Returns:
- a List of SubGraphs which are the solutions to this search
setSeeds
public void setSeeds(java.util.List<Graph<NodeType,java.lang.Double>> newSeeds)