Class ExprProfile

java.lang.Object
  |
  +--ExprProfile

class ExprProfile

extends java.lang.Object

The class creates an nEPsamples sample expression profile object for a gene. The gene is specified by its pid for the samples in sample-E condition list of samples. Note these arrays are indexed [0:nEPsamples-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 and Djamel Medjahed (SAIC-Frederick). 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.

Version:

$Date: 2002/10/14 20:17:17 $ $Revision: $

Author:

P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD

See Also:

ProtPlot Home

This work was derived from prpxplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://prpxplorer.sourceforge.org/

Field Summary

(package private) float	cvExpr CV (stdDevExpr/meanExpr) of expression of the sampleData[] values.
(package private) boolean	didDataSetupFlag flag: set by setupData() if successful
long	exprProfileBits selected expression list bits of selected samples
(package private) float	maxExpr maximum of the sampleData[] values
(package private) float	meanExpr mean expression of the sampleData[] values.
(package private) float	minExpr minimum of the sampleData[] values
(package private) int	mPid ARG: Master Protein ID (pid) for gene we are creating if != -1
(package private) int	nEPpresent # of sample's in subset to plot that don't have 0.0 expression
(package private) int	nEPsamples # of sample's to draw after setup
(package private) boolean	normToOneFlag flag: normalize sampleData[] to 1.0
private ProtPlot	prp link to global prpxplorer instance
(package private) float[]	sampleData normalized quantified data for all sample-E samples
(package private) int	sampleDataNbr opt.
(package private) java.lang.String[]	sampleLabel (sampleName,sampleData) sample-E samples
(package private) java.lang.String[]	sampleName names for all sample-E samples
(package private) float	stdDevExpr StdDev of expression of the sampleData[] values.
(package private) int[]	xCoord X coords for all sample 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(ProtPlot prp, int pid, boolean normToOneFlag) ExprProfile() - Constructor to create expresion profile object

Method Summary

(package private) boolean	setupData(int mPid) setupData() - setup the data arrays for the other computations
(package private) boolean	updateData(int mPid) updateData() - update expression profile with new gene data

Methods inherited from class java.lang.Object

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

Field Detail

prp

private ProtPlot prp

link to global prpxplorer instance

normToOneFlag

boolean normToOneFlag

flag: normalize sampleData[] to 1.0

didDataSetupFlag

boolean didDataSetupFlag

flag: set by setupData() if successful

mPid

int mPid

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

exprProfileBits

public long exprProfileBits

selected expression list bits of selected samples

nEPsamples

int nEPsamples

# of sample's to draw after setup

nEPpresent

int nEPpresent

# of sample's in subset to plot that don't have 0.0 expression

sampleLabel

java.lang.String[] sampleLabel

(sampleName,sampleData) sample-E samples

sampleName

java.lang.String[] sampleName

names for all sample-E samples

sampleDataNbr

int sampleDataNbr

opt. # quant data for all sample-E samples

maxExpr

float maxExpr

maximum of the sampleData[] values

minExpr

float minExpr

minimum of the sampleData[] values

meanExpr

float meanExpr

mean expression of the sampleData[] values. Don't count 0.0 samples

stdDevExpr

float stdDevExpr

StdDev of expression of the sampleData[] values. Don't count 0.0 samples

cvExpr

float cvExpr

CV (stdDevExpr/meanExpr) of expression of the sampleData[] values. Don't count 0.0 samples

sampleData

float[] sampleData

normalized quantified data for all sample-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 sample vert lines in canvas for event handler...

Constructor Detail

ExprProfile

ExprProfile(ProtPlot prp,
            int pid,
            boolean normToOneFlag)

ExprProfile() - Constructor to create expresion profile object

Parameters:

prp - is the ProtPlot instance

mPid - is the Master Protein Index if not -1

normToOneFlag - normalize data to 1.0 if set

See Also:

setupData(int)

Method Detail

updateData

boolean updateData(int mPid)

updateData() - update expression profile with new gene data

Parameters:

pid - is the Master Protein Index to use in computing expr. profile

See Also:

setupData(int)

setupData

boolean setupData(int mPid)

setupData() - setup the data arrays for the other computations

Parameters:

pid - is the Master Protein Index to use in compouting expr. profile

Returns:

false if an illegal pid or no expr profile list of samples