Class HPxyData

java.lang.Object
  |
  +--HPxyData

class HPxyData

extends java.lang.Object

The HPxyData class creates HP-X and HP-Y data 'sets' for a given gene mid. If the useHPxySetDataFlag is not set, then it treats the F1 and F2 channels of the HP-X and HP-Y samples as the 2 instance sets (using msX and msY). If useHPxySetDataFlag is set, it gets the data from the HP-X 'set' hps.msListX[1:hps.nHP_X] and the HP-Y 'set' hps.msListY[1:hps.nHP_Y].

Summary data for each class is saved in hpDataX[0:nX-1], hpDataY[0:nY-1], f1f2CV_X[0:nX-1], f1f2CV_Y[0:nY-1].

You can then call @see #calcXYstatistics to compute

    (mnXdata, mnYdata)        -  mean intensity HP-X, HP-Y 
    (cvXdata,cvYdata)         -  Coeff. of variation all HP-X, HP-Y  
    (stdDevXdata,stdDevYdata) -  std deviation intensity HP-X, HP-Y 

The HP-X and HP-Y labels (hpLabelX, hpLabelY) may be set using

Version:

$Date: 2003/07/07 21:40:41 $ $Revision: 1.9 $

Author:

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

See Also:

to generate labels for various displays and reports.

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/.

, MAExplorer Home, MaHybridSample, SampleSets

Field Summary

(package private) boolean	alsoCalcEPdataFlag flag: use to also compute HP list statistics as well as XY stats
(package private) float	cvEdata Coefficient of variation all HP-E list data
(package private) float	cvXdata Coefficient of variation all HP-X set data
(package private) float	cvYdata Coefficient of variation all HP-Y set data
(package private) boolean	didDataSetupFlag flag: set by setupXYdata() if successful
(package private) boolean	didStatisticsFlag flag: set by calcXYstatistics() and calcEPstatistics() if successful
(package private) float[]	f1f2CV_E Coefficient of variation each HP-E f1 f2 sample in the set data
(package private) float[]	f1f2CV_X Coefficient of variation each HP-X f1 f2 sample in the set data
(package private) float[]	f1f2CV_Y Coefficient of variation each HP-Y f1 f2 sample in the set data
(package private) int	gid1 GID derived from mid
(package private) int	gid2 Ggang ID derived from mid
(package private) float[]	hpDataE quant data for all HP-E (list) members
(package private) float[]	hpDataX quant data for all HP-X (set) members
(package private) float[]	hpDataY quant data for all HP-Y (set) members
(package private) java.lang.String	hpLabelX plot label: (className,mnData,sdData,cvData) HP-X (set)
(package private) java.lang.String	hpLabelY plot label: (className,mnData,stdData,cvData) HP-Y (set)
(package private) java.lang.String	hpNameE names for all HP-Y (set) members
(package private) java.lang.String	hpNameX name for all HP-X (set) members
(package private) java.lang.String	hpNameY names for all HP-Y (set) members
private SampleSets	hps Global instance of HP-X, HP-Y and HP-E sets and lists
private MAExplorer	mae link to global MAExplorer instance
private Maps	map Global instance of lookup table maps populated elsewhere
(package private) int	mid ARG: gene MID idx we are creating if != -1
(package private) float	mnEdata mean intensity HP-EP list data
(package private) float	mnXdata mean intensity HP-X set data
(package private) float	mnYdata mean intensity HP-Y set data
(package private) int	nE # of HP-EP list members after setup
(package private) int	nX # of HP-X set members after setup
(package private) int	nY # of HP-Y set members after setup
(package private) float	stdDevEdata std deviation HP-EP list data
(package private) float	stdDevXdata std deviation intensity HP-X set data
(package private) float	stdDevYdata std deviation HP-Y set data
(package private) boolean	useHPxySetDataFlag flag: get data from msListX/Y else msX/Y

Constructor Summary

(package private)

HPxyData(MAExplorer mae, int mid, boolean useHPxySetDataFlag) HPxyData() - Constructor to create HP XY data object.

Method Summary

(package private) boolean	calcEPstatistics() calcEPstatistics() - compute the the EP statistics.
(package private) boolean	calcXYstatistics() calcXYstatistics() - setup the data arrays depending on useHPxySetDataFlag.
(package private) void	clearXYdata() clearXYdata() - clear X and Y mn, cv, stdDev data
(package private) boolean	getCalcEPdataFlag() getCalcEPdataFlag() - get the also calculate EP data flag status.
(package private) void	setCalcEPdataFlag(boolean flag) setCalcEPdataFlag() - set the also calculate EP data when do updates.
(package private) void	setupDataStruct(boolean useHPxySetDataFlag) setupDataStruct() - setup or change array allocations
(package private) boolean	setupEPdata(int mid) setupEPdata() - setup the HP-EP data arrays.
(package private) boolean	setupXYdata(int mid) setupXYdata() - setup the data arrays depending on useHPxySetDataFlag.
(package private) boolean	setupXYlabels() setupXYlabels() - set the XY labels based on samples selected.
(package private) boolean	updateData(int mid, boolean updateLabelsFlag) updateData() - update HP XY data with new gene data and calculate (mn,StdDev,CV) statistics, and update the labels (suitable for display)
(package private) boolean	updateDataAndStat(int mid) updateDataAndStat() - update HP XY data with new data and calculate (mn,StdDev,CV) statistics.

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

Global instance of lookup table maps populated elsewhere

hps

private SampleSets hps

Global instance of HP-X, HP-Y and HP-E sets and lists

useHPxySetDataFlag

boolean useHPxySetDataFlag

flag: get data from msListX/Y else msX/Y

didDataSetupFlag

boolean didDataSetupFlag

flag: set by setupXYdata() if successful

didStatisticsFlag

boolean didStatisticsFlag

flag: set by calcXYstatistics() and calcEPstatistics() if successful

alsoCalcEPdataFlag

boolean alsoCalcEPdataFlag

flag: use to also compute HP list statistics as well as XY stats

mid

int mid

ARG: gene MID idx we are creating if != -1

gid1

int gid1

GID derived from mid

gid2

int gid2

Ggang ID derived from mid

nX

int nX

# of HP-X set members after setup

nY

int nY

# of HP-Y set members after setup

nE

int nE

# of HP-EP list members after setup

hpLabelX

java.lang.String hpLabelX

plot label: (className,mnData,sdData,cvData) HP-X (set)

hpLabelY

java.lang.String hpLabelY

plot label: (className,mnData,stdData,cvData) HP-Y (set)

hpNameX

java.lang.String hpNameX

name for all HP-X (set) members

hpNameY

java.lang.String hpNameY

names for all HP-Y (set) members

hpNameE

java.lang.String hpNameE

names for all HP-Y (set) members

hpDataX

float[] hpDataX

quant data for all HP-X (set) members

hpDataY

float[] hpDataY

quant data for all HP-Y (set) members

hpDataE

float[] hpDataE

quant data for all HP-E (list) members

f1f2CV_X

float[] f1f2CV_X

Coefficient of variation each HP-X f1 f2 sample in the set data

f1f2CV_Y

float[] f1f2CV_Y

Coefficient of variation each HP-Y f1 f2 sample in the set data

f1f2CV_E

float[] f1f2CV_E

Coefficient of variation each HP-E f1 f2 sample in the set data

mnXdata

float mnXdata

mean intensity HP-X set data

mnYdata

float mnYdata

mean intensity HP-Y set data

mnEdata

float mnEdata

mean intensity HP-EP list data

stdDevXdata

float stdDevXdata

std deviation intensity HP-X set data

stdDevYdata

float stdDevYdata

std deviation HP-Y set data

stdDevEdata

float stdDevEdata

std deviation HP-EP list data

cvXdata

float cvXdata

Coefficient of variation all HP-X set data

cvYdata

float cvYdata

Coefficient of variation all HP-Y set data

cvEdata

float cvEdata

Coefficient of variation all HP-E list data

Constructor Detail

HPxyData

HPxyData(MAExplorer mae,
         int mid,
         boolean useHPxySetDataFlag)

HPxyData() - Constructor to create HP XY data object.

Parameters:

mae - is instance of MAExplorer

mid - is the Master Gene ID (MID) if not -1

useHPxySetDataFlag - to use msListX/Y else msX/Y

See Also:

setupXYdata(int)

Method Detail

getCalcEPdataFlag

boolean getCalcEPdataFlag()

getCalcEPdataFlag() - get the also calculate EP data flag status. The flag is checked when do updates and compute statistics. It defaults to false to save time with unnecessary computations.

Returns:

value of the flag

See Also:

setCalcEPdataFlag(boolean), #setEPdata, calcEPstatistics()

setCalcEPdataFlag

void setCalcEPdataFlag(boolean flag)

setCalcEPdataFlag() - set the also calculate EP data when do updates. This defaults to false to save time with unnecessary computations.

Parameters:

flag - is new value to set the flag

See Also:

getCalcEPdataFlag(), #setEPdata, calcEPstatistics()

updateData

boolean updateData(int mid,
                   boolean updateLabelsFlag)

updateData() - update HP XY data with new gene data and calculate (mn,StdDev,CV) statistics, and update the labels (suitable for display)

Parameters:

mid - is the Master Gene ID (MID) if not -1

updateLabelsFlag - to do labels as well

Returns:

false if any problems.

See Also:

calcXYstatistics(), calcEPstatistics(), setupXYdata(int), setupEPdata(int), setupXYlabels()

updateDataAndStat

boolean updateDataAndStat(int mid)

updateDataAndStat() - update HP XY data with new data and calculate (mn,StdDev,CV) statistics. Do NOT update the labels (suitable for display)

Parameters:

mid - is the Master Gene ID (MID) if not -1

Returns:

false if any problems.

See Also:

calcXYstatistics(), calcEPstatistics(), setupXYdata(int), setupEPdata(int)

setupDataStruct

void setupDataStruct(boolean useHPxySetDataFlag)

setupDataStruct() - setup or change array allocations

Parameters:

useHPxySetDataFlag - to use msListX/Y else msX/Y

See Also:

setupXYdata(int)

setupXYdata

boolean setupXYdata(int mid)

setupXYdata() - setup the data arrays depending on useHPxySetDataFlag. NOTE: does NOT compute (mn, stdDev, CV) of samples. You MUST do that in separate call to calcXYstatistics().

Parameters:

mid - is the Master Gene ID (MID) if not -1

Returns:

false if an illegal mid

See Also:

MaHybridSample.getDataByGID(int, boolean, int), MenuBarFrame.setHP_XYlabels(), setupDataStruct(boolean)

setupEPdata

boolean setupEPdata(int mid)

setupEPdata() - setup the HP-EP data arrays. NOTE: does NOT compute (mn, stdDev, CV) of samples. You MUST do that in separate call to calcEPstatistics().

Parameters:

mid - is the Master Gene ID (MID) if not -1

Returns:

false if an illegal mid

See Also:

MaHybridSample.getDataByGID(int, boolean, int), MenuBarFrame.setHP_XYlabels(), setupDataStruct(boolean)

calcXYstatistics

boolean calcXYstatistics()

calcXYstatistics() - setup the data arrays depending on useHPxySetDataFlag. Using double precision arithmetic and the shortcut method for computing variance, it computes:

    (mnXdata, mnYdata)        -  mean intensity HP-X, HP-Y 
    (cvXdata,cvYdata)         -  Coeff. of variation all HP-X, HP-Y  
    (stdDevXdata,stdDevYdata) - std deviation intensity HP-X, HP-Y 

Returns:

false if an illegal mid

calcEPstatistics

boolean calcEPstatistics()

calcEPstatistics() - compute the the EP statistics. Using double precision arithmetic and the shortcut method for computing variance, it computes:

    (mnEdata)         -  mean intensity HP-EP
    (cvEdata)         -  Coeff. of variation all HP-EP
    (stdDevEdata)     - std deviation intensity HP-EP

Returns:

false if an illegal mid or alsoCalcEPdataFlag is false.

clearXYdata

void clearXYdata()

clearXYdata() - clear X and Y mn, cv, stdDev data

setupXYlabels

boolean setupXYlabels()

setupXYlabels() - set the XY labels based on samples selected. This sets (hpLabelX, hpLabelY) which may be used for various displays.

Returns:

false if any problems.

See Also:

Util.cvf2s(float, int)