Class Filter

java.lang.Object
  |
  +--Filter

public class Filter

extends java.lang.Object

Class Filter.java - Filter the current ProtPlot data. 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 MAExplorer 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://maexplorer.sourceforge.org/

Field Summary

double	cvEPdata computed Coefficient of variation all EP set data for current protein
double	cvXdata computed Coefficient of variation all X set data for current protein
double	cvYdata computed Coefficient of variation all Y set data for current protein
boolean	didDataSetupFlag flag: set by setupData() if successful
boolean	didStatisticsFlag flag: set by calcPrimaryStatisticss() if successful
boolean	doingXYscatterPlotFlag set if doing display X vs Y in ratio mode
private DrawProtScatterPlot	dwSP instance of DrawProtScatterPlot
double[]	epData quant data for all EP (set) members
double	mnEPdata computed mean intensity EP set data for current protein
double	mnXdata computed mean intensity X set data for current protein
double	mnYdata computed mean intensity Y set data for current protein
int	nEP # of EP set members after setup
int	nEPsamplesPassedMinProteins Compute the min # of EP set samples passing > S proteins/Sample test
int	nSamplesPassedMinProteins Compute the min # of X&Y or EP set samples passing > S proteins/Sample test
int	nX # of X set members after setup
int	nXsamplesPassedMinProteins Compute the min # of X set samples passing > S proteins/Sample test
int	nY # of Y set members after setup
int	nYsamplesPassedMinProteins Compute the min # of Y set samples passing > S proteins/Sample test
boolean	passedDisplayXYRangeTest set if doing display X vs Y in ratio mode AND (exprX,exprY) in X and Y range of scatterplot
int	passedEPminSamplesCtr counters for missing samples protein test for EP set
int	passedExprCtr counters Expr counter
int	passedFamilyCtr counters Family counter
int	passedFilterCtr counters Filter counter
int	passedKStestCtr counters for KS-test
int	passedMaxMWsizeCtr counters max MW size counter
boolean	passedMissingProteins Combined flag for both X & Y or EP missing proteins tests
int	passedMwPIRangeCtr counter for test of (pM.pI,pM.mw) within pI and Mw scroller range limits
boolean	passedMwPIRangeTest Flag that tests if (pM.pI,pM.mw) is within the pI and Mw scroller range limits
int	passedNsamplesCtr counters N samples counter
int	passedRatioCtr counters Ratio counter
int	passedSavedClusterCtr counter for proteins in saved Cluster set of proteins
int	passedSavedFilterCtr counter for proteins in saved Filter set of proteins
int	passedTissueCtr counters Tissue counter
int	passedTtestCtr counters for t-test
int	passedXYmissingProteinsCtr counter for missing X and Y set protein test
private ProtPlot	prp instance of ProtPlot
float	pValue computed Computed pValue when use the t-Test for current protein
float	ratioXYsets computed ratio of mnXdata/mnYdata if mnYdata NEQ 0 for current protein
private StatisticsPRP	stat instance of StatisticsPRP
double	stdDevEPdata computed std deviation EP set data for current protein
double	stdDevXdata computed std deviation X set data for current protein
double	stdDevYdata computed std deviation Y set data for current protein
private UtilPRP	util instance of UtilPRP
double[]	xData quant data for all X (set) members.
double[]	xDataP1 quant data for all X (set) members.
double[]	yData quant data for all Y (set) members.
double[]	yDataP1 quant data for all Y (set) members.

Constructor Summary

Filter(ProtPlot prp)
Filter() - constructor

Method Summary

boolean	allocLocalEPdataArrays(boolean allocAnywaysFlag) allocLocalEPdataArrays() - setup or change EP sets array allocations used by Filter
boolean	allocLocalXYdataArrays(boolean allocAnywaysFlag) allocLocalXYdataArrays() - setup or change X, Y, or EP sets array allocations used by Filter
(package private) boolean	calcEPstatistics() calcEPstatistics() - compute primary statistics for EP set data in epData[0:nEP-1].
(package private) boolean	calcXYstatistics() calcXYstatistics() - compute primary statistics for X and Y sets for current x(y)Data[].
boolean	checkSamplesFilter(int mPid) checkSamplesFilter() - check Proteins (pX,pY) to see if it passed filter.
(package private) java.lang.String	getExtraFilterData(int mPid) getExtraFilterData() - get extra Filter data from t-Test, KS-test etc.
java.lang.String[]	getSampleListBySubstring(java.lang.String sMatch) getSampleListBySubstring() - return a list of sample names by substring matching
int	resetFilterCounters() resetFilterCounters() - reset the filter counters
void	saveFilter() saveFilter() - save current Filtered proteins into prp.savedFilterMPIDs[]
(package private) boolean	setupLocalEPsetData(int mPid, boolean allocAnywaysFlag) setupLocalEPsetData() - setup local EP sets data arrays for pM
(package private) boolean	setupLocalXYsetData(int mPid, boolean allocAnywaysFlag) setupLocalXYsetData() - setup local X, and Y sets data arrays for pM
boolean	setupXYlabels() setupXYlabels() - set the XY labels based on samples selected.
boolean	test_XYsets_KS_Test(int mPid, float pValueThr, boolean getDataFlag) test_XYsets_KS_Test() - test if X and Y sets pass Kolmogorov-Smirnov Test with a pValue better than pValueThr.
boolean	test_XYsets_t_Test(int mPid, float pValueThr, boolean getDataFlag) test_XYsets_t_Test() - test if X and Y sets pass the t-Test with a pValue better than pValueThr.

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

instance of ProtPlot

stat

private StatisticsPRP stat

instance of StatisticsPRP

util

private UtilPRP util

instance of UtilPRP

dwSP

private DrawProtScatterPlot dwSP

instance of DrawProtScatterPlot

didDataSetupFlag

public boolean didDataSetupFlag

flag: set by setupData() if successful

didStatisticsFlag

public boolean didStatisticsFlag

flag: set by calcPrimaryStatisticss() if successful

nX

public int nX

# of X set members after setup

nY

public int nY

# of Y set members after setup

nEP

public int nEP

# of EP set members after setup

xData

public double[] xData

quant data for all X (set) members. xDataP1[j+1]= xData[j]

xDataP1

public double[] xDataP1

quant data for all X (set) members. xDataP1[j+1]= xData[j]

yData

public double[] yData

quant data for all Y (set) members. yDataP1[j+1]= yData[j]

yDataP1

public double[] yDataP1

quant data for all Y (set) members. yDataP1[j+1]= yData[j]

epData

public double[] epData

quant data for all EP (set) members

mnXdata

public double mnXdata

computed mean intensity X set data for current protein

mnYdata

public double mnYdata

computed mean intensity Y set data for current protein

mnEPdata

public double mnEPdata

computed mean intensity EP set data for current protein

ratioXYsets

public float ratioXYsets

computed ratio of mnXdata/mnYdata if mnYdata NEQ 0 for current protein

stdDevXdata

public double stdDevXdata

computed std deviation X set data for current protein

stdDevYdata

public double stdDevYdata

computed std deviation Y set data for current protein

stdDevEPdata

public double stdDevEPdata

computed std deviation EP set data for current protein

cvXdata

public double cvXdata

computed Coefficient of variation all X set data for current protein

cvYdata

public double cvYdata

computed Coefficient of variation all Y set data for current protein

cvEPdata

public double cvEPdata

computed Coefficient of variation all EP set data for current protein

pValue

public float pValue

computed Computed pValue when use the t-Test for current protein

nSamplesPassedMinProteins

public int nSamplesPassedMinProteins

Compute the min # of X&Y or EP set samples passing > S proteins/Sample test

nXsamplesPassedMinProteins

public int nXsamplesPassedMinProteins

Compute the min # of X set samples passing > S proteins/Sample test

nYsamplesPassedMinProteins

public int nYsamplesPassedMinProteins

Compute the min # of Y set samples passing > S proteins/Sample test

nEPsamplesPassedMinProteins

public int nEPsamplesPassedMinProteins

Compute the min # of EP set samples passing > S proteins/Sample test

passedMissingProteins

public boolean passedMissingProteins

Combined flag for both X & Y or EP missing proteins tests

passedMwPIRangeTest

public boolean passedMwPIRangeTest

Flag that tests if (pM.pI,pM.mw) is within the pI and Mw scroller range limits

doingXYscatterPlotFlag

public boolean doingXYscatterPlotFlag

set if doing display X vs Y in ratio mode

passedDisplayXYRangeTest

public boolean passedDisplayXYRangeTest

set if doing display X vs Y in ratio mode AND (exprX,exprY) in X and Y range of scatterplot

passedSavedClusterCtr

public int passedSavedClusterCtr

counter for proteins in saved Cluster set of proteins

passedSavedFilterCtr

public int passedSavedFilterCtr

counter for proteins in saved Filter set of proteins

passedMwPIRangeCtr

public int passedMwPIRangeCtr

counter for test of (pM.pI,pM.mw) within pI and Mw scroller range limits

passedXYmissingProteinsCtr

public int passedXYmissingProteinsCtr

counter for missing X and Y set protein test

passedEPminSamplesCtr

public int passedEPminSamplesCtr

counters for missing samples protein test for EP set

passedTtestCtr

public int passedTtestCtr

counters for t-test

passedKStestCtr

public int passedKStestCtr

counters for KS-test

passedMaxMWsizeCtr

public int passedMaxMWsizeCtr

counters max MW size counter

passedNsamplesCtr

public int passedNsamplesCtr

counters N samples counter

passedRatioCtr

public int passedRatioCtr

counters Ratio counter

passedExprCtr

public int passedExprCtr

counters Expr counter

passedFamilyCtr

public int passedFamilyCtr

counters Family counter

passedTissueCtr

public int passedTissueCtr

counters Tissue counter

passedFilterCtr

public int passedFilterCtr

counters Filter counter

Constructor Detail

Filter

public Filter(ProtPlot prp)

Filter() - constructor

Parameters:

prp - is instance of ProtPlot

Method Detail

resetFilterCounters

public int resetFilterCounters()

resetFilterCounters() - reset the filter counters

Returns:

# proteins passing S test

checkSamplesFilter

public boolean checkSamplesFilter(int mPid)

checkSamplesFilter() - check Proteins (pX,pY) to see if it passed filter. If no data exists for samples, (expr==0.0) then return false.

 The data filter takes the intersection of the following filters.
 By definition, a filter that is disabled is true so the intersection
 ignores it. Note the Ratio test and the Expression test are mutually
 exclusive.
   passed Ratio X/Y range (based on ratio, ratio-range and 
          inside/outside flag) test
   passed Expression range test
   passed t-test for X and Y sets
   passed minimum number of samples for both X and Y set if used 
          else EP list test
   passed Tissue membership test
   passed Family membership test

Parameters:
mPid - is the master protein id to check
dataMustExistFlag - makes sure that data exists for ratio data
  (X or Y or both X and Y exists)
Returns:
true value if passed the filter in various ways

getSampleListBySubstring

public java.lang.String[] getSampleListBySubstring(java.lang.String sMatch)

getSampleListBySubstring() - return a list of sample names by substring matching

Parameters:

sMatch - is the substring to match (e.g " normal" or " cancer")

Returns:

list of sample names if there is a substring match else null

allocLocalXYdataArrays

public boolean allocLocalXYdataArrays(boolean allocAnywaysFlag)

allocLocalXYdataArrays() - setup or change X, Y, or EP sets array allocations used by Filter

Parameters:

allocAnywaysFlag - to the X and Y sample index lists

Returns:

true if succeed

allocLocalEPdataArrays

public boolean allocLocalEPdataArrays(boolean allocAnywaysFlag)

allocLocalEPdataArrays() - setup or change EP sets array allocations used by Filter

Parameters:

allocAnywaysFlag - to recalculate the EP sample index list

Returns:

true if succeed

test_XYsets_t_Test

public boolean test_XYsets_t_Test(int mPid,
                                  float pValueThr,
                                  boolean getDataFlag)

test_XYsets_t_Test() - test if X and Y sets pass the t-Test with a pValue better than pValueThr. If there are not enough members of the X or Y sets, then return true.

Parameters:

mPid - is the Master Protein Id to test

pValueThr - is the p-value threshold to use

getDataFlag - get the data, else assume that precalculated

Returns:

true if succeed, else false if a problem.

See Also:

StatisticsPRP.calcTandPvalues(int, int, double, double, double, double)

test_XYsets_KS_Test

public boolean test_XYsets_KS_Test(int mPid,
                                   float pValueThr,
                                   boolean getDataFlag)

test_XYsets_KS_Test() - test if X and Y sets pass Kolmogorov-Smirnov Test with a pValue better than pValueThr. If there are not enough members of the X or Y sets, then return true.

Parameters:

mPid - is the Master Protein Id to test

pValueThr - is the p-value threshold to use

getDataFlag - get the data, else assume that precalculated

Returns:

true if succeed, else false if a problem.

See Also:

StatisticsPRP.calcTandPvalues(int, int, double, double, double, double)

setupLocalXYsetData

boolean setupLocalXYsetData(int mPid,
                            boolean allocAnywaysFlag)

setupLocalXYsetData() - setup local X, and Y sets data arrays for pM

Parameters:

mPid - is the Master Protein ID if not -1

allocAnywaysFlag - allocate anyways even if < 2 samples for X or Y set

Returns:

false if an illegal mPid

See Also:

allocLocalXYdataArrays(boolean)

getExtraFilterData

java.lang.String getExtraFilterData(int mPid)

getExtraFilterData() - get extra Filter data from t-Test, KS-test etc. for mid if in XY sets mode.

Parameters:

mid - for protein to get extra info

Returns:

extra info if any, else ""

setupLocalEPsetData

boolean setupLocalEPsetData(int mPid,
                            boolean allocAnywaysFlag)

setupLocalEPsetData() - setup local EP sets data arrays for pM

Parameters:

mPid - is the Master Protein ID if not -1

allocAnywaysFlag - allocate anyways even if < 2 samples for RP set

Returns:

false if an illegal mPid

See Also:

allocLocalEPdataArrays(boolean)

calcXYstatistics

boolean calcXYstatistics()

calcXYstatistics() - compute primary statistics for X and Y sets for current x(y)Data[]. Use double precision arithmetic and the shortcut method for computing variance. It computes:

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

Parameters:

allowAnySizeNflag - allow any size nX or NY

Returns:

false if any problems

calcEPstatistics

boolean calcEPstatistics()

calcEPstatistics() - compute primary statistics for EP set data in epData[0:nEP-1]. Use double precision arithmetic and the shortcut method for computing variance. It computes:

    mnEPdata         -  mean intensity of epData[0:nEP-1].
    cvEPdata         -  Coeff. of variation all data epData[0:nEP-1].
    stdDevEPdata     - std deviation of epData[0:nEP-1].

Returns:

false if any problems

setupXYlabels

public boolean setupXYlabels()

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

Returns:

false if any problems.

See Also:

UtilPRP.cvf2s(float, int)

saveFilter

public void saveFilter()

saveFilter() - save current Filtered proteins into prp.savedFilterMPIDs[]