Class Cluster

Object

Cluster

public class Cluster
extends Object

An instance of the Cluster class represents a group of genes.

Constructor Summary

Constructors

Constructor and Description
Cluster() Creates a Cluster initially containing zero genes.

Method Summary

Modifier and Type	Method and Description
void	absorbCluster(Cluster c) Adds all genes in the specified Cluster to this Cluster.
void	addGene(Gene g) Adds the specified Gene to this Cluster.
java.util.Vector<Double>	getClusterMean() Returns the mean (i.e., average) of the expression vectors of all Genes in this Cluster.
double	getDistanceToCluster(Cluster c) Computes and returns the distance between this Cluster and the specified Cluster.
Gene	getGene(int i) Returns a Gene in this Cluster.
int	getSizeOfCluster() Returns the number of genes in this Cluster.
void	initialize() Clears all genes from this Cluster so that it contains zero genes.
boolean	isGeneInCluster(Gene g) Returns a boolean value indicating if the specified Gene is in this Cluster.
void	removeGene(Gene g) Removes the specified Gene from this Cluster.
String	toString() Returns a String representation of this Cluster.

Methods inherited from class Object

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

Constructor Detail

Cluster

public Cluster()

Creates a Cluster initially containing zero genes.

Method Detail

initialize

public void initialize()

Clears all genes from this Cluster so that it contains zero genes.

getSizeOfCluster

public int getSizeOfCluster()

Returns the number of genes in this Cluster.

Returns:

an integer representing the size of this Cluster

addGene

public void addGene(Gene g)

Adds the specified Gene to this Cluster.

If the specified Gene is already in this Cluster then the Gene is not added again (i.e,. there should be no duplicate Genes in the Cluster).

Parameters:

g - a Gene to be added to this Cluster

removeGene

public void removeGene(Gene g)

Removes the specified Gene from this Cluster.

If the specified Gene is not in this Cluster then this Cluster is not changed.

Parameters:

g - a Gene to be removed from this Cluster

getGene

public Gene getGene(int i)

Returns a Gene in this Cluster.

The ith Gene in this Cluster is returned.

Parameters:

i - the index of the Gene in this Cluster to be returned

Returns:

the Gene at index i in this Cluster

isGeneInCluster

public boolean isGeneInCluster(Gene g)

Returns a boolean value indicating if the specified Gene is in this Cluster.

Parameters:

g - a Gene that may or may not be in this Cluster

Returns:

true if g is in this Cluster, false otherwise

getClusterMean

public java.util.Vector<Double> getClusterMean()

Returns the mean (i.e., average) of the expression vectors of all Genes in this Cluster.

Returns:

a collection of doubles corresponding to the average expression of each Gene in this Cluster in each experiment

getDistanceToCluster

public double getDistanceToCluster(Cluster c)

Computes and returns the distance between this Cluster and the specified Cluster.

Each Cluster has a vector representing the Cluster's mean expression across all experiments. The distance between two Clusters is computed as the Euclidean distance between the two Clusters' means.

Parameters:

c - a Cluster for which we wish to compute to the distance to this Cluster

Returns:

a double representing the distance between the specified Cluster and this Cluster

absorbCluster

public void absorbCluster(Cluster c)

Adds all genes in the specified Cluster to this Cluster.

Thus, this Cluster grows in size by the number of genes in Cluster c. The specified Cluster is not altered.

Parameters:

c - a Cluster to be absorbed by this Cluster

toString

public String toString()

Returns a String representation of this Cluster.

The name of each Gene in this Cluster along with each Gene's function are included in the String representation of this Cluster.

Overrides:

toString in class Object

Returns:

a String represenation of this Cluster