org.gephi.statistics.plugin

Class Modularity

java.lang.Object

org.gephi.statistics.plugin.Modularity

All Implemented Interfaces:

Statistics, LongTask

public class Modularity
extends Object
implements Statistics, LongTask

Author:

pjmcswee

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	Modularity.Community
(package private) class	Modularity.CommunityStructure
(package private) class	Modularity.ModEdge

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	isCanceled
private boolean	isRandomized
private double	modularity
static String	MODULARITY_CLASS
private double	modularityResolution
private ProgressTicket	progress
private double	resolution
private Modularity.CommunityStructure	structure
private boolean	useWeight

Constructor Summary

Constructors

Constructor and Description
Modularity()

Method Summary

Modifier and Type	Method and Description
boolean	cancel() Cancel the task.
protected HashMap<String,Double>	computeModularity(org.gephi.graph.api.Graph hgraph, Modularity.CommunityStructure theStructure, int[] comStructure, double currentResolution, boolean randomized, boolean weighted)
void	execute(org.gephi.graph.api.Graph hgraph)
void	execute(org.gephi.graph.api.GraphModel graphModel) Executes the statistics algorithm.
(package private) int[]	fillComStructure(org.gephi.graph.api.Graph hgraph, Modularity.CommunityStructure theStructure, int[] comStructure)
(package private) double[]	fillDegreeCount(org.gephi.graph.api.Graph hgraph, Modularity.CommunityStructure theStructure, int[] comStructure, double[] nodeDegrees, boolean weighted)
private double	finalQ(int[] struct, double[] degrees, org.gephi.graph.api.Graph hgraph, Modularity.CommunityStructure theStructure, double totalWeight, double usedResolution, boolean weighted)
double	getModularity()
boolean	getRandom()
String	getReport() Returns an HTML string that displays the statistics result.
double	getResolution()
boolean	getUseWeight()
private double	q(int node, Modularity.Community community, Modularity.CommunityStructure theStructure, double currentResolution)
private void	saveValues(int[] struct, org.gephi.graph.api.Graph hgraph, Modularity.CommunityStructure theStructure)
void	setProgressTicket(ProgressTicket progressTicket) Set the progress ticket for the long task.
void	setRandom(boolean isRandomized)
void	setResolution(double resolution)
void	setUseWeight(boolean useWeight)
(package private) Modularity.Community	updateBestCommunity(Modularity.CommunityStructure theStructure, int i, double currentResolution)

Methods inherited from class java.lang.Object

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

Field Detail

MODULARITY_CLASS

public static final String MODULARITY_CLASS

See Also:

Constant Field Values

progress

private ProgressTicket progress

isCanceled

private boolean isCanceled

structure

private Modularity.CommunityStructure structure

modularity

private double modularity

modularityResolution

private double modularityResolution

isRandomized

private boolean isRandomized

useWeight

private boolean useWeight

resolution

private double resolution

Constructor Detail

Modularity

public Modularity()

Method Detail

setRandom

public void setRandom(boolean isRandomized)

getRandom

public boolean getRandom()

setUseWeight

public void setUseWeight(boolean useWeight)

getUseWeight

public boolean getUseWeight()

setResolution

public void setResolution(double resolution)

getResolution

public double getResolution()

cancel

public boolean cancel()

Description copied from interface: LongTask

Cancel the task. Returns true if the task has been sucessfully cancelled, false otherwise.

Specified by:

cancel in interface LongTask

Returns:

true if the task has been sucessfully cancelled, false otherwise

setProgressTicket

public void setProgressTicket(ProgressTicket progressTicket)

Description copied from interface: LongTask

Set the progress ticket for the long task. Can't be null.

Specified by:

setProgressTicket in interface LongTask

Parameters:

progressTicket - the progress ticket for this task

execute

public void execute(org.gephi.graph.api.GraphModel graphModel)

Description copied from interface: Statistics

Executes the statistics algorithm.

It is preferable to work on visible graphs, to be synchronized with the visualization.

Specified by:

execute in interface Statistics

Parameters:

graphModel - The graph model

execute

public void execute(org.gephi.graph.api.Graph hgraph)

computeModularity

protected HashMap<String,Double> computeModularity(org.gephi.graph.api.Graph hgraph,
                                                   Modularity.CommunityStructure theStructure,
                                                   int[] comStructure,
                                                   double currentResolution,
                                                   boolean randomized,
                                                   boolean weighted)

updateBestCommunity

Modularity.Community updateBestCommunity(Modularity.CommunityStructure theStructure,
                                         int i,
                                         double currentResolution)

fillComStructure

int[] fillComStructure(org.gephi.graph.api.Graph hgraph,
                       Modularity.CommunityStructure theStructure,
                       int[] comStructure)

fillDegreeCount

double[] fillDegreeCount(org.gephi.graph.api.Graph hgraph,
                         Modularity.CommunityStructure theStructure,
                         int[] comStructure,
                         double[] nodeDegrees,
                         boolean weighted)

finalQ

private double finalQ(int[] struct,
                      double[] degrees,
                      org.gephi.graph.api.Graph hgraph,
                      Modularity.CommunityStructure theStructure,
                      double totalWeight,
                      double usedResolution,
                      boolean weighted)

saveValues

private void saveValues(int[] struct,
                        org.gephi.graph.api.Graph hgraph,
                        Modularity.CommunityStructure theStructure)

getModularity

public double getModularity()

getReport

public String getReport()

Description copied from interface: Statistics

Returns an HTML string that displays the statistics result. Can contains complex HTML snippets and images.

Specified by:

getReport in interface Statistics

Returns:

An HTML string that displays the results for this Statistics

q

private double q(int node,
                 Modularity.Community community,
                 Modularity.CommunityStructure theStructure,
                 double currentResolution)