Class CompositeDatabase

java.lang.Object
  |
  +--CompositeDatabase

class CompositeDatabase

extends java.lang.Object

Class to operate on composite sets of Hybridized Samples lists HP-X set, HP-Y set and HP-E list. It computes global statistics and also is used to access list of averaged genes from these lists.

The current gene associated parameters are defined in this class and include: (isValidObjFlag, objMID, objGID, objGIDG, objField, objGrid, objRow, objCol, objX, objY).

It includes many primary methods used throughout MAExplorer for accessing this data including:

List of methods
 setCurrentGenes() - set current genes to those in the GeneClass database
 calcRatioHistVal() - compute histogram bin value & increment ratio histogram
 calcRatioHists() - compute ratio histogram of d1List[]/d2List[] data
 calcHistOfHP_XYRatios() - compute histogram of HP-X/-Y (or 'sets') spot ratios of filtered data
 setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range
 setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range
 setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range
 setRatioHistCLfromHP_XYsetRatios() - set GeneList of X/Y set ratios in ratio range
 lookupHPcoords() - lookup closest gene name by (x,y) in sample pseudoarray and set current gene
 setOBJtoGID() - set the current gene xxxOBJ values to the specified GID
 setObjCoordFromMaster_ID() - set gene xxxOBJ values from Master_ID name
 setObjCoordFromMID() - set gene xxxOBJ values from MID for current HP sample
 getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing the data filter
 getRawHP_XandYdata() - get raw list spot (HP-X,HP-Y) data passing the data filter
 getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter
 calAllSamples() - compute (meanCalDNA, stdDevCalDNA) calibration for all samples
 recalcNorms() - recompute normalizations for all samples
 calcHP_HPcorrelations() - compute HP vs. HP samples correlation coefficients table 
 createHPmeanAndVarTable() - create table (HP,mn,stdDev,min,max,median) of raw intensity data
 recalcGlobalStats() - recompute global array statistics with all or just good spots

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: 1.17 $

Author:

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

See Also:

MAExplorer Home, Filter, GeneList, HPxyData, MaHybridSample, SampleSets

Field Summary

(package private) java.awt.Color[]	color_textHP text HP labels shared colors
private Filter	fc link to global Filter instance
(package private) java.awt.Font[]	font_textHP text HP labels shared fonts
(package private) float	grandMeanCalDNA grand mean HP Calib.DNA means for normalization.
(package private) float	grandMeanUseGeneSet grand mean HP 'User Filter Gene Set' means for normalization.
private SampleSets	hps link to global SamplesSets instance
(package private) static HPxyData	hpXYdata generic HP-X/Y set object
(package private) static boolean	isValidObjFlag Flag to indicate that the current gene (i.e.
private MAExplorer	mae link to global MAExplorer instance
private Maps	map link to global Maps instance
(package private) float	maxDataHP_X max intensity HP_X in getNormHP_XandYdata
(package private) float	maxDataHP_Y max intensity HP_Y in getNormHP_XandYdata
(package private) int	maxRatioHistIdx max value found in ratioHist[]
(package private) int	maxTextItems Common Grid labels for drawing onto the canvas.
(package private) float	minDataHP_X min intensity HP_X in getNormHP_XandYdata
(package private) float	minDataHP_Y min intensity HP_Y in getNormHP_XandYdata
(package private) int	minRatioHistIdx min value found in ratioHist[]
(package private) int	nRatioHistBins # of bins in ratioHist[]
(package private) int	nTextItems
(package private) int	objCol object Grid-Column that best matches xy coords if isValidObj is TRUE
(package private) int	objField object Field that best matches xy coords if isValidObj is TRUE
(package private) static int	objGID GridCoords gid of object if isValidObj is TRUE
(package private) int	objGIDG Gang f' GridCoords gid of object if isValidObj is TRUE
(package private) int	objGrid object Grid that best matches xy coords if isValidObj is TRUE
(package private) static int	objMID Gene index mid of object if isValidObj is TRUE
(package private) int	objRow object Grid-Row that best matches xy coords if isValidObj is TRUE
(package private) int	objX optimal spot X position if isValidObj is TRUE
(package private) int	objY optimal spot Y position if isValidObj is TRUE
(package private) int[]	ratioHist histogram of g1/g2 ratios [0:nRatioHistBins] in range 0.01:100.0
(package private) double[]	ratioValue scale of ratio histogram of g1/g2 ratios
(package private) boolean	recursionFlag flag: track last updated object to avoid recursion problems
(package private) float[][]	rSqHP_HP [1:nRows][1:nCols] rSq, HP vs HP correlation coefficient
private GeneList	tempCD_CL temporary GeneList used in local gene list operations

Constructor Summary

(package private)

CompositeDatabase(MAExplorer mae) CompositeDatabase() - constructor to set up data structures.

Method Summary

(package private) boolean	calAllSamples() calAllSamples() - compute (meanCalDNA, stdDevCalDNA) calibration for all samples
(package private) boolean	calcHistOfF1F2Ratios(GeneList ml, MaHybridSample ms) calcHistOfF1F2Ratios() - compute histogram of F1/F2 ratios for spots which are selected in the GeneList ml.
(package private) boolean	calcHistOfHP_XYratios(GeneList ml, boolean useXYsetsFlag) calcHistOfHP_XYRatios() - compute histogram of HP-X/-Y (or 'sets') spot ratios of filtered data
(package private) SimpleTable	calcHP_HPcorrelations() calcHP_HPcorrelations() - compute HP vs.
(package private) void	calcRatioHists(int nList, float[] d1List, float[] d2List, GeneList ml) calcRatioHists() - compute ratio histogram of d1List[]/d2List[] data.
(package private) double	calcRatioHistVal(float g1, float g2) calcRatioHistVal() - compute histogram bin value & increment ratio histogram
(package private) SimpleTable	calDNAhybSamplesTable() calDNAhybSamplesTable() - calc.
(package private) void	cleanup() cleanup() - cleanup global static allocated variables in this class.
(package private) Table	createHPmeanAndVarTable() createHPmeanAndVarTable() - create table (HP,mn,stdDev,min,max,median) of raw intensity data.
(package private) int	getHP_XandYsetData(float[] xList, float[] yList, int[] propList, GeneList ml, boolean setPropsFlag, boolean filterByMLflag) getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter mae.fc.workingCL.
(package private) int	getNormHP_XandYdata(float[] xList, float[] yList, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) int	getRawHP_XandYdata(float[] xData, float[] yData, float[] xBkgd, float[] yBkgd, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getRawHP_XandYdata() - get list raw spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) java.lang.String	lookupHPcoords(int x, int y, int distThreshold, boolean useFieldNameFlag, MaHybridSample ms) lookupHPcoords() - lookup closest gene name by (x,y) in sample pseudoarray and set current gene if < distThreshold away, else return "".
(package private) void	recalcGlobalStats(boolean useGoodSpotsForGlobalStatsFlag) recalcGlobalStats() - recompute global array statistics with all or just good spots.
(package private) void	recalcNorms(java.lang.String sMethod, boolean recomputeNormalizationExtremaFlag) recalcNorms() - recompute normalizations for all samples in the hps.msList[].
(package private) void	setCurrentGenes(int curGenesMode) setCurrentGenes() - set current genes to those in the GeneClass database if the curGenesMode is true.
(package private) boolean	setIntensHistCLfromIntenRange(GeneList resultCL, MaHybridSample ms, float intensLB, float intensUB, boolean outsideRangeFlag) setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range
(package private) void	setObjCoordFromMaster_ID(java.lang.String masterID) setObjCoordFromMaster_ID() - set gene xxxOBJ values from Master_ID name
(package private) void	setObjCoordFromMID(int mid, java.lang.Object sObj) setObjCoordFromMID() - set gene xxxOBJ values from MID for current HP sample.
(package private) void	setOBJtoGID(int gid, MaHybridSample ms) setOBJtoGID() - set the current gene xxxOBJ values to the specified GID.
(package private) boolean	setRatioHistCLfromF1F2Ratios(GeneList resultCL, MaHybridSample ms, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range
(package private) boolean	setRatioHistCLfromHP_XYratios(GeneList resultCL, MaHybridSample msX, MaHybridSample msY, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range
(package private) boolean	setRatioHistCLfromHP_XYsetRatios(GeneList resultCL, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromHP_XYsetRatios() - set GeneList of X/Y set ratios in ratio range

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

fc

private Filter fc

link to global Filter instance

hps

private SampleSets hps

link to global SamplesSets instance

ratioHist

int[] ratioHist

histogram of g1/g2 ratios [0:nRatioHistBins] in range 0.01:100.0

ratioValue

double[] ratioValue

scale of ratio histogram of g1/g2 ratios

maxRatioHistIdx

int maxRatioHistIdx

max value found in ratioHist[]

minRatioHistIdx

int minRatioHistIdx

min value found in ratioHist[]

nRatioHistBins

int nRatioHistBins

# of bins in ratioHist[]

hpXYdata

static HPxyData hpXYdata

generic HP-X/Y set object

minDataHP_X

float minDataHP_X

min intensity HP_X in getNormHP_XandYdata

minDataHP_Y

float minDataHP_Y

min intensity HP_Y in getNormHP_XandYdata

maxDataHP_X

float maxDataHP_X

max intensity HP_X in getNormHP_XandYdata

maxDataHP_Y

float maxDataHP_Y

max intensity HP_Y in getNormHP_XandYdata

tempCD_CL

private GeneList tempCD_CL

temporary GeneList used in local gene list operations

grandMeanUseGeneSet

float grandMeanUseGeneSet

grand mean HP 'User Filter Gene Set' means for normalization.

grandMeanCalDNA

float grandMeanCalDNA

grand mean HP Calib.DNA means for normalization.

rSqHP_HP

float[][] rSqHP_HP

[1:nRows][1:nCols] rSq, HP vs HP correlation coefficient

isValidObjFlag

static boolean isValidObjFlag

Flag to indicate that the current gene (i.e. object) is valid. If MouseReleased selected object matches xy coords within radius, then the objXXX values defined below are valid.

objMID

static int objMID

Gene index mid of object if isValidObj is TRUE

objGID

static int objGID

GridCoords gid of object if isValidObj is TRUE

objGIDG

int objGIDG

Gang f' GridCoords gid of object if isValidObj is TRUE

objField

int objField

object Field that best matches xy coords if isValidObj is TRUE

objGrid

int objGrid

object Grid that best matches xy coords if isValidObj is TRUE

objRow

int objRow

object Grid-Row that best matches xy coords if isValidObj is TRUE

objCol

int objCol

object Grid-Column that best matches xy coords if isValidObj is TRUE

objX

int objX

optimal spot X position if isValidObj is TRUE

objY

int objY

optimal spot Y position if isValidObj is TRUE

maxTextItems

int maxTextItems

Common Grid labels for drawing onto the canvas. NOTE: this is specific for each microarray. Computed as: maxFIELDS*maxGRIDS+2 (includes title) actual # text items to display

nTextItems

int nTextItems

color_textHP

java.awt.Color[] color_textHP

text HP labels shared colors

font_textHP

java.awt.Font[] font_textHP

text HP labels shared fonts

recursionFlag

boolean recursionFlag

flag: track last updated object to avoid recursion problems

Constructor Detail

CompositeDatabase

CompositeDatabase(MAExplorer mae)

CompositeDatabase() - constructor to set up data structures. Access is then performed using various methods.

Parameters:

mae - is the MAExplorer instance

See Also:

GeneList, GeneList.clear(), HPxyData

Method Detail

setCurrentGenes

void setCurrentGenes(int curGenesMode)

setCurrentGenes() - set current genes to those in the GeneClass database if the curGenesMode is true. Else set all genes as current.

Parameters:

curGenesMode -

See Also:

GeneList.addGene(Gene), GeneList.clear()

calcRatioHistVal

double calcRatioHistVal(float g1,
                        float g2)

calcRatioHistVal() - compute histogram bin value & increment ratio histogram

Parameters:

g1 - intensity value

g2 - intensity value

Returns:

the ratio defined as: g1/g2.

calcRatioHists

void calcRatioHists(int nList,
                    float[] d1List,
                    float[] d2List,
                    GeneList ml)

calcRatioHists() - compute ratio histogram of d1List[]/d2List[] data. Compute the ratio histogram and set ratio values for genes in ml.

Parameters:

nList - is the size of the data arrays

d1List - ARG: is list of data1 data

d2List - ARG: is list of data2 data

ml - RTN: is GeneList to use in filtering the data

See Also:

Gene.setGeneData(float), GeneList.clear(), calcRatioHistVal(float, float)

calcHistOfF1F2Ratios

boolean calcHistOfF1F2Ratios(GeneList ml,
                             MaHybridSample ms)

calcHistOfF1F2Ratios() - compute histogram of F1/F2 ratios for spots which are selected in the GeneList ml.

Parameters:

ml - is gene list to use in filtering

ms - is the Sample to use

Returns:

true if succeed

See Also:

MaHybridSample.getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean), calcRatioHists(int, float[], float[], GeneList)

calcHistOfHP_XYratios

boolean calcHistOfHP_XYratios(GeneList ml,
                              boolean useXYsetsFlag)

calcHistOfHP_XYRatios() - compute histogram of HP-X/-Y (or 'sets') spot ratios of filtered data

Parameters:

ml - is gene list to use in filtering

ms - is the Sample to use

Returns:

true if succeed

See Also:

getHP_XandYsetData(float[], float[], int[], GeneList, boolean, boolean), getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean), calcRatioHists(int, float[], float[], GeneList)

setIntensHistCLfromIntenRange

boolean setIntensHistCLfromIntenRange(GeneList resultCL,
                                      MaHybridSample ms,
                                      float intensLB,
                                      float intensUB,
                                      boolean outsideRangeFlag)

setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range

Parameters:

resultCL - RTN: is the resulting gene list

ms - is the Sample to use

intensLB - is lower bound of intensity

intensUB - is upper bound of intensity

outsideRangeFlag - test if outside of range else inside range

Returns:

true if succeed

See Also:

Filter.isMIDinWorkingCL(int), GeneList.addGene(Gene), GeneList.clear(), MaHybridSample.getDataByGID(int, boolean, int), getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean), calcRatioHistVal(float, float)

setRatioHistCLfromF1F2Ratios

boolean setRatioHistCLfromF1F2Ratios(GeneList resultCL,
                                     MaHybridSample ms,
                                     float ratioLB,
                                     float ratioUB,
                                     boolean outsideRangeFlag)

setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range

Parameters:

resultCL - RTN: is the resulting gene list

ms - is the Sample to use

ratioLB - is lower bound of intensity

ratioUB - is upper bound of intensity

outsideRangeFlag - test if outside of range else inside range

Returns:

true if succeed

See Also:

GeneList.addGene(Gene), GeneList.clear(), MaHybridSample.getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean), calcRatioHistVal(float, float)

setRatioHistCLfromHP_XYratios

boolean setRatioHistCLfromHP_XYratios(GeneList resultCL,
                                      MaHybridSample msX,
                                      MaHybridSample msY,
                                      float ratioLB,
                                      float ratioUB,
                                      boolean outsideRangeFlag)

setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range

Parameters:

resultCL - RTN: is the resulting gene list

msX - is the X Sample to use

msY - is the Y Sample to use

ratioLB - is lower bound of intensity

ratioUB - is upper bound of intensity

outsideRangeFlag - test if outside of range else inside range

Returns:

true if succeed

See Also:

GeneList.addGene(Gene), GeneList.clear(), calcRatioHistVal(float, float), getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean)

setRatioHistCLfromHP_XYsetRatios

boolean setRatioHistCLfromHP_XYsetRatios(GeneList resultCL,
                                         float ratioLB,
                                         float ratioUB,
                                         boolean outsideRangeFlag)

setRatioHistCLfromHP_XYsetRatios() - set GeneList of X/Y set ratios in ratio range

Parameters:

resultCL - RTN: is the resulting gene list

ratioLB - is lower bound of intensity

ratioUB - is upper bound of intensity

outsideRangeFlag - test if outside of range else inside range

Returns:

true if succeed

See Also:

GeneList.addGene(Gene), GeneList.clear(), calcRatioHistVal(float, float), getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean)

lookupHPcoords

java.lang.String lookupHPcoords(int x,
                                int y,
                                int distThreshold,
                                boolean useFieldNameFlag,
                                MaHybridSample ms)

lookupHPcoords() - lookup closest gene name by (x,y) in sample pseudoarray and set current gene if < distThreshold away, else return "". If it finds it, it also sets the isValidObj flag and updates (objField, objGrid, objRow, objCol) and ( objGID, objGIDG, objMID). It also sets (objX,objY) to (xC[], yC[]) values. It looks up the associated GeneBank, dbEST data in dbESTid, cloneId, ESTname, GeneBankId (Acc)

Parameters:

x - coordinage

y - coordinates

distThreshold - of distance of (x,y) to nearest spot in sample

useFieldNameFlag - to generate the field name (if > 1 field)

ms - is sample to test coordinates

Returns:

string of coordinates data

See Also:

GridCoords.cvtGID2str(int, boolean), Component.repaint(), setOBJtoGID(int, MaHybridSample)

setOBJtoGID

void setOBJtoGID(int gid,
                 MaHybridSample ms)

setOBJtoGID() - set the current gene xxxOBJ values to the specified GID. It updates: (objField, objGrid, objRow, objCol, objGID, objGIDG, objMID, objX, objY).

setObjCoordFromMaster_ID

void setObjCoordFromMaster_ID(java.lang.String masterID)

setObjCoordFromMaster_ID() - set gene xxxOBJ values from Master_ID name

Parameters:

masterID - is the Master_ID for the current gene

See Also:

GipoTable.getMIDfromMaster_IDhashTable(java.lang.String), setObjCoordFromMID(int, java.lang.Object)

setObjCoordFromMID

void setObjCoordFromMID(int mid,
                        java.lang.Object sObj)

setObjCoordFromMID() - set gene xxxOBJ values from MID for current HP sample. Also update the pseudoarray image and any popup plots.

Parameters:

mid - gene MID to set as the current gene (obj)

sObj - to pass onto updateCurGene()

See Also:

PopupRegistry.updateCurGene(int, int, java.lang.Object), ScrollableImageCanvas.setObjPos(int, int), Component.repaint()

getNormHP_XandYdata

int getNormHP_XandYdata(float[] xList,
                        float[] yList,
                        int[] propList,
                        GeneList ml,
                        MaHybridSample msX,
                        MaHybridSample msY,
                        boolean setPropsFlag,
                        boolean filterByMLflag)

getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.

If msX==msY, then get msX.f1 for msX and msX.f2 for msY else get (msX.f1+msX.f2)/2 for msX and (msY.f1+msY.f2)/2 for msY. The assumption is made that grid structure is same for both msX and msY. Also set the (min/max)(DataHP_X,DataHP_Y) values. Return the number of points nList in the list[0:nList-1].

Parameters:

xList[max - # genes to get] to return HP-X values

yList[max - # genes to get] to return optional HP-Y values

propList[max - # genes to get] gene property values

ml - is the GeneList to save genes or to filter by. To filter by all genes, set ml to set of all genes.

msX - is HP-X sample to use

msY - is HP-Y sample to use - optional

setPropsFlag - set the propList[] data from fc.workingCL as IS_FILTERED or IS_NOT_FILTERED. If filterByMLflag, then copy the gene.prop field.

filterByMLflag - if true, then filter by ml GeneList. To filter by all genes, set ml to set of all genes mae.gct.allGenesCL

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

See Also:

Filter.isMIDinWorkingCL(int), Gene.setGeneData(float), GeneList.clearNull(), GeneList.setGene(Gene, int), GeneBitSet.isItemInGeneBitSet(int), MaHybridSample.getDataByGID(int, boolean, int), MaHybridSample.getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean), getHP_XandYsetData(float[], float[], int[], GeneList, boolean, boolean)

getRawHP_XandYdata

int getRawHP_XandYdata(float[] xData,
                       float[] yData,
                       float[] xBkgd,
                       float[] yBkgd,
                       int[] propList,
                       GeneList ml,
                       MaHybridSample msX,
                       MaHybridSample msY,
                       boolean setPropsFlag,
                       boolean filterByMLflag)

getRawHP_XandYdata() - get list raw spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL. If msX==msY, then get msX.f1 for msX and msX.f2 for msY else get (msX.f1+msX.f2)/2 for msX and (msY.f1+msY.f2)/2 for msY. The assumption is made that grid structure is same for both msX and msY. Also set the (min/max)(DataHP_X, DataHP_Y) values. It will also return the background data values if the xBkgd[] and/or yBkgd[] are not null.

NOTE: This method does NOT get 'set' data since it is ambiguous how to "average" raw data (that is why we normalize it :-). So this method ignores mae.useHPxySetDataFlag. Use getNormHP_XandYdata() to set mean set data.

Return the number of points nList in the list[0:nList-1].

Parameters:

xData[max - # genes to get] to return HP-X intensity values

yData[max - # genes to get] to return optional HP-Y intensity values

xBkgd[max - # genes to get] to return HP-X background values

yBkgd[max - # genes to get] to return optional HP-Y background values

propList[max - # genes to get] gene property values

ml - is the GeneList to save genes or to filter by. To filter by all genes, set ml to set of all genes.

msX - is HP-X sample to use

msY - is HP-Y sample to use - optional

setPropsFlag - set the propList[] data from fc.workingCL as IS_FILTERED or IS_NOT_FILTERED. If filterByMLflag, then copy the gene.prop field.

filterByMLflag - if true, then filter by ml GeneList. To filter by all genes, set ml to set of all genes mae.gct.allGenesCL

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xData[], yData[]) sizes.

See Also:

Filter.isMIDinWorkingCL(int), Gene.setGeneData(float), GeneList.clearNull(), GeneList.setGene(Gene, int), GeneBitSet.isItemInGeneBitSet(int), MaHybridSample.getDataByGID(int, boolean, int), MaHybridSample.getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean), getHP_XandYsetData(float[], float[], int[], GeneList, boolean, boolean)

getHP_XandYsetData

int getHP_XandYsetData(float[] xList,
                       float[] yList,
                       int[] propList,
                       GeneList ml,
                       boolean setPropsFlag,
                       boolean filterByMLflag)

getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter mae.fc.workingCL. If msX==msY, then get msX.f1 for msX and msX.f2 for msY else get (msX.f1+msX.f2)/2 for msX and (msY.f1+msY.f2)/2 for msY. The assumption is made that grid structure is same for both msX and msY. It computes and returns the number of points nList in the list[1:nList].

Parameters:

xList[max - # genes to get] HP-X values

yList[max - # genes to get] return optional HP-Y values

propList[max - # genes to get] optional property values

ml - is the GeneList to save genes in or filter by.To filter by all genes, set ml to set of all genes mae.gct.allGenesCL

setPropsFlag - set the propList[] data from fc.workingCL as IS_FILTERED or IS_NOT_FILTERED

filterByMLflag - if true, then filter by ml

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got the all if them return size equals the (xList[], yList[]) sizes.

See Also:

Filter.isMIDinWorkingCL(int), Gene.setGeneData(float), GeneList.clear(), GeneList.clearNull(), GeneList.setGene(Gene, int), GeneBitSet.isItemInGeneBitSet(int), HPxyData.setupDataStruct(boolean), HPxyData.updateDataAndStat(int)

calAllSamples

boolean calAllSamples()

calAllSamples() - compute (meanCalDNA, stdDevCalDNA) calibration for all samples

Returns:

true if successful.

See Also:

MaHybridSample.calcMeanCalDNA(), MaHybridSample.calcMeanUseNormGeneSet()

recalcNorms

void recalcNorms(java.lang.String sMethod,
                 boolean recomputeNormalizationExtremaFlag)

recalcNorms() - recompute normalizations for all samples in the hps.msList[]. Recalculate intensity scale factor extrema depending on normalization mode.

Parameters:

sMethod - is the name of the current normalization method

recomputeNormalizationExtremaFlag - if set

See Also:

Component.repaint(), MaHybridSample.calcIntensScaleExtrema(), PopupRegistry.updateFilter(GeneList), StateScrollers.regenerateScrollers(boolean), StateScrollers.setRangeMaps(), Util.showMsg(java.lang.String), calAllSamples()

calDNAhybSamplesTable

SimpleTable calDNAhybSamplesTable()

calDNAhybSamplesTable() - calc. (meanCalDNA, stdDevCalDNA) Table for all samples

Returns:

SimplleTable if successful else null.

See Also:

MaHybridSample, PopupRegistry.updateFilter(GeneList), SimpleTable, Util.cvf2s(float, int), calAllSamples()

calcHP_HPcorrelations

SimpleTable calcHP_HPcorrelations()

calcHP_HPcorrelations() - compute HP vs. HP samples correlation coefficients table for all loaded HPs. It is computed only on the Filtered data.

Returns:

SimpleTable if successful else null.

See Also:

MathMAE.calcXYstat(int, float[], float[], int[], java.lang.String, java.lang.String), SimpleTable, Util.showMsg3(java.lang.String), getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean)

createHPmeanAndVarTable

Table createHPmeanAndVarTable()

createHPmeanAndVarTable() - create table (HP,mn,stdDev,min,max,median) of raw intensity data.

Returns:

table if successful, else null.

See Also:

Table, Util.cvf2s(float, int)

recalcGlobalStats

void recalcGlobalStats(boolean useGoodSpotsForGlobalStatsFlag)

recalcGlobalStats() - recompute global array statistics with all or just good spots. This recalculates the statistics for each array in the database using its local good spot data status. This also includes a call to ms.cvtRawQdataToMAEdata() to compute additional derived statistics. It then updates the PopupRegistry current gene, data filter and display.

Parameters:

useGoodSpotsForGlobalStatsFlag - if true

See Also:

MaHybridSample.recalcGlobalStats(boolean), PopupRegistry.updateCurGene(int, int, java.lang.Object), PopupRegistry.updateFilter(GeneList)

cleanup

void cleanup()

cleanup() - cleanup global static allocated variables in this class. If statics are added later to this class, then set them to null here.