org.wallerlab.yoink.clustering

Class LouvainClusteringFacade<T>

java.lang.Object

org.wallerlab.yoink.clustering.LouvainClusteringFacade<T>

Type Parameters:

T - Type of graph populator

public class LouvainClusteringFacade<T>
extends java.lang.Object

Convenience class to start, populate, cluster and return the results.

Constructor Summary

Constructors

Constructor and Description
LouvainClusteringFacade(java.lang.String databaseFile)

Method Summary

Modifier and Type	Method and Description
java.util.Map<java.lang.Long,java.lang.Integer>	cluster(int maxCommunities)
java.util.List<java.util.Set<T>>	getResult(int level) Return the set of communities at a certain hierarchy/aggregation level.
void	populate(java.util.List<InteractionTriple<T>> interactions)
void	populate(java.util.Set<java.util.Set<T>> interactions) Creates the graph from the provided interacting pairs.
void	shutdown()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LouvainClusteringFacade

public LouvainClusteringFacade(java.lang.String databaseFile)

Method Detail

populate

public void populate(java.util.Set<java.util.Set<T>> interactions)

Creates the graph from the provided interacting pairs. The set has to be in the format [[a,b], [b,d],[a,e],...]

Parameters:

interactions - as defined by DORI

populate

public void populate(java.util.List<InteractionTriple<T>> interactions)

cluster

public java.util.Map<java.lang.Long,java.lang.Integer> cluster(int maxCommunities)

Parameters:

maxCommunities - the max number of communities

Returns:

map of hierarchy level and corresponding number of communities {hierarchylevel : number of communites}

getResult

public java.util.List<java.util.Set<T>> getResult(int level)

Return the set of communities at a certain hierarchy/aggregation level.

Parameters:

level - for getting communities

Returns:

List of Communities

shutdown

public void shutdown()