Clustering (networkanalysis 1.3.0 API)

java.lang.Object
- nl.cwts.networkanalysis.Clustering

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class Clustering
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable
```
Clustering of the nodes in a network.
Each node belongs to exactly one cluster.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

protected int[] clusters
Cluster of each node.

protected int nClusters
Number of clusters.

protected int nNodes
Number of nodes.

Fields
Modifier and Type	Field and Description
`protected int[]`	`clusters` Cluster of each node.
`protected int`	`nClusters` Number of clusters.
`protected int`	`nNodes` Number of nodes.

Constructor Summary

Constructors
Constructor and Description
`Clustering(int nNodes)` Constructs a singleton clustering for a specified number of nodes.
`Clustering(int[] clusters)` Constructs a clustering using a specified cluster for each node.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`calcNormalizedMutualInformation(Clustering clustering)` Calculates the normalized mutual information relative to another clustering.
`double`	`calcVariationOfInformation(Clustering clustering)` Calculates the variation of information relative to another clustering.
`Clustering`	`clone()` Clones the clustering.
`int`	`getCluster(int node)` Returns the cluster of a node.
`boolean[]`	`getClusterIsNotEmpty()` Returns whether the cluster is empty or not for each cluster.
`int[]`	`getClusters()` Returns the cluster of each node.
`double[]`	`getClusterWeights(double[] nodeWeights)` Determine the total node weight of all nodes per cluster.
`double[]`	`getClusterWeights(Network network)` Determine the total node weight of all nodes per cluster.
`int`	`getNClusters()` Returns the number of clusters.
`int`	`getNNodes()` Returns the number of nodes.
`int[]`	`getNNodesPerCluster()` Returns the number of nodes per cluster.
`int`	`getNNonEmptyClusters()` Returns the number of non-empty clusters.
`int[][]`	`getNodesPerCluster()` Returns a list of nodes per cluster.
`void`	`initSingletonClusters()` Initializes a singleton clustering.
`static Clustering`	`load(java.lang.String filename)` Loads a clustering from a file.
`void`	`mergeClusters(Clustering clustering)` Merges the clusters based on a clustering of the clusters.
`void`	`orderClustersByNNodes()` Orders the clusters in decreasing order of their number of nodes.
`void`	`orderClustersByWeight(double[] nodeWeights)` Orders the clusters in decreasing order of their total node weight.
`void`	`removeEmptyClusters()` Removes empty clusters.
`void`	`removeEmptyClustersLargerThan(int minimumCluster)` Removes empty clusters and relabels clusters to follow consecutive numbering only for clusters larger than the specified minimum number of clusters.
`void`	`save(java.lang.String filename)` Saves the clustering in a file.
`void`	`setCluster(int node, int cluster)` Assigns a node to a cluster.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - nNodes
```
protected int nNodes
```
    Number of nodes.
  - nClusters
```
protected int nClusters
```
    Number of clusters.
  - clusters
```
protected int[] clusters
```
    Cluster of each node.
- Constructor Detail
  - Clustering
```
public Clustering(int nNodes)
```
    Constructs a singleton clustering for a specified number of nodes.
    
    Parameters:
    
    nNodes - Number of nodes
  - Clustering
```
public Clustering(int[] clusters)
```
    Constructs a clustering using a specified cluster for each node.
    
    Parameters:
    
    clusters - Cluster of each node
- Method Detail
  - load
```
public static Clustering load(java.lang.String filename)
                       throws java.lang.ClassNotFoundException,
                              java.io.IOException
```
    Loads a clustering from a file.
    
    Parameters:
    
    filename - File from which a clustering is loaded
    
    Returns:
    
    Loaded clustering
    
    Throws:
    
    java.lang.ClassNotFoundException - Class not found
    
    java.io.IOException - Could not read the file
    
    See Also:
    
    save(String filename)
  - clone
```
public Clustering clone()
```
    Clones the clustering.
    
    Overrides:
    
    clone in class java.lang.Object
    
    Returns:
    
    Cloned clustering
  - save
```
public void save(java.lang.String filename)
          throws java.io.IOException
```
    Saves the clustering in a file.
    
    Parameters:
    
    filename - File in which the clustering is saved
    
    Throws:
    
    java.io.IOException - Could not write to the file
    
    See Also:
    
    load(String filename)
  - getNNodes
```
public int getNNodes()
```
    Returns the number of nodes.
    
    Returns:
    
    Number of nodes
  - getNClusters
```
public int getNClusters()
```
    Returns the number of clusters.
    
    Returns:
    
    Number of clusters
  - getClusterIsNotEmpty
```
public boolean[] getClusterIsNotEmpty()
```
    Returns whether the cluster is empty or not for each cluster.
    
    Returns:
    
    Cluster is empty for each cluster
  - getNNonEmptyClusters
```
public int getNNonEmptyClusters()
```
    Returns the number of non-empty clusters.
    
    Returns:
    
    Number of non-empty clusters
    
    See Also:
    
    getClusterIsNotEmpty()
  - getClusters
```
public int[] getClusters()
```
    Returns the cluster of each node.
    
    Returns:
    
    Cluster of each node
  - getCluster
```
public int getCluster(int node)
```
    Returns the cluster of a node.
    
    Parameters:
    
    node - Node
    
    Returns:
    
    Cluster
  - getNNodesPerCluster
```
public int[] getNNodesPerCluster()
```
    Returns the number of nodes per cluster.
    
    Returns:
    
    Number of nodes per cluster
  - getNodesPerCluster
```
public int[][] getNodesPerCluster()
```
    Returns a list of nodes per cluster.
    
    Returns:
    
    List of nodes per cluster
  - setCluster
```
public void setCluster(int node,
                       int cluster)
```
    Assigns a node to a cluster.
    
    Parameters:
    
    node - Node
    
    cluster - Cluster
  - initSingletonClusters
```
public void initSingletonClusters()
```
    Initializes a singleton clustering.
    Each node i is assigned to a cluster i.
  - removeEmptyClusters
```
public void removeEmptyClusters()
```
    Removes empty clusters.
    Clusters are relabeled to follow a strictly consecutive numbering 0, ..., nClusters - 1.
  - removeEmptyClustersLargerThan
```
public void removeEmptyClustersLargerThan(int minimumCluster)
```
    Removes empty clusters and relabels clusters to follow consecutive numbering only for clusters larger than the specified minimum number of clusters.
    Each empty cluster larger that minimumCluster is reassigned to the lowest available cluster, in the order of the existing clusters. For example, if minimumCluster = 5 and cluster 2 and 7 are empty, then cluster 8 is relabeled to 7 (and 9 to 8, etc...), but clusters 0-4 remain as they are.
    
    Parameters:
    
    minimumCluster - Minimum cluster to start relabeling from
  - getClusterWeights
```
public double[] getClusterWeights(Network network)
```
    Determine the total node weight of all nodes per cluster.
    
    Parameters:
    
    network - Network with node weights
    
    Returns:
    
    Total node weight per cluster
    
    See Also:
    
    getClusterWeights(double[] nodeWeight)
  - getClusterWeights
```
public double[] getClusterWeights(double[] nodeWeights)
```
    Determine the total node weight of all nodes per cluster.
    
    Parameters:
    
    nodeWeights - Array of node weights
    
    Returns:
    
    Total node weight per cluster
  - orderClustersByNNodes
```
public void orderClustersByNNodes()
```
    Orders the clusters in decreasing order of their number of nodes.
    
    See Also:
    
    orderClustersByWeight(double[] nodeWeights)
  - orderClustersByWeight
```
public void orderClustersByWeight(double[] nodeWeights)
```
    Orders the clusters in decreasing order of their total node weight.
    The total node weight of a cluster equals the sum of the weights of the nodes belonging to the cluster.
    
    Parameters:
    
    nodeWeights - Node weights
    
    See Also:
    
    orderClustersByNNodes()
  - mergeClusters
```
public void mergeClusters(Clustering clustering)
```
    Merges the clusters based on a clustering of the clusters.
    
    Parameters:
    
    clustering - Clustering of the clusters
  - calcNormalizedMutualInformation
```
public double calcNormalizedMutualInformation(Clustering clustering)
```
    Calculates the normalized mutual information relative to another clustering.
    
    Parameters:
    
    clustering - Other clustering
    
    Returns:
    
    Normalized mutual information
  - calcVariationOfInformation
```
public double calcVariationOfInformation(Clustering clustering)
```
    Calculates the variation of information relative to another clustering.
    
    Parameters:
    
    clustering - Other clustering
    
    Returns:
    
    Variation of information

Class Clustering

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

nNodes

nClusters

clusters

Constructor Detail

Clustering

Clustering

Method Detail

load

clone

save

getNNodes

getNClusters

getClusterIsNotEmpty

getNNonEmptyClusters

getClusters

getCluster

getNNodesPerCluster

getNodesPerCluster

setCluster

initSingletonClusters

removeEmptyClusters

removeEmptyClustersLargerThan

getClusterWeights

getClusterWeights

orderClustersByNNodes

orderClustersByWeight

mergeClusters

calcNormalizedMutualInformation

calcVariationOfInformation