Class ClusterGenes.Cluster

java.lang.Object
  |
  +--ClusterGenes.Cluster

Enclosing class:

ClusterGenes

class ClusterGenes.Cluster

extends java.lang.Object

[FUTURE] Class Cluster holds an ordered list of genes for a particular cluster. It also holds other metrics describing that cluster.

[TODO] Split out this class into a separate file so can keep many clusters around and manipulate them. Note Clusters are not just GeneBitSets but may be ordered gene lists (or HP lists) where the order is sorted by an associated cluster similarity etc. feature.

[NOTE] This class is not currenly used. The cluster methods should be rewritten to use it.

Field Summary

(package private) GeneList	clusterCL optional list of genes in this cluster
(package private) java.lang.String	cName optional cluster name
(package private) float	covDist coefficient of variation computed as stDist/meanDist
(package private) float[]	distToMeanDP [0:nGenes-1] distance to meanEP
(package private) int	id id # of this cluster
(package private) float	meanDist mean distance to meanEP
(package private) ExprProfile	meanEP mean expr profile of this cluster
(package private) float	medianDist median distance to medianEP
(package private) ExprProfile	medianEP median expr profile of this cluster
(package private) Gene[]	mList ordered list of genes in this cluster
(package private) float	nearestClusterDist distance to nearest cluster
(package private) int	nearestClusterID id # of nearest cluster
(package private) int	nEP # of objects (eg.
(package private) int	nGenes # of genes in this cluster
(package private) float	sdDist stdDev distance to meanDP
(package private) ExprProfile	sdEP stdDev expr profile (to meanEP) of cluster

Constructor Summary

(package private)

ClusterGenes.Cluster(int id, int nGenes, int nEP, java.lang.String cName, Gene[] mList) Cluster() - constructor.

Methods inherited from class java.lang.Object

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

Field Detail

id

int id

id # of this cluster

nearestClusterID

int nearestClusterID

id # of nearest cluster

nGenes

int nGenes

# of genes in this cluster

nEP

int nEP

# of objects (eg. HPs) in cluster

cName

java.lang.String cName

optional cluster name

mList

Gene[] mList

ordered list of genes in this cluster

clusterCL

GeneList clusterCL

optional list of genes in this cluster

distToMeanDP

float[] distToMeanDP

[0:nGenes-1] distance to meanEP

nearestClusterDist

float nearestClusterDist

distance to nearest cluster

covDist

float covDist

coefficient of variation computed as stDist/meanDist

medianDist

float medianDist

median distance to medianEP

meanDist

float meanDist

mean distance to meanEP

sdDist

float sdDist

stdDev distance to meanDP

medianEP

ExprProfile medianEP

median expr profile of this cluster

meanEP

ExprProfile meanEP

mean expr profile of this cluster

sdEP

ExprProfile sdEP

stdDev expr profile (to meanEP) of cluster

Constructor Detail

ClusterGenes.Cluster

ClusterGenes.Cluster(int id,
                     int nGenes,
                     int nEP,
                     java.lang.String cName,
                     Gene[] mList)

Cluster() - constructor.

Parameters:

id - is the cluster ID

nGenes - is the # of genes in the cluster

nEP - is the # of samples in the expression profile.

cName - is the name of the cluster

mList - is list of genes in the cluster