Package ffx.numerics.clustering

Class ClusterPair

java.lang.Object

ffx.numerics.clustering.ClusterPair

All Implemented Interfaces:

Comparable<ClusterPair>

public class ClusterPair
extends Object
implements Comparable<ClusterPair>

Immutable-like holder describing a pair of clusters and the linkage distance between them; used as entries within the DistanceMap during agglomeration.

Since:

1.0

Author:

Lars Behnke, 2013, Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
ClusterPair()	Creates an empty ClusterPair.
ClusterPair(Cluster left, Cluster right, Double distance)	Creates a ClusterPair linking two clusters at a given distance.

Method Summary

Modifier and Type	Method	Description
Cluster	agglomerate(int clusterIdx)	Agglomerates left and right clusters under an auto-generated name.
Cluster	agglomerate(String name)	Agglomerates left and right clusters into a new parent with the given name.
int	compareTo(ClusterPair o)
Cluster	getlCluster()	Gets the left cluster.
Double	getLinkageDistance()	Gets the linkage distance.
Cluster	getOtherCluster(Cluster c)	Returns the opposite cluster of the provided one in this pair.
Cluster	getrCluster()	Gets the right cluster.
ClusterPair	reverse()	Creates a new ClusterPair with left and right clusters swapped.
void	setlCluster(Cluster lCluster)	Sets the left cluster.
void	setLinkageDistance(Double distance)	Sets the linkage distance.
void	setrCluster(Cluster rCluster)	Sets the right cluster.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

ClusterPair

public ClusterPair()

Creates an empty ClusterPair.

ClusterPair

public ClusterPair(Cluster left,
 Cluster right,
 Double distance)

Creates a ClusterPair linking two clusters at a given distance.

Parameters:

left - the left cluster

right - the right cluster

distance - the linkage distance between clusters

Method Details

getOtherCluster

public Cluster getOtherCluster(Cluster c)

Returns the opposite cluster of the provided one in this pair.

Parameters:

c - one cluster in this pair

Returns:

the other cluster in the pair

getlCluster

public Cluster getlCluster()

Gets the left cluster.

Returns:

the left cluster

setlCluster

public void setlCluster(Cluster lCluster)

Sets the left cluster.

Parameters:

lCluster - the left cluster

getrCluster

public Cluster getrCluster()

Gets the right cluster.

Returns:

the right cluster

setrCluster

public void setrCluster(Cluster rCluster)

Sets the right cluster.

Parameters:

rCluster - the right cluster

getLinkageDistance

public Double getLinkageDistance()

Gets the linkage distance.

Returns:

the linkage distance

setLinkageDistance

public void setLinkageDistance(Double distance)

Sets the linkage distance.

Parameters:

distance - the linkage distance to set

reverse

public ClusterPair reverse()

Creates a new ClusterPair with left and right clusters swapped.

Returns:

a new ClusterPair with the two left/right inverted

compareTo

public int compareTo(ClusterPair o)

Specified by:

compareTo in interface Comparable<ClusterPair>

agglomerate

public Cluster agglomerate(int clusterIdx)

Agglomerates left and right clusters under an auto-generated name.

Parameters:

clusterIdx - index appended to the generated cluster name

Returns:

the new parent Cluster

agglomerate

public Cluster agglomerate(String name)

Agglomerates left and right clusters into a new parent with the given name.

Parameters:

name - name of the new parent cluster

Returns:

the new parent Cluster

toString

public String toString()

Overrides:

toString in class Object