Class ClusterSamples

java.lang.Object
  |
  +--ClusterSamples

class ClusterSamples

extends java.lang.Object

This class generates a cluster tree of HP samples from the active gene list. [FUTURE] The class represents an individual ClusterSamples entry. Model this class after ClusterGenes.java, use it as a model for this class. *

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/06/04 21:48:20 $ $Revision: 1.8 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Field Summary

(package private) float[][]	HPdistances Euclidean distance or correlation coefficient of sample HP pattern vector from another gene.
(package private) float[][]	HPvector normalized quantitation gene vector for all HPs
private MAExplorer	mae link to global MAExplorer instance
(package private) GeneList	mList list of genes used in pattern vector
(package private) MaHybridSample[]	msList list of samples H.P.s to cluster
(package private) int[]	nearestHP index of nearest HP
(package private) int	nMlist # of genes in mList
(package private) int	nMSlist size of msList[]

Constructor Summary

(package private)

ClusterSamples(MAExplorer mae, GeneList mList, MaHybridSample[] msList, int nMSlist) ClusterSamples() - constructor

Methods inherited from class java.lang.Object

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

Field Detail

mae

private MAExplorer mae

link to global MAExplorer instance

mList

GeneList mList

list of genes used in pattern vector

nMlist

int nMlist

# of genes in mList

msList

MaHybridSample[] msList

list of samples H.P.s to cluster

nMSlist

int nMSlist

size of msList[]

HPvector

float[][] HPvector

normalized quantitation gene vector for all HPs

HPdistances

float[][] HPdistances

Euclidean distance or correlation coefficient of sample HP pattern vector from another gene.

nearestHP

int[] nearestHP

index of nearest HP

Constructor Detail

ClusterSamples

ClusterSamples(MAExplorer mae,
               GeneList mList,
               MaHybridSample[] msList,
               int nMSlist)

ClusterSamples() - constructor

Parameters:

mae - is the MAExplorer instance

mList - is the GeneList defining the per sample expression lists

msList - is the list of samples to cluster

nMSlist - is the # of samples