com.chemaxon.clustering.common

Class IDBasedClusterBuilder

java.lang.Object

com.chemaxon.clustering.common.IDBasedClusterBuilder

@Beta
 @PublicAPI
public final class IDBasedClusterBuilder
extends java.lang.Object

Builder for ID based non-hierarchic clustering. The represented clustering have the following properties:

• Cluster and structure IDs are nonnegative integers
• All clusters are contained from 0 ID to the highest cluster ID ever added
• No empty clusters allowed

Licensing: this class is part of the JKlustor suite; it can be used with valid JKlustor license.

Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Author:

Gabor Imre

Constructor Summary

Constructors

Constructor and Description
IDBasedClusterBuilder() Instantiate an empty builder.

Method Summary

Modifier and Type	Method and Description
int	addNewCluster() Allocate a new cluster.
void	addStructuresToCluster(java.util.Collection<java.lang.Integer> structureIDs, int clusterID) Add multiple structures to a cluster.
void	addStructureToCluster(int structureID, int clusterID) Set a structure to be a part of a cluster as a leaf.
IDBasedSingleLevelClustering	build() Build immutable clustering representation.
boolean	isRepresentantSet(int clusterId) Check if cluster representant is set.
void	removeStructure(int structureID) Remove a structure from its respective cluster.
static java.lang.String	toDetailedString(IDBasedSingleLevelClustering clustering) Utility method to create a detailed string representation of a clustering.
void	updateRepresentant(int structureID, int clusterID) Set/update the cluster representant structure.

Methods inherited from class java.lang.Object

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

Constructor Detail

IDBasedClusterBuilder

public IDBasedClusterBuilder()
                      throws chemaxon.license.LicenseException

Instantiate an empty builder.

Throws:

chemaxon.license.LicenseException - when appropriate license is not available

Method Detail

addNewCluster

public int addNewCluster()

Allocate a new cluster.

Note that it is not necessary to call this method; clusters are added implicitly.

Returns:

ID of a new empty cluster, considered as root.

updateRepresentant

public void updateRepresentant(int structureID,
                               int clusterID)

Set/update the cluster representant structure.

Parameters:

structureID - Structure to pintpoint as representant

clusterID - Associated cluster

isRepresentantSet

public boolean isRepresentantSet(int clusterId)

Check if cluster representant is set.

Parameters:

clusterId - Cluster ID

Returns:

true when cluster representant structure is set.

addStructureToCluster

public void addStructureToCluster(int structureID,
                                  int clusterID)

Set a structure to be a part of a cluster as a leaf.

Parameters:

structureID - ID of the structure to add

clusterID - ID of the cluster of the structure

Throws:

java.lang.IllegalStateException - when structure is already a member of any other cluster

addStructuresToCluster

public void addStructuresToCluster(java.util.Collection<java.lang.Integer> structureIDs,
                                   int clusterID)

Add multiple structures to a cluster.

Parameters:

structureIDs - Structure IDs to add

clusterID - ID of the immediate parent cluster for the structures

Throws:

java.lang.IllegalStateException - when a structure is already a member of any other cluster

removeStructure

public void removeStructure(int structureID)

Remove a structure from its respective cluster.

Parameters:

structureID - ID of the structure to add

Throws:

java.lang.IllegalStateException - when given structure is not a member of any cluster

toDetailedString

public static java.lang.String toDetailedString(IDBasedSingleLevelClustering clustering)

Utility method to create a detailed string representation of a clustering.

Parameters:

clustering - Clustering to traverse

Returns:

Detailed multiline String representation

build

public IDBasedSingleLevelClustering build()

Build immutable clustering representation.

Returns:

Immutable clustering representation