com.chemaxon.clustering.common

Interface IDBasedHierarchicClustering

All Superinterfaces:

HierarchicClustering<Integer,IDBasedHierarchicCluster>

@Beta
 @PublicAPI
public interface IDBasedHierarchicClustering
extends HierarchicClustering<Integer,IDBasedHierarchicCluster>

A Hierarchic clustering over integers, preferably IDs.

Please note that in order to help the implementation of higher level clustering representations represented clusters have associated, unique integer IDs.

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

Nested Class Summary

Nested classes/interfaces inherited from interface com.chemaxon.clustering.common.HierarchicClustering

HierarchicClustering.Alignment

Method Summary

Modifier and Type	Method and Description
int	getClusterIndexOf(int leafId) Cluster ID of a leaf.
int	getMaxClusterID() Maximal ClusterID present in this clustering.
int	getMaxLeafID() Maximal leaf ID referenced in this clustering.
int	getParentClusterIndexOf(int clusterId) Cluster ID of a cluster's parent.
IDBasedAssigner	getPreferredAssigner() Preferred assigner.
IDBasedAssigner	unitPathAssigner() Assigner which consider parent-child edges as unit length.

Methods inherited from interface com.chemaxon.clustering.common.HierarchicClustering

clusterOf, maxHeight, preferredAlignment, roots

Method Detail

getMaxClusterID

int getMaxClusterID()

Maximal ClusterID present in this clustering.

Returns:

Maximal cluster ID present.

getMaxLeafID

int getMaxLeafID()

Maximal leaf ID referenced in this clustering.

Returns:

Maximal leaf ID referenced.

getClusterIndexOf

int getClusterIndexOf(int leafId)

Cluster ID of a leaf. Functionality is similar to HierarchicClustering.clusterOf(java.lang.Object).

Parameters:

leafId - A leaf

Returns:

Lowest level Cluster ID or -1 when the leaf is not present in the clustering

getParentClusterIndexOf

int getParentClusterIndexOf(int clusterId)

Cluster ID of a cluster's parent.

Parameters:

clusterId - A cluster ID

Returns:

Parent cluster ID or -1 when the specified cluster is a root or when the specified cluster is not contained

unitPathAssigner

IDBasedAssigner unitPathAssigner()

Description copied from interface: HierarchicClustering

Assigner which consider parent-child edges as unit length.

Specified by:

unitPathAssigner in interface HierarchicClustering<Integer,IDBasedHierarchicCluster>

Returns:

The unit path assigner.

getPreferredAssigner

IDBasedAssigner getPreferredAssigner()

Description copied from interface: HierarchicClustering

Preferred assigner.

Some clustering algorithms may assign meaningful levels for clusters/leaves. If no such assignment s done the implementations should fall back the unit path assigner.

Specified by:

getPreferredAssigner in interface HierarchicClustering<Integer,IDBasedHierarchicCluster>

Returns:

The preferred assigner