: Class ExprProfile

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Class ExprProfile

java.lang.Object
  |
  +--ExprProfile

class ExprProfile
extends java.lang.Object

The class creates an nHP_E sample expression profile object for a gene. The gene is specified by its mid for the HPs in HP-E condition list of samples. Note these arrays are indexed [0:nHP_E-1]. This contains data, but no graphics.

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: 2003/07/07 21:40:41 $ $Revision: 1.10 $
Author:: P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD
See Also:: MAExplorer Home, ExprProfileCanvas, ExprProfileOverlay, Filter.setGeneListBySpotCV(GeneList, GeneList, float, int), Filter.setPostiveQuantData(GeneList, GeneList, int), Report.createTableOfExprProfiles(Gene[], int, boolean)

Field Summary

(package private) float[] cvData
          Coefficient of variation all HP-E samples

(package private) boolean didDataSetupFlag
          flag: set by setupData() if successful

(package private) boolean doMeanPlotsFlag
          flag: generate mean plots (of the clusters) else individual plots

(package private) int gid1
          GID derived from mid

(package private) int gid2
          (opt) ganged GID derived from mid

(package private) float[] hpData
          normalized quantified data for all HP-E samples

(package private) float[] hpDataMn
          opt.

(package private) int hpDataNbr
          opt.

(package private) float[] hpDataSD
          opt.

(package private) java.lang.String[] hpLabel
          (hpName,hpData,cvData) HP-E samples

(package private) java.lang.String[] hpName
          names for all HP-E samples

private MAExplorer mae
          link to global MAExplorer instance

private Maps map
          link to global Maps instance

(package private) float maxHPdataMn
          opt.

(package private) float maxMean
          maximum of the hpDataMn[] values

(package private) int mid
          ARG: Master Gene ID (MID) for gene we are creating if != -1

(package private) int nGeneClustersCnt
          # clustered genes to this mid

(package private) int nHP_E
          # of HP's to draw after setup

(package private) boolean normToOneFlag
          flag: normalize hpData[] & cvData[] to 1.0

(package private) int[] xCoord
          X coords for all HP-E vert lines in canvas for event handler...

(package private) int y1Coord
          Y coord for horizontal axis for vertical line, else is label for setting current gene

Constructor Summary

(package private) ExprProfile(MAExplorer mae, int mid, boolean normToOneFlag)
          ExprProfile() - Constructor to create expresion profile object

Method Summary

(package private) boolean setupData(int mid)
          setupData() - setup the data arrays for the other computations

(package private) boolean updateData(int mid)
          updateData() - update expression profile with new gene data

(package private) boolean updateData(int mid, boolean doMeanPlotsFlag, int hpDataNbr, float maxHPdataMn, float[] hpDataMn, float[] hpDataSD)
          updateData() - update expression profile with new gene and mean data

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

map

private Maps map

link to global Maps instance

normToOneFlag

boolean normToOneFlag

flag: normalize hpData[] & cvData[] to 1.0

doMeanPlotsFlag

boolean doMeanPlotsFlag

flag: generate mean plots (of the clusters) else individual plots

didDataSetupFlag

boolean didDataSetupFlag

flag: set by setupData() if successful

mid

int mid

ARG: Master Gene ID (MID) for gene we are creating if != -1

gid1

int gid1

GID derived from mid

gid2

int gid2

(opt) ganged GID derived from mid

nGeneClustersCnt

int nGeneClustersCnt

# clustered genes to this mid

nHP_E

int nHP_E

# of HP's to draw after setup

hpLabel

java.lang.String[] hpLabel

(hpName,hpData,cvData) HP-E samples

hpName

java.lang.String[] hpName

names for all HP-E samples

hpDataNbr

int hpDataNbr

opt. # quant data for all HP-E samples

maxMean

float maxMean

maximum of the hpDataMn[] values

hpData

float[] hpData

normalized quantified data for all HP-E samples

maxHPdataMn

float maxHPdataMn

opt. max mean normalized quantified data for all samples and genes

hpDataMn

float[] hpDataMn

opt. Mean quant data for all HP-E samples

hpDataSD

float[] hpDataSD

opt. S.D. quant data for all HP-E samples

cvData

float[] cvData

Coefficient of variation all HP-E samples

y1Coord

int y1Coord

Y coord for horizontal axis for vertical line, else is label for setting current gene

xCoord

int[] xCoord

X coords for all HP-E vert lines in canvas for event handler...

Constructor Detail

ExprProfile

ExprProfile(MAExplorer mae,
            int mid,
            boolean normToOneFlag)

ExprProfile() - Constructor to create expresion profile object

Parameters:: mae - is the MAExplorer instance; mid - is the Master Gene Index if not -1; normToOneFlag - normalize data to 1.0 if set
See Also:: setupData(int)

Method Detail

updateData

boolean updateData(int mid)

updateData() - update expression profile with new gene data

Parameters:: mid - is the Master Gene Index to use in computing expression profile
See Also:: setupData(int)