Package org.nlpub.watset.graph

Class MarkovClusteringExternal<V,E>

java.lang.Object

org.nlpub.watset.graph.MarkovClusteringExternal<V,E>

Type Parameters:

V - the type of nodes in the graph

E - the type of edges in the graph

All Implemented Interfaces:

org.jgrapht.alg.interfaces.ClusteringAlgorithm<V>

public class MarkovClusteringExternal<V,E>
extends Object
implements org.jgrapht.alg.interfaces.ClusteringAlgorithm<V>

A wrapper for the official implementation of the Markov Clustering (MCL) algorithm in C.

This is a weird thing. The official implementation of MCL is very fast, but we need to run the separate process and speak to it over standard input/output redirection.

See Also:

• van Dongen (2000)
• van Dongen (2008)
• MCL - a cluster algorithm for graphs

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MarkovClusteringExternal.Builder<V,E>	Builder for MarkovClusteringExternal.
static class	MarkovClusteringExternal.Implementation<V,E>	Actual implementation of the Markov Clustering wrapper.

Nested classes/interfaces inherited from interface org.jgrapht.alg.interfaces.ClusteringAlgorithm

org.jgrapht.alg.interfaces.ClusteringAlgorithm.Clustering<V extends Object>, org.jgrapht.alg.interfaces.ClusteringAlgorithm.ClusteringImpl<V extends Object>

Field Summary

Fields

Modifier and Type	Field	Description
protected org.jgrapht.alg.interfaces.ClusteringAlgorithm.Clustering<V>	clustering	The cached clustering result.
protected final org.jgrapht.Graph<V,E>	graph	The graph.
protected final Path	path	The path to the MCL binary.
protected final double	r	The inflation parameter.
protected final int	threads	The number of threads.

Constructor Summary

Constructors

Constructor	Description
MarkovClusteringExternal(org.jgrapht.Graph<V,E> graph, Path path, double r, int threads)	Create an instance of the Markov Clustering algorithm wrapper.

Method Summary

Modifier and Type	Method	Description
static <V, E> MarkovClusteringExternal.Builder<V,E>	builder()	Create a builder.
org.jgrapht.alg.interfaces.ClusteringAlgorithm.Clustering<V>	getClustering()

Methods inherited from class java.lang.Object

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

Field Details

graph

protected final org.jgrapht.Graph<V,E> graph

The graph.

path

protected final Path path

The path to the MCL binary.

r

protected final double r

The inflation parameter.

threads

protected final int threads

The number of threads.

clustering

protected org.jgrapht.alg.interfaces.ClusteringAlgorithm.Clustering<V> clustering

The cached clustering result.

Constructor Details

MarkovClusteringExternal

public MarkovClusteringExternal(org.jgrapht.Graph<V,E> graph,
 Path path,
 double r,
 int threads)

Create an instance of the Markov Clustering algorithm wrapper.

Parameters:

graph - the graph

path - the path to the MCL binary

r - the inflation parameter

threads - the number of threads

Method Details

builder

public static <V,
E>
MarkovClusteringExternal.Builder<V,E> builder()

Create a builder.

Type Parameters:

V - the type of nodes in the graph

E - the type of edges in the graph

Returns:

a builder

getClustering

public org.jgrapht.alg.interfaces.ClusteringAlgorithm.Clustering<V> getClustering()

Specified by:

getClustering in interface org.jgrapht.alg.interfaces.ClusteringAlgorithm<V>