A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a2a1Diff - Variable in class O2Plib.db.DbBoundary

angle difference of notch will be < 180 in a notch

a_count - Variable in class O2Plib.image.WriteGifEncoder

acc - Static variable in class O2Plib.db.CSD.CSDacc

Accession database if it exists

acc - Variable in class O2Plib.db.DbAccession.AccContentHandler

where most of the data is

acc - Variable in class O2Plib.db.DbSample

The DbAccession database instance.

accFieldNames - Variable in class O2Plib.db.DbSample

Accession database fields for this sample if not null

accFields - Static variable in class O2Plib.db.DbAccession

Accession database table fields.

accFieldsDynamic - Static variable in class O2Plib.db.DbAccession

Dynamic accession database table fields.

accFieldsNames - Variable in class O2Plib.db.DbAccession

Sample accession fields if available in accession database

accFieldsRequired - Static variable in class O2Plib.db.DbAccession

Required accession database table fields

accFile - Variable in class O2Plib.db.CSD.CSDacc

Accession database file if it exists

accFilePath - Variable in class O2Plib.db.CSD.CSDacc

Full Accession database file if it exists

accFormatModeA - Variable in class O2Plib.db.DbAccession

accession file data mode IO_FORMAT_xxxx

accRowData - Variable in class O2Plib.db.DbAccession

Sample accession data if available in accession database

accRowData - Variable in class O2Plib.db.DbSample

Accession database data for this sample if not null

accum - Variable in class O2Plib.image.WriteGifEncoder

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupDialogQuery

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupOptions

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupTableEditDialog

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

actionPerformed() - handle action events

actionPerformed(ActionEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

actionPerformed() - handle action events

actualSubHeaders - Variable in class O2Plib.db.CSD.CSDio

actual# of CSD DB subheaders and it should be LEQ MAXSUBHEADERS.

add(DbSample, String) - Method in class O2Plib.db.CSD.CSDcond

add() - add sample to condition.

add(DbSample) - Method in class O2Plib.db.CSD.CSDcond

add() - add sample to condition.

add(String) - Method in class O2Plib.db.CSD.CSDcond

add() - add sample name to condition.

add(int, CSDRspot, String) - Method in class O2Plib.db.CSD.CSDRmap

add() - add entry to the Rmap

add(DbPspot) - Method in class O2Plib.db.CSD.CSDRspot

add() - add DbPspot to the Rspot set spotList[] list if the pairing code is SP, PP, AP, or (US with (xRmom,yRmom) NEQ 0).

add(CSDRspot, int) - Method in class O2Plib.db.CSD.CSDRspotList

add() - add Rspot to RSL.

add(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspotList

add() - add Rspot to RSL.

add(int) - Method in class O2Plib.db.CSD.CSDRspotList

add() - add Rspot number to RSL.

add2ERspot(DbPspot) - Method in class O2Plib.db.CSD.CSDRspot

add2ERspot() - add DbPspot to ERspot set.

addButtonsCnt - Variable in class O2Plib.gui.PopupDialogQuery

# of buttons to add.

addChoicesList(int, Panel) - Method in class O2Plib.gui.PopupOptions

addChoicesList() - add Choices lists add Choice list "{A|B|C...Z}1,{A|B|C...Z}2,..."

addColumnsToTable(String[]) - Method in class O2Plib.table.SimpleTable

addColumnsToTable() - add new columns to the table with the specified field names list.

addColumnToTable(String, String[]) - Method in class O2Plib.table.SimpleTable

addColumnToTable() - add a new column to the table with the specified field name.

addDbug(CSDRspot, int, int) - Method in class O2Plib.db.CSD.CSDRspotList

addDbug() - DBUG version.

addExpr(CSDexpr) - Method in class O2Plib.db.CSD.CSDexprList

addExpr() - add Expr to ExprList.

addLandmarkToLMset(int, int, int, int) - Method in class O2Plib.db.LMset

addLandmarkToLMset() - add landmark at (x1,y1,x2,y2) to the landmark set up to maxLMS.

addLMS(LMset, String) - Method in class O2Plib.db.CSD.CSDlms

addLMS() - add LMset to list of LMsets.

addLMS(LMset) - Method in class O2Plib.db.CSD.CSDlms

addLMS() - add LMset to list of LMsets.

addNewEntry(String, String, String) - Method in class O2Plib.db.DbAccession

addNewEntry() - add a new row of data to accession table.

addRoi(Roi, boolean, int, Color) - Method in class O2Plib.image.RoiList

addRoi() - add new Roi to Roi list

addRspotToHashtable(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspotList

addRspotToHashtable() - Add Rspot to Rspot list hashtable.

addRspotToHashtableDbug(CSDRspot, int) - Method in class O2Plib.db.CSD.CSDRspotList

addRspotToHashtableDbug() - DBUG version.

addSlidersList(int, Panel) - Method in class O2Plib.gui.PopupOptions

addSlidersList() - add slider triple(s).

addStringToStringList(String[], String) - Static method in class O2Plib.misc.Util

addStringToStringList() - arg string to string array.

addSwitch(String[], String) - Static method in class O2Plib.misc.Switches

addSwitch() - add switch to the sw[]list, by extending the list and then appending the new switch.

addTableToTableList() - Method in class O2Plib.table.Table

addTableToTableList() - add Table to tblList.

adjustmentValueChanged(AdjustmentEvent) - Method in class O2Plib.gui.PopupOptions

adjustmentValueChanged() - handle ImageScroller scroll events.

adjustmentValueChanged(AdjustmentEvent) - Method in class O2Plib.gui.PopupTableEditDialog

adjustmentValueChanged() - handle ImageScroller scroll events.

aH - Variable in class O2Plib.gui.PopupTableEditDialog

Scroll pane to hold the Name-Value scrollable panel

alertDone - Variable in class O2Plib.gui.PopupDialogQuery

button pressed flag

alertTimeout(String) - Method in class O2Plib.gui.PopupDialogQuery

alertTimeout() - update popup dialog msg - wait for "Continue"

allocSpotTotals() - Method in class O2Plib.db.CSD.CSDtotals

allocSpotTotals() - allocate spot total arrays for nSamples

allSetSamples - Static variable in class O2Plib.db.CSD.CSDglb

SEt of all samples.

altLMset - Variable in class O2Plib.db.DbSpot

Sorted list of next nearest LM sets [0:nbrAltLMs-1] to this spot

altLMsetDistSq - Variable in class O2Plib.db.DbSpot

corresponding distances of next nearest landmarks [0:nbrAltLMs-1]

altMod - Variable in class O2Plib.image.ScrollableImage

ALT/Mouse

annotation - Variable in class O2Plib.db.CSD.CSDRspot

Spot annotation

answer - Variable in class O2Plib.gui.PopupTextFieldDialog

Returned value from text field

AP - Static variable in class O2Plib.db.CSD.CSDglb

Ambiguous Pair - pairing program generated label

AP - Static variable in class O2Plib.db.DbBaseSpot

Ambiguous Pair - pairing program generated label

AP - Static variable in class O2Plib.db.DbLM

Ambiguous Pair - pairing program generated label

AP - Static variable in class O2Plib.db.DbPairSamples

Ambiguous Pair - pairing program generated label

APCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Ambiguous Pair spot label

appendLandmarkToLMset(int, int, int, int) - Method in class O2Plib.db.LMset

appendLandmarkToLMset() - append landmark at (x1,y1,x2,y2) to the landmark set up to maxLMS.

appendPRmsg(String) - Static method in class O2Plib.misc.Util

appendPRmsg() - append message to report text area window if it exists.

appendRowToTable(String[]) - Method in class O2Plib.db.DbAccession

appendRowToTable() - append accRowData[] data to accession table.

appendRowToTable(String[]) - Method in class O2Plib.table.SimpleTable

appendRowToTable() - append row of data to table.

applicationName - Static variable in class O2Plib.misc.Util

Name of this application

area - Variable in class O2Plib.db.DbSpot

spot area in pixels

areaCalibFlag - Variable in class O2Plib.db.CSD.CSDcal

use Area calibration in OD/mm**2 if set

areaIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

areaMax - Variable in class O2Plib.db.CSD.CSDtotals

areaMin - Variable in class O2Plib.db.CSD.CSDtotals

Minimum area of any spot in DB

arrclr(byte[], byte, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the byte array to byte value

arrclr(char[], char, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the char array to char value

arrclr(short[], short, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the short array to short value

arrclr(int[], int, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the int array to int value

arrclr(long[], long, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the long array to long value

arrclr(float[], float, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the float array to float value

arrclr(String[], String, int) - Static method in class O2Plib.misc.Util

arrclr() - set all values of the String array to short value

assignAccessionDB(DbAccession) - Method in class O2Plib.db.DbSample

assignAccessionDB() - assign the accession database

assignRsampleToAllSpotsInSpotList(DbSample) - Method in class O2Plib.db.DbSample

assignRsampleToAllSpotsInSpotList() - assign the dbRsample field in all spots in the current spot list

atMostOneFlag - Variable in class O2Plib.gui.PopupNameListSelectorDialog

atomicFileCopy(String, String) - Static method in class O2Plib.io.FileIO

atomicFileCopy() - do an atomic file move where we delete the toFile PRIOR to copying the fromFile to the toFile.

aV - Variable in class O2Plib.gui.PopupTableEditDialog

B

b - Variable in class O2Plib.image.WriteGifEncoder

badArgExit(String, String, boolean) - Static method in class O2Plib.misc.Util

badArgExit() - print switch arg error message and exit with -1 if exitFlag is set.

baseSampleName - Variable in class O2Plib.db.DbSample

base sample name of the sample without either the path prefix or the file extension.

baseSSFimageFileName - Variable in class O2Plib.db.DbSample

name of SSF input base file name from file [FUTURE]

baseStatusTime - Static variable in class O2Plib.misc.Util

base starting time in epoch msec time for the status reports

batchDir - Static variable in class O2Plib.db.CSD.CSDglb

Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/

batchDir - Variable in class O2Plib.io.FileIO

Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/

bestPairedSpot - Variable in class O2Plib.db.DbBaseSpot

ptr to best paired spot for spot-pairing, if not null

bestPairedSpot - Variable in class O2Plib.db.DbSpot

ptr to best paired spot for spot-pairing, if not null

BF_DISPLAY_SPOT - Static variable in class O2Plib.db.DbBaseSpot

Bit feature to display spot

BF_FAILED_SXSYR1RANGE - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed sX/Sy range lower bound

BF_FAILED_SXSYR2RANGE - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed sX/Sy range upper bound

BF_FAILED_T1AREA - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T1 area lower bound

BF_FAILED_T1DENSITY - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T1 density lower bound

BF_FAILED_T1DENSRANGE - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T1 density range lower bound

BF_FAILED_T2AREA - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T2 area upper bound

BF_FAILED_T2DENSITY - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T2 density upper bound

BF_FAILED_T2DENSRANGE - Static variable in class O2Plib.db.DbBaseSpot

Bit feature failed T2 density range upper bound

BF_IS_LMS_SPOT - Static variable in class O2Plib.db.CSD.CSDglb

Bit feature of a spot.

BF_ISVALIDSPOT - Static variable in class O2Plib.db.CSD.CSDglb

Bit feature of a spot.

BF_ISVALIDSPOT - Static variable in class O2Plib.db.DbBaseSpot

Bit feature of a spot

bitFeatures - Variable in class O2Plib.db.DbBaseSpot

bit features of a spot is the OR of BF_xxxx bits

bitpp - Variable in class O2Plib.image.PpxLoader

bits per pixel (one band)

BITS - Static variable in class O2Plib.image.WriteGifEncoder

bkgrdFilterSize - Variable in class O2Plib.db.DbSample

size of NxN zonal notch filter background estimator

blackIsZeroFlag - Variable in class O2Plib.image.PpxLoader

1 if BLACK is gray value 0, else 0 if WHITE is gray value 0

blackIsZeroFlag - Variable in class O2Plib.image.TiffPixelLoader

Black is Zero flag

blkaln - Variable in class O2Plib.image.PpxLoader

block alignment flag 0 = aligned)

bLsqTerm - Variable in class O2Plib.db.CSD.CSDnorm

Least Square normalization intercept: bj to estimate djR'=mj*d'j+bj.

blueBits(int) - Method in class O2Plib.image.MedianCut

blueBits() - Get 8-bit blue component of a 15-bit color 8-bit pixel with low 3 bits zero.

bLUT - Variable in class O2Plib.image.MedianCut

[0:255] Blue Color map look up table

bmax - Variable in class O2Plib.image.MC_Cube

bmin - Variable in class O2Plib.image.MC_Cube

bnd - Variable in class O2Plib.db.DbSpot

Spot boundary for the CC if used

BND_SMOOTHING_FILTER_WIDTH - Static variable in class O2Plib.db.DbBoundary

For 180 micron/pixel.

bPixels - Variable in class O2Plib.image.PpxLoader

pixels [0:nPixels-1] for the image

bubbleSort(String[], int) - Static method in class O2Plib.misc.Sort

bubbleSort() - Sort String array via bubble sort w/len

bubbleSortIndex(String[], int, boolean) - Static method in class O2Plib.misc.Sort

bubbleSortIndex() - sort copy of String[0:len-1] data with bubble sort, return index[].

bubbleSortIndex(float[], int, boolean) - Static method in class O2Plib.misc.Sort

bubbleSortIndex() - sort copy of float[0:len-1] data with bubble sort, return index[].

bubbleSortIndex(int[], int, boolean) - Static method in class O2Plib.misc.Sort

bubbleSortIndex() - sort copy of int[0:len-1] data with bubble sort, return index[].

bufSize - Variable in class O2Plib.table.Table

size of input buffer when read file

buildAccWizardGUI() - Method in class O2Plib.gui.PopupTableEditDialog

buildAccWizardGUI() - Build the ImageViewer GUI

buildFullFieldLists() - Method in class O2Plib.db.DbAccession

buildFullFieldLists() - build full accFields[] and helpList[] arrays [TODO] Big time add MIAPE fields here...

buildGUI() - Method in class O2Plib.gui.PopupYesNoDialogBox

buildGUI() - Build GUI

buildOptionsGUI(String[], boolean[], String[], String) - Method in class O2Plib.gui.PopupOptions

buildOptionsGUI() - build the popup selector.

bytePix - Variable in class O2Plib.image.PixReader

8-bits/pixel image if it exists

bytpp - Variable in class O2Plib.image.PpxLoader

bytes per pixel (one band)

C

cacheBufSizeBlocks - Variable in class O2Plib.db.CSD.CSDsizes

Rspot cache file buffer size

cacheDir - Static variable in class O2Plib.db.CSD.CSDglb

Cache database directory {projDir}/cache/

cacheDir - Variable in class O2Plib.io.FileIO

Cache database directory {projDir}/cache/

cal2gray - Variable in class O2Plib.misc.CalibrateOD

map pixel gray values to calibrated value (e.g., OD) by scaling it as: calibration value*1000 to gray size [0:maxGrayPixel]

calcCalib() - Method in class O2Plib.misc.CalibrateOD

calcCalib() - continuous piecewise linear calibration od(gray)

calcDensPrime(boolean, boolean) - Method in class O2Plib.db.DbSample

calcDensPrime() - For all spots update the spotList with background corrections by computing D' = Density - Area*MeanBkgrdDensity

calcFindHistPeaksAndExtrapolate(int[]) - Method in class O2Plib.misc.CalibrateOD

calcFindHistPeaksAndExtrapolate() - set up histogram, peaks and extrapolate map for the current Wedge ROI histogram.

calcHistFindPeaksAndExtrapolate() - Method in class O2Plib.misc.CalibrateOD

calcHistFindPeaksAndExtrapolate() - set up histogram, peaks and extrapolate map for the current Wedge ROI.

calcHistogram(DbSample, Roi) - Method in class O2Plib.image.PixFunctions

calcHistogram() - compute grayscale histogram from image pixel data for sample dbS.

calcHistogram(DbSample, int, int, int, int) - Method in class O2Plib.image.PixFunctions

calcHistogram() - compute grayscale histogram from image pixel data for sample dbS.

calcHistogramFromPeaks(float[], int[], int, int) - Method in class O2Plib.misc.CalibrateOD

calcHistogramFromPeaks() - compute "pseudo" grayscale histogram from lists peaks of peaks.

calcMeanGrayValue(DbSample, int, int, int, DbSpot) - Static method in class O2Plib.image.PixFunctions

calcMeanGrayValue() - compute mean gray value of spot and return the values in a DbSpot instance for sample dbS with (sp.area, sp.density, sp.xMom, sp.yMom, sp.density, sp.mnDensity, sp.dMax, sp.dMin, sp.sxy) Note: the std-deviation of sp.density is saved in sp.sxy.

calcMinEnclosingRectangle(Point[], int) - Static method in class O2Plib.db.DbBoundary

calcMinEnclosingRectangle() - compute minimum rectangle from the xyList[] of (x,y) points.

calcO2CandC2OscaledMaps() - Method in class O2Plib.misc.CalibrateOD

calcO2CandC2OscaledMaps() - setup gray2cal[] and cal2gray[] scaled maps given mapGrayToCal[] map.

calcStatistics() - Method in class O2Plib.db.DbPairSamples

calcStatistics() - compute the paired spot statistics

calcStatusTimesReport() - Static method in class O2Plib.misc.Util

calcStatusTimesReport() - compute the status times and memory usage report if the timer is on.

calcWedgeHistogram(int, int, int, int) - Method in class O2Plib.misc.CalibrateOD

calcWedgeHistogram() - compute grayscale histogram in the image specified as dbSample.pix under the specified by the Wedge computing window region of interest (ROI)[x1:x2, y1:y2].

calCWx1 - Variable in class O2Plib.misc.CalibrateOD

calibration wedge computing window ULHC coordinate x

calCWx1A - Variable in class O2Plib.db.DbAccession

ULHC X computing window for input sample image wedge if any, else -1

calCWx1Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

calCWx2 - Variable in class O2Plib.misc.CalibrateOD

( calibration wedge computing window LRHC coordinate x

calCWx2A - Variable in class O2Plib.db.DbAccession

LRHC X computing window for input sample image wedge if any, else -1

calCWx2Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

calCWy1 - Variable in class O2Plib.misc.CalibrateOD

calibration wedge computing window ULHC coordinate y

calCWy1A - Variable in class O2Plib.db.DbAccession

ULHC Y computing window for input sample image wedge if any, else -1

calCWy1Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

calCWy2 - Variable in class O2Plib.misc.CalibrateOD

calibration wedge computing window LRHC coordinate y

calCWy2A - Variable in class O2Plib.db.DbAccession

LRHC Y computing window for input sample image wedge if any, else -1

calCWy2Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

calcXYeRspotCentroid() - Method in class O2Plib.db.CSD.CSDRspot

calcXYeRspotCentroid() - compute (xERspot,yERspot) estimated centroid of ERspot data using non-Rsample Pspots which must exist.

calFileDate - Variable in class O2Plib.misc.CalibrateOD

Date associated with the .cal file.

calib - Variable in class O2Plib.db.CSD.CSDcal

(Optional) list of sample's grayscale to calibrated units calibrations.

calib - Variable in class O2Plib.db.DbSample

(Opt) CalibrateOD instance

CALIB_MHZ_RT - Static variable in class O2Plib.db.CSD.CSDcal

(MHZ,RT) calibration type

CALIB_MW_PIE - Static variable in class O2Plib.db.CSD.CSDcal

(MW,pIE) calibration type

CALIB_PIECEWISE_LINEAR - Static variable in class O2Plib.db.CSD.CSDcal

Piecewise-linear curve fitting type

CALIB_SMOOTH - Static variable in class O2Plib.db.CSD.CSDcal

Smooth curve fitting type

calibCtr - Static variable in class O2Plib.misc.CalibrateOD

Master Calibration counter

calibName - Variable in class O2Plib.db.CSD.CSDcal

name of calibration

CalibrateOD - Class in O2Plib.misc

Class CalibrateOD calibrates image grayscale to OD or other unigs values where calibration standards are available.

CalibrateOD() - Constructor for class O2Plib.misc.CalibrateOD

CalibrateOD() - constructor for base instance.

CalibrateOD(int) - Constructor for class O2Plib.misc.CalibrateOD

CalibrateOD() - constructor to set up the initial map.

CalibrateOD(DbSample, int) - Constructor for class O2Plib.misc.CalibrateOD

CalibrateOD() - constructor to set up the initial map.

calibType - Variable in class O2Plib.db.CSD.CSDcal

domain type of calibration: CALIB_MW_PIE or CALIB_MHZ_RT

calImageFile - Variable in class O2Plib.misc.CalibrateOD

Image file associated with the .cal file if not null.

cancelFlag - Variable in class O2Plib.gui.PopupOptions

pressed Cancel

cancelFlag - Variable in class O2Plib.gui.PopupYesNoDialogBox

flag set by cancel button

cancelMsg - Variable in class O2Plib.gui.PopupYesNoDialogBox

Cancel label for dialog box

cbmi - Variable in class O2Plib.gui.MenuSupport.ChkBoxMenuData

Menu item

ccMinSize - Variable in class O2Plib.db.DbSample

Minimum central core component size area threshold in pixels

ccNumber - Variable in class O2Plib.db.DbSpot

Spot connected component number (CC#) from spot list .

ccNumberIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

ccOfGroup - Variable in class O2Plib.db.DbPspot

cc of group Rsample spot belongs to if any

ccRsampleIdx - Variable in class O2Plib.db.DbSpot

[DEPRICATE] Seg2Dgel CC# index for Rsample spot

ccSampleIdx - Variable in class O2Plib.db.DbSpot

[DEPRICATE] Seg2Dgel CC# index for Rsample spot

cdbIsOpenFlag - Static variable in class O2Plib.db.CSD.CSDglb

Flag indicates CSD DB is opened

centerPt - Variable in class O2Plib.image.ScrollableImage

center point

chainCode - Variable in class O2Plib.db.DbBoundary

chain code [0:lth-1]

changeArgVswitchData(String[], String, String, boolean) - Static method in class O2Plib.misc.Switches

changeArgVswitchData() change the switch data to the new switch.

changedTableFieldsDataFlag - Variable in class O2Plib.gui.PopupTableEditDialog

Flag indicating that the data fields were edited

changedUserData - Variable in class O2Plib.gui.PopupOptions

Changed user data [0:nData-1] if not null, then make a TextField with this data on the right else empty Label.

changedValueData - Variable in class O2Plib.gui.PopupTableEditDialog

Changed user data [0:nData-1] if not null, then make a TextField with this data on the right else empty Label.

changeGuiFlag - Variable in class O2Plib.gui.PopupTableEditDialog

flag to indicating that the GUI may have changed and that it should be rebuilt.

changeLandmarkToLMset(int, int, int, int, int) - Method in class O2Plib.db.LMset

changeLandmarkToLMset() - change landmark lmN to (x1,y1,x2,y2) in the landmark set.

char4x6table - Static variable in class O2Plib.image.DrawPix

Small 4x6 character set [0:127,1:2]

char5x7table - Static variable in class O2Plib.image.DrawPix

Large 5x7 character set was designed by Jonathan Merril.

char_init() - Method in class O2Plib.image.WriteGifEncoder

char_init() - Set up the 'byte output' routine

char_out(byte, FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

char_out() - add char to end of current packet, and if it is 254 characters, flush the packet to disk.

characters(char[], int, int) - Method in class O2Plib.db.DbAccession.AccContentHandler

characters() - This reports character data (within an element).

characters(char[], int, int) - Method in class O2Plib.db.DbLM.LmsContentHandler

characters() - This reports character data (within an element).

characters(char[], int, int) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

characters() - This reports character data (within an element).

characters(char[], int, int) - Method in class O2Plib.db.DbSample.SsfContentHandler

characters() - This reports character data (within an element).

charPix - Variable in class O2Plib.image.PixReader

16-bits/pixel image if it exists.

checkBoxPanel - Variable in class O2Plib.gui.PopupNameListSelectorDialog

checkBoxPanel - Variable in class O2Plib.gui.PopupOptions

checkIfChangedAndSave() - Method in class O2Plib.gui.PopupTableEditDialog

checkIfChangedAndSave() - copy current valueData[] to valueDataOrig[]

chkBoxMenuItemCmdHT - Variable in class O2Plib.gui.MenuSupport

Hashtable of ALL checkboxItem menu items.

chkBoxMenuItemDataHT - Variable in class O2Plib.gui.MenuSupport

Hashtable of ALL checkboxItem menu items.

chkPairingBits(CSDRspot) - Method in class O2Plib.db.CSD.CSDfilterState

chkPairingBits() - test the pairing bits agains the Rspot.

chkPairingBits(CSDRspotList) - Method in class O2Plib.db.CSD.CSDfilterState

chkPairingBits() - test the pairing bits agains the list of Rspots.

chkPspotLimits(DbPspot) - Method in class O2Plib.db.CSD.CSDlimits

chkPspotLimits() - check a DbPspot's Sample values for MW, pIe, (or RT, MZ) area, density (D'), density range, dP and dL limits.

chkRspotLimits(CSDRspot) - Method in class O2Plib.db.CSD.CSDlimits

chkRspotLimits() - check if all DbPspots in the Rspot set meet the Sample values for MW, pIe, area, density (D'), density range, dP and dL limits.

chkSampleImageExists() - Method in class O2Plib.db.DbSample

chkSampleImageExists() - test if the original image file exists for the sample

cl_block(FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

cl_block() - table clear for block compress Clear out the hash table.

cl_hash(int) - Method in class O2Plib.image.WriteGifEncoder

cl_hash() - reset code table

clean() - Method in class O2Plib.misc.CalibrateOD

clean() - clean up before init or when kill instance before GC

clear() - Method in class O2Plib.db.CSD.CSDannotation

clear() - clear instance.

clear() - Method in class O2Plib.db.CSD.CSDcond

clear() - clear condition list

clear() - Method in class O2Plib.db.CSD.CSDexpr

clear() - clear object list

clear() - Method in class O2Plib.db.CSD.CSDexprList

clear() - clear the expression list

clear() - Method in interface O2Plib.db.CSD.CSDlistInterface

clear() - clear object list

clear() - Method in class O2Plib.db.CSD.CSDlms

clear() - clear condition.

clear() - Method in class O2Plib.db.CSD.CSDRmap

clear() - clear Rmap

clear() - Method in class O2Plib.db.CSD.CSDRspot

clear() - clear CSDRspot.

clear() - Method in class O2Plib.db.CSD.CSDRspotList

clear() - clear the RSL.

clear() - Method in class O2Plib.image.Roi

clear() - clear ROI by setting all coordinates to -1

clear_flg - Variable in class O2Plib.image.WriteGifEncoder

80% occupancy

ClearCode - Variable in class O2Plib.image.WriteGifEncoder

clearCSD() - Method in class O2Plib.db.CSD.CSD

clearCSD() - clear the CSD [TODO]

clearFlags() - Method in class O2Plib.gui.PopupOptions

clearFlags() - clear all of the return status flags

clearImageReader(String) - Method in class O2Plib.image.PixReader

clearImageReader() - init the state of the image reader

clearLMset(boolean) - Method in class O2Plib.db.LMset

clearLMset() - reset the LMset state to contain no entries.

clearPairingBit(int) - Method in class O2Plib.db.CSD.CSDfilterState

clearPairingBit() - clear the search pairing bit

clearRsampleValues() - Method in class O2Plib.db.DbPspot

clearRsampleValues() - clear Rsample values in this spot.

clearSampleLMset() - Method in class O2Plib.db.LMset

clearSampleLMset() - reset only the Sample LMset state to contain no entries.

clearSizingBit(int) - Method in class O2Plib.db.CSD.CSDlimits

clearSizingBit() - clear the search sizing limits bit

clearSpotList() - Method in class O2Plib.db.DbSample

clearSpotList() - clear spot list

clearSpotPairList() - Method in class O2Plib.db.DbSample

clearSpotPairList() - clear spot list

clearSublistChkMenuItemStates(String) - Method in class O2Plib.gui.MenuSupport

clearSublistChkMenuItemStates() - clear all of the checkbox menu items in the radio group.

clearSublistChkMenuItemStates(CheckboxMenuItem) - Method in class O2Plib.gui.MenuSupport

clearSublistChkMenuItemStates() - clear all of the checkbox menu items in the radio group.

clearTableList() - Static method in class O2Plib.table.Table

clearTableList() - clear the table List of all instances.

cloneExprList() - Method in class O2Plib.db.CSD.CSDexprList

cloneExprList() - make a cloned copy of an ExprList.

cloneIt() - Method in class O2Plib.db.CSD.CSDcond

cloneIt() - make a cloned copy of a condition.

cloneIt() - Method in class O2Plib.db.CSD.CSDRspot

cloneIt() - clone the contents of this Rspot.

cloneIt() - Method in class O2Plib.db.CSD.CSDRspotList

cloneIt() - make a cloned copy of a RSL.

cloneLMset() - Method in class O2Plib.db.LMset

cloneLMset() - clone a new instance of this LM set.

clonePspot() - Method in class O2Plib.db.DbPspot

clonePspot() - clone spot sp into this spot.

clonePspotRsample() - Method in class O2Plib.db.DbPspot

clonePspotRsample() - clone spot sp into this spot.

close() - Method in class O2Plib.gui.PopupTableEditDialog

close() - close this popup and reset flags

close() - Method in class O2Plib.gui.PopupTextFieldDialog

close() - close this popup

close() - Method in class O2Plib.gui.PopupYesNoDialogBox

close() - close this popup

closeCSD() - Method in class O2Plib.db.CSD.CSDio

closeCSD() - flush the database and close it.

cm - Variable in class O2Plib.image.PpxLoader

cm - Variable in class O2Plib.image.TiffPixelLoader

cMapMode - Variable in class O2Plib.image.PpxLoader

color map flag.

cmd - Variable in class O2Plib.gui.MenuSupport.ChkBoxMenuData

CheckboxMenuItem command

cmd - Variable in class O2Plib.gui.MenuSupport.MenuCmdData

Menu command

cnt - Variable in class O2Plib.image.MC_Cube

code - Variable in class O2Plib.db.DbBaseSpot

Spot Pairing code DbLM.(SP,PP,AP,US,CP,EP,LM,GS)

codetab - Variable in class O2Plib.image.WriteGifEncoder

color - Variable in class O2Plib.image.Roi

color to display the ROI if enabled

color - Variable in class O2Plib.image.RoiList

working Roi color.

colorMax - Variable in class O2Plib.image.MedianCut

# of non-zero bins in hist15[]

colSize - Variable in class O2Plib.gui.PopupDialogQuery

# of columns to display

columnView - Variable in class O2Plib.image.ScrollableImage

column pixel size rulers

commutativeLMSflag - Variable in class O2Plib.db.DbLM

flag to allow searching for commutative database entries

compress(int, FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

compress() - GIF Image compression - modified 'compress'.

compressChainCode() - Method in class O2Plib.db.DbBoundary

compressChainCode() - Compress the bnd.chainCode[] and from 8-bits to 4-bit nibbles and shrink the arrays.

computeAllLMSradii() - Method in class O2Plib.db.CSD.CSDlms

computeAllLMSradii() -compute the LMS radii for a sample pairs.

computeLMSradii() - Method in class O2Plib.db.LMset

computeLMSradii() - compute minimum half radii for each valid LM and save them in 'minEffectiveRadius[-]' and then their nearest neighbor's landmark number in 'nearestLM[-]'.

condListDB - Static variable in class O2Plib.db.CSD.CSDglb

Database of list of condition lists of samples in the CSD either by data filtering or by computation (e.g., boolean computation of conditions from other condition sets).

CONSOLE_FLAG - Static variable in class O2Plib.db.CSD.CSDglb

CONSOLE_FLAG - Variable in class O2Plib.image.ScrollableImage

CONSOLE_FLAG - Static variable in class O2Plib.misc.Util

containsRoi(String) - Method in class O2Plib.image.RoiList

containsRoi() - see if roiName is in RoiList

contents - Variable in class O2Plib.db.DbAccession.AccContentHandler

contents - Variable in class O2Plib.db.DbLM.LmsContentHandler

contents - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

contents - Variable in class O2Plib.db.DbSample.SsfContentHandler

controlPanel - Variable in class O2Plib.gui.PopupNameListSelectorDialog

button box control panel

controlPanel - Variable in class O2Plib.gui.PopupOptions

controlPanel - Variable in class O2Plib.gui.PopupTableEditDialog

Control panel for the main frame

copy(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspot

copy() - copy the contents of Rspot r to this Rspot.

copyBaseValues(DbBaseSpot, boolean) - Method in class O2Plib.db.DbBaseSpot

copyBaseValues() - copy values in spot sp into this spot.

copyFile(String, String, String, int) - Static method in class O2Plib.io.FileIO

copyFile() - binary copy of one file or URL to a local file

copyFile(String, String, String, int, boolean) - Static method in class O2Plib.io.FileIO

copyFile() - binary copy of one file or URL to a local file

copyLMset(LMset) - Method in class O2Plib.db.LMset

copyLMset() - copy specified LMset into this LM set.

copyRsampleLMset(LMset) - Method in class O2Plib.db.LMset

copyRsampleLMset() - copy only Rsample (x,y) data in specified LMset into this LM set.

copyRsampleToSampleBaseValues() - Method in class O2Plib.db.DbBaseSpot

copyRsampleToSampleBaseValues() - copy Rsample base field field values in this Pspot to the Sample base field values.

copyRsampleToSampleSpotValues() - Method in class O2Plib.db.DbPspot

copyRsampleToSampleSpotValues() - copy Rsample field values in this Pspot to the Sample field values.

copySampleLMset(LMset) - Method in class O2Plib.db.LMset

copySampleLMset() - copy only Sample (x,y) data in specified LMset into this LM set.

copySpotValues(DbPspot, boolean) - Method in class O2Plib.db.DbPspot

copySpotValues() - copy values in spot sp into this spot.

copyTable(SimpleTable) - Method in class O2Plib.table.Table

copyTable() - copy SimpleTable data to this Table.

copyValues(DbSpot, boolean) - Method in class O2Plib.db.DbSpot

copyValues() - copy values in spot sp into this spot.

corCoefLsqTerm - Variable in class O2Plib.db.CSD.CSDnorm

Correlation coefficient when computing Least Square normalization terms:

corruptedFlag - Variable in class O2Plib.db.CSD.CSDio

normally set false.

count - Static variable in class O2Plib.image.TiffPixelLoader

instance # of TiffPixelLoader

count - Variable in class O2Plib.image.WriteGifEncoderHashitem

countG - Variable in class O2Plib.db.DbSample

# spots in list.

countPairG - Variable in class O2Plib.db.DbSample

# spots in list.

countsFailedFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(3.1) when the begining of is found

covAreaLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] COV area limits

covDensLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] COV density limits

CP - Static variable in class O2Plib.db.CSD.CSDglb

Composite Sample Database spot pair.

CP - Static variable in class O2Plib.db.DbBaseSpot

Composite Sample Database spot pair.

CP - Static variable in class O2Plib.db.DbLM

Composite Sample Database spot pair.

CP - Static variable in class O2Plib.db.DbPairSamples

Composite Sample Database spot pair.

CPCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Composite (averaged) spot label

create(int) - Method in class O2Plib.db.CSD.CSDRmap

create() - create the empty Rmap lists and hash tables of size nRmapSize

createAltLMset(int) - Method in class O2Plib.db.DbSpot

createAltLMset() - create alternate landmark set for this spot.

createCalibrationMaps(int) - Method in class O2Plib.db.CSD.CSDcal

createCalibrationMaps() - calibrate X and Y calibration sets using either piecewise-linear or smooth curve fitting [TODO]

createFileTable(String, String[], boolean) - Method in class O2Plib.table.Table

createFileTable() - create table from file on this Table.

createLMsetListFromDbLMtable(DbLM) - Method in class O2Plib.db.CSD.CSDlms

createLMsetListFromDbLMtable() - build LM set list from DbLM table

createNewDbLMtable(String) - Method in class O2Plib.db.DbLM

createNewDbLMtable() - create a new tlm Table.

createNewEmptyCGLdbFile(String, long) - Method in class O2Plib.db.CSD.CSDcache

createNewEmptyCGLdbFile() - Create a zeroed CSD cache database file called fileName.

createScroller(ScrollableImage.ImageCanvas, int, int, boolean) - Method in class O2Plib.image.ScrollableImage

createScroller() - Create JScroller with/without pixel ruler, or zoom buttons

createZoomedImage(Image, int, int, int, int) - Method in class O2Plib.image.ScrollableImage

createZoomedImage() - create zoomed image using getScaledInstance.

CSD - Class in O2Plib.db.CSD

Class CSD supports a Composite Samples Database data structure for Open2Dprot programs.

CSD() - Constructor for class O2Plib.db.CSD.CSD

CSD() - Constructor for new CSD.

CSD(String, String, String, int) - Constructor for class O2Plib.db.CSD.CSD

CSD() - Constructor for new CSD.

CSD_DBTYPE_CACHE - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is cache data

CSD_DBTYPE_RDBMS - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is RDBMS data

CSD_DBTYPE_TAB_DELIM - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is Tab-delimited data

CSD_DBTYPE_UNKNOWN - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is unknown data

CSD_DBTYPE_XML - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is XML data

CSDacc - Class in O2Plib.db.CSD

Class CSDacc contains the accession database information for the Composite Samples Database (CSD).

CSDacc() - Constructor for class O2Plib.db.CSD.CSDacc

CSDacc() - Constructor for new CSDacc.

csdAcc - Static variable in class O2Plib.db.CSD.CSDglb

Accession/MAIPE sample information related data

CSDannotation - Class in O2Plib.db.CSD

Class CSDannotation defines protein/peptide spot identification and annotation for an Rspot set in the Composite Samples Database (CSD).

CSDannotation() - Constructor for class O2Plib.db.CSD.CSDannotation

CSDannotation() - Constructor for new CSDannotation.

csdBINfile - Variable in class O2Plib.db.CSD.CSDio

full path CSD binary random access database file (.csd)

CSDcache - Class in O2Plib.db.CSD

Class CSDcache supports multiple memory and multiple disk caches for supporting a single Composite Samples Database for Open2Dprot programs.

CSDcache() - Constructor for class O2Plib.db.CSD.CSDcache

CSDcache() - Constructor for new CSDcache.

CSDcache(int, int, int, int) - Constructor for class O2Plib.db.CSD.CSDcache

CSDcache() - Constructor for new CSD.

csdCache - Static variable in class O2Plib.db.CSD.CSDglb

This supports multiple memory and multiple disk caches for a single Composite Sample Database (CSD).

csdCacheFile - Static variable in class O2Plib.db.CSD.CSDglb

Full path binary cache file for the CSD without the path.

CSDcal - Class in O2Plib.db.CSD

Class CSDcal contains sample calibration data for the Composite Samplex Database (CSD).

CSDcal() - Constructor for class O2Plib.db.CSD.CSDcal

CSDcal() - Constructor for new CSDcal.

CSDcond - Class in O2Plib.db.CSD

Class CSDcond contains a list of Samples for a condition set of samples for the Composite Samples Database (CSD).

CSDcond() - Constructor for class O2Plib.db.CSD.CSDcond

CSDcond() - Constructor for new CSDcond with a cleared list.

CSDcond(String, String, String) - Constructor for class O2Plib.db.CSD.CSDcond

CSDcond() - Constructor for new CSDcond with a cleared list.

csdDatabaseFile - Static variable in class O2Plib.db.CSD.CSDglb

Composite Sample Database file (CSD) without the path.

CSDexpr - Class in O2Plib.db.CSD

Class CSDexpr contains an expression profile vector data for the Composite Samples Database (CSD).

CSDexpr() - Constructor for class O2Plib.db.CSD.CSDexpr

CSDexpr() - Constructor for new CSDexpr.

CSDexprList - Class in O2Plib.db.CSD

Class CSDexprListList contains a list of expression profiles (vectors) data for the Composite Samples Database (CSD).

CSDexprList() - Constructor for class O2Plib.db.CSD.CSDexprList

CSDexprList() - Constructor for new CSDexprList.

CSDexprList(String, String, String) - Constructor for class O2Plib.db.CSD.CSDexprList

CSDexprList() - Constructor for new CSDexprList.

csdFD - Variable in class O2Plib.db.CSD.CSDio

Random access file descriptor for the bindary CSD

CSDfilterState - Class in O2Plib.db.CSD

Class CSDfilterState contains the state for a named data filter parameter subset.

CSDfilterState() - Constructor for class O2Plib.db.CSD.CSDfilterState

CSDfilterState() - Constructor for new CSDfilterState.

csdFormatMode - Static variable in class O2Plib.db.CSD.CSDglb

CSD database type is CSD_DBTYPE_UNKNOWN, CSD_DBTYPE_XML, CSD_DBTYPE_CACHE, or CSD_DBTYPE_RDBMS

CSDglb - Class in O2Plib.db.CSD

Class CSDglb contains global variables for the support of the Composite Samples Database data structure for Open2Dprot programs.

CSDglb() - Constructor for class O2Plib.db.CSD.CSDglb

csdIO - Static variable in class O2Plib.db.CSD.CSDglb

Name of the CSD I/O database

CSDio - Class in O2Plib.db.CSD

Class CSDio contains the I/O methods for the Composite Samples Database (CSD).

CSDio() - Constructor for class O2Plib.db.CSD.CSDio

CSDio() - Constructor for new CSDio.

csdLength - Variable in class O2Plib.db.CSD.CSDio

size of the file when opened

CSDlimits - Class in O2Plib.db.CSD

Class CSDlimits contains the sizing spot/Rspot set feature limits for the Composite Samples Database (CSD).

CSDlimits() - Constructor for class O2Plib.db.CSD.CSDlimits

CSDlimits() - Constructor for new CSDlimits.

CSDlistInterface - Interface in O2Plib.db.CSD

Interface CSDlistInterface defines required methods implemented in list classes for the Composite Samples Database (CSD).

csdLMS - Static variable in class O2Plib.db.CSD.CSDglb

Landmark database for all of the CSD samples database if landmarks are used.

CSDlms - Class in O2Plib.db.CSD

Class CSDlms contains lists of LMset landmark database for the Composite Samples Database (CSD).

CSDlms() - Constructor for class O2Plib.db.CSD.CSDlms

CSDlms() - Constructor for new CSDlms.

csdName - Static variable in class O2Plib.db.CSD.CSDglb

Name of the CSD database

CSDnorm - Class in O2Plib.db.CSD

Class CSDnorm contains a normalization for a sample for the Composite Samples Database (CSD).

CSDnorm() - Constructor for class O2Plib.db.CSD.CSDnorm

CSDnorm() - Constructor for new CSDnorm.

CSDnorm(String) - Constructor for class O2Plib.db.CSD.CSDnorm

CSDnorm() - Constructor for new CSDnorm.

csdRdbmsFile - Static variable in class O2Plib.db.CSD.CSDglb

Full path RDBMS file for the CSD without the path.

csdRDBMSname - Variable in class O2Plib.db.CSD.CSDio

Name of the CSD RDBMS database

CSDRmap - Class in O2Plib.db.CSD

Class CSDRmap contains the state Rmap information on the Composite Samples Database (CSD).

CSDRmap() - Constructor for class O2Plib.db.CSD.CSDRmap

CSDRmap() - Constructor for new CSDRmap.

CSDRmap(String, String, String) - Constructor for class O2Plib.db.CSD.CSDRmap

CSDRmap() - Constructor for new CSDRmap.

CSDRspot - Class in O2Plib.db.CSD

Class CSDRspot is an ERspot for the Composite Samples Database (CSD).

CSDRspot() - Constructor for class O2Plib.db.CSD.CSDRspot

CSDRspot() - Constructor for new CSDRspot.

CSDRspot(int) - Constructor for class O2Plib.db.CSD.CSDRspot

CSDRspot() - Constructor for new CSDRspot.

CSDRspotList - Class in O2Plib.db.CSD

Class CSDRspotList contains a Rspot List or (RSL).

CSDRspotList() - Constructor for class O2Plib.db.CSD.CSDRspotList

CSDRspotList() - Constructor for new CSDRspotList with a cleared list.

CSDRspotList(String, String, String) - Constructor for class O2Plib.db.CSD.CSDRspotList

CSDRspotList() - Constructor for new CSDRspotList with a cleared list.

csdSizes - Static variable in class O2Plib.db.CSD.CSDglb

CSD sizes related data

CSDsizes - Class in O2Plib.db.CSD

Class CSDsizes contains the state header information on the Composite Samples Database (CSD).

CSDsizes() - Constructor for class O2Plib.db.CSD.CSDsizes

csdTabDelimFile - Static variable in class O2Plib.db.CSD.CSDglb

Full path Tab-Delim file for the CSD without the path.

csdTotals - Static variable in class O2Plib.db.CSD.CSDglb

CSD totals statistics and SSF and SFP statistics related data

CSDtotals - Class in O2Plib.db.CSD

Class CSDtotals contains the state totals information on the Composite Samples Database (CSD).

CSDtotals() - Constructor for class O2Plib.db.CSD.CSDtotals

CSDtotals() - Constructor for new CSDtotals.

csdURL - Variable in class O2Plib.db.CSD.CSDio

[FUTURE] optional URL path to relational database

CSDversion - Static variable in class O2Plib.db.CSD.CSDglb

contains the version of the CSD.

csdXMLfile - Static variable in class O2Plib.db.CSD.CSDglb

Full path XML file for the CSD without the path.

ctrArea1Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed area1 sizing, i.e., below lower threshold

ctrArea1Failed - Variable in class O2Plib.db.DbSample

# spots failed area1 sizing, i.e., below lower threshold

ctrArea2Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed area2 sizing, i.e., above lower threshold

ctrArea2Failed - Variable in class O2Plib.db.DbSample

# spots failed area2 sizing, i.e., above lower threshold

ctrDensity1Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed density1 sizing, i.e., below lower threshold

ctrDensity1Failed - Variable in class O2Plib.db.DbSample

# spots failed density1 sizing, i.e., below lower threshold

ctrDensity2Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed density2 sizing, i.e., above lower threshold

ctrDensity2Failed - Variable in class O2Plib.db.DbSample

# spots failed density2 sizing, i.e., above lower threshold

ctrDR1Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed DR1 sizing, i.e., below lower threshold

ctrDR1Failed - Variable in class O2Plib.db.DbSample

# spots failed DR1 sizing, i.e., below lower threshold

ctrDR2Failed - Variable in class O2Plib.db.CSD.CSDtotals

# spots failed DR2 sizing, i.e., above lower threshold

ctrDR2Failed - Variable in class O2Plib.db.DbSample

# spots failed DR2 sizing, i.e., above lower threshold

ctrlMod - Variable in class O2Plib.image.ScrollableImage

CTRL/Mouse

ctrlShiftMod - Variable in class O2Plib.image.ScrollableImage

CTRL-SHIFT/Mouse

ctrSxSy1Failed - Variable in class O2Plib.db.DbSample

# spots failed Sx/Sy sizing, i.e., above lower threshold

ctrSxSy2Failed - Variable in class O2Plib.db.DbSample

# spots failed Sx/Sy sizing, i.e., below upper threshold

cubeList - Variable in class O2Plib.image.MedianCut

list of cubes

cur_accum - Variable in class O2Plib.image.WriteGifEncoder

cur_bits - Variable in class O2Plib.image.WriteGifEncoder

curHT - Variable in class O2Plib.misc.ParamHash

Current hash table of values read

curNormMethod - Variable in class O2Plib.db.CSD.CSDnorm

Current normalization method set by NORM_xxx

curPixHeight - Variable in class O2Plib.image.ScrollableImage

pixel height

curPixWidth - Variable in class O2Plib.image.ScrollableImage

pixel width

curPos - Variable in class O2Plib.image.ScrollableImage

current position of scrollers

curveFittingType - Variable in class O2Plib.db.CSD.CSDcal

smoothing type of calibration: CALIB_PIECEWISE_LINEAR or CALIB_SMOOTH

cvByte2Int(byte) - Method in class O2Plib.image.PpxLoader

cvByte2Int() - convert unsigned byte [0:255] to int in range [0:255]

cvByte2Int(byte) - Static method in class O2Plib.misc.Util

cvByte2Int() - convert unsigned byte [0:255] to int in range [0:255]

cvChainCode2Str(int, boolean) - Method in class O2Plib.db.DbBoundary

cvChainCode2Str() - If a chain code exists in a boundary data structure then map it to a String:

cvCodes(int) - Static method in class O2Plib.db.DbLM

cvCodes() - map landmark codes to 2 character String names for printing

cvd2s(double, int) - Static method in class O2Plib.misc.Util

cvd2s() - convert double to string with precision # of digits If precision > 0 then limit # of digits in fraction

cvDeltaTime2str(long, boolean) - Static method in class O2Plib.misc.Util

cvDeltaTime2str() - convert a delta epoch time msec to a string "00:01:30 (H:M:S) or 90.0 seconds"

cvf2s(float, int) - Static method in class O2Plib.misc.Util

cvf2s() - convert float to string with exact precision # of digits.

cvf2sVariable(float, int) - Static method in class O2Plib.misc.Util

cvf2sVariable() - convert float to string with precision # of digits.

cvi2hexs(int, int) - Static method in class O2Plib.misc.Util

cvi2hexs() - convert integer number to hex string

cvi2hexs(int) - Static method in class O2Plib.misc.Util

cvi2hexs() - convert integer number to hex string

cvi2os(int, int) - Static method in class O2Plib.misc.Util

cvi2os() - convert integer number to octal string.

cvi2os(int) - Static method in class O2Plib.misc.Util

cvi2os() - convert integer number to octal string with leading 0.

cvi2s(int) - Static method in class O2Plib.misc.Util

cvi2s() - convert integer number to integer string

cvi2s(int, int) - Static method in class O2Plib.misc.Util

cvi2s() - convert integer number to string with left spaces filled

cviByRadix(int, int, int, CalibrateOD) - Static method in class O2Plib.misc.Util

cviByRadix() - convert int by radix to specific space filled from left

cvInt2Byte(int) - Method in class O2Plib.image.PpxLoader

cvInt2Byte() - convert unsignged int [0:255] to signed byte [-128:+127]

cvInt2Byte(int) - Static method in class O2Plib.misc.Util

cvInt2Byte() - convert unsignged int [0:255] to signed byte [-128:+127]

cvLMsetToPrintStr(int) - Method in class O2Plib.db.LMset

cvLMsetToPrintStr() - get the basic landmark data for a landmark k with just xy coords and landmark name.

cvLMSIdx2Name(int) - Static method in class O2Plib.db.LMset

cvLMSIdx2Name() - map an internal LMSet landmark number in the range of [0:nlandmarks-1] to a LMS letter name [0:25] maps to ["A":"Z"] and [26:51] maps to ["a":"z"].

cvLMSname2Idx(String) - Static method in class O2Plib.db.LMset

cvLMSname2Idx() - maps landmark String letter name to a landmark index number.

cvLMtoDetailedPrintStr(int) - Method in class O2Plib.db.DbLM

cvLMtoDetailedPrintStr() - get the full landmark data for a landmark k

cvLMtoDetailedPrintStr(int) - Method in class O2Plib.db.LMset

cvLMtoDetailedPrintStr() - get the full landmark data for a landmark k

cvLMtoPrintStr(int) - Method in class O2Plib.db.DbLM

cvLMtoPrintStr() - get the basic landmark data for a landmark k with just xy coords and landmark name.

cvP2Ihdr(byte[]) - Method in class O2Plib.image.PpxLoader

cvP2Ihdr() - Convert portable header byteData[0:511] into PpxLoader state.

cvPairCode2PairingBit(int) - Method in class O2Plib.db.CSD.CSDfilterState

cvPairCode2PairingBit() - set the search pairing bit

cvPairingCodeName2Code(String) - Static method in class O2Plib.db.DbLM

cvPairingCodeName2Code() - convert pairing code string to pairing code.

cvPrettyPrintSpot() - Method in class O2Plib.db.DbSpot

cvPrettyPrintSpot() - pretty print a spot if it exists else return "Null".

cvs2Array(String, int, String) - Static method in class O2Plib.misc.Util

cvs2Array() - cvt arg list "1,4,3,6,..." to "," - delim String[].

cvs2d(String) - Static method in class O2Plib.misc.Util

cvs2d() - convert String to double

cvs2d(String, double) - Static method in class O2Plib.misc.Util

cvs2d() - convert String to double with default value

cvs2f(String) - Static method in class O2Plib.misc.Util

cvs2f() - convert String to float

cvs2f(String, float) - Static method in class O2Plib.misc.Util

cvs2f() - convert String to float with default value

cvs2fArray(String, int, String) - Static method in class O2Plib.misc.Util

cvs2fArray() - convert String arg list "1,4,3,6,..." to int[]

cvs2i(String) - Static method in class O2Plib.misc.Util

cvs2i() - convert integer String to int

cvs2i(String, int) - Static method in class O2Plib.misc.Util

cvs2i() - convert String to int with default value

cvs2iArray(String, int, String) - Static method in class O2Plib.misc.Util

cvs2iArray() - convert String arg list "1,4,3,6,..." to int[]

cvs2o(String) - Static method in class O2Plib.misc.Util

cvs2o() - convert octal String to int

cvs2o(String, int) - Static method in class O2Plib.misc.Util

cvs2o() - convert octal String to int with default value

cvSpotToPrettyPrintListStr(DbSpot, boolean) - Static method in class O2Plib.db.DbSpot

cvSpotToPrettyPrintListStr() - get the pretty-print features of the specified spot and its pair spot if it is paired.

cvSpotToPrettyPrintListStr(DbSpot, boolean, boolean) - Static method in class O2Plib.db.DbSpot

cvSpotToPrettyPrintListStr() - get the pretty-print features of the specified spot and its pair spot if it is paired.

cvSpotToPrintStr(DbSpot, int) - Static method in class O2Plib.db.DbSpot

cvSpotToPrintStr() - Debugging print the features of the specified spot and print its paired spot features if it is paired.

cvSpotToPrintStr(DbSpot, int, boolean) - Static method in class O2Plib.db.DbSpot

cvSpotToPrintStr() - Debugging print the features of the specified spot and print its paired spot features if it is paired.

cvtBoundaryToChainCode() - Method in class O2Plib.db.DbBoundary

cvtBoundaryToChainCode() - Compute the clockwise chain code from the boundary.

cvtChainCode_to_nextXY(int, int, int) - Method in class O2Plib.db.DbBoundary

cvtChainCode_to_nextXY() - Given (x,y) and the i'th chainCode generate a new (x,y) based on the chain code direction.

cvtCSDformatCodeToStr(int) - Static method in class O2Plib.misc.Switches

cvtCSDformatCodeToStr() - convert CSD.CSD_DBTYPE_xxxx to letter code

cvtCSDformatCodeToStr(String) - Static method in class O2Plib.misc.Switches

cvtCSDformatCodeToStr() - convert letter code to CSD.CSD_DBTYPE_xxxx value

cvtFormatCodeToStr(int) - Static method in class O2Plib.misc.Switches

cvtFormatCodeToStr() -convert IO_FORMAT_xxxx to letter code

cvtFormatCodeToStr(String) - Static method in class O2Plib.misc.Switches

cvtFormatStrToCode() - convert letter code to IO_FORMAT_xxxx value

cvtImg24toImg8(int) - Method in class O2Plib.image.MedianCut

cvtImg24toImg8() - Uses Heckbert's median-cut algorithm to divide the color space defined by "hist15[]" into "maxcubes" cubes.

cvtLMsetSpotsToStr(String, int, int) - Method in class O2Plib.db.DbLM

cvtLMsetSpotsToStr() - convert ONLY k'throws LM set spots for specified sample to a readable formated string.

cvtLMsetSpotsToStr(String, int, int, Roi, boolean, boolean) - Method in class O2Plib.db.DbLM

cvtLMsetSpotsToStr() - convert ONLY k'th LM set spots for specified sample to a readable formated string.

cvtMER_RLMs_to_chainCode(int, int, int, int, int[], int[], int[], int[]) - Method in class O2Plib.db.DbBoundary

cvtMER_RLMs_to_chainCode() - given the M.E.R., R.L.Ms, convert a boundary and compressed chain code in a DbBoundary boundary object.

cvtNullsToEmptyStrings(String[]) - Static method in class O2Plib.misc.Util

cvtNullsToEmptyStrings() - convert nulls to "" in string array

cvtPairBit2PairCode(int) - Static method in class O2Plib.db.DbLM

cvtPairBit2PairCode() - convert pairing-bit to pairing label code US, SP, PP, AP, EP, CP, GS, LM

cvtPairCode2Color(int) - Static method in class O2Plib.db.DbLM

cvtPairCode2Color() - convert pairing label code to Color

cvtPairCode2PairBit(int) - Static method in class O2Plib.db.DbLM

cvtPairCode2PairBit() - convert pairing label code to pairing-bit

cvtQuoteNullsToEmptyStrings(String[]) - Static method in class O2Plib.misc.Util

cvtQuoteNullsToEmptyStrings() - convert "null"s to "" in string array

cvtSpotToSpotRecordStr(DbSpot, int) - Method in class O2Plib.db.DbSample

cvtSpotToSpotRecordStr() - convert spot statistics to string depending on the SSF conversion mode.

cvtSpotToSpotRecordStr(DbSpot) - Method in class O2Plib.db.DbSample

cvtSpotToSpotRecordStr() - convert spot statistics to string depending on the SSF conversion mode.

cvtSpotToSpotRecordStr(StringBuffer, DbSpot) - Method in class O2Plib.db.DbSample

cvtSpotToSpotRecordStr() - convert spot statistics to string depending on the SSF conversion mode.

cvtSwitchListToStr(String[]) - Static method in class O2Plib.misc.Switches

cvtSwitchListToStr() - convert switch list to a string <= 60 cols/line.

cvtTblToDelimData(String) - Method in class O2Plib.table.SimpleTable

cvtTblToDelimData() - convert the table to a delimited string table where delim could be tab or comma or some other character or substring.

cvtTblToHTML(String, int, String[], String[], String) - Method in class O2Plib.table.SimpleTable

cvtTblToHTML() - convert the table to a HTML string

cvtTblToXML(String, String, String, String, String) - Method in class O2Plib.table.SimpleTable

cvtTblToXML() - convert the table to a XML string.

cvtTblToXML(String, String, String, String) - Method in class O2Plib.table.SimpleTable

cvtTblToXML() - convert the table to a XML string.

cvXYtoOtherSample(int, int, int, int, int) - Method in class O2Plib.db.LMset

cvXYtoOtherSample() - maps (x,y) from source sample to the destination sample

cwx1 - Variable in class O2Plib.db.DbSample

computing window ULHC coordinate x

cwx1A - Variable in class O2Plib.db.DbAccession

ULHC X computing window for entire input sample image

cwx1Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

cwx2 - Variable in class O2Plib.db.DbSample

computing window LRHC coordinate x

cwx2A - Variable in class O2Plib.db.DbAccession

LRHC X computing window for entire input sample image

cwx2Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

cwy1 - Variable in class O2Plib.db.DbSample

computing window ULHC coordinate y

cwy1A - Variable in class O2Plib.db.DbAccession

ULHC Y computing window for entire input sample image

cwy1Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

cwy2 - Variable in class O2Plib.db.DbSample

computing window LRHC coordinate y

cwy2A - Variable in class O2Plib.db.DbAccession

LRHC Y computing window for entire input sample image

cwy2Idx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

D

data - Variable in class O2Plib.gui.PopupDialogQuery

for returning data back to caller

dataCheckbox - Variable in class O2Plib.gui.PopupOptions

Left [0:nData-1] checkboxes

dataChoice - Variable in class O2Plib.gui.PopupOptions

Left [0:nChoices-1] Choices

dataChoiceSwitchIdx - Variable in class O2Plib.gui.PopupOptions

Left [0:nChoices-1] is the index of corresponding switch option

dataChoiceVarNbr - Variable in class O2Plib.gui.PopupOptions

Left [0:nChoices-1] is the variable number for this choice

dataDirDButton - Variable in class O2Plib.gui.PopupOptions

Left [0:nData-1] Directory dialog buttons

dataFileDButton - Variable in class O2Plib.gui.PopupOptions

Left [0:nData-1] File dialog buttons

dataFiltersListDB - Static variable in class O2Plib.db.CSD.CSDglb

Database list of data filter parameter subset.

dataLabel - Variable in class O2Plib.gui.PopupOptions

Left [0:nData-1] labels if not using checkbox

dataLabel - Variable in class O2Plib.gui.PopupTableEditDialog

Left [0:nData-1] labels if not using checkbox

dataSlider - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] Sliders

dataSliderLabel - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the Label associated with this Slider

dataSliderMax - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the Maximum scroller value

dataSliderMin - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the Minimum scroller value

dataSliderPrecision - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the precision in format statement 0 means cvi2s() else cvf2s(,precision)

dataSliderScale - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the scale factor to map back to user space

dataSliderSwitchIdx - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the index of the corresponding switch option

dataSliderText - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the text label associated with this Slider

dataSliderVarNbr - Variable in class O2Plib.gui.PopupOptions

Right [0:nSliders-1] is the variable number for this Slider

dataTextField - Variable in class O2Plib.gui.PopupOptions

Right [0:nData-1] TextFields if used

dataTextField - Variable in class O2Plib.gui.PopupTableEditDialog

Right [0:nData-1] TextFields if used

dataType - Variable in class O2Plib.image.TiffPixelLoader

data type from sampleModel.getDataType() The types are defined as DataBuffer.TYPE_xxxx where xxxx is (BYTE, DOUBLE, FLOAT, INT, SHORT, UNDEFINED, USHORT)

dateCreation - Static variable in class O2Plib.db.CSD.CSDglb

Date at time of initial creation

dateLastSession - Static variable in class O2Plib.db.CSD.CSDglb

Date of last session

dateSPF - Variable in class O2Plib.db.DbPairSamples

date read from SPF file

dateStr() - Static method in class O2Plib.misc.Util

dateStr() - return a new Date string of the current day and time

DbAccession - Class in O2Plib.db

Class DbAccession accesses the Open2Dprot accession database.

DbAccession() - Constructor for class O2Plib.db.DbAccession

Accession() - constructor for Accession

DbAccession.AccContentHandler - Class in O2Plib.db

This class implements the SAX ContentHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's content, stuffing data structures with correct data from xml files.

DbAccession.AccContentHandler() - Constructor for class O2Plib.db.DbAccession.AccContentHandler

AccContentHandler() - constructor()

DbAccession.AccErrorHandler - Class in O2Plib.db

AccErrorHandlerclass implements the SAX ErrorHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's warnings and errors.

DbAccession.AccErrorHandler() - Constructor for class O2Plib.db.DbAccession.AccErrorHandler

AccErrorHandler() - constructor()

DbBaseSpot - Class in O2Plib.db

Class DbBaseSpot is the base class used to define a spot.

DbBaseSpot() - Constructor for class O2Plib.db.DbBaseSpot

DbBaseSpot() - Constructor for new DbSpot.

DbBaseSpot(DbSample) - Constructor for class O2Plib.db.DbBaseSpot

DbBaseSpot() - Constructor for new DbBaseSpot.

DbBaseSpot(DbSample, DbSample) - Constructor for class O2Plib.db.DbBaseSpot

DbBaseSpot() - Constructor for new DbBaseSpot.

DbBoundary - Class in O2Plib.db

Class DbBoundary supports spot boundary analysis data structures (chain-coded) and functions for representing spot boundaries in DbSpot for the Open2Dprot system.

DbBoundary(DbSample) - Constructor for class O2Plib.db.DbBoundary

DbBoundary() - Constructor

DbBoundary(DbSample, DbSpot) - Constructor for class O2Plib.db.DbBoundary

DbBoundary() - Constructor

dbLM - Variable in class O2Plib.db.CSD.CSDlms

landmark database if it exists

DbLM - Class in O2Plib.db

Class DbLM is the Landmark database for Open2Dprot.

DbLM() - Constructor for class O2Plib.db.DbLM

DbLM() - set up lndmark part of the database of size nbrLandmarks.

DbLM(int) - Constructor for class O2Plib.db.DbLM

DbLM() - set up lndmark part of the database of size nbrLandmarks.

dbLM - Variable in class O2Plib.db.DbLM.LmsContentHandler

where most of the data is

dbLM - Variable in class O2Plib.db.DbPairSamples

Landmark database object

dbLM - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Landmark database object

DbLM.LmsContentHandler - Class in O2Plib.db

This class implements the SAX ContentHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's content, stuffing data structures with correct data from xml files.

DbLM.LmsContentHandler() - Constructor for class O2Plib.db.DbLM.LmsContentHandler

LmsContentHandler() - constructor()

DbLM.LmsErrorHandler - Class in O2Plib.db

LmsErrorHandler class implements the SAX ErrorHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's warnings and errors.

DbLM.LmsErrorHandler() - Constructor for class O2Plib.db.DbLM.LmsErrorHandler

LmsErrorHandler() - constructor()

DbPairSamples - Class in O2Plib.db

Class DbPairSamples is the Sample Paired-spots File (SPF) state for spot pairing modules in Open2Dprot.

DbPairSamples() - Constructor for class O2Plib.db.DbPairSamples

DbPairSamples() - setup DbPairSamples database

DbPairSamples(DbSample, DbSample, DbLM) - Constructor for class O2Plib.db.DbPairSamples

DbPairSamples() - setup DbPairSamples instance of the database

DbPairSamples.SpfContentHandler - Class in O2Plib.db

This class implements the SAX ContentHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's content, stuffing data structures with correct data from xml files.

DbPairSamples.SpfContentHandler() - Constructor for class O2Plib.db.DbPairSamples.SpfContentHandler

SpfContentHandler() - constructor for XML reader

DbPairSamples.SpfErrorHandler - Class in O2Plib.db

SpfErrorHandlerclass implements the SAX ErrorHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's warnings and errors.

DbPairSamples.SpfErrorHandler() - Constructor for class O2Plib.db.DbPairSamples.SpfErrorHandler

SpfErrorHandler() - constructor()

DbPspot - Class in O2Plib.db

Class DbPspot contains the Composite Sample Database (CSD) spot.

DbPspot() - Constructor for class O2Plib.db.DbPspot

DbPspot(DbSample) - Constructor for class O2Plib.db.DbPspot

DbPspot() - Constructor for new DbPspot.

DbPspot(DbSample, DbSample) - Constructor for class O2Plib.db.DbPspot

DbPspot() - Constructor for new DbPspot.

dbRsample - Static variable in class O2Plib.db.CSD.CSDglb

dbRsample - Variable in class O2Plib.db.DbBaseSpot

dbRsample - Variable in class O2Plib.db.DbPairSamples

Rsample object

dbRsample - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Rsample instance

dbSample - Static variable in class O2Plib.db.CSD.CSDglb

dbSample - Variable in class O2Plib.db.CSD.CSDnorm

dbSample - Variable in class O2Plib.db.DbBaseSpot

dbSample - Variable in class O2Plib.db.DbBoundary

dbSample - Variable in class O2Plib.db.DbPairSamples

Sample object

dbSample - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Sample instance

DbSample - Class in O2Plib.db

Class DbSample defines information about a sample.

DbSample() - Constructor for class O2Plib.db.DbSample

DbSample() - create null DbSample

DbSample(int) - Constructor for class O2Plib.db.DbSample

DbSample() - setup DbSample part of the database

DbSample(int, String, String, String, int) - Constructor for class O2Plib.db.DbSample

DbSample() - setup DbSample part of the database

dbSample - Variable in class O2Plib.db.DbSample.SsfContentHandler

where most of the data is

dbSample - Variable in class O2Plib.misc.CalibrateOD

Global instances

DbSample.SsfContentHandler - Class in O2Plib.db

This class implements the SAX ContentHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's content, stuffing data structures with correct data from xml files.

DbSample.SsfContentHandler() - Constructor for class O2Plib.db.DbSample.SsfContentHandler

SsfContentHandler() - constructor()

DbSample.SsfErrorHandler - Class in O2Plib.db

SsfErrorHandlerclass implements the SAX ErrorHandler interface and defines callback behavior for the SAX callbacks associated with an XML document's warnings and errors.

DbSample.SsfErrorHandler() - Constructor for class O2Plib.db.DbSample.SsfErrorHandler

SsfErrorHandler() - constructor()

dbSamplesListDB - Static variable in class O2Plib.db.CSD.CSDglb

dbSPFlistsDB - Static variable in class O2Plib.db.CSD.CSDglb

List of SPF pairs read from SPF files [0:nSPFlist-1].

dbSpot - Variable in class O2Plib.db.DbBoundary

DbSpot - Class in O2Plib.db

Class DbSpot supports a spot data structure for spot features in Open2Dprot programs.

DbSpot(DbSample, int) - Constructor for class O2Plib.db.DbSpot

DbSpot() - Constructor for new DbSpot.

DbSpot(DbSample, DbSample, int) - Constructor for class O2Plib.db.DbSpot

DbSpot() - Constructor for new DbSpot.

DbSpot(DbSample, DbSample) - Constructor for class O2Plib.db.DbSpot

DbSpot() - Constructor for new DbSpot.

DbSpot(DbSample) - Constructor for class O2Plib.db.DbSpot

DbSpot() - Constructor for new DbSpot.

DbSpot() - Constructor for class O2Plib.db.DbSpot

DbSpot() - Constructor for new DbSpot.

DBUG_CALIB - Static variable in class O2Plib.misc.CalibrateOD

Local debugging flag set in CalibrateOD.main() test code

DBUG_DEF_DATA - Static variable in class O2Plib.misc.CalibrateOD

debugging

DBUG_FULL_BND - Static variable in class O2Plib.db.DbBoundary

Debugging

dbugBitName - Static variable in class O2Plib.misc.Switches

Debug bits name from the parsed Open2Dprot.dbug file

dbugBitValues - Static variable in class O2Plib.misc.Switches

Debug bits values from the parsed Open2Dprot.dbug file

dbugConsoleFlag - Static variable in class O2Plib.misc.Util

Debug console flag adds additional output to console

dbugEpilogueFlag - Variable in class O2Plib.db.DbPairSamples

epilogue debug flag

dbugFlag - Static variable in class O2Plib.db.DbBoundary

Debugging flag

dbugFlag - Variable in class O2Plib.db.DbPairSamples

generic debug flag

dbugFlag - Variable in class O2Plib.db.DbSample

Debugging flag

dbugFlag - Variable in class O2Plib.image.PixReader

To track additional loading info

dbugFlag - Variable in class O2Plib.image.PixWriter

To track additional loading info

dbugFlag - Static variable in class O2Plib.image.TiffPixelLoader

debugging flag

dbugFlag - Static variable in class O2Plib.table.SimpleTable

Debugging flag

dBugLMnbr - Variable in class O2Plib.db.DbPairSamples

-DEBUG:bits,LMset# (not letter)

dBugLMsetNbr - Static variable in class O2Plib.db.CSD.CSDglb

The LMset number to be debugged.

dbugPairsFlag - Variable in class O2Plib.db.DbPairSamples

pairs of spots debug flag

dbugPrefaceFlag - Variable in class O2Plib.db.DbPairSamples

preface debug flag

dBugPspotNbr - Static variable in class O2Plib.db.CSD.CSDglb

The Pspot number to be debugged.

dBugRspotNbr - Static variable in class O2Plib.db.CSD.CSDglb

The Rspot number to be debugged.

dBugSampleNbr - Static variable in class O2Plib.db.CSD.CSDglb

The Sample number to be debugged.

dbx1 - Variable in class O2Plib.db.DbSample

Debugging window for -debug: window

dbx2 - Variable in class O2Plib.db.DbSample

Debugging window for -debug: window

dby1 - Variable in class O2Plib.db.DbSample

Debugging window for -debug: window

dby2 - Variable in class O2Plib.db.DbSample

Debugging window for -debug: window

DEBUG_CH - Variable in class O2Plib.db.DbAccession.AccContentHandler

local debug flag

DEBUG_CH - Variable in class O2Plib.db.DbLM.LmsContentHandler

local debug flag

DEBUG_CH - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

local debug flag

DEBUG_CH - Variable in class O2Plib.db.DbSample.SsfContentHandler

local debug flag

DEBUG_TOP_LEVEL - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

local debug flag to printout top level start/end

decoder - Variable in class O2Plib.image.TiffPixelLoader

Tiff Image Decoder

DEF_COL_SIZE - Static variable in class O2Plib.gui.PopupDialogQuery

default # of columns

DEF_MAX_ROIS - Static variable in class O2Plib.image.RoiList

max # of Rois

DEF_MIN_ACCEPTABLE_DIST - Static variable in class O2Plib.db.CSD.CSDRspotList

Default value of minimum distance for a best fit search by (x,y) coordinates to be valid.

DEFAULT_PIPELINE_XML - Static variable in interface O2Plib.db.xml.PipeLineDefault

defaultDouble - Static variable in class O2Plib.misc.Util

defaultFloat - Static variable in class O2Plib.misc.Util

defaultInt - Static variable in class O2Plib.misc.Util

defLegalImageFileExtens - Static variable in class O2Plib.db.DbAccession

List of legal gel image file extensions

defMinAcceptableDist - Variable in class O2Plib.db.CSD.CSDRspotList

Default minimum acceptable (x,y) search distance.

defNbrAltLMs - Variable in class O2Plib.db.DbPairSamples

default # of alternate paired landmarks (N3).

deleteBnd() - Method in class O2Plib.db.DbBoundary

deleteBnd() - delete the boundary data structure data, but keep the empty object.

deleteLMsetFromLmsTable(DbSample, DbSample, boolean) - Method in class O2Plib.db.DbLM

deleteLMsetFromLmsTable() - delete old landmark set from the landmark database table.

deleteLocalFile(String) - Static method in class O2Plib.io.FileIO

deleteLocalFile() - delete local file.

deleteRowsFromTable(int[]) - Method in class O2Plib.table.SimpleTable

deleteRowsFromTable() - delete rows from the table and resize the table.

delLandmarkFromLMset(int, int, int) - Method in class O2Plib.db.LMset

delLandmarkFromLMset() - delete landmark at (x1,y1,x2,y2) from the landmark set if the two coordinates for the specified.

delLandmarkFromLMset(int, int, int, int) - Method in class O2Plib.db.LMset

delLandmarkFromLMset() - delete landmark at (x1,y1,x2,y2) from landmark set if the two pairs of coordinates are within THR_LATCH_DISTANCE.

demo_setDefaultWedgeData_LeukemiaGels() - Method in class O2Plib.misc.CalibrateOD

demo_setDefaultWedgeData_LeukemiaGels() - setup the ND wedge data for the 4 demo GELLAB-II PPX leukemia gels release with Open2Dprot.

density - Variable in class O2Plib.db.DbSpot

Note: store the various density modes in the same array! This could be selected from (densityPrime, %density, volume).

densityIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

densityPct - Variable in class O2Plib.db.DbSpot

percent spot density

densityPrime - Variable in class O2Plib.db.DbSpot

density' is density corrected for background and is computed as (density - mnBackground*area).

densityPrimeIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

densRangeDiffLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] (maxDensity-mnBkground) diff calibrated density limits/pixel

dialogQuery(String, String) - Method in class O2Plib.gui.PopupDialogQuery

dialogQuery() - query String variable requested

dialogQuery(String, String, String[], int) - Method in class O2Plib.gui.PopupDialogQuery

dialogQuery() - query String variable int requested

didLeastSqCalibFlag - Variable in class O2Plib.db.CSD.CSDnorm

true if EVER did a SET LEAST SQUARES calibration

didRatioListCalibFlag - Variable in class O2Plib.db.CSD.CSDnorm

true if EVER did a SET RATIO LIST calibration

difference(CSDcond, CSDcond) - Method in class O2Plib.db.CSD.CSDcond

difference() - do the intersection of two condition lists r3= difference(r1,r2).

difference(CSDexprList, CSDexprList) - Method in class O2Plib.db.CSD.CSDexprList

difference() - do the intersection of two ExprList lists r3= difference(r1,r2).

difference(CSDRspotList, CSDRspotList) - Method in class O2Plib.db.CSD.CSDRspotList

difference() - do the intersection of two RSL lists r3= difference(r1,r2).

dirDBindex - Variable in class O2Plib.gui.PopupOptions

The index of dataXXX[index] associated with the file browswer button prompt list dirDBPrompt[].

dirDBPrompt - Variable in class O2Plib.gui.PopupOptions

The file browswer button prompt list [0:nDirDBPrompt-1] but allocated [0:nData-1].

discoverFileExtension(String, String, String[]) - Static method in class O2Plib.io.FileIO

discoverFileExtension() - discover file extension by trying to lookup the file discoverFileExtension(dir,fileName,legalExtens)

diskCacheFD - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of disk cache Random Access Files

diskCacheFilePtr - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of disk cache file pointers in CSD database

diskCacheList - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1][0:diskCacheSize-1(variable)] list of CSD disk caches

diskCacheName - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of disk cache file names

diskCacheSize - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of disk cache list sizes

diskCacheTimeStamp - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of disk cache time stamps

diskCacheValid - Variable in class O2Plib.db.CSD.CSDcache

[0:nDiskCaches-1] list of valid disk caches

diskTimeStampCtr - Static variable in class O2Plib.db.CSD.CSDcache

disk cache time stamp for aging cache

displayImg - Variable in class O2Plib.image.ScrollableImage

image to display, can be zoomed

DIST_THR_LANDMARK - Static variable in class O2Plib.db.LMset

Default distance to accept (x,y) to existing landmark

distNearestLM - Variable in class O2Plib.db.LMset

distance between closest landmarks [0:nbrLandmarks-1][RSAMPLE:SAMPLE] for each sample and that landmark

distNextNearestLM - Variable in class O2Plib.db.LMset

distance between next closest landmarks [0:nbrLandmarks-1][RSAMPLE:SAMPLE] for each sample and that landmark

dL - Variable in class O2Plib.db.DbBaseSpot

distance from spot pair to their landmark

dLlimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] dL limits

dLmax - Variable in class O2Plib.db.CSD.CSDtotals

Maximum dL of any spot in DB

dLmax - Variable in class O2Plib.db.DbPairSamples

Maximum dL of any spot in DB

dLthr - Variable in class O2Plib.db.CSD.CSDlimits

Maximum threshold distance from spot-pair center to their corresponding landmark.

dLx - Variable in class O2Plib.db.DbSpot

relative X distance from Rsample spot to LM

dLy - Variable in class O2Plib.db.DbSpot

relative Y distance from Rsample spot to LM

dMax - Variable in class O2Plib.db.DbSpot

spot MAX OD

dMin - Variable in class O2Plib.db.DbSpot

spot MIN OD

DO_CLIP_DP_DL - Static variable in class O2Plib.db.DbPairSamples

set true if clip max of dP and dL

DO_CLIP_DX_DY - Static variable in class O2Plib.db.DbPairSamples

If true, then clip dX and dY

domain - Variable in class O2Plib.image.PpxLoader

0 = optical density, 1 = transmittance 2 = gray value ...

doneFlag - Variable in class O2Plib.gui.PopupNameListSelectorDialog

doneFlag - Variable in class O2Plib.gui.PopupTableEditDialog

Flag indicating that the editing is finished.

doTiffLoad(String, boolean, boolean) - Method in class O2Plib.image.TiffPixelLoader

doTiffLoad() - load the image and array grab of TIFF files

dP - Variable in class O2Plib.db.DbBaseSpot

distance between spots in a pair

dPlimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] dP limits

dPmax - Variable in class O2Plib.db.CSD.CSDtotals

Maximum dP of any spot in DB

dPmax - Variable in class O2Plib.db.DbPairSamples

Maximum dP of any spot in DB

dPmTot - Variable in class O2Plib.db.DbPairSamples

global spot statistics: sum dP for Rsample only

dPrimeMax - Variable in class O2Plib.db.CSD.CSDtotals

Maximum dPrime (density) of any spot in DB

dPrimeMin - Variable in class O2Plib.db.CSD.CSDtotals

Minimum dPrime (density) of any spot in DB

dPthr - Variable in class O2Plib.db.CSD.CSDlimits

Maximum threshold distance between spots in a spot-pair

drawBoundariesForSpots(DbSample, char[], int, int) - Static method in class O2Plib.image.DrawPix

drawBoundariesForSpots() - If generating the segmented spot image in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set, draw a white boundary around each spot in the 'O'riginal or segmented 'Z' image (-DRAWSPOTS:BO default).

drawBoundariesForSpots(DbSample, int[], int, int) - Static method in class O2Plib.image.DrawPix

drawBoundariesForSpots() - If generating the segmented spot image in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set, draw a white boundary around each spot in the 'O'riginal or segmented 'Z' image (-DRAWSPOTS:BO default).

drawBox(Graphics, int, int, int, int, Color) - Method in class O2Plib.image.DrawOverlays

drawBox() - draw box of size w X w sign at the specified color.

drawCircle(Graphics, int, int, int, Color) - Method in class O2Plib.image.DrawOverlays

drawCircle() - draw circle at the specified color and radius.

drawDotsInSpots(DbSample, int[], int, int, boolean, boolean, boolean) - Static method in class O2Plib.image.DrawPix

drawDotsInSpots() - draw symbol indicating the spots in the spot list in the pix.

drawDotsInSpots(DbSample, char[], int, int, boolean, boolean, boolean) - Static method in class O2Plib.image.DrawPix

drawDotsInSpots() - draw symbol indicating the spots in the spot list in the pix.

drawHorizSlice(Graphics, int, int, int, int, int, int, char[]) - Method in class O2Plib.image.DrawOverlays

drawHorizSlice() - draw horizontal slice of image at (xImg,yImg) if defined.

drawLowerRoiTickmark(Graphics, Point, Color, int) - Method in class O2Plib.image.DrawOverlays

drawLowerRoiTickmark() - draw region of interest tick marks if either ULHC or LRHC but not both exist.

DrawOverlays - Class in O2Plib.image

DrawOverlays() - Constructor for class O2Plib.image.DrawOverlays

DrawOverlays() - Constructor, use default min & max zoom values

DrawOverlays(float, float) - Constructor for class O2Plib.image.DrawOverlays

DrawOverlays() - Constructor for setting different min max values for zoom

DrawPix - Class in O2Plib.image

DrawPix() - Constructor for class O2Plib.image.DrawPix

DrawPix() - Constructor

drawPlus(Graphics, int, int, int, Color) - Method in class O2Plib.image.DrawOverlays

drawPlus() - draw plus sign at the specified color.

drawROIrectangle(Graphics, int, int, int, int, Color, int, int, int) - Method in class O2Plib.image.DrawOverlays

drawROIrectangle() - draw a Region Of Interest rectangle if legal

drawROIrectangle(Graphics, Roi, Color, int, int, int) - Method in class O2Plib.image.DrawOverlays

drawROIrectangle() - draw a Region Of Interest rectangle if legal

drawROIrectangle(Graphics, Roi, Color, int, int) - Method in class O2Plib.image.DrawOverlays

drawROIrectangle() - draw a Region Of Interest rectangle if legal

drawRoiTickmarks(Graphics, Roi, int) - Method in class O2Plib.image.DrawOverlays

drawRoiTickmarks() - draw region of interest tick marks if either ULHC or LRHC but not both exist.

drawTextInPix(int[], int, int, String, int, int, int, int, int, boolean) - Static method in class O2Plib.image.DrawPix

drawTextInPix() - Display the string 'str' starting at (x0,y0) in specified 'gray' value in either of two charcter sizes 4x6 (upper case only: font=0); or 5x7 (upper/lower case: font=1) and a 'zoom' factor of 1X (default) to 64X.

drawTextInPix(char[], int, int, String, int, int, int, int, int, boolean) - Static method in class O2Plib.image.DrawPix

drawTextInPix() - Display the string 'str' starting at (x0,y0) in specified 'gray' value in either of two charcter sizes 4x6 (upper case only: font=0); or 5x7 (upper/lower case: font=1) and a 'zoom' factor of 1X (default) to 64X.

drawVertSlice(Graphics, int, int, int, int, int, int, char[]) - Method in class O2Plib.image.DrawOverlays

drawVertSlice() - draw vertical slice of image at (xImg,yImg) if defined.

dt1Threshold - Variable in class O2Plib.db.DbPairSamples

distance threshold T1 for determining SP pairs.

dt2Threshold - Variable in class O2Plib.db.DbPairSamples

distance threshold T2 for determining PP pairs.

DYNAMIC_FIELDS - Static variable in class O2Plib.db.DbAccession

Use hash table for dynamic fields

E

editPane - Variable in class O2Plib.gui.PopupTableEditDialog

Scrollable edit pane that holds the gridPanel

editRsampleLMSFlag - Variable in class O2Plib.db.LMset

To enble editing Rsample landmark values.

editType - Variable in class O2Plib.gui.PopupTableEditDialog

Type of editing being performed

endDataDict - Variable in class O2Plib.image.PpxLoader

(unsigned int) if non-zero, then byte # of file where data dictionary ends.

endDocument() - Method in class O2Plib.db.DbAccession.AccContentHandler

endDocument() - This indicates the end of a Document parse-this occurs after all callbacks in all SAX Handlers..

endDocument() - Method in class O2Plib.db.DbLM.LmsContentHandler

endDocument() - This indicates the end of a Document parse-this occurs after all callbacks in all SAX Handlers..

endDocument() - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

endDocument() - This indicates the end of a Document parse-this occurs after all callbacks in all SAX Handlers..

endDocument() - Method in class O2Plib.db.DbSample.SsfContentHandler

endDocument() - This indicates the end of a Document parse-this occurs after all callbacks in all SAX Handlers..

endElement(String, String, String) - Method in class O2Plib.db.DbAccession.AccContentHandler

endElement() - Indicates the end of an element (</[element name]>) is reached.

endElement(String, String, String) - Method in class O2Plib.db.DbLM.LmsContentHandler

endElement() - Indicates the end of an element (</[element name]>) is reached.

endElement(String, String, String) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

endElement() - Indicates the end of an element (</[element name]>) is reached.

endElement(String, String, String) - Method in class O2Plib.db.DbSample.SsfContentHandler

endElement() - Indicates the end of an element (</[element name]>) is reached.

endPrefixMapping(String) - Method in class O2Plib.db.DbAccession.AccContentHandler

endPrefixMapping() - This indicates the end of a prefix mapping, when the namespace reported in a DbAccession.AccContentHandler.startPrefixMapping(java.lang.String, java.lang.String) callback is no longer available.

endPrefixMapping(String) - Method in class O2Plib.db.DbLM.LmsContentHandler

endPrefixMapping() - This indicates the end of a prefix mapping, when the namespace reported in a DbLM.LmsContentHandler.startPrefixMapping(java.lang.String, java.lang.String) callback is no longer available.

endPrefixMapping(String) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

endPrefixMapping() - This indicates the end of a prefix mapping, when the namespace reported in a DbPairSamples.SpfContentHandler.startPrefixMapping(java.lang.String, java.lang.String) callback is no longer available.

endPrefixMapping(String) - Method in class O2Plib.db.DbSample.SsfContentHandler

endPrefixMapping() - This indicates the end of a prefix mapping, when the namespace reported in a DbSample.SsfContentHandler.startPrefixMapping(java.lang.String, java.lang.String) callback is no longer available.

entranceX - Variable in class O2Plib.db.DbBoundary

entranceY - Variable in class O2Plib.db.DbBoundary

EOF - Static variable in class O2Plib.image.WriteGifEncoder

EOFCode - Variable in class O2Plib.image.WriteGifEncoder

EP - Static variable in class O2Plib.db.CSD.CSDglb

Extrapolated Pair - by CSD database program

EP - Static variable in class O2Plib.db.DbBaseSpot

Extrapolated Pair - by CSD database program

EP - Static variable in class O2Plib.db.DbLM

Extrapolated Pair - by CSD database program

EP - Static variable in class O2Plib.db.DbPairSamples

Extrapolated Pair - by CSD database program

EPCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Extrapolated spot label

epList - Variable in class O2Plib.db.CSD.CSDexprList

[0:nEPlist-1] list of expression profiles

epSetSamples - Static variable in class O2Plib.db.CSD.CSDglb

Expression Profile set of samples.

equivLMspotPtr - Variable in class O2Plib.db.DbLM

Linked list of latched DbSpots that correspond to landmarks in the LM set [nbrLandmarks][2].

errCode - Static variable in class O2Plib.io.FileIO

error code is 0 if succeed

errFlag - Variable in class O2Plib.table.Table

Error message Flag

errMsg - Variable in class O2Plib.db.DbAccession

Error message if not null

errMsg - Static variable in class O2Plib.misc.ParamHash

error code string if an error occurred, else null

errMsg - Variable in class O2Plib.table.Table

Error message string if not null

error(SAXParseException) - Method in class O2Plib.db.DbAccession.AccErrorHandler

error() - This will report an error that has occurred; this indicates that a rule was broken, typically in validation, but that parsing can reasonably continue.

error(SAXParseException) - Method in class O2Plib.db.DbLM.LmsErrorHandler

error() - This will report an error that has occurred; this indicates that a rule was broken, typically in validation, but that parsing can reasonably continue.

error(SAXParseException) - Method in class O2Plib.db.DbPairSamples.SpfErrorHandler

error() - This will report an error that has occurred; this indicates that a rule was broken, typically in validation, but that parsing can reasonably continue.

error(SAXParseException) - Method in class O2Plib.db.DbSample.SsfErrorHandler

error() - This will report an error that has occurred; this indicates that a rule was broken, typically in validation, but that parsing can reasonably continue.

errorLoadingImageFlag - Variable in class O2Plib.image.PixReader

set after image loaded

ERSPOT_DIST_THR - Static variable in class O2Plib.db.CSD.CSDRspot

Default distance threshold for restricting adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.

eRspotDistThr - Static variable in class O2Plib.db.CSD.CSDRspot

Restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.

eRspotFlag - Variable in class O2Plib.db.CSD.CSDRspot

This Rspot is an eRspot (extrapolated Rspot)

estBufsize - Variable in class O2Plib.db.CSD.CSDsizes

estimated cache file buffer size

exitX - Variable in class O2Plib.db.DbBoundary

exitY - Variable in class O2Plib.db.DbBoundary

exposureCorrectionFactor - Variable in class O2Plib.db.CSD.CSDcal

(Optional) exposure correction or decay factor such as might be used to correct for delays in scanning after a pulse label.

expRawValues - Variable in class O2Plib.db.CSD.CSDexpr

exprListsDB - Static variable in class O2Plib.db.CSD.CSDglb

Database list of expression profile lists [0:nExprListsDB-1] if not null.

expValues - Variable in class O2Plib.db.CSD.CSDexpr

extrapolatedFlag - Variable in class O2Plib.db.DbSpot

set if spot is an extrapolated EP spot.

extrapolateNDwedgeMap() - Method in class O2Plib.misc.CalibrateOD

extrapolateNDwedgeMap() - extrapolate the maxCalSteps ND wedge peaks in wedgeCalValues[0:maxCalSteps-1] with corresponding gray values wedgeGrayValues[0:maxCalSteps-1] into a piecewise linear mapGrayToCal[0:maxGray] array.

extrapolateNDwedgeMap(int, int, int, int[], float[]) - Method in class O2Plib.misc.CalibrateOD

extrapolateNDwedgeMap() - extrapolate the maxCalSteps ND wedge peaks in wedgeCalValues[0:maxCalSteps-1] with corresponding gray values wedgeGrayValues[0:maxCalSteps-1] into a piecewise linear mapGrayToCal[0:maxGray] array.

F

f - Variable in class O2Plib.gui.PopupTextFieldDialog

Frame where dialog box is added

fatalError(SAXParseException) - Method in class O2Plib.db.DbAccession.AccErrorHandler

fatalError() - This will report a fatal error that has occurred; this indicates that a rule has been broken that makes continued parsing either impossible or an almost certain waste of time.

fatalError(SAXParseException) - Method in class O2Plib.db.DbLM.LmsErrorHandler

fatalError() - This will report a fatal error that has occurred; this indicates that a rule has been broken that makes continued parsing either impossible or an almost certain waste of time.

fatalError(SAXParseException) - Method in class O2Plib.db.DbPairSamples.SpfErrorHandler

fatalError() - This will report a fatal error that has occurred; this indicates that a rule has been broken that makes continued parsing either impossible or an almost certain waste of time.

fatalError(SAXParseException) - Method in class O2Plib.db.DbSample.SsfErrorHandler

fatalError() - This will report a fatal error that has occurred; this indicates that a rule has been broken that makes continued parsing either impossible or an almost certain waste of time.

fatalExit(String, boolean) - Static method in class O2Plib.misc.Util

fatalExit() - print error message and exit with -1 if exitFlag set.

fatalMsg - Variable in class O2Plib.image.TiffPixelLoader

Msg why failed if not null

fieldNameData - Variable in class O2Plib.gui.PopupTableEditDialog

FieldName data [0:nData-1] has a Label with the data.

fieldsIdxHT - Variable in class O2Plib.db.DbAccession

Hashtable for field names for accession database.

fileDBindex - Variable in class O2Plib.gui.PopupOptions

The index of dataXXX[index] associated with the file browswer button prompt list fileDBindex[].

fileDBPrompt - Variable in class O2Plib.gui.PopupOptions

The file browswer button prompt list [0:nFileDBPrompt-1] but allocated [0:nData-1].

fileDialog - Variable in class O2Plib.gui.PopupFileDialog

for use in popup FileDialog

FileIO - Class in O2Plib.io

Class FileIO is used to read file I/O from local disk or URLs for the Open2Dprot projects.

FileIO() - Constructor for class O2Plib.io.FileIO

FileIO() - constructor.

FileIO(String) - Constructor for class O2Plib.io.FileIO

FileIO() - constructor.

FileIO(String, boolean) - Constructor for class O2Plib.io.FileIO

FileIO() - constructor.

FileIO(boolean) - Constructor for class O2Plib.io.FileIO

FileIO() - constructor

fileName - Variable in class O2Plib.image.TiffPixelLoader

filename path of image file

fileOKflag - Variable in class O2Plib.table.Table

File exists and was able to be read

fileSeparator - Static variable in class O2Plib.misc.Util

File separator: Property("file.separator")

filterHash - Static variable in class O2Plib.db.CSD.CSDfilterState

hashTable for filter lookup

filtyp - Variable in class O2Plib.image.PpxLoader

type of file.

findBoundary(Point[], int, boolean) - Method in class O2Plib.db.DbBoundary

findBoundary() - given the xyList of points in a spot, search the list to to find a boundary.

findBoundary2(Point[], int, boolean) - Method in class O2Plib.db.DbBoundary

findBoundary2() - given the xyList of points in a spot, search the list to to find a boundary.

findFreeDiskCache(int) - Method in class O2Plib.db.CSD.CSDcache

findFreeDiskCache() - find first free disk cache.

findFreeMemCache(int) - Method in class O2Plib.db.CSD.CSDcache

findFreeMemCache() - find first free memory cache.If no cache is free, then pick the oldest one and flush it to the CSD database if valid and reuse that cache.

findLMbyXYcoords(int, int, int) - Method in class O2Plib.db.LMset

findLMbyXYcoords() - find the (x,y) in the landmark set if the smallest distance between (x,y) and the landmark is <= DIST_THR_LANDMARK.

findLMbyXYcoords(int, int, int, int) - Method in class O2Plib.db.LMset

findLMbyXYcoords() - find the (x,y) in the landmark set if the smallest distance between (x,y) and the landmark is <= distThr.

findPeaks(int, int, int[], int, int, int, int, float, int, boolean, boolean) - Method in class O2Plib.misc.CalibrateOD

findPeaks() - Find the peaks in the histogram sHist[].

findPeakTableSizes() - Method in class O2Plib.misc.CalibrateOD

findPeakTableSizes() - find the current maxPeaks and maxNDvalues from non-zero values in the peaks table.

findSpotByXY(int, int, int, boolean) - Method in class O2Plib.db.DbSample

findSpotByXY() - find a spot in the spot list that is within distThr of the (x,y) coordinate specified.

findSpotPairByXY(int, int, int, int, boolean) - Method in class O2Plib.db.DbSample

findSpotPairByXY() - find a spot in the spot-pair list that is within distThr of the (x,y) coordinate specified.

fioErrStr - Static variable in class O2Plib.io.FileIO

error code string if an error occurred, else null

firstERspot - Variable in class O2Plib.db.CSD.CSDio

Rspot index of first eRspot if not 0

firstSpot - Variable in class O2Plib.db.DbSample

first spot allocated in the linked spot list.

firstSpotPair - Variable in class O2Plib.db.DbSample

first spot allocated in the linked spotPairList[] spot-pair list.

flush_char(FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

flush_char() - flush packet to disk, and reset the accumulator

flushAllCachesToCSDdbFile() - Method in class O2Plib.db.CSD.CSDcache

flushAllCachesToCSDdbFile() - flush the cache (memory and disk) to the CSD database file.

flushAllMemCacheToDiskCache() - Method in class O2Plib.db.CSD.CSDcache

flushAllMemCacheToDiskCache() - flush the memory cache to the disk cache.

flushBinCSD() - Method in class O2Plib.db.CSD.CSDio

flushBinCSD() - flush the CSD if it is open and clear the state.

flushMemCacheToDiskCache(int) - Method in class O2Plib.db.CSD.CSDcache

flushMemCacheToDiskCache() - flush the memory cache to the disk cache.

FONT4X6 - Static variable in class O2Plib.image.DrawPix

Font size codes for drawtext...()

FONT5X7 - Static variable in class O2Plib.image.DrawPix

Font size codes for drawtext...()

fontFamily - Variable in class O2Plib.gui.PopupTableEditDialog

foreignSpotName - Variable in class O2Plib.db.CSD.CSDRmap

[0:nRmapSize-1] list of foreign spot names mapped by rspotNbr

foreignSpotName2RpotNbrHT - Variable in class O2Plib.db.CSD.CSDRmap

map of foreign spot name to Rspot set #

frame - Variable in class O2Plib.gui.PopupDialogQuery

popup frame instance

free_ent - Variable in class O2Plib.image.WriteGifEncoder

freeTable() - Method in class O2Plib.table.SimpleTable

freeTable() - free Table tData[][] and tFields so can garbage collect it.

fullFileName - Variable in class O2Plib.table.SimpleTable

Optional full file name associated with table

fversn - Variable in class O2Plib.image.PpxLoader

(unsigned short) Set to PPX_VRSION by program creating header

G

g - Variable in class O2Plib.image.WriteGifEncoder

g_init_bits - Variable in class O2Plib.image.WriteGifEncoder

gcAndMemoryStats(String, boolean) - Static method in class O2Plib.misc.Util

gcAndMemoryStats() - String garbage collect & print memory statistics.

genNdwvalues - Variable in class O2Plib.image.PpxLoader

ND (od) or CPM wedge step values

get2D(int[], int, int, int) - Static method in class O2Plib.image.DrawPix

get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)

get2D(char[], int, int, int) - Static method in class O2Plib.image.DrawPix

get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)

getAccEntryValueByFieldName(String[], String) - Method in class O2Plib.db.DbAccession

getAccEntryValueByFieldName() - lookup accession entry data by field name (prefix) in the current ta.

getAccEntryValueByIndex(String[], int) - Method in class O2Plib.db.DbAccession

getAccEntryValueByFieldIndex() - lookup entry in row data by field index in the current table.

getAllSSFspotsStr(String, DbSample, int[]) - Static method in class O2Plib.db.DbSpot

getAllSSFspotsStr() - get the printable list of all spots the specified sample..

getAltLMsetStr() - Method in class O2Plib.db.DbSpot

getAltLMsetStr() - create an alternate landmark set list string for this spot.

getArrayOfTabDelimitedTokens(String, int) - Method in class O2Plib.table.Table

getArrayOfTabDelimitedTokens() - get array of tab-delim tokens from table.

getBytePixels() - Method in class O2Plib.image.PpxLoader

getBytePixels() - get pixels from the raster

getCalibratedXvalue(float) - Method in class O2Plib.db.CSD.CSDcal

getCalibratedXvalue() - map X coordinate to calibrated value [TODO]

getCalibratedYvalue(float) - Method in class O2Plib.db.CSD.CSDcal

getCalibratedYvalue() - map X coordinate to calibrated value [TODO]

getCalTable() - Method in class O2Plib.misc.CalibrateOD

getCalTable() - get calibration wedgeCalValues[0:maxCalSteps-1] values

getChangedUserData() - Method in class O2Plib.gui.PopupOptions

getChangedUserData() get the changed user data from text fields into local array so caller can get it.

getCharPix() - Method in class O2Plib.image.PixReader

getCharPix() - map the image to char[].

getCmdListCBMIbyPreface(String) - Method in class O2Plib.gui.MenuSupport

getCmdListCBMIbyPreface() - get list of all of the commands in the checkbox menu items with a common command prefix ending with a ':'.

getCurDateStr() - Static method in class O2Plib.misc.Util

getCurDateStr() - return date string in the format of YYMMDDHHMMSS.

getData(String, String[], boolean) - Method in class O2Plib.table.Table

getData() - read the data and store it in the table.

getdBugBitsHelpStr() - Static method in class O2Plib.misc.Switches

getdBugBitsHelpStr() - make a help string from the parsed debug bits

getDefaultSwitches(String[], String) - Static method in class O2Plib.misc.Switches

getDefaultSwitches() - get the default swtich list from the properties file if any.

getDirPathByDirBrowser(String, String) - Static method in class O2Plib.io.FileIO

getDirPathByDirBrowser() - set the output path by directory browser

getDumpLMsetSpotsStr(int, String) - Method in class O2Plib.db.DbLM

getDumpLMsetSpotsStr() - get a printable LM set k string of spots for both samples in readable format.

getDumpLMsetSpotsStr(int, String, Roi, Roi, boolean, boolean) - Method in class O2Plib.db.DbLM

getDumpLMsetSpotsStr() - get a printable LM set k string of spots for both samples in readable format.

getExprList() - Method in class O2Plib.db.CSD.CSDexprList

getExprList() - get the list of Expression listS

getFieldIdxRowDatum(int, int) - Method in class O2Plib.table.SimpleTable

getFieldIdxRowDatum() - get datum by field idx with row index

getFieldRowDatum(int, String) - Method in class O2Plib.table.SimpleTable

getFieldRowDatum() - get datum by field in row by Table row index

getFileName(String) - Static method in class O2Plib.misc.Util

getFileName() - get the file name after last '/' if any

getFileNameFromPath(String) - Static method in class O2Plib.misc.Util

getFileNameFromPath() - extract the filename from the path

getFilesInDir(String, String) - Static method in class O2Plib.io.FileIO

getFilesInDir() - get list of files in directory with specified file extension

getFullInfo() - Static method in class O2Plib.misc.Util

getFullInfo() - get the full file info on the program and exit.

getFullPathPixFileName(String, String, String[]) - Static method in class O2Plib.io.FileIO

getFullPathPixFileName() - get the full path pix file name

getGrayValueTable() - Method in class O2Plib.misc.CalibrateOD

getGrayValueTable() - get calibration grayscale[0:maxPeaks-1]

getHasCalMapFlag() - Method in class O2Plib.misc.CalibrateOD

getHasCalMapFlag() - return the status of the Gray to calibration map.

getHorizontalScrollBarVal() - Method in class O2Plib.image.ScrollableImage

getHorizontalScrollBarVal() -

getImage() - Method in class O2Plib.image.PpxLoader

getImage() - get pixels from the raster

getImage() - Method in class O2Plib.image.TiffPixelLoader

getImage() - get AWT Image from the raster.

getIncrement() - Method in class O2Plib.image.ScrollableImage.Rule

getIncrement() - get increment

getLandmarkDBstr() - Method in class O2Plib.db.DbLM

getLandmarkDBstr() - get the printable report for all landmarks

getListOfLMSlists() - Method in class O2Plib.db.CSD.CSDlms

getListOfLMSlists() - get the list of LMset objects

getListOfRowsDataByFieldNameValuePairs(String, String, String, String) - Method in class O2Plib.table.SimpleTable

getListOfRowsDataByFieldNameValuePairs() - lookup a list of rows data by (fieldName1,fieldValue1) and (fieldName2,fieldValue2) matches.

getListOfRowsIdxByFieldNameValuePairs(String, String, String, String) - Method in class O2Plib.table.SimpleTable

getListOfRowsIdxByFieldNameValuePairs() - lookup a list of rows of data by (fieldName1,fieldValue1) and (fieldName2,fieldValue2) matches.

getLMSDBbyNamestr(String, String) - Method in class O2Plib.db.LMset

getLMSDBbyNamestr() - get the LMset summary as a printable string.

getLMSDBbyNamestr(String, String, int) - Method in class O2Plib.db.LMset

getLMSDBbyNamestr() - get the LMset summary as a printable string.

getLMSDBstr(DbSample, DbSample) - Method in class O2Plib.db.DbLM

getLMSDBstr() - get landmark set summary as a printable string.

getLMsetsDBradiiReport(int) - Method in class O2Plib.db.CSD.CSDlms

getLMsetsDBradiiReport() - get LMset half-radii report for all (sample, Rsample) landmarks for all CSDlms LMsets.

getLMsetsDBxyValuesReport(int) - Method in class O2Plib.db.CSD.CSDlms

getLMsetsDBxyValuesReport() - get LMset(x,y) values report for all (sample, Rsample) landmarks for all CSDlms LMsets.

getLMsetSpotList(DbSample, int) - Method in class O2Plib.db.DbLM

getLMsetSpotList() - get a list of spots in landmark set k for sample dbS if it exists.

getLMsetStr() - Method in class O2Plib.db.LMset

getLMsetStr() - get the printable report for all landmarks in the LM set.

getLMSlistsNames() - Method in class O2Plib.db.CSD.CSDlms

getLMSlistsNames() - get the list of LMset names

getLmsSetEntryFromDBtable(String, String) - Method in class O2Plib.db.DbLM

getLmsSetEntryFromDBtable() - lookup and get landmark set in the database table in memory.

getLmsSetEntryFromDBtable(String, String, boolean) - Method in class O2Plib.db.DbLM

getLmsSetEntryFromDBtable() - lookup and get landmark set in the database table in memory.

getLMSstr() - Method in class O2Plib.db.LMset

getLMSstr() - get the landmark set summary as a printable string.

getLocatorPrevTag() - Method in class O2Plib.db.DbAccession.AccContentHandler

getLocatorPrevTag() - get locator and previous tag for debugging.

getLocatorPrevTag() - Method in class O2Plib.db.DbLM.LmsContentHandler

getLocatorPrevTag() - get locator and previous tag for debugging.

getLocatorPrevTag() - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

getLocatorPrevTag() - get locator and previous tag for debugging.

getLocatorPrevTag() - Method in class O2Plib.db.DbSample.SsfContentHandler

getLocatorPrevTag() - get locator and previous tag for debugging.

getMapGrayToCal() - Method in class O2Plib.misc.CalibrateOD

getmapGrayToCal() - return the mapGrayToCal[0:maxGray-1].

getMaximumHorizontalSB() - Method in class O2Plib.image.ScrollableImage

getMaximumHorizontalSB() -

getMaximumSize() - Method in class O2Plib.image.ScrollableImage

getMaximumSize() - getMaximumSize, must be implemented for ScrollPane to be displayed correctly.

getMaximumSize() - Method in class O2Plib.image.ScrollableImage.ImageCanvas

getMaximumSize() - getMaximumSize, must be implemented for ScrollPane to be displayed correctly.

getMaximumVerticalSB() - Method in class O2Plib.image.ScrollableImage

getMaximumVerticalSB() -

getMemCacheFromDiskCache(int, int) - Method in class O2Plib.db.CSD.CSDcache

getMemCacheFromDiskCache() - get the memory cache from the disk cache up to the maximum memory cache size if needed.

getMenuLabelListCBMIbyPreface(String) - Method in class O2Plib.gui.MenuSupport

getMenuLabelListCBMIbyPreface() - get list of all of the menu labels in the checkbox menu items with a common command prefix endinting with a ':'.

getMinimumSize() - Method in class O2Plib.image.ScrollableImage

getMinimumSize() - getMinimumSize, must be implemented for ScrollPane to be displayed correctly.

getMinimumSize() - Method in class O2Plib.image.ScrollableImage.ImageCanvas

getMinimumSize() - getMinimumSize, must be implemented for ScrollPane to be displayed correctly.

getNbrRGBpixels(int[], int) - Method in class O2Plib.image.TiffPixelLoader

getNbrRGBpixels() - test if red==green==blue for all pixels

getNewValueDataResults() - Method in class O2Plib.gui.PopupTableEditDialog

getNewValueDataResults() - get changedValueData[] from the text fields.

getNormalization() - Method in class O2Plib.db.CSD.CSDRspot

getNormalization() - set normalization for Rspot set.

getNormalizedDprimeData() - Method in class O2Plib.db.CSD.CSDRspot

getNormalizedDprimeData() - get normalized D' spot intensity for Rspot set.

getNthCommaSeparatedArg(String, int) - Static method in class O2Plib.misc.Util

getNthCommaSeparatedArg() - get n'th arg in comma separated list.

getPairingBit() - Method in class O2Plib.db.CSD.CSDfilterState

getPairingBit() - get the search pairing bits

getPairingBitStr(int) - Static method in class O2Plib.db.CSD.CSDfilterState

getPairingBitStr() - get the search pairing bits as a string

getPixelDataFromImage(Image, int, int) - Static method in class O2Plib.image.PixReader

getPixelDataFromImage() - get the pixel data from the image

getPixelDataFromImage(Image, int, int) - Method in class O2Plib.image.ScrollableImage

getPixelDataFromImage() - get the pixel data from the image

getPixels() - Method in class O2Plib.image.TiffPixelLoader

getPixels() - get unpacked pixels array from the raster.

getPreferredSize() - Method in class O2Plib.gui.PopupOptions

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

getPreferredSize() - Method in class O2Plib.gui.PopupTableEditDialog

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

getPreferredSize() - Method in class O2Plib.image.ScrollableImage

getPreferredSize() - getPreferredSize, must be implemented for ScrollPane to be displayed correctly.

getPreferredSize() - Method in class O2Plib.image.ScrollableImage.ImageCanvas

getPreferredSize() - getPreferredSize, must be implemented for ScrollPane to be displayed correctly.

getPrettyPrintCurrentDateStr() - Static method in class O2Plib.misc.Util

getPrettyPrintCurrentDateStr() - get a printable current date string

getPrettyPrintSpotStr(DbSpot) - Static method in class O2Plib.db.DbSpot

getPrettyPrintSpotStr() - get the pretty-print spot features of specified

getPrettyPrintSpotStr(DbSpot, boolean) - Static method in class O2Plib.db.DbSpot

getPrettyPrintSpotStr() - get the pretty-print spot features of specified

getProjectDirPaths() - Method in class O2Plib.io.FileIO

getProjectDirPaths() - get printable string of project directory (batch/ cache/ ppx/ rdbms/ tmp/ xml/).

getRadioSublistChkMenuItemStates(CheckboxMenuItem) - Method in class O2Plib.gui.MenuSupport

getRadioSublistChkMenuItemStates() - Do radio function by clearing all of the checkbox menu items except the one mentioned which is set to true.

getResults() - Method in class O2Plib.gui.PopupOptions

getResults() - get results array by returning an array of switches merging promptData with userData and setting the "-no" switch accordingly.

getROIStr() - Method in class O2Plib.image.Roi

getROIstr() - get the ROI printable string

getRowData(int) - Method in class O2Plib.table.SimpleTable

getRowData() - get row of data[] for specific row in the table

getRowDataByFieldNameValue(String, String) - Method in class O2Plib.table.SimpleTable

getRowDataByFieldNameValue() - get row of data by (fieldName,fieldValue).

getRsample_xLM(int, int) - Method in class O2Plib.db.CSD.CSDlms

getRsample_xLM() - get the Rsample's nbrLM landmark X value

getRsample_yLM(int, int) - Method in class O2Plib.db.CSD.CSDlms

getRsample_yLM() - get the Rsample's nbrLM landmark Y value

getRspotsList() - Method in class O2Plib.db.CSD.CSDRspotList

getRspotsList() - get the list of Rspot CSDRspot objects

getRspotsNbrs() - Method in class O2Plib.db.CSD.CSDRspotList

getRspotsNbrs() - get the list of Rspot numbers

getSample_xLM(int, int) - Method in class O2Plib.db.CSD.CSDlms

getSample_xLM() - get the Sample's nbrLM landmark X value

getSample_yLM(int, int) - Method in class O2Plib.db.CSD.CSDlms

getSample_yLM() - get the Sample's nbrLM landmark Y value

getSampleAccStr() - Method in class O2Plib.db.DbSample

getSampleAccStr() - get printable data including accession name/value row for this sample

getSampleNames() - Method in class O2Plib.db.CSD.CSDcond

getSampleNames() - get the list of sample namess

getSampleOnlyHeaderNames() - Static method in class O2Plib.db.DbPspot

getSampleOnlyHeaderNames() - get row of space-separated names of fields used in either toStringSampleOnly() or toStringRsampleOnly() calls.

getSamplesList() - Method in class O2Plib.db.CSD.CSDcond

getSampleList() - get the list of sample DbSample objects

getSampleSPFstr() - Method in class O2Plib.db.DbPairSamples

getSampleSPFstr() - get printable data including SPF name/value row for this sample

getSampleSpotNbr(int, int) - Method in class O2Plib.db.CSD.CSDlms

getSampleSpotNbr() - get the Sample's nbrLM landmark spotNumber value [TODO- REFACTORE] since dbLM list not in CSD with DbSpots.

getSampleUseLMflag(int, int) - Method in class O2Plib.db.CSD.CSDlms

getSampleUseLMflag() - get the sample's useLM flag

getSelectedList() - Method in class O2Plib.gui.PopupNameListSelectorDialog

getSelectedList() - get the current selectedNames[] list.

getSizingBitStr(int) - Static method in class O2Plib.db.CSD.CSDlimits

getSizingBitStr() - get the search sizing limits bits as a string

getSpotLMsetRadiiStr() - Method in class O2Plib.db.LMset

getSpotLMsetRadiiStr() - get the printable report mapping all landmarks effective radii.

getSpotLMsetRadiiStr(String, String, int) - Method in class O2Plib.db.LMset

getSpotLMsetRadiiStr() - get the printable report mapping all landmarks effective radii.

getSpotLMSradiiStr() - Method in class O2Plib.db.LMset

getSpotLMSradiiStr() - get the printable report mapping all landmarks effective radii.

getSpotPairStr(DbSpot) - Method in class O2Plib.db.DbPairSamples

getSpotPairStr() - get the paired spot string that identifies the samples, LM sets, LM coords,, dP, dL

getSpotTotalsFromSamples() - Method in class O2Plib.db.CSD.CSDtotals

getSpotTotalsFromSamples() - compile totals from individual sample instances

getStateStr() - Method in class O2Plib.misc.CalibrateOD

getStateStr() - get this calibration state as a string

getStateValue(String, String) - Method in class O2Plib.misc.ParamHash

getStateValue() - get PARAM and use default if not found or the value is "null" string.

getStateValue(String, int) - Method in class O2Plib.misc.ParamHash

getStateValue() - get int PARAM and use default if not found.

getStateValue(String, short) - Method in class O2Plib.misc.ParamHash

getStateValue() - get short PARAM and use default if not found.

getStateValue(String, long) - Method in class O2Plib.misc.ParamHash

getStateValue() - get float PARAM and use default if not found.

getStateValue(String, float) - Method in class O2Plib.misc.ParamHash

getStateValue() - get float PARAM and use default if not found.

getStateValue(String, boolean) - Method in class O2Plib.misc.ParamHash

getStateValue() - get boolean PARAM and use default if not found.

getStudyDataForAllSamples() - Method in class O2Plib.db.CSD.CSDacc

getStudyDataForAllSamples() - get the accession database study data for all samples

getStudyDataForSample(int) - Method in class O2Plib.db.CSD.CSDacc

getStudyDataForSample() - get the accession database study data for a particular sample

getStudyFields() - Method in class O2Plib.db.CSD.CSDacc

getStudyFields() - get the accession database study fields

getSubListSpotsPairedWithThisSpot(DbSpot, int) - Static method in class O2Plib.db.DbSpot

getSubListSpotsPairedWithThisSpot() - get a sublist of spots (in the other sample) that are paired with this spot.

getSwitchOptionsTableStr(String, String[], boolean[], String[]) - Static method in class O2Plib.misc.Switches

getSwitchOptionsTableStr() - get list ALL switch options listing on/off status, name and value if any

getTabDelimFields() - Static method in class O2Plib.db.CSD.CSDtotals

getTabDelimFields() - get a string representation of this instance as tab delimited fields.

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDacc

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDannotation

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDcal

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDcond

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDexpr

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDnorm

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDRmap

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields(boolean, boolean) - Static method in class O2Plib.db.CSD.CSDRspot

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.CSD.CSDsizes

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFields() - Static method in class O2Plib.db.DbPspot

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

getTabDelimitedFieldsAndData() - Method in class O2Plib.db.CSD.CSDcond

getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.

getTabDelimitedFieldsAndData() - Method in class O2Plib.db.CSD.CSDRmap

getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.

getTabDelimitedFieldsAndData(boolean, boolean) - Method in class O2Plib.db.CSD.CSDRspotList

getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.

getTabDelimitedFieldsAndData() - Method in class O2Plib.db.CSD.CSDsizes

getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.

getTabDelimitedFieldsAndData() - Method in class O2Plib.db.CSD.CSDtotals

getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.

getTableRowsSubset(SimpleTable, String, String, String) - Method in class O2Plib.table.Table

getTableRowsSubset() - make new table subset of table by (field,key)

getTableRowsSubset(Table, String[], String[], String[], String[], int, String) - Method in class O2Plib.table.Table

getTableRowsSubset() - make new table of specified fields by fieldList[] and in the order in which they appear in the fieldList[].

getTiffPixels(Raster, boolean) - Method in class O2Plib.image.TiffPixelLoader

getTiffPixels() - get pixels from the raster

getTiffProperties(Raster) - Method in class O2Plib.image.TiffPixelLoader

getTiffProperties() - get properties of the Tiff image

getUnits() - Method in class O2Plib.misc.CalibrateOD

getUnits() - get Wedge units, e.g.

getUnitsAbbrev() - Method in class O2Plib.misc.CalibrateOD

getUnitsAbbrev() - get Wedge units abbreviation, e.g.

getUnitsManufacturerPartNbr() - Method in class O2Plib.misc.CalibrateOD

getUnitsManufacturerPartNbr() - get Wedge manufacturerPartNbr

getUnNormalizedDprimeData() - Method in class O2Plib.db.CSD.CSDRspot

getUnNormalizedDprimeData() - get unnormalized D' spot intensity for Rspot set.

getUsageStr(String, String[]) - Static method in class O2Plib.misc.Switches

getUsageStr() - get usage message string of command line switches

getUserSwitchData() - Method in class O2Plib.gui.PopupOptions

getUserSwitchData() - get user data array

getUserTextData() - Method in class O2Plib.gui.PopupOptions

getUserTextData() - get user text field data array

getVerticalScrollBarVal() - Method in class O2Plib.image.ScrollableImage

getVerticalScrollBarVal() -

gHist - Variable in class O2Plib.misc.CalibrateOD

Histogram of pix4 AVERAGE Size [0:maxGrayPixel+1]

GIFEncode(FileOutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class O2Plib.image.WriteGifEncoder

GIFEncode() - encode the image Adapted from ppmtogif, which is based on GIFENCOD by David Rowley .

GIFNextPixel() - Method in class O2Plib.image.WriteGifEncoder

GIFNextPixel() - Return the next pixel from the image

glbIdCondCounter - Static variable in class O2Plib.db.CSD.CSDcond

Global Condition list ID counter

glbIdExprListCounter - Static variable in class O2Plib.db.CSD.CSDexprList

Global expression list ID counter

glbIdRmapCounter - Static variable in class O2Plib.db.CSD.CSDRmap

Global Rmap ID counter

glbIdRSLcounter - Static variable in class O2Plib.db.CSD.CSDRspotList

Global RSL ID counter

glbPercentThr - Variable in class O2Plib.db.DbSample

Saturation threshold [0.0:1.0] , i.e.

globalRspotCtr - Static variable in class O2Plib.db.CSD.CSDRspot

global Rspot set counter to generate new Rspot set IDs in the init() method.

globalStats - Variable in class O2Plib.db.DbPairSamples

global statistics generated by pairing analysis

globalStats - Variable in class O2Plib.db.DbSample

Global statistics created at the preface and end of segmentation

globalStatsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(3) when the begining of is found

gLUT - Variable in class O2Plib.image.MedianCut

[0:255] Green Color map look up table

gmax - Variable in class O2Plib.image.MC_Cube

gmin - Variable in class O2Plib.image.MC_Cube

goParse(String, DbAccession) - Method in class O2Plib.db.DbAccession.AccContentHandler

goParse() - parse XML file for prologue, spot, and epilogue data.

goParse(String, DbLM) - Method in class O2Plib.db.DbLM.LmsContentHandler

goParse() - parse XML file for prologue, spot, and epilogue data.

goParse(String, DbPairSamples) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

goParse() - parse XML file for prologue, spot, and epilogue data.

goParse(String, DbSample) - Method in class O2Plib.db.DbSample.SsfContentHandler

goParse() - parse XML file for prologue, spot, and epilogue data.

gray2cal - Variable in class O2Plib.misc.CalibrateOD

grayCalWedge - Variable in class O2Plib.image.PpxLoader

(16-bit unsigned) gray scale peaks calibration corresponding to step wedge values.

greenBits(int) - Method in class O2Plib.image.MedianCut

greenBits() - Get 8-bit green component of a 15-bit color 8-bit pixel with low 3 bits zero.

gridPanel - Variable in class O2Plib.gui.PopupTableEditDialog

Where put the grid of (Label,TextField) name value pairs

growLMset(int) - Method in class O2Plib.db.LMset

growLMset() - regrow the landmark set up to newSize.

GS - Static variable in class O2Plib.db.CSD.CSDglb

Garbage Spot - generated by CSD database or editing programs

GS - Static variable in class O2Plib.db.DbBaseSpot

Garbage Spot - generated by CSD database or editing programs

GS - Static variable in class O2Plib.db.DbLM

Garbage Spot - generated by CSD database or editing programs

GS - Static variable in class O2Plib.db.DbPairSamples

Garbage Spot - generated by CSD database or editing programs

guiBuilderSpec - Variable in class O2Plib.gui.PopupOptions

Gui Builder Spec data [0:nData-1] if not "".

H

hAP1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hAP2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hasCalMapAFlag - Variable in class O2Plib.db.DbAccession

has valid mapGrayToCalA[] data

hasCalMapFlag - Variable in class O2Plib.misc.CalibrateOD

Indicates that there is an valid mapGrayToCal map else if it was set to 1:1 the flag is set false.

hCP1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hCP2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

height - Variable in class O2Plib.image.MedianCut

width size of image

height - Variable in class O2Plib.image.WriteGifEncoder

helpData - Variable in class O2Plib.gui.PopupOptions

Prompt help data [0:nData-1] if not null, then make a TextField with this data on the right else empty Label.

helpData - Variable in class O2Plib.gui.PopupTableEditDialog

Optional help data [0:nData-1] if not null, then this is info on the corresponding fieldNameData.

helpList - Static variable in class O2Plib.db.DbAccession

Accession table help list

helpList - Static variable in class O2Plib.db.DbLM

Help list for the landmark table

helpListDynamic - Static variable in class O2Plib.db.DbAccession

Dynamic accession table fields help list

helpListRequired - Static variable in class O2Plib.db.DbAccession

Required accession table fields help list

helpTextArea - Variable in class O2Plib.gui.PopupOptions

Text area for help for individual switch entries

hEP1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hEP2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hexToAscii - Static variable in class O2Plib.db.DbBoundary

hex mapping array: {"0123456789abcdef"}

hist - Variable in class O2Plib.misc.CalibrateOD

histogram of pixel data in ND computing window of [0:255]

hist15 - Variable in class O2Plib.image.MedianCut

[0:32K] 15-bit RGB hist.

histCode - Variable in class O2Plib.db.DbPairSamples

Histogram [0:11] of SPF label frequencies:

histPtr - Variable in class O2Plib.image.MedianCut

[0:colorMax-1] points to colors in "hist15[]"

histSize - Variable in class O2Plib.misc.CalibrateOD

Histogram size is maxGrayPixel+1

HORIZONTAL - Static variable in class O2Plib.image.ScrollableImage.Rule

ohorizontal rientation

hPosOld - Variable in class O2Plib.image.ScrollableImage

old horizontal position

hPP1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hPP2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

HSIZE - Static variable in class O2Plib.image.MedianCut

max size of image histogram

HSIZE - Static variable in class O2Plib.image.WriteGifEncoder

hsize - Variable in class O2Plib.image.WriteGifEncoder

hSP1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hSP2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

htab - Variable in class O2Plib.image.WriteGifEncoder

hUS1 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

hUS2 - Variable in class O2Plib.db.DbPairSamples

Histogram label statistics

I

id - Variable in class O2Plib.image.MC_Cube

idCond - Variable in class O2Plib.db.CSD.CSDcond

Condition list id for this instance

idExprList - Variable in class O2Plib.db.CSD.CSDexprList

Expression list id for this instance

idIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

idNbr - Variable in class O2Plib.db.CSD.CSDRspot

Rspot set number [1:max # of Rspots].

idRmap - Variable in class O2Plib.db.CSD.CSDRmap

Rmap id for this instance

idRsampleSpot - Variable in class O2Plib.db.CSD.CSDRspot

The DbPspot rSpotNbr idNbr from the Rsample spot if it exists (i.e.

idRSL - Variable in class O2Plib.db.CSD.CSDRspotList

RSL id for this Rspot set list instance

idxCondList - Variable in class O2Plib.db.CSD.CSDRspot

List of indices constituting the corresponding CSDcond for each entry in the Rspot set.

idxRsample - Variable in class O2Plib.db.DbBaseSpot

index of Rsample this spot is paired with.

idxRsample - Variable in class O2Plib.db.DbPairSamples

index of Rsample instance in CSD database.

idxSample - Variable in class O2Plib.db.DbBaseSpot

Index of Sample for this spot.

idxSample - Variable in class O2Plib.db.DbPairSamples

Index of Sample instance in CSD database.

idxSample - Variable in class O2Plib.db.DbSample

Index of this Sample instance in CSD database.

idxSampleList - Variable in class O2Plib.db.CSD.CSDacc

index values of the samples [0:nSamples-1]

idxSampleList - Variable in class O2Plib.db.CSD.CSDexpr

idxSampleList - Variable in class O2Plib.db.CSD.CSDexprList

List of indices [0:nEPlist-1] constituting the corresponding DbSamples for each entry in the Rspot set.

idxSampleList - Variable in class O2Plib.db.CSD.CSDRspot

List of indices [0:nSpots-1] constituting the corresponding DbSamples for each entry in the Rspot set.

ignorableWhitespace(char[], int, int) - Method in class O2Plib.db.DbAccession.AccContentHandler

ignorableWhitespace() -

ignorableWhitespace(char[], int, int) - Method in class O2Plib.db.DbLM.LmsContentHandler

ignorableWhitespace() -

ignorableWhitespace(char[], int, int) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

ignorableWhitespace() -

ignorableWhitespace(char[], int, int) - Method in class O2Plib.db.DbSample.SsfContentHandler

ignorableWhitespace() -

image - Variable in class O2Plib.image.PixReader

image instance

imagePanel - Variable in class O2Plib.image.ScrollableImage

actual object to be displayed

imageUpdate(Image, int, int, int, int, int) - Method in class O2Plib.image.PixReader.PixObserver

imageUpdate() - called when loading reporting progress by printing "..." Set by ImageObserver.

imEncode - Variable in class O2Plib.image.PpxLoader

Image encoding method 0 = none (just raw raster data) 1 = UNIX 'compress/uncompress' 2 = run length 3 = 1D modified Huffman 4 = 2D modified Huffman 5 = delta coding 6 = run length with delta coding ...

img - Variable in class O2Plib.image.PpxLoader

Image structure required for PPX loader

img - Variable in class O2Plib.image.TiffPixelLoader

Image structure.

imgFile - Variable in class O2Plib.image.PixReader

full file path name of the input image

imgType - Variable in class O2Plib.image.PixReader

image type: "TIFF", "JPG", "GIF", "PPX"

imOrientation - Variable in class O2Plib.image.PpxLoader

Image orientation bits where: Default 00==>011: 01 = left to right 02 = bottom to top 04 = right to left 010= top to bottom

increment - Variable in class O2Plib.image.ScrollableImage.Rule

rule increment size

index - Variable in class O2Plib.image.WriteGifEncoderHashitem

indexRsample - Variable in class O2Plib.db.CSD.CSDRspot

Index of Rsample in this.idxSampleList[].

init() - Method in class O2Plib.db.CSD.CSD

init() - setup the related sub class object instances

init(int) - Method in class O2Plib.db.CSD.CSDcond

init() - initialize Condition list to specified size if > 0.

init(int) - Method in class O2Plib.db.CSD.CSDexpr

init() - initialize expression list to specified size if > 0.

init(int) - Method in class O2Plib.db.CSD.CSDexprList

init() - initialize list of expression lists to specified size if > 0.

init(int) - Method in interface O2Plib.db.CSD.CSDlistInterface

init() - initialize object list to specified size if > 0.

init(int) - Method in class O2Plib.db.CSD.CSDRmap

init() - initialize Rmap list to specified size if > 0.

init(int) - Method in class O2Plib.db.CSD.CSDRspot

init() - initialize CSDRspot structures.

init(int) - Method in class O2Plib.db.CSD.CSDRspotList

init() - initialize Rspot list list to specified size if > 0.

init() - Method in class O2Plib.db.DbBoundary

init() - init any globals required on a per-spot basis.

init() - Method in class O2Plib.db.DbLM

init() - reset the DbLM state for both samples.

init() - Method in class O2Plib.db.DbPairSamples

init() - init the DbSPF state.

init() - Method in class O2Plib.db.DbSample

init() - init the DbSample instance state sample names.

init(String, int, int) - Method in class O2Plib.gui.MenuSupport

init() - create empty hash tables.

init() - Method in class O2Plib.misc.CalibrateOD

init() - init the calibration, default to 256 gray value 1:1

init(int) - Method in class O2Plib.misc.CalibrateOD

init() - init the calibration with calibration map

init(int, float[]) - Method in class O2Plib.misc.CalibrateOD

init() - init the calibration with calibration map

init(int) - Static method in class O2Plib.misc.Switches

init() - reset the switches database

initAccTblDynamicIndices() - Method in class O2Plib.db.DbAccession

initAccTblDynamicIndices() - init dynamic indices for accession table.

initAccTblIndices() - Method in class O2Plib.db.DbAccession

initAccTblIndices() - init the indices for the accession table.

initAccTblRequiredIndices() - Method in class O2Plib.db.DbAccession

initAccTblRequiredIndices() - init required indices for accession table.

initCacheLists() - Method in class O2Plib.db.CSD.CSDcache

initCacheLists() - init cache lists.

initCal(String, int) - Method in class O2Plib.db.CSD.CSDcal

initCal() - initialize calibration [TODO] add data...

initGlb() - Method in class O2Plib.db.CSD.CSDglb

initGlb() - reset all variables to initial state.

INITIAL_MAXBND - Static variable in class O2Plib.db.DbBoundary

Initial boundary size

initialMaxPeaks - Variable in class O2Plib.misc.CalibrateOD

the value of maxPeaks BEFORE running the peak finder

initialPairingStatsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(3.3) when the begining of initial pairing statistics is found.

initl - Variable in class O2Plib.image.PpxLoader

initials of person doing scan

initLMset() - Method in class O2Plib.db.LMset

initLMset() - reset the LMset state for both samples.

initMaxima() - Method in class O2Plib.db.DbPairSamples

initMaxima() - initialize the feature maxima and minima

inPixFile - Variable in class O2Plib.db.DbSample

full path name of the sample image file.

insertSpot(DbSpot, DbSpot) - Method in class O2Plib.db.DbSample

insertSpot() - insert spot r BEFORE spot sp and update spotList[0:nTopSpot-1].

insertSpotPair(DbPspot, DbPspot) - Method in class O2Plib.db.DbSample

insertSpotPair() - insert DbPspot r BEFORE sp and update spotPairList[0:nTopSpotPair-1].

insertTblInULHCtable(int, int, String) - Method in class O2Plib.table.Table

insertTblInULHCtable() - insert table into U.L.H.C.

interlace - Variable in class O2Plib.image.WriteGifEncoder

80% occupancy

internalZoomButtonsFlag - Variable in class O2Plib.image.ScrollableImage

FUTURE: special internal buttons for zoom

intersection(CSDcond, CSDcond) - Method in class O2Plib.db.CSD.CSDcond

intersection() - do the intersection of two condition lists r3= intersection(r1,r2).

intersection(CSDexprList, CSDexprList) - Method in class O2Plib.db.CSD.CSDexprList

intersection() - do the intersection of two ExprList lists r3= intersection(r1,r2).

intersection(CSDRspotList, CSDRspotList) - Method in class O2Plib.db.CSD.CSDRspotList

intersection() - do the intersection of two RSL lists r3= intersection(r1,r2).

intPix - Variable in class O2Plib.image.PixReader

16-bits/pixel image if it exists packed in LSB of 232-bit int Data may be 8-bits to 16/bits/pixel

invalidCentroidsTot - Variable in class O2Plib.db.CSD.CSDtotals

# of invalid spot centroids found during spot quantification

invalidCentroidsTot - Variable in class O2Plib.db.DbSample

# of invalid spot centroids found during spot quantification

invoke(Object, String, Class[], Object[]) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

invoke() - method call to parent class.

INVOKE_METHOD_NAME - Static variable in class O2Plib.image.ScrollableImage

name of method that parent needs to have implemented for remote painting

IO_EXCEPTION - Static variable in class O2Plib.io.FileIO

IO_FILE_NOT_FOUND - Static variable in class O2Plib.io.FileIO

IO_FILE_NOT_READ_ENABLED - Static variable in class O2Plib.io.FileIO

IO_FILE_WRITE_ERROR - Static variable in class O2Plib.io.FileIO

IO_FORMAT_FULL - Static variable in class O2Plib.io.FileIO

File format for full tab-delimited format that includes data BEFORE the spot list and summary data AFTER the spot list

IO_FORMAT_GELLAB - Static variable in class O2Plib.io.FileIO

File format for old GELLAB-II formats

IO_FORMAT_TAB_DELIM - Static variable in class O2Plib.io.FileIO

File format for tab-delimited format for use with spreadsheets such as Excel.

IO_FORMAT_XML - Static variable in class O2Plib.io.FileIO

File format for XML for use with the Open2Dprot project

IO_OK - Static variable in class O2Plib.io.FileIO

I/O error codes

IO_SECURITY_VIOLATION - Static variable in class O2Plib.io.FileIO

isColorImageFlag - Static variable in class O2Plib.image.PixReader

The image was a RGB color image converted to grayscale using the NTSC color transform.

isComponentCMflag - Variable in class O2Plib.image.TiffPixelLoader

set if has ComponentColorModel

isComponentSMflag - Variable in class O2Plib.image.TiffPixelLoader

set if has ComponentSampleModel

isCompressedChainCode - Variable in class O2Plib.db.DbBoundary

Sizes of sub-objects.

isDBwindow(int, int) - Method in class O2Plib.db.DbSample

isDBwindow() - test if (x,y) is inside the debug window.

isDynamicField(String) - Method in class O2Plib.db.DbAccession

isDynamicField() - lookup dynamic Accession DB field data that is required (not dynamic)

isLandmarkSpot(DbPspot) - Method in class O2Plib.db.CSD.CSDlms

isLandmarkSpot() - test if sample's ccNbr spot is a landmark spot.

isLandmarkSpot() - Method in class O2Plib.db.DbPspot

isLandmarkSpot() - test if sample's ccNbr spot is a landmark spot.

isLoadedFlag - Variable in class O2Plib.image.PixReader

set after image loaded

isMultiplePixelPackedSMflag - Variable in class O2Plib.image.TiffPixelLoader

set if has a MultiplePixelPackedSampleModel

isPackedCMflag - Variable in class O2Plib.image.TiffPixelLoader

set if PackedColorModel

isPackedFlag - Variable in class O2Plib.image.TiffPixelLoader

set if pixel can be packed into a byte array

isptsz - Variable in class O2Plib.image.PpxLoader

(unsigned short) s.s.d in microns*1024

isRequiredField(String) - Method in class O2Plib.db.DbAccession

isRequiredField() - lookup required Accession DB field data that is required (not dynamic)

isRGBcolorImageFlag - Variable in class O2Plib.image.TiffPixelLoader

set if this is a RGB color image

isSinglePixelPackedSMflag - Variable in class O2Plib.image.TiffPixelLoader

set if has a SinglePixelPackedSampleModel

istpx - Variable in class O2Plib.image.PpxLoader

(unsigned short) X step sizes in microns*1024

istpy - Variable in class O2Plib.image.PpxLoader

(unsigned short) Y step sizes in microns*1024

isTransparent - Variable in class O2Plib.image.WriteGifEncoderHashitem

isValid() - Method in class O2Plib.image.Roi

isValid() - test if the ROI is well defined such that all entries are < 0 and (x1 < = x2) and (y1 < = y2).

isValid(int, int, int, int) - Method in class O2Plib.image.Roi

isValid() - test if these coordinates are a valid region

isValidROI(int, int, int, int) - Method in class O2Plib.db.DbSample

isValidROI() - check if current region of interest (ROI) is valid

isValidROI(int, int, int, int) - Method in class O2Plib.misc.CalibrateOD

isValidROI() - check if current region of interest (ROI) is valid

isValidWedgeROI() - Method in class O2Plib.misc.CalibrateOD

isValidWedgeROI() - check if Wedge ROI is valid

isValInList(int, int[]) - Static method in class O2Plib.misc.Util

isValInList() - test if val is in list of values.

isValInList(float, float[]) - Static method in class O2Plib.misc.Util

isValInList() - test if val is in list of values.

isVisibleFlag - Variable in class O2Plib.gui.PopupTableEditDialog

Set true if window is visible

isXYinROI(int, int) - Method in class O2Plib.image.Roi

isXYinROI() - test if XY is in the valid ROI region

itemStateChanged(ItemEvent) - Method in class O2Plib.gui.PopupDialogQuery

itemStateChanged() - event handler for Choices

itemStateChanged(ItemEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

itemStateChanged() - handle item state checkbox selectors.

itemStateChanged(ItemEvent) - Method in class O2Plib.gui.PopupOptions

itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.

itemStateChanged(ItemEvent) - Method in class O2Plib.gui.PopupTableEditDialog

itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.

J

jsp - Variable in class O2Plib.image.ScrollableImage

Scroll pane to hold the image

justPixelsFlag - Static variable in class O2Plib.image.TiffPixelLoader

K

keyPressed(KeyEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

keyPressed() - handle key down events, pass to parent

keyPressed(KeyEvent) - Method in class O2Plib.image.ScrollableImage

keyPressed() - handle key down events

keyReleased(KeyEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

keyReleased(KeyEvent) - Method in class O2Plib.image.ScrollableImage

keyTyped(KeyEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

keyTyped(KeyEvent) - Method in class O2Plib.image.ScrollableImage

L

label - Variable in class O2Plib.gui.PopupDialogQuery

for data label

landmarkFile - Variable in class O2Plib.db.CSD.CSDlms

Landmark file name

landmarkSetSizeStatsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(3.2) when the begining of the list of statistics is found.

largeFont - Variable in class O2Plib.gui.PopupTableEditDialog

lastCacheBlock - Variable in class O2Plib.db.CSD.CSDio

last block in CSD cache file

lastSpot - Variable in class O2Plib.db.DbSample

last spot allocated (optional)

lastSpotPair - Variable in class O2Plib.db.DbSample

last spot allocated in the spotPairList[] spot-pair list (optional)

lastTaTableRowIdx - Variable in class O2Plib.db.DbAccession

Last row found with lookupAccEntry()

LB - Static variable in class O2Plib.db.CSD.CSDfilterState

Lower bound index constant

LB - Static variable in class O2Plib.db.CSD.CSDlimits

Lower bound index constant

leftFillWithSpaces(String, int) - Static method in class O2Plib.misc.Util

leftFillWithSpaces() - left fill the string with spaces to size n.

legalImageFileExtens - Static variable in class O2Plib.db.DbSample

List of legal sample image file extensions

legalImageFileExtensA - Variable in class O2Plib.db.DbAccession

List of legal input image file extensions.

limits - Variable in class O2Plib.db.CSD.CSDfilterState

LIMITS_COV_AREA - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: coefficient of variation of area

LIMITS_COV_DENSITY - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: coefficient of variation of density

LIMITS_DL - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: dL

LIMITS_DP - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: dP

LIMITS_MN_AREA - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: mean area

LIMITS_MN_DENS_RANGE - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: mean density range (maxdensity-bkgrd density)/pixel

LIMITS_MN_DENSITY - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: mean density

LIMITS_MW - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: MW

LIMITS_MZ - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: MZ (2D-LC-MS)

LIMITS_N_SAMPLES_PER_COND - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: # of samples/condition (minimum)

LIMITS_P_VALUE - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: pValue

LIMITS_PIE - Static variable in class O2Plib.db.CSD.CSDlimits

LIMITS_REL_DIST - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: relative distance from the landmark indicating that the pairing has more certainty if closer.

LIMITS_RT - Static variable in class O2Plib.db.CSD.CSDlimits

Sizing limits: RT (retention time 2D LC-MS)

listAllSpots(boolean, boolean) - Method in class O2Plib.db.DbSample

listAllSpots() - list all spots in the spot list.

listener - Variable in class O2Plib.gui.PopupDialogQuery

Tried this instead of "this"

listG - Variable in class O2Plib.db.DbSample

point to first spot of full spot list - initialized to nulls.

listPairG - Variable in class O2Plib.db.DbSample

point to first spot of full spot list - initialized to nulls.

listSamplePairs(DbAccession) - Method in class O2Plib.db.DbLM

ListSamplePairs() - generate a unique list of sample pairs in the database.

listSamples() - Method in class O2Plib.db.DbAccession

listSamples() - list samples (one/line) in the accession file

listUniqueSamplesInLandmarkDB(DbAccession) - Method in class O2Plib.db.DbLM

listUniqueSamplesInLandmarkDB() - generate a unique list of sample pairs in the database.

LM - Static variable in class O2Plib.db.CSD.CSDglb

LandMark spot [could be virtual landmark] - by CSD database program

LM - Static variable in class O2Plib.db.DbBaseSpot

LandMark spot [could be virtual landmark] - by CSD database program.

LM - Static variable in class O2Plib.db.DbLM

LandMark spot [could be virtual landmark] - by CSD database program

LM - Static variable in class O2Plib.db.DbPairSamples

LandMark spot [could be virtual landmark] - by CSD database program

LMCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Landmark spot label

lmErrDist - Variable in class O2Plib.db.LMset

LSQ error of landmarks to latched spots from SSF [0:nbrLandmarks-1][RSAMPLE:SAMPLE]

lmFlag - Variable in class O2Plib.db.DbPspot

set true if spot is a landmark spot

lmFlag - Variable in class O2Plib.db.DbSpot

set true if spot is a landmark spot

lmNbrI - Variable in class O2Plib.db.DbBaseSpot

Landmark number as int index [0:51].

lmNbrIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

lmNbrS - Variable in class O2Plib.db.DbBaseSpot

Landmark number String as index [0:51] encoded as a name character "A" : "Z or "a" : "z".

LMset - Class in O2Plib.db

Class LMset maintains the Landmark database for Open2Dprot.

LMset() - Constructor for class O2Plib.db.LMset

LMset() - set up lndmark part of the database of size nbrLandmarks.

LMset(int) - Constructor for class O2Plib.db.LMset

LMset() - set up lndmark part of the database of size nbrLandmarks.

LMSETCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Color of spots in the landmark set

lmSetPtr - Variable in class O2Plib.db.DbLM

Points to first spot of each LM set in each Sample [0:PARAM_MAXLANDMARKS-1][RSAMPLE:SAMPLE]

lmSetRsample - Variable in class O2Plib.db.CSD.CSDRspot

LMset that the Rsample belongs to

lmSetsList - Variable in class O2Plib.db.CSD.CSDlms

list of LMsets [0:nLMsetsList-1]

lmSetsNames - Variable in class O2Plib.db.CSD.CSDlms

Names of the LMsets [0:nLMsetsList-1]

lmsFields - Static variable in class O2Plib.db.DbLM

Landmark table fields

lmsFile - Variable in class O2Plib.db.DbLM

loadAccessionDatabase(String, String, String[], int) - Method in class O2Plib.db.DbAccession

loadAccessionDatabase() - lookup and load the accession database.

loadGifOrJpegPix(String) - Method in class O2Plib.image.PixReader

loadGifOrJpegPix() - read GIF or JPEG pix file into this obj as bytePix[] and return as intPix[].

loadJpeg2000Pix(String) - Method in class O2Plib.image.PixReader

loadJpeg2000Pix() - read JPEG2000 pix file into this obj as either charPix[] or bytePix[] depending on whether it is > 8-bits/pixel or not.

loadLandmarkDatabase(String, int) - Method in class O2Plib.db.DbLM

loadLandmarkDatabase() - load landmarks database table

loadPPXpix(String) - Method in class O2Plib.image.PixReader

loadPPXpix() - read GELLAB-II PPX pix file into this obj as bytePix[] and return as int{ox[].

loadTiffPix(String) - Method in class O2Plib.image.PixReader

loadTiffPix() - read Tiff pix file into this obj as a grayscale intPix[].

locator - Variable in class O2Plib.db.DbAccession.AccContentHandler

Hold onto the locator for location information - for debugging

locator - Variable in class O2Plib.db.DbLM.LmsContentHandler

Hold onto the locator for location information - for debugging

locator - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Hold onto the locator for location information - for debugging

locator - Variable in class O2Plib.db.DbSample.SsfContentHandler

Hold onto the locator for location information for debugging

lookupAccEntry(String, String) - Method in class O2Plib.db.DbAccession

lookupAccEntry() - lookup accession row entry data in the accession database specified by the accFile.

lookupAccEntryNoExtn(String, String) - Method in class O2Plib.db.DbAccession

lookupAccEntryNoExtn () - lookup accession row entry data in the accession database specified by the accFieldName's value of accNameData.

lookupAccessionTableIndices() - Method in class O2Plib.db.DbAccession

lookupAccessionTableIndices() - lookup SSF data table indices There may be additional fields.

lookupAccTableFields() - Method in class O2Plib.db.DbAccession

lookupAccTableFields() - lookup accession database fields

lookupBestDbPspotBySampleIdx(int) - Method in class O2Plib.db.CSD.CSDRspot

lookupBestDbPspotBySampleIdx() - find best DbPspot from Rspot set by sample index.

lookupChkboxMenuItem(String) - Method in class O2Plib.gui.MenuSupport

lookupChkboxMenuItem() - lookup CheckboxMenuItem entry in menu list by searching (key,value)=(cmd,ChkBoxMenuData) and returning the CheckboxMenuItem if found.

lookupChkboxMenuItem(CheckboxMenuItem) - Method in class O2Plib.gui.MenuSupport

lookupChkboxMenuItem() - lookup String command entry in checkbox menu item list by searching (key,value)=(CheckboxMenuItem,ChkBoxMenuData) and returning the command if found.

lookupChkboxMenuItemLabel(String) - Method in class O2Plib.gui.MenuSupport

lookupChkboxMenuItemLabel() - lookup CheckboxMenuItem entry label in menu list by searching (key,value)=(cmd,ChkBoxMenuData) and returning the menu label if found.

lookupDynamicAccTableIndices() - Method in class O2Plib.db.DbAccession

lookupDynamicAccTableIndices() - lookup dynamic SSF data table indices There may be additional fields.

lookupFieldIdx(String) - Method in class O2Plib.table.SimpleTable

lookupFieldIdx() - lookup column index of field if exists.

lookupFieldIdxFromHT(String) - Method in class O2Plib.db.DbAccession

lookupFieldIdxFromHT() - lookup accession database field column index.

lookupFieldPrefixIdx(String) - Method in class O2Plib.table.SimpleTable

lookupFieldPrefixIdx() - lookup column index of fieldNamePrefix if exists in the table.

lookupIdxByLMS(String) - Method in class O2Plib.db.CSD.CSDlms

lookupIdxByLMS() - lookup index of LMset name in list of LMsets.

lookupIdxByLMS(LMset) - Method in class O2Plib.db.CSD.CSDlms

lookupIdxByLMS() - lookup index of LMset name in list of LMsets.

lookupIdxByRspot(CSDexpr) - Method in class O2Plib.db.CSD.CSDexprList

lookupIdxByRspot() - lookup index of Rspot object in ExprList.

lookupIdxByRspot(int) - Method in class O2Plib.db.CSD.CSDRspotList

lookupIdxByRspot() - lookup index of Rspot number in RSL.

lookupIdxByRspot(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspotList

lookupIdxByRspot() - lookup index of Rspot object in RSL.

lookupIdxBySample(String) - Method in class O2Plib.db.CSD.CSDcond

lookupIdxBySample() - lookup index of sample name in condition.

lookupIdxBySample(DbSample) - Method in class O2Plib.db.CSD.CSDcond

lookupIdxBySample() - lookup index of sample object in condition.

lookupLandmarkTableIndices() - Method in class O2Plib.db.DbLM

lookupLandmarkTableIndices() - lookup SSF data table indices Note: the table contains (pixRsample,pixSample,lmNbr,xRsample,yRsample,xSample,ySample) So look for both field name sets.

lookupMenuItem(String) - Method in class O2Plib.gui.MenuSupport

lookupMenuItem() - lookup MenuItem entry in menu list.

lookupMenuItem(MenuItem) - Method in class O2Plib.gui.MenuSupport

lookupMenuItem() - lookup MenuItem entry by MenuItem in menu list.

lookupMenuItemLabel(String) - Method in class O2Plib.gui.MenuSupport

lookupMenuItemLabel() - lookup CheckboxMenuItem entry label in menu list by searching (key,value)=(cmd,MenuCmdData) and returning the menu label if found.

lookupPairedSamplesList(String) - Method in class O2Plib.db.DbLM

lookupPairedSamplesList() - lookup list of all pairs of (Rsample,Sample) pairs in the landmark database such that the Rsample is rName.

lookupRequiredAccTableIndices() - Method in class O2Plib.db.DbAccession

lookupRequiredAccTableIndices() - lookup required SSF data table indices.

lookupRowByFieldNameValue(String, String) - Method in class O2Plib.table.SimpleTable

lookupRowByFieldNameValue() - lookup the row of data by (fieldName,fieldValue).

lookupRowByFieldNameValuePairs(String, String, String, String) - Method in class O2Plib.table.SimpleTable

lookupRowByFieldNameValuePairs() - lookup the row of data by (fieldName1,fieldValue1) and (fieldName2,fieldValue2) matches.

lookupRspotByExactRspotXYcoord(float, float) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByExactRspotXYcoord() - lookup Rspot set by exact Rspot set (xRspot,yRspot) coordinates.

lookupRspotByExactRspotXYcoordDbug(float, float, int, int) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByExactRspotXYcoordDbug() - DBUG version.

lookupRspotByNearestERspotXYcoord(float, float, float) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByNearestERspotXYcoord() - lookup nearest ERspot set by (xERspot,yERspot) coordinates.

lookupRspotByNearestRspotXYcoord(int, int, float) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.

lookupRspotByNearestRspotXYcoord(float, float, float) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.

lookupRspotByNearestRspotXYcoord(float, float, float, boolean) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.

lookupRspotByRspotIDnbr(int) - Method in class O2Plib.db.CSD.CSDRspotList

lookupRspotByRspotIDnbr() - lookup Rspot set by ID number

lookupSampleInAccDB(String, String, String) - Method in class O2Plib.db.DbAccession

lookupSampleInAccDB() - lookup the sample accNameData in the accession DB by the accession database accFieldName key.

lookupSampleInAccDB(String, String, String) - Method in class O2Plib.db.DbSample

lookupSampleInAccDB() - lookup the sample by (nave,value) pair for this sample in the accession DB.

lookupSamplePairLMS(DbSample, DbSample, boolean) - Method in class O2Plib.db.DbLM

lookupSamplePairLMS() - lookup specific LMset pair (Rsample,Sample) from landmarks data table.

lookupSsfSpotlistTableIndices() - Method in class O2Plib.db.DbSample

lookupSsfSpotlistTableIndices() - lookup SSF data table indices

lookupTableByName(String) - Static method in class O2Plib.table.Table

lookupTableByName() - lookup the table by name

lookupTableListIdxByTableName(String) - Static method in class O2Plib.table.Table

lookupTableListIdxByTableName() - lookup TableList[] index by Table name if the name is in the table list.

low - Variable in class O2Plib.image.MC_Cube

lsqMcoef - Variable in class O2Plib.db.CSD.CSDnorm

Least Square normalization slope: mj to estimate djR'=mj*d'j+bj

lth - Variable in class O2Plib.db.DbBoundary

length of boundary

lvl - Variable in class O2Plib.image.MC_Cube

M

main(String[]) - Static method in class O2Plib.misc.CalibrateOD

main() - for testing and optimizing parameters for findPeak method using preset data from GELLAb-II Leukemia-AML gel image (gel 0324.1).

make8BitImage() - Method in class O2Plib.image.MedianCut

make8BitImage() - Generate 8-bit image from interla 15-bit image.

makeChkBoxMenuItem(Frame, Menu, String, String, int, boolean) - Method in class O2Plib.gui.MenuSupport

makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list.

makeInverseMap(int[], int) - Method in class O2Plib.image.MedianCut

makeInverseMap() - for all cubes, compute centroid of colors in cube.

makeMenuItem(Frame, Menu, String, String, int) - Method in class O2Plib.gui.MenuSupport

makeMenuItem() - make menuItem entry in menu list.

makePPXimage() - Method in class O2Plib.image.PpxLoader

makePPXimage() - make img and pixels[] from the byte bPixels[] data

makeProjectDirs(String, boolean) - Method in class O2Plib.io.FileIO

makeProjectDirs() - make a project directory and sub directories and create directory and sub directories: batch/ cache/ ppx/ rdbms/ tmp/ xml/.

makeSubMenu(Frame, Menu, String, String, int) - Method in class O2Plib.gui.MenuSupport

makeSubMenu() - make submenu entry in menu list.

makeTabDelimReport(String) - Method in class O2Plib.table.Table

makeTabDelimReport() - make tab-delimited string report string from this Table

manufacturerPartNbr - Variable in class O2Plib.misc.CalibrateOD

optional manufacturer part number for the step wedge

mapGrayToCal - Variable in class O2Plib.misc.CalibrateOD

mapGrayToCalA - Variable in class O2Plib.db.DbAccession

Gray to calibration value calibration map if it exists.

mappingModeFlag - Variable in class O2Plib.db.CSD.CSDfilterState

using Rspot name mapping to foreign Fspot mapping

mapRelXYtoImage(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mapRelXYtoImage() - map (x,y)Mouse in current canvas to (xImg,yImg) as well as updating the parent.(xImg,yImg) values.

mapRsampleXYtoSample(int, int) - Method in class O2Plib.db.LMset

mapRsampleXYtoSample() - map Rsample (x,y) to coordinate system of Sample.

mapRsampleXYtoSampleLMset(int, int, int) - Method in class O2Plib.db.LMset

mapRsampleXYtoSampleLMset() - map Rsample (x,y) to coordinate system of Sample.

mapRspotToStdSpotFlag - Variable in class O2Plib.db.CSD.CSDRmap

false is standard Rspot mapping, true is standard Foreign Fspot mapping

mapSampleXYtoRsample(int, int) - Method in class O2Plib.db.LMset

mapSampleXYtoRsample() - map Sample (x,y) to coordinate system of Rsample.

mapSampleXYtoRsampleLMset(int, int, int) - Method in class O2Plib.db.LMset

mapSampleXYtoRsampleLMset() - map Sample (x,y) to coordinate system of Rsample.

mapStateToZoom(float, Point) - Method in class O2Plib.image.DrawOverlays

mapStateToZoom() - map state point to zoomed/dezoomed point This can be used for remapping overlays.

mapStateToZoom(int, Point) - Method in class O2Plib.image.DrawOverlays

mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal.

mapStateToZoom(int, int) - Method in class O2Plib.image.DrawOverlays

mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal.

mapStateToZoom(float, Point) - Method in class O2Plib.image.ScrollableImage

mapStateToZoom() - map state point to zoomed/dezoomed point This can be used for remapping overlays.

mapStateToZoom(int, Point) - Method in class O2Plib.image.ScrollableImage

mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal.

mapZoomToState(float, Point) - Method in class O2Plib.image.DrawOverlays

mapZoomToState() - map zoom point to state point This can be used for remapping overlays.

mapZoomToState(int, Point) - Method in class O2Plib.image.DrawOverlays

mapZoomToState() - map zoom point to state point based on zoomMagVal.

mapZoomToState(int, int) - Method in class O2Plib.image.DrawOverlays

mapZoomToState() - map zoom point to state point based on zoomMagVal.

mapZoomToState(float, Point) - Method in class O2Plib.image.ScrollableImage

mapZoomToState() - map zoom point to state point This can be used for remapping overlays.

mapZoomToState(int, Point) - Method in class O2Plib.image.ScrollableImage

mapZoomToState() - map zoom point to state point based on zoomMagVal.

masks - Variable in class O2Plib.image.WriteGifEncoder

masterPairSpotCtr - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

master paired spot counter reset to 0 when start XML reader

MAX_BUFFERED_SPOTS - Static variable in class O2Plib.db.DbSample

max # spots to buffer in memory when converting the list of spots to string representations.

MAX_CHKBOX_CMDS - Static variable in class O2Plib.gui.MenuSupport

max number of menu checkbox items allowed

MAX_CHOICES - Variable in class O2Plib.gui.PopupOptions

MAX_CMDS - Static variable in class O2Plib.gui.MenuSupport

Initial max number of menu items allowed.

MAX_DL - Static variable in class O2Plib.db.DbPairSamples

max dL value allowed if clip

MAX_DP - Static variable in class O2Plib.db.DbPairSamples

max dP value allowed if clip

MAX_DX_DY - Static variable in class O2Plib.db.DbPairSamples

|dX| and |dY| if clip

MAX_GRAY - Static variable in class O2Plib.misc.CalibrateOD

Maximum gray value possible defaults to 8-bits, but could overide if the image has more bits/pixel (i.e.

MAX_NODE_SAFTY_FACTOR - Static variable in class O2Plib.db.CSD.CSDglb

MAX_RATIO_ALT_DIST_THRESHOLD - Static variable in class O2Plib.db.LMset

Default distance threshold to use to ignore alternate landmarks > distance

MAX_SLIDERS - Variable in class O2Plib.gui.PopupOptions

MAX_SPOT_SUBLIST_SIZE - Static variable in class O2Plib.db.DbBaseSpot

max size of spot sublist when they are created locally

MAX_STATUS_TIMES - Static variable in class O2Plib.misc.Util

Max # of report timer status names

MAX_TEXT_FIELD_WIDTH - Variable in class O2Plib.gui.PopupOptions

MAX_TEXT_FIELD_WIDTH - Variable in class O2Plib.gui.PopupTableEditDialog

MAX_WEDGE_STEPS - Static variable in class O2Plib.misc.CalibrateOD

Maximum # of calibration Wedge and peak values in the peak table

MAX_ZOOM_MAG_VAL - Static variable in class O2Plib.image.DrawOverlays

min zoomMag value (zoom/dezoom) X magnification

MAX_ZOOM_MAG_VAL - Static variable in class O2Plib.image.ScrollableImage

max zoomMag value (zoom/dezoom) X magnification

maxAreaFound - Variable in class O2Plib.db.CSD.CSDtotals

Max area found in accepted spot

maxAreaFound - Variable in class O2Plib.db.DbSample

Max area found in accepted spot

maxbits - Variable in class O2Plib.image.WriteGifEncoder

maxBkgrdDensity - Variable in class O2Plib.db.CSD.CSDtotals

max background seen in any spot

maxBkgrdDensity - Variable in class O2Plib.db.DbSample

max background seen in any spot

maxBkgrdTot - Variable in class O2Plib.db.CSD.CSDtotals

Max sample background grayscale (computed elsewhere)

maxBkgrdTot - Variable in class O2Plib.db.DbSample

Max sample background grayscale (computed elsewhere)

maxBndAlloc - Static variable in class O2Plib.db.DbBoundary

initial boundary size allocation

maxCalib - Variable in class O2Plib.db.CSD.CSDsizes

# pIe and MW calibration objects.

maxCalibGrayFound - Variable in class O2Plib.db.CSD.CSDtotals

Max calibrated grayvalue found in accepted spot

maxCalibGrayFound - Variable in class O2Plib.db.DbSample

Max calibration grayscale found in accepted spot

maxCalibrations - Variable in class O2Plib.db.CSD.CSDcal

Number of calibrations

maxCalSteps - Variable in class O2Plib.misc.CalibrateOD

eg.

maxCalStepsA - Variable in class O2Plib.db.DbAccession

Number of wedge list calibration values if not 0

maxCheckboxMenuItems - Variable in class O2Plib.gui.MenuSupport

initial max number of menu checkbox items allowed

maxcode - Variable in class O2Plib.image.WriteGifEncoder

MAXCODE(int) - Method in class O2Plib.image.WriteGifEncoder

MAXCODE() - return n bits

MAXCOLORS - Static variable in class O2Plib.image.MedianCut

maximum # of output colors

maxConditions - Variable in class O2Plib.db.CSD.CSDsizes

max # of sample condition lists

maxDensityFound - Variable in class O2Plib.db.CSD.CSDtotals

Max density found in accepted spot

maxDensityFound - Variable in class O2Plib.db.DbSample

Max density found in accepted spot

maxDensityIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

maxDensityPrimeFound - Variable in class O2Plib.db.CSD.CSDtotals

Max densityPrime found in accepted spot

maxDensityPrimeFound - Variable in class O2Plib.db.DbSample

Max densityPrime found in accepted spot

maxDiskCaches - Variable in class O2Plib.db.CSD.CSDcache

maximum number of CSD disk caches

maxDiskCachesSize - Variable in class O2Plib.db.CSD.CSDcache

maximum number of CSD disk caches

maxDmax - Variable in class O2Plib.db.CSD.CSDtotals

Maximum maxD of any spot in DB

maxEPlist - Variable in class O2Plib.db.CSD.CSDexprList

the maximum number of expression profiles in list if any.

maxFailcodes - Variable in class O2Plib.db.CSD.CSDsizes

max # PREFILTER failure codes

maxFields - Variable in class O2Plib.db.CSD.CSDacc

maximum # of MIAPE accession fields used to define the study string, Size of miapeStudyFields[] (optional).

maxFileSize - Variable in class O2Plib.db.CSD.CSDsizes

Maximum CSD DB cache file sizein # of Rspots

maxFspots - Variable in class O2Plib.db.CSD.CSDsizes

max # of Foreign Fspots lists in the CSD DB

maxGhist - Variable in class O2Plib.misc.CalibrateOD

Histogram statistics [for use in FUTURE]

maxGrayPixel - Variable in class O2Plib.db.DbSample

max Gray Pixel value in the image1 is (1<maxGrayPixel - Variable in class O2Plib.image.PixReader

maxGrayPixel pixel value in the image

maxGrayPixelA - Variable in class O2Plib.db.DbAccession

max gray value allowed

maxGrayValue - Variable in class O2Plib.misc.CalibrateOD

max gray value found in the image and it is <= 255

maxHorOld - Variable in class O2Plib.image.ScrollableImage

maxImageCols - Variable in class O2Plib.db.CSD.CSDsizes

max # of columns in an image

maxImageRows - Variable in class O2Plib.db.CSD.CSDsizes

max # of rows in an image

maxLMS - Variable in class O2Plib.db.CSD.CSDlms

the actual number of LMS used if any.

maxLms - Variable in class O2Plib.db.CSD.CSDsizes

max # LM sets can use

maxLMS - Variable in class O2Plib.db.LMset

maximum size of the landmarks read from the landmark DB

maxmaxcode - Variable in class O2Plib.image.WriteGifEncoder

maxMemCaches - Variable in class O2Plib.db.CSD.CSDcache

maximum number of CSD memory caches

maxMemCachesSize - Variable in class O2Plib.db.CSD.CSDcache

maximum number of CSD memory caches

maxMenuItems - Variable in class O2Plib.gui.MenuSupport

Initial max number of menu items allowed.

maxNbrAltLMs - Static variable in class O2Plib.db.DbSpot

Maximum # of alternate paired landmarks (N3).

maxNodesPerRspotSet - Variable in class O2Plib.db.CSD.CSDsizes

i.e.

maxNodesSaftyFactor - Variable in class O2Plib.db.CSD.CSDsizes

# of nodes to create per Rspot set estimate by multiplying by the # of samples

maxOCL - Variable in class O2Plib.db.CSD.CSDsizes

max # of OCL or Ordered Condition Lists

maxPeaks - Variable in class O2Plib.misc.CalibrateOD

eg.

maxPeaksA - Variable in class O2Plib.db.DbAccession

Number of wedge list gray values if not 0

maxRmapSize - Variable in class O2Plib.db.CSD.CSDRmap

The maximum # of spots in the preallocated map lists

maxRoi - Variable in class O2Plib.image.RoiList

max roi, max array size.

maxRSLs - Variable in class O2Plib.db.CSD.CSDsizes

max # of RspotList RSL sub sets lists

maxRspotBitSetFeatures - Variable in class O2Plib.db.CSD.CSDsizes

max # of Rspot bit-set features

maxRspots - Static variable in class O2Plib.db.CSD.CSDRspotList

Maximum total number of Rspots in the rspotList[0:maxRspots-1].

maxRspots - Variable in class O2Plib.db.CSD.CSDsizes

max # of Rspots lists in the CSD DB

maxSamples - Variable in class O2Plib.db.CSD.CSDacc

maximum # of samples in accession database (optional).

maxSamples - Variable in class O2Plib.db.CSD.CSDcond

maximum # of samples in allocated condition list.

maxSamples - Variable in class O2Plib.db.CSD.CSDexpr

maximum size of the preallocated arrays

maxSamples - Variable in class O2Plib.db.CSD.CSDsizes

max number of samples allowed

maxSpotPairs - Variable in class O2Plib.db.DbSample

size of spotPairList[]

maxSpots - Variable in class O2Plib.db.CSD.CSDRspot

Maximum number of spots in the Rspot set

MAXSPOTS - Static variable in class O2Plib.db.DbSample

Default maximum number of spots (i.e.) in initial spot list These are the number of CC's.

maxSpots - Variable in class O2Plib.db.DbSample

size of spotList

maxStatusTimes - Static variable in class O2Plib.misc.Util

max # of times to track with setReportStatus().

maxSubHeaders - Variable in class O2Plib.db.CSD.CSDio

# of CSD DB subheaders and it should be equal to MAXSUBHEADERS

maxVertOld - Variable in class O2Plib.image.ScrollableImage

maxX - Static variable in class O2Plib.db.DbBoundary

Minimum enclosing rectangle: RIGHT most x

maxY - Static variable in class O2Plib.db.DbBoundary

Minimum enclosing rectangle: BOTTOM most y

maxZoomMagVal - Variable in class O2Plib.image.DrawOverlays

MC_Cube - Class in O2Plib.image

MC_Cube() - Constructor for class O2Plib.image.MC_Cube

MC_Cube() - constructor

meanBackgroundIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

meanDensityIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

meanDP_SP_PP - Variable in class O2Plib.db.DbPairSamples

global spot statistics: mean dP for Rsample only

meanDPprime_SP_PP - Variable in class O2Plib.db.DbPairSamples

global spot statistics: adjusted mean meanDP_SP_PP for Rsample only

meanDprimeRatioMeanSpots - Variable in class O2Plib.db.CSD.CSDnorm

Median of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization

meanGhist - Variable in class O2Plib.misc.CalibrateOD

Histogram statistics [for use in FUTURE]

MedianCut - Class in O2Plib.image

MedianCut converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.

MedianCut(int[], int, int) - Constructor for class O2Plib.image.MedianCut

MedianCut() - Constructor Then call cvtImg24toImg8() to get the 8-bit image.

medianDprimeRatioMeanSpots - Variable in class O2Plib.db.CSD.CSDnorm

Median of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization

mediumFont - Variable in class O2Plib.gui.PopupTableEditDialog

memCacheFilePtr - Variable in class O2Plib.db.CSD.CSDcache

[0:nMemCaches-1] list of cache file pointers in CSD database

memCacheList - Variable in class O2Plib.db.CSD.CSDcache

[0:nMemCaches-1][0:memCacheSize-1(variable)] list of CSD memory caches

memCacheSize - Variable in class O2Plib.db.CSD.CSDcache

[0:nMemCaches-1] list of memory cache list sizes

memCacheTimeStamp - Variable in class O2Plib.db.CSD.CSDcache

[0:nMemCaches-1] list of memory cache time stamps

memCacheValid - Variable in class O2Plib.db.CSD.CSDcache

[0:nMemCaches-1] list of valid memory caches

memTimeStampCtr - Static variable in class O2Plib.db.CSD.CSDcache

memory cache time stamp for aging cache

menuItemCmdHT - Variable in class O2Plib.gui.MenuSupport

Hashtable of ALL menu items.

menuItemDataHT - Variable in class O2Plib.gui.MenuSupport

Hashtable of ALL menu items.

menuLabel - Variable in class O2Plib.gui.MenuSupport.ChkBoxMenuData

CheckboxMenuItem label

menuLabel - Variable in class O2Plib.gui.MenuSupport.MenuCmdData

Menu label

MenuSupport - Class in O2Plib.gui

Class MenuSupport contains various Menu support functions for helping implement and support dynamic submenus of MenuItem or CheckboxMenuItem types.

MenuSupport() - Constructor for class O2Plib.gui.MenuSupport

MenuSupport() - Constructor.

MenuSupport(String) - Constructor for class O2Plib.gui.MenuSupport

MenuSupport() - Constructor.

MenuSupport(String, int, int) - Constructor for class O2Plib.gui.MenuSupport

MenuSupport() - Constructor.

MenuSupport.ChkBoxMenuData - Class in O2Plib.gui

MenuSupport.ChkBoxMenuData(String, String, CheckboxMenuItem) - Constructor for class O2Plib.gui.MenuSupport.ChkBoxMenuData

ChkBoxMenuData() - create menu data instance

MenuSupport.MenuCmdData - Class in O2Plib.gui

MenuSupport.MenuCmdData(String, String, MenuItem) - Constructor for class O2Plib.gui.MenuSupport.MenuCmdData

MenuCmdData() - create menu data instance

mergeSwitches(String[], String[], String) - Static method in class O2Plib.misc.Switches

mergeSwitches() - merge switches where new switches overide old switches.

merx1 - Variable in class O2Plib.db.DbSpot

Spot minimum enclosing rectangle x1 in pixel coordinates

merX1Idx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

merx2 - Variable in class O2Plib.db.DbSpot

Spot minimum enclosing rectangle x2 in pixel coordinates

merX2Idx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

mery1 - Variable in class O2Plib.db.DbSpot

Spot minimum enclosing rectangle y1 in pixel coordinates

merY1Idx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

mery2 - Variable in class O2Plib.db.DbSpot

Spot minimum enclosing rectangle y2 in pixel coordinates

merY2Idx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

mi - Variable in class O2Plib.gui.MenuSupport.MenuCmdData

Menu item

miapeStudyData - Variable in class O2Plib.db.CSD.CSDacc

[0:nSamples-1][0:nMiapeFields-1] A short version of a samples's accession info is assembled from MIAPE/accession fields specified by miapeStudyFields[].

miapeStudyFields - Variable in class O2Plib.db.CSD.CSDacc

[0:nMiapeFields-1] list of names of MIAPE accession fields used to define the study string

MIN_ZOOM_MAG_VAL - Static variable in class O2Plib.image.DrawOverlays

MIN_ZOOM_MAG_VAL - Static variable in class O2Plib.image.ScrollableImage

min zoomMag value (zoom/dezoom) X magnification

minBestFitXYdistance - Variable in class O2Plib.db.CSD.CSDRspotList

Distance of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call.

minBestFitXYIdx - Variable in class O2Plib.db.CSD.CSDRspotList

Index in rspotsList[] of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call.

minBkgrdDensity - Variable in class O2Plib.db.CSD.CSDtotals

min background seen in any spot

minBkgrdDensity - Variable in class O2Plib.db.DbSample

min background seen in any spot

minBkgrdTot - Variable in class O2Plib.db.CSD.CSDtotals

Min sample background grayscale (computed elsewhere)

minBkgrdTot - Variable in class O2Plib.db.DbSample

Min sample background grayscale (computed elsewhere)

minDensityIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

minDmax - Variable in class O2Plib.db.CSD.CSDtotals

Minimum maxD of any spot in DB

minEffectiveRadius - Variable in class O2Plib.db.LMset

Min effective radius distance between closest landmarks [0:nbrLandmarks-1][RSAMPLE:SAMPLE] is the min of the half radius of the two samples for that landmark.

minGhist - Variable in class O2Plib.misc.CalibrateOD

Histogram statistics [for use in FUTURE]

minGrayPixel - Variable in class O2Plib.image.PixReader

minGrayPixel pixel value in the image

minNbrLMSspots - Variable in class O2Plib.db.DbPairSamples

Math.min(nbrRsampleSpotsInLMS,nbrSampleSpotsInLMS);

minRspotCacheBlocks - Variable in class O2Plib.db.CSD.CSDsizes

Rspot cache file i.e.

minX - Static variable in class O2Plib.db.DbBoundary

Minimum enclosing rectangle: LEFT most x

minX - Variable in class O2Plib.image.TiffPixelLoader

X upper left hand corner of image origin

minY - Static variable in class O2Plib.db.DbBoundary

Minimum enclosing rectangle: TOP most y

minY - Variable in class O2Plib.image.TiffPixelLoader

Y upper left hand corner of image origin

minZoomMagVal - Variable in class O2Plib.image.DrawOverlays

mnAreaLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] mean area limits

mnBackground - Variable in class O2Plib.db.DbSpot

spot mean background density in calibrated OD if available.

mnBkgrdGrayvalue - Variable in class O2Plib.db.DbSpot

spot mean background grayvalue

mnCarea - Variable in class O2Plib.db.CSD.CSDRspot

Mean area for Rspots being analyzed for condition subsets.

mnCdPrime - Variable in class O2Plib.db.CSD.CSDRspot

Mean D' for entire Rspot set for condition subsets.

mnCnormDensity - Variable in class O2Plib.db.CSD.CSDRspot

mean normalized density for Rspots being analyzed for condition subsets.

mnCVdensity - Variable in class O2Plib.db.CSD.CSDRspot

Mean Coef.

mnDensity - Variable in class O2Plib.db.DbSpot

mean spot density

mnDensLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] mean density limits

mnXcentroid - Variable in class O2Plib.db.CSD.CSDRspot

Mean Xabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.

mnYcentroid - Variable in class O2Plib.db.CSD.CSDRspot

Mean Yabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.

modeDensity - Variable in class O2Plib.db.CSD.CSDnorm

[TODO-REFACTOR] Density mode String 'A P R L C'

mouseClicked(MouseEvent) - Method in class O2Plib.gui.PopupOptions

mouseClicked(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseClicked() - Pass this event to the parent class.

mouseClicked(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseClicked() - Pass this event to the parent class.

mouseDragged(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseDragged() - display data

mouseDragged(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseDragged() - Pass this event to the parent class.

mouseEntered(MouseEvent) - Method in class O2Plib.gui.PopupOptions

mouseEntered(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseEntered() - Pass this event to the parent class.

mouseEntered(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseEntered() - Pass this event to the parent class.

mouseExited(MouseEvent) - Method in class O2Plib.gui.PopupOptions

mouseExited(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseExited() - Pass this envent to the parent class.

mouseExited(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseExited() - Pass this envent to the parent class.

mouseMoved(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseMoved() - Pass this event to the parent class.

mouseMoved(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseMoved() - Pass this event to the parent class.

mousePressed(MouseEvent) - Method in class O2Plib.gui.PopupOptions

mousePressed() - display data

mousePressed(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mousePressed() - display data

mousePressed(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mousePressed() - display data

mouseReleased(MouseEvent) - Method in class O2Plib.gui.PopupOptions

mouseReleased(MouseEvent) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

mouseReleased() - display data

mouseReleased(MouseEvent) - Method in class O2Plib.image.ScrollableImage

mouseReleased() - Pass this event to the parent class.

mrl - Static variable in class O2Plib.db.CSD.CSDglb

Master database list of all Rspots sets.

msg - Variable in class O2Plib.gui.PopupTextFieldDialog

Message to display

msg - Variable in class O2Plib.gui.PopupYesNoDialogBox

Message for dialog box

MSG_COLS - Static variable in class O2Plib.gui.PopupTableEditDialog

MSG_ROWS - Static variable in class O2Plib.gui.PopupTableEditDialog

size of the text area in characters

msgTextArea - Variable in class O2Plib.gui.PopupTableEditDialog

Text area GUI for message rporting

mwLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] mw (y) region limits

mzLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] mz (2D LC-MS) (y) region limits

N

n_bits - Variable in class O2Plib.image.WriteGifEncoder

name - Variable in class O2Plib.db.CSD.CSDcond

Name of the condition

name - Variable in class O2Plib.db.CSD.CSDexprList

Name of expression profile list

name - Variable in class O2Plib.db.CSD.CSDfilterState

Name of the data-mining filter state

name - Variable in class O2Plib.db.CSD.CSDnorm

Name of the normalization

name - Variable in class O2Plib.db.CSD.CSDRmap

Name of the condition

name - Variable in class O2Plib.db.CSD.CSDRspotList

Name of the list of Rspots

name - Variable in class O2Plib.gui.MenuSupport

Name of this MenuSupport instance

name - Variable in class O2Plib.image.PpxLoader

name of the picture - was [16]

name - Variable in class O2Plib.table.SimpleTable

Optional table name associated with table

nameListCB - Variable in class O2Plib.gui.PopupNameListSelectorDialog

[0:nNames-1] checkboxes

names - Variable in class O2Plib.gui.PopupNameListSelectorDialog

list of all names to select from

namespaceMappings - Variable in class O2Plib.db.DbAccession.AccContentHandler

Store URI to prefix mappings

namespaceMappings - Variable in class O2Plib.db.DbLM.LmsContentHandler

Store URI to prefix mappings

namespaceMappings - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Store URI to prefix mappings

namespaceMappings - Variable in class O2Plib.db.DbSample.SsfContentHandler

Store URI to prefix mappings

nbands - Variable in class O2Plib.image.PpxLoader

# of scanning bands (colors)

nBands - Variable in class O2Plib.image.TiffPixelLoader

# of samples/pixel

nBitsPerPixel - Variable in class O2Plib.db.DbSample

# of bits/pixel in the image1

nBitsPerPixel - Variable in class O2Plib.image.PixReader

# of bits/pixel in the image

nBitsPerPixel - Variable in class O2Plib.image.TiffPixelLoader

# bits/pixel is sampleModel.sampleSize[0]

nbr - Variable in class O2Plib.db.CSD.CSDannotation

Annotation ID number

NBR_INVOKE_PARAMS - Static variable in class O2Plib.image.ScrollableImage

number of parameters used to invoke for remote painting

nbrAltLMs - Variable in class O2Plib.db.DbSpot

The # of alternate paired landmarks for this spot.

nbrERspots - Static variable in class O2Plib.db.CSD.CSDRspotList

Number of ERspots in the send part of the rspotList[nbrERspots:totRspots-1].

nbrLandmarks - Variable in class O2Plib.db.LMset

actual size of the landmarks read from the landmark DB

nbrLblAP - Variable in class O2Plib.db.CSD.CSDtotals

# AP labeled spots in DB (from all samples)

nbrLblCP - Variable in class O2Plib.db.CSD.CSDtotals

# CP labeled spots in DB (from All samples)

nbrLblEP - Variable in class O2Plib.db.CSD.CSDtotals

# EP labeled spots in DB (from All samples)

nbrLblGP - Variable in class O2Plib.db.CSD.CSDtotals

# GS labeled spots in DB (from All samples)

nbrLblPP - Variable in class O2Plib.db.CSD.CSDtotals

# PP labeled spots in DB (from all samples)

nbrLblSP - Variable in class O2Plib.db.CSD.CSDtotals

# SP labeled spots in DB (from all samples)

nbrLblUS - Variable in class O2Plib.db.CSD.CSDtotals

# US labeled spots in DB (from all samples)

nbrRsampleSpotsInLMS - Variable in class O2Plib.db.DbPairSamples

total # spots we hold in the LM sets for Rsample

nbrRsampleSpotsInLMSPairedSPorPP - Variable in class O2Plib.db.DbPairSamples

# spots paired with the Rsample SP or PP label

nbrRspots - Static variable in class O2Plib.db.CSD.CSDRspotList

Number of non-EP Rspots in the first part of the [0:nbrRspots-1].

nbrRspotSets - Variable in class O2Plib.db.CSD.CSDio

# of R-spot sets (ie==> max file size)

nbrSampleSpotsInLMS - Variable in class O2Plib.db.DbPairSamples

total # spots we hold in the LM sets for Sample

nbrTimesInitialized - Static variable in class O2Plib.db.CSD.CSDglb

Count # times initialized

nbrWedgePeaks - Variable in class O2Plib.misc.CalibrateOD

Number of peaks in the calibration step wedge if it is not 0.

nBytesPerPixel - Variable in class O2Plib.db.DbSample

# of bytes/pixel in the image1

nBytesPerPixel - Variable in class O2Plib.image.PixReader

# of bytes/pixel in the image

nCCread - Variable in class O2Plib.db.DbSample

# spots actually read from the SSF data file

nChoices - Variable in class O2Plib.gui.PopupOptions

# of choices

nCols - Variable in class O2Plib.image.PixReader

# of columns in the image

ncols - Variable in class O2Plib.image.PpxLoader

(unsigned short) full image size # columns in pixels

nCols - Variable in class O2Plib.image.TiffPixelLoader

# of columns in the image

nCondListDB - Static variable in class O2Plib.db.CSD.CSDglb

size of condList

nCsample - Variable in class O2Plib.db.CSD.CSDRspot

# of samples in the Condition subset of the Rspot set.

nCsample - Variable in class O2Plib.db.DbSpot

# of samples in Cspot Csample' estimate if not 0.

ncubes - Variable in class O2Plib.image.MedianCut

# of color cubes

nData - Variable in class O2Plib.gui.PopupOptions

# of data items

nData - Variable in class O2Plib.gui.PopupTableEditDialog

# of name-value pair data items

nDataFiltersDB - Static variable in class O2Plib.db.CSD.CSDglb

size of dataFilterList

nDirDBPrompt - Variable in class O2Plib.gui.PopupOptions

# of active dirDBPrompt[] prompts

nDiskCaches - Variable in class O2Plib.db.CSD.CSDcache

number of CSD disk caches

nearestLM - Variable in class O2Plib.db.LMset

LM nearest to this one [0:nbrLandmarks-1][RSAMPLE:SAMPLE]

needToSaveCSDdataFlag - Static variable in class O2Plib.db.CSD.CSDglb

Flag indicates need to save the CSD DB data

nEntries - Variable in class O2Plib.misc.ParamHash

# of hash table entries after call readNameValuesHashTableFromFile()

nEPlist - Variable in class O2Plib.db.CSD.CSDexprList

the actual number of expression profiles in list if any.

NEVER - Static variable in class O2Plib.db.CSD.CSDglb

NEVER and CONSOLE_FLAG - debugging variables - must not be final!

NEVER - Static variable in class O2Plib.image.PixReader

Debugging

NEVER - Variable in class O2Plib.image.ScrollableImage

NEVER and CONSOLE_FLAG - debugging variables - must not be final!

NEVER - Static variable in class O2Plib.misc.Util

NEVER and CONSOLE_FLAG - debugging variables - must not be final!

nexcpt - Variable in class O2Plib.image.PpxLoader

(unsigned int) number of exception entries

nExprListsDB - Static variable in class O2Plib.db.CSD.CSDglb

The size of exprListsDB[] expression profile lists.

nextID - Static variable in class O2Plib.image.MC_Cube

nextLMspot - Variable in class O2Plib.db.DbBaseSpot

ptr to Next LM-set spot if not null

nextLMspot - Variable in class O2Plib.db.DbSpot

ptr to Next LM-set spot if not null

nextNearestLM - Variable in class O2Plib.db.LMset

NEXT nearest LM [0:nbrLandmarks-1][RSAMPLE:SAMPLE]

nextPrime(int) - Static method in class O2Plib.misc.Util

nextPrime() - find the next prime # >= n.

nextRspot - Variable in class O2Plib.db.CSD.CSDRspot

Next instance for list of Rspots linked list

nextSpot - Variable in class O2Plib.db.DbBaseSpot

ptr to Next spot instance in spot list if not null

nextSpot - Variable in class O2Plib.db.DbSpot

ptr to Next spot instance in spot list if not null

nFileDBPrompt - Variable in class O2Plib.gui.PopupOptions

# of active fileDBindex[] prompts

nLMsetsList - Variable in class O2Plib.db.CSD.CSDlms

Size of list of LMsets

nMemCaches - Variable in class O2Plib.db.CSD.CSDcache

number of CSD memory caches

nMiapeFields - Variable in class O2Plib.db.CSD.CSDacc

# of MIAPE accession fields used to define the study string, Size of miapeStudyFields[].

nNames - Variable in class O2Plib.gui.PopupNameListSelectorDialog

# of all names

nOclDB - Static variable in class O2Plib.db.CSD.CSDglb

the number of Ordered condition lists

nodeSaftyFactor - Static variable in class O2Plib.db.CSD.CSDglb

default to MAX_NODE_SAFTY_FACTOR - free space in the spot node

noMsg - Variable in class O2Plib.gui.PopupYesNoDialogBox

No label for dialog box

nOptions - Variable in class O2Plib.gui.PopupDialogQuery

optionValues[0:nOptions]

norm - Variable in class O2Plib.db.CSD.CSDfilterState

current density normalization mode

norm - Variable in class O2Plib.db.CSD.CSDRspot

Rspot set normalization method

NORM_LOESS - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by LOESS

NORM_LSQ - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by linear least square fit

NORM_NONE - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization - none.

NORM_OTHER - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by an other (possible plugin) method

NORM_PCT_TOT_DENS - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by percent of total density'

NORM_RATO_MEANS - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by ratio means

NORM_RATO_MEDIANS - Static variable in class O2Plib.db.CSD.CSDnorm

Normalization by ratio means

normalizeData(CSDRspot, float, int) - Method in class O2Plib.db.CSD.CSDnorm

normalizeData() - normalize data by this normalization.

normalizeData(float, int) - Method in class O2Plib.db.CSD.CSDnorm

normalizeData() - normalize data by this normalization.

normHash - Static variable in class O2Plib.db.CSD.CSDnorm

hashTable for normalization lookup

normListDB - Static variable in class O2Plib.db.CSD.CSDglb

[0:nSamplesDB-1] lists of sample normalizations for CSD database

normLSQspotNbrs - Variable in class O2Plib.db.CSD.CSDnorm

[0:nSpotsLsq-1] Ratio-mean spot #'s of spots in ratioMeans for normalization.

normLSQspots - Variable in class O2Plib.db.CSD.CSDnorm

[0:nSpotsLsq-1] list of spots used in least-square fit norm.

normMethod - Variable in class O2Plib.db.CSD.CSDexpr

Normalization method used to compute the expValues[]

normMode - Variable in class O2Plib.db.CSD.CSDexpr

Normalization method which is CSDnorm.NORM_PCT_xxxx

nPairCCread - Variable in class O2Plib.db.DbSample

# spots actually read from the SSF data file

nPixels - Variable in class O2Plib.db.DbSample

total # of pixels in image1 = pixWidth*pixHeight

nPixels - Variable in class O2Plib.image.PixReader

# of columns X # rows in the image

nPixels - Variable in class O2Plib.image.PpxLoader

# of pixels for the image is (nrows*ncols)

nPixels - Variable in class O2Plib.image.TiffPixelLoader

# of pixels/image (is nRows*nCols)

nRatioMeanSpots - Variable in class O2Plib.db.CSD.CSDnorm

#'s of spots in ratioMean normalization.

nRmapsDB - Static variable in class O2Plib.db.CSD.CSDglb

Database number of Rmap entries in the rMapList[0:nRmaps-1].

nRmapSize - Variable in class O2Plib.db.CSD.CSDRmap

The # of spots in the map

nRoi - Variable in class O2Plib.image.RoiList

current number of ROIs in the roiList[]

nRows - Variable in class O2Plib.image.PixReader

# of rows in the image

nrows - Variable in class O2Plib.image.PpxLoader

(unsigned short) full image size # rows in pixels

nRows - Variable in class O2Plib.image.TiffPixelLoader

# of rows in the image

nRspotListsDB - Static variable in class O2Plib.db.CSD.CSDglb

size of rspotListsDB

nSample - Variable in class O2Plib.db.DbBaseSpot

Sample# (RSAMPLE or SAMPLE) to identify type of sample

nSampleLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] # samples/class

nSamples - Variable in class O2Plib.db.CSD.CSDacc

# samples

nSamples - Variable in class O2Plib.db.CSD.CSDcond

# of samples in condition.

nSamples - Variable in class O2Plib.db.CSD.CSDexpr

size of the dbSamples

nSamples - Variable in class O2Plib.db.CSD.CSDexprList

# of samples in condition.

nSamplesDB - Static variable in class O2Plib.db.CSD.CSDglb

size of the dbSampleList

nSelectedNames - Variable in class O2Plib.gui.PopupNameListSelectorDialog

# of all samples

nSliders - Variable in class O2Plib.gui.PopupOptions

# of slider Scrollbar

nSPFfilesUsedDB - Static variable in class O2Plib.db.CSD.CSDglb

# of SPF files actual PSL used to create DB

nSPFlistsDB - Static variable in class O2Plib.db.CSD.CSDglb

size of the dbSPFlist

nSpots - Variable in class O2Plib.db.CSD.CSDRspot

Number of spots in the Rspot set

nSpotsAborted - Variable in class O2Plib.db.CSD.CSDtotals

# of spots aborted during assembly.

nSpotsAborted - Variable in class O2Plib.db.DbSample

# of spots aborted during assembly.

nSpotsLsq - Variable in class O2Plib.db.CSD.CSDnorm

Number of spots used in computing Least Square normalization terms

nStateEntries - Variable in class O2Plib.misc.ParamHash

# of hash table entries

nStatusName - Static variable in class O2Plib.misc.Util

# of Report status names saved when do setReportStatus(name) calls.

nSwitches - Static variable in class O2Plib.misc.Switches

the number of Command line switches

nth - Static variable in class O2Plib.image.DrawPix

picture file iteration #

nth - Static variable in class O2Plib.image.PixReader

dump sequantially named pictures using numbered image files

nTopSpot - Variable in class O2Plib.db.DbSample

number of spots current spotList[] that were defined.

nTopSpotPair - Variable in class O2Plib.db.DbSample

number of spot pairs current spotPairList[] that were defined.

numDataElements - Variable in class O2Plib.image.TiffPixelLoader

# raster DataBuffer data elements/pixel

numPages - Variable in class O2Plib.image.TiffPixelLoader

# of TIFF pages

numPixels - Variable in class O2Plib.image.WriteGifEncoder

nUniquePairs - Variable in class O2Plib.db.DbLM

Size of list of all pairs of samples in the landmark DB samplePairList[RSAMPLE:SAMPLE][0:nUniquePairs-1]

nUniqueSamplesInLmsDBlist - Variable in class O2Plib.db.DbLM

Size of list of all pairs of samples in the landmark DB sampleInLmsDBlist[0:nUniqueSamplesInLmsDBlist-1]

nWedgeSteps - Variable in class O2Plib.image.PpxLoader

will contain WEDGE_PPX to be set by user

nx - Variable in class O2Plib.image.PpxLoader

(unsigned short) X size of region of interest

nXRspots - Variable in class O2Plib.db.CSD.CSDcal

# of pIe or RT X calib spots

ny - Variable in class O2Plib.image.PpxLoader

(unsigned short) Y size of region of interest

nYRspots - Variable in class O2Plib.db.CSD.CSDcal

# of MW or mhz Y calib spots

O

O2Plib.db - package O2Plib.db

O2Plib.db.CSD - package O2Plib.db.CSD

O2Plib.db.xml - package O2Plib.db.xml

O2Plib.gui - package O2Plib.gui

O2Plib.image - package O2Plib.image

O2Plib.io - package O2Plib.io

O2Plib.misc - package O2Plib.misc

O2Plib.table - package O2Plib.table

O2PLIB_VERSION - Static variable in class O2Plib.misc.Util

O2Plib version number

objInstance - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

objParams - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

oclListDB - Static variable in class O2Plib.db.CSD.CSDglb

Database meta-list of ordered lists of sample conditions each of which contains lists of samples.

oclNameDB - Static variable in class O2Plib.db.CSD.CSDglb

[0:nOclDB-1] is list of names of ordered lists of sample conditions

odmn - Variable in class O2Plib.image.PpxLoader

Min Pixel value.

odmx - Variable in class O2Plib.image.PpxLoader

Max Pixel value.

off_timer() - Static method in class O2Plib.misc.Util

off_timer() - Compute the time banner String using the previously set startTime.

off_timer(long) - Static method in class O2Plib.misc.Util

off_timer() - Compute the time banner String assuming that a on_timer(cpuTime,runTime) was done previously.

offScreenImg - Variable in class O2Plib.image.ScrollableImage

image for double buffer TODO: should be able to draw offscreen

ok - Variable in class O2Plib.image.WriteGifEncoder

80% occupancy

okFlag - Variable in class O2Plib.gui.PopupTextFieldDialog

Returned true if pressed DONE

okFlag - Variable in class O2Plib.gui.PopupYesNoDialogBox

flag set by the yes button (no or cancel button set to false)

oldScrollerHeight - Variable in class O2Plib.image.ScrollableImage

for calc Scroller Positions height

oldScrollerWidth - Variable in class O2Plib.image.ScrollableImage

for calc Scroller Positions width

omittedArea - Variable in class O2Plib.db.CSD.CSDtotals

omittedArea - Variable in class O2Plib.db.DbSample

omittedDensity - Variable in class O2Plib.db.CSD.CSDtotals

Data statistics read from the SSF files.

omittedDensity - Variable in class O2Plib.db.DbSample

Data statistics read from the SSF files.

omittedNumberSpots - Variable in class O2Plib.db.CSD.CSDtotals

omittedNumberSpots - Variable in class O2Plib.db.DbSample

on_timer() - Static method in class O2Plib.misc.Util

on_timer() - Get the current time (in milliseconds)

openBinCSD(String, String, boolean) - Method in class O2Plib.db.CSD.CSDio

openBinCSD() - open a new CSD file.

openCSDdbFile() - Method in class O2Plib.db.CSD.CSD

openCSDdbFile() - Open the CSD RDBMS, XML or cache file Don't open if it is already opened.

openReadFile(String, String) - Static method in class O2Plib.io.FileIO

openReadFile() - Try to open an input File for reading.

optionChoice - Variable in class O2Plib.gui.PopupDialogQuery

opt.

optionPanel - Variable in class O2Plib.gui.PopupDialogQuery

for options

optionValues - Variable in class O2Plib.gui.PopupDialogQuery

list of option values if present

orientation - Variable in class O2Plib.image.ScrollableImage.Rule

vertical or horizontal orientation takes values HORIZONTAL or VERTICAL

origImg - Variable in class O2Plib.image.ScrollableImage

original image

origPixHeight - Variable in class O2Plib.image.ScrollableImage

original pixel height

origPixWidth - Variable in class O2Plib.image.ScrollableImage

pixel width

osName - Static variable in class O2Plib.misc.Util

name of this operating system: Property("os.name")

otherNormMethod - Variable in class O2Plib.db.CSD.CSDnorm

out_it(String, FileWriter) - Static method in class O2Plib.io.FileIO

out_it() - Output a String to the output channel 'oChan'.

output(int, FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

output() - Output the given code.

P

p - Variable in class O2Plib.db.DbSample.SsfContentHandler

instance of current DbSpot

paint(Graphics) - Method in class O2Plib.gui.PopupTableEditDialog

paint() - repaint scrollable canvas in region defined by scroll bars

paintComponent(Graphics) - Method in class O2Plib.image.ScrollableImage.Corner

paintComponent(Graphics) - Method in class O2Plib.image.ScrollableImage.ImageCanvas

paintComponent() -

paintComponent(Graphics) - Method in class O2Plib.image.ScrollableImage

paintComponent() - paint

paintComponent(Graphics) - Method in class O2Plib.image.ScrollableImage.Rule

paintComponent() - Swing paint method

paintCtr - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

for debugging

PAIRBIT_AP - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair AP

PAIRBIT_AP - Static variable in class O2Plib.db.DbLM

Pairing Bit: Ambiguous Pair - pairing program generated label

PAIRBIT_CP - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair CP

PAIRBIT_CP - Static variable in class O2Plib.db.DbLM

PAIRBIT_EP - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair EP

PAIRBIT_EP - Static variable in class O2Plib.db.DbLM

Pairing Bit: Extrapolated Pair - by CSD database program

PAIRBIT_GS - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair GS

PAIRBIT_GS - Static variable in class O2Plib.db.DbLM

Pairing Bit:Garbage Spot - generated by CSD database or editing programs.

PAIRBIT_LM - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair LM

PAIRBIT_LM - Static variable in class O2Plib.db.DbLM

Pairing Bit: LandMark spot [could be virtual LM] - by CSD program

PAIRBIT_PP - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair PP

PAIRBIT_PP - Static variable in class O2Plib.db.DbLM

Pairing Bit: Possible Pair - pairing program generated label

PAIRBIT_SP - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair SP

PAIRBIT_SP - Static variable in class O2Plib.db.DbLM

Pairing Bit: Sure Pair - pairing program generated label

PAIRBIT_US - Static variable in class O2Plib.db.CSD.CSDfilterState

Pairing-bit Sure-Pair US

PAIRBIT_US - Static variable in class O2Plib.db.DbLM

Pairing Bit: Unresolved Spot - pairing program generated label

pairingBits - Variable in class O2Plib.db.CSD.CSDfilterState

spot pair label bits: from DbLM.PAIRBIT_xx where xx is US, SP, PP, AP, EP, CP, GS, LM.

pairingParamsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(1) when the begining of the list of is found

pairingStats - Variable in class O2Plib.db.DbPairSamples

Complete pairing statistics multiline string

PARAM_DEF_NBR_ALT_LMS - Static variable in class O2Plib.db.LMset

Default # of alternate landmarks to try for secondary pairing

PARAM_MAX_ALT_LMS - Static variable in class O2Plib.db.LMset

Default max # of alternate landmarks to try for secondary pairing

PARAM_MAXLANDMARKS - Static variable in class O2Plib.db.LMset

Default maximum number of landmarks i.e LM set A:Z or A:Za:z

ParamHash - Class in O2Plib.misc

ParamHash() - Constructor for class O2Plib.misc.ParamHash

ParamHash() - Constructor

parentObj - Variable in class O2Plib.image.ScrollableImage

pass parent instance down

parsedBugBitsFile(String) - Static method in class O2Plib.misc.Switches

parsedBugBitsFile() - parse the debug bits values from the parsed Open2Dprot.dbug file.

parsedBugBitsHelpStr(String) - Static method in class O2Plib.misc.Switches

parsedBugBitsHelpStr() - parse the debug bits values from the parsed debug bits help string.

pctOmittedToDprimeAcceptedSpots - Variable in class O2Plib.db.DbSample

Pct omitToAccepted/densityPrime_spots failing_t1Density_resizing computed as: (100.0*omittedDensity/totSampleDensityPrime).

pi - Variable in class O2Plib.image.TiffPixelLoader

List of PixelAccessors from the RenderedImages'

pieLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] pIe (x) region limits

PipeLineDefault - Interface in O2Plib.db.xml

PipeLineDefault Place holder if pipeline can not be loaded

pix - Variable in class O2Plib.db.DbSample

sample source sample image

pix - Variable in class O2Plib.image.PixReader.PixObserver

Global instances

PIXEL_RULERS - Variable in class O2Plib.image.ScrollableImage

FUTURE: To display rulers with pixel size in JScrollPane

pixel_x_coordIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

pixel_y_coordIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

pixelIndex - Variable in class O2Plib.image.WriteGifEncoder

pixelResolutionMicrons - Variable in class O2Plib.db.CSD.CSDcal

Resolution of scan data.

pixels - Variable in class O2Plib.image.PpxLoader

pixels [0:nPixels-1] for the image

pixels - Variable in class O2Plib.image.TiffPixelLoader

image of size nRows of nCols pixels.

pixels - Variable in class O2Plib.image.WriteGifEncoder

pixels32 - Variable in class O2Plib.image.MedianCut

32-bit image[width*height] (Alpha,Red,Green,Blue) pixels

pixels8 - Variable in class O2Plib.image.MedianCut

8-bit image[width*height] using LUTs

pixelSizeMicrons - Variable in class O2Plib.db.DbSample

Pixel resolution in the sample image in microns/pixel

PixFunctions - Class in O2Plib.image

PixFunctions() - Constructor for class O2Plib.image.PixFunctions

PixFunctions() - constructor

pixHeight - Variable in class O2Plib.db.DbSample

Sample image size height from SSF file

pixHeightA - Variable in class O2Plib.db.DbAccession

Input sample image size: height

PixHeightIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

PixReader - Class in O2Plib.image

PixReader() - Constructor for class O2Plib.image.PixReader

PixReader() - Constructor to use when reading an image file

PixReader(int[]) - Constructor for class O2Plib.image.PixReader

PixReader() - Constructor to use when converting an int[] pix to a char[] pixel array using getCharPix().

PixReader(String) - Constructor for class O2Plib.image.PixReader

PixReader() - init the state of the image reader

PixReader.PixObserver - Class in O2Plib.image

PixObserver implements our own (rather than default) image observer

PixReader.PixObserver(PixReader) - Constructor for class O2Plib.image.PixReader.PixObserver

PixObserver() - Constructor

pixRsampleIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

pixRsampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

pixSampleIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

pixSampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

pixWidth - Variable in class O2Plib.db.DbSample

Sample image size width from SSF file

pixWidthA - Variable in class O2Plib.db.DbAccession

Input sample image size: width

PixWidthIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

PixWriter - Class in O2Plib.image

PixWriter() - Constructor for class O2Plib.image.PixWriter

PixWriter() - Constructor to use when reading an image file

pixXsize - Variable in class O2Plib.db.CSD.CSDcal

max # columns in CSD virtual database

pixYsize - Variable in class O2Plib.db.CSD.CSDcal

max # rows in CSD virtual database

popupAlertMsg(String, Color) - Static method in class O2Plib.misc.Util

popupAlertMsg() - display msg in status and popup up an Alert message

PopupDialogQuery - Class in O2Plib.gui

PopupDialogQuery(Frame, int) - Constructor for class O2Plib.gui.PopupDialogQuery

PopupDialogQuery() - Constructor

popupDirectoryDialog(String, String, boolean) - Method in class O2Plib.gui.PopupFileDialog

popupDirectoryDialog() - popup directory dialog and get directory name.

PopupFileDialog - Class in O2Plib.gui

PopupFileDialog() - Constructor for class O2Plib.gui.PopupFileDialog

PopupFileDialog() - constructor

popupFileDialog(String, String, boolean) - Method in class O2Plib.gui.PopupFileDialog

popupFileDialog() - popup file dialog and get file name.

PopupHTMLbrowser - Class in O2Plib.gui

Class PopupHTMLbrowser is the popup a web browser on the specified URL string.

PopupHTMLbrowser(String, String) - Constructor for class O2Plib.gui.PopupHTMLbrowser

PopupHTMLbrowser() - constructor

popupHTMLbrowser(String, String) - Method in class O2Plib.gui.PopupHTMLbrowser

popupHTMLbrowser() - Display URL file in system Web browser.

PopupNameListSelectorDialog - Class in O2Plib.gui

Class PopupNameListSelectorDialog is a popup window to select a list of names.

PopupNameListSelectorDialog(Frame, String, String, String[], String[], boolean, boolean, boolean) - Constructor for class O2Plib.gui.PopupNameListSelectorDialog

PopupNameListSelectorDialog() - popup selector for a subset list of names.

PopupOptions - Class in O2Plib.gui

Class PopupOptions creates and displays a popup window of pairs of (-options, data) and scrollbars for assigning command line switches and threshold parameters for some of the switches.

PopupOptions(String[], boolean[], String[], String, String) - Constructor for class O2Plib.gui.PopupOptions

PopupOptions() - constructor for popup options selector

PopupTableEditDialog - Class in O2Plib.gui

Class PopupTableEditDialog implements a popup GUI to create and edit the sample annotation used in the accessioning program.

PopupTableEditDialog(Frame, String, Table, String, String, int, boolean, boolean) - Constructor for class O2Plib.gui.PopupTableEditDialog

PopupTableEditDialog() - Constructor

popupTextField() - Method in class O2Plib.gui.PopupTextFieldDialog

popupTextField() - popup text field

PopupTextFieldDialog - Class in O2Plib.gui

Class PopupTextFieldDialog provides a popup text field with a Done and Cancel buttons.

PopupTextFieldDialog(Frame, String, String) - Constructor for class O2Plib.gui.PopupTextFieldDialog

PopupTextFieldDialog () - constructor

PopupYesNoDialogBox - Class in O2Plib.gui

Class PopupYesNoDialogBox is a dialog box with with 1, 2 or 3 yesMsg, noMsg, and cancelMsg.

PopupYesNoDialogBox(Frame, String, String, String, String, Color) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup YES/NO/CANCEL modal dialog.

PopupYesNoDialogBox(Frame, String, String, String, String) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup YES/NO/CANCEL modal dialog.

PopupYesNoDialogBox(Frame, String, String, String, Color) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup YES/NO modal dialog.

PopupYesNoDialogBox(Frame, String, String, String) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup YES/NO modal dialog.

PopupYesNoDialogBox(Frame, String, String, Color) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup OK modal dialog.

PopupYesNoDialogBox(Frame, String, String) - Constructor for class O2Plib.gui.PopupYesNoDialogBox

PopupYesNoDialogBox() - Constructor for popup OK modal dialog.

positionImageWindow() - Method in class O2Plib.gui.PopupTableEditDialog

positionImageWindow() - position image window on the screen

positionWindow() - Method in class O2Plib.gui.PopupYesNoDialogBox

positionWindow() - position window on the screen

PP - Static variable in class O2Plib.db.CSD.CSDglb

Possible Pair - pairing program generated label

PP - Static variable in class O2Plib.db.DbBaseSpot

Possible Pair - pairing program generated label

PP - Static variable in class O2Plib.db.DbLM

Possible Pair - pairing program generated label

PP - Static variable in class O2Plib.db.DbPairSamples

Possible Pair - pairing program generated label

PPCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Possible Pair spot label

PPX_VRSION - Static variable in class O2Plib.image.PpxLoader

Code version 3.5 as 35

ppxDir - Static variable in class O2Plib.db.CSD.CSDglb

Original sample images directory {projDir}/ppx/

ppxDir - Variable in class O2Plib.io.FileIO

Original sample images directory {projDir}/ppx/

ppxDirA - Variable in class O2Plib.db.DbAccession

Directory where input images are kept

ppxFileName - Variable in class O2Plib.image.PpxLoader

full path of PPX input file

PpxLoader - Class in O2Plib.image

PpxLoader() - Constructor for class O2Plib.image.PpxLoader

PpxLoader() - constuctor()

PpxLoader(byte[]) - Constructor for class O2Plib.image.PpxLoader

PpxLoader() - constuctor to parse the PPX header and set up the state

preferedSize - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

preferred size of canvas

preferedSize - Variable in class O2Plib.image.ScrollableImage

preferred size of canvas

preferredHeight - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

preferred size of canvas

preferredHeight - Variable in class O2Plib.image.ScrollableImage

preferred size of canvas

preferredWidth - Variable in class O2Plib.image.ScrollableImage.ImageCanvas

preferred size of canvas

preferredWidth - Variable in class O2Plib.image.ScrollableImage

preferred size of canvas

prettyPrintDateStr(String) - Static method in class O2Plib.misc.Util

prettyPrintDateStr() - pretty-print date string.

previousTag - Variable in class O2Plib.db.DbAccession.AccContentHandler

previous tag found - for debugging

previousTag - Variable in class O2Plib.db.DbLM.LmsContentHandler

previous tag found - for debugging

previousTag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

previous non-group state end-tag 'xxxx' by found.

previousTag - Variable in class O2Plib.db.DbSample.SsfContentHandler

previous tag found

prevLMnbr - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

previous end-tag found

prevSpot - Variable in class O2Plib.db.DbBaseSpot

ptr to Previous spot instance in spot list if not null

prevSpot - Variable in class O2Plib.db.DbSpot

ptr to Previous spot instance in spot list if not null

primary_SP_PP_pairRate - Variable in class O2Plib.db.DbPairSamples

Percentage: (50.0F*(hSP1+hPP1))/minNbrLMSspots Where minNbrLMSspots= min(nbrRsampleSpotsInLMS,nbrSampleSpotsInLMS)

printCurrentMemoryUsage(String) - Static method in class O2Plib.misc.Util

printCurrentMemoryUsage() - print: %free, total memory usage and time of day to stdout.

printErrMsgFlag - Static variable in class O2Plib.io.FileIO

To display error messages.

processingInstruction(String, String) - Method in class O2Plib.db.DbAccession.AccContentHandler

processingInstruction() - This indicates that a processing instruction (other than the XML declaration) has been encountered.

processingInstruction(String, String) - Method in class O2Plib.db.DbLM.LmsContentHandler

processingInstruction() - This indicates that a processing instruction (other than the XML declaration) has been encountered.

processingInstruction(String, String) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

processingInstruction() - This indicates that a processing instruction (other than the XML declaration) has been encountered.

processingInstruction(String, String) - Method in class O2Plib.db.DbSample.SsfContentHandler

processingInstruction() - This indicates that a processing instruction (other than the XML declaration) has been encountered.

processingXMLdataFlag - Variable in class O2Plib.db.DbAccession

Processing the XML file

processingXMLdataFlag - Variable in class O2Plib.db.DbLM

projDir - Static variable in class O2Plib.db.CSD.CSDglb

Project directory path

projDir - Variable in class O2Plib.db.DbPairSamples

Project directory set by main program

projDir - Variable in class O2Plib.gui.PopupOptions

project directory

projDir - Variable in class O2Plib.io.FileIO

Project directory that is either userDir, specified by -projDir:{path}, or extracted from the input file path it the image is in a "/ppx/" subdirectory.

projDirSPF - Variable in class O2Plib.db.DbPairSamples

Project directory read from SPF file

promptData - Variable in class O2Plib.gui.PopupOptions

Prompt data [0:nData-1] has a "-", then make a CheckBox, else a Label with the data.

pTileGhist - Variable in class O2Plib.misc.CalibrateOD

Histogram statistics [for use in FUTURE]

pushSpot(DbSpot) - Method in class O2Plib.db.DbSample

pushSpot() - push DbSpot spot into spotList[0:nTopSpot-1].

pushSpotPair(DbSpot, DbSpot) - Method in class O2Plib.db.DbPairSamples

pushSpotPair() - push DbSpot spots pair into spotLists and adjust spot pairing data.

pushSpotPair(DbPspot) - Method in class O2Plib.db.DbPairSamples

pushSpotPair() - push DbPspot spots pair of into spotLists and adjust spot pairing data.

pushSpotPair(DbPspot) - Method in class O2Plib.db.DbSample

pushSpotPair() - push DbPspot spot-pair into spotPairList[0:nTopSpotPair-1].

pushXYbndInterpolateLine(DbBoundary, int, int, int, int) - Method in class O2Plib.db.DbBoundary

pushXYbndInterpolateLine() - interpolate two int points (x1,y1) to point (x2,y2) into a list of x,y coordinates which are pushed into bnd.

pushXYboundary(int, int) - Method in class O2Plib.db.DbBoundary

pushXYboundary() - push (x,y) into this boundary if (x,y)[1:lth] NEQ top pixel.

Putbyte(byte, FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

Putbyte() - Write out a byte to the GIF file

Putword(int, FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

Putword() - Write out a word to the GIF file

pValueLimit - Variable in class O2Plib.db.CSD.CSDlimits

PREFILTER: continus p-value limits

Q

quickSort(int[], int, int) - Method in class O2Plib.image.MedianCut

quickSort() - sort the map Based on the QuickSort method by James Gosling from Sun's SortDemo applet

quickSort(int[], int, int) - Static method in class O2Plib.misc.Sort

quickSort() - sort the int[] array.

quit(boolean) - Method in class O2Plib.gui.PopupNameListSelectorDialog

quit() - kill this frame

quit() - Method in class O2Plib.gui.PopupOptions

close() - kill this frame

R

r - Variable in class O2Plib.image.WriteGifEncoder

rArea - Variable in class O2Plib.db.DbPspot

spot Rsample area in pixels

rAreaMax - Variable in class O2Plib.db.DbPairSamples

rAreaMin - Variable in class O2Plib.db.DbPairSamples

Minimum Rsample area of any spot in DB

ras - Variable in class O2Plib.image.TiffPixelLoader

Raster image read

ratioMean - Variable in class O2Plib.db.CSD.CSDnorm

Slope mj OR Tot D'/sample's ratio list.

ratioMeanSpotNbrs - Variable in class O2Plib.db.CSD.CSDnorm

[0:nRatioMeanSpots-1] Ratio-mean spot #'s of spots in ratioMeans for normalization.

ratioMeanSpots - Variable in class O2Plib.db.CSD.CSDnorm

[0:nRatioMeanSpots-1] list of spots used in ratio mean normalization

ratioOmittedToAccepted - Variable in class O2Plib.db.CSD.CSDtotals

"Omitted(D')/Accepted(D')"

ratioOmittedToAccepted - Variable in class O2Plib.db.DbSample

"Omitted(D')/Accepted(D')"

rdbmsDir - Static variable in class O2Plib.db.CSD.CSDglb

RDBMS database directory {projDir}/rdbms/

rdbmsDir - Variable in class O2Plib.io.FileIO

RDBMS database directory {projDir}/rdbms/

rDensity - Variable in class O2Plib.db.DbPspot

Rsample spot density not corrected for background

rDprime - Variable in class O2Plib.db.DbPspot

Rsample Spot density in D' (density corrected for background by subtracting mnBackground*area .

rDprimeMax - Variable in class O2Plib.db.DbPairSamples

Maximum Rsample dPrime (density) of any spot in DB

rDprimeMin - Variable in class O2Plib.db.DbPairSamples

Minimum Rsample dPrime (density) of any spot in DB

rDxLM - Variable in class O2Plib.db.DbPspot

X distance Rsample spot (x,y) relative to Rsample LM(x,y)

rDyLM - Variable in class O2Plib.db.DbPspot

Y distance Rsample spot (x,y) relative to Rsample LM(x,y)

readAccessionXML(String) - Method in class O2Plib.db.DbAccession

readAccessionXML() - read accession database data from XML file

readAccTable(String) - Method in class O2Plib.db.DbAccession

readAccTable() - read the accession table from accFile

readAllSsfSpotlistTables() - Method in class O2Plib.db.DbSample

readAllSsfSpotlistTables() - read SSF data, preface and epilogue tables Note: this reads the SSF data produced by "Seg2Dgel -ssfFormat:F" which produces three files.

readBytesFromURL(String, String) - Static method in class O2Plib.io.FileIO

readBytesFromURL() - read binary data from URL

readImageFile(String) - Method in class O2Plib.image.PixReader

readImageFile() - read an image fileread new image file.

readLandmarkDatabase(String, String, String, int, boolean) - Method in class O2Plib.db.DbLM

readLandmarkDatabase() - read landmark database data from tab-delimited data file or XML data file into the Table tlm.

readLandmarkDatabase(String, int, boolean) - Method in class O2Plib.db.DbLM

readLandmarkDatabase() - read landmark database data from tab-delimited data file or XML data file into the Table tlm.

readLandmarksTable(int) - Method in class O2Plib.db.DbLM

readLandmarksTable() - find (Rsample,Sample) in landmarks database table using the previously definedlmsFile path.

readLandmarkXML(String) - Method in class O2Plib.db.DbLM

readLandmarkXML() - read landmark database data from XML file into Table.

readNameValuesHashTableFromFile(String, String, int) - Method in class O2Plib.misc.ParamHash

readNameValuesHashTableFromFile() - read a hashtable of tab-delimited name-value pairs from a file.

readNameValuesHashTableFromFile(String, String, int, boolean) - Method in class O2Plib.misc.ParamHash

readNameValuesHashTableFromFile() - read a hashtable of tab-delimited name-value pairs from a file.

readOnlyCSDflag - Variable in class O2Plib.db.CSD.CSDio

may not write CSD

readOnlyFlag - Variable in class O2Plib.gui.PopupNameListSelectorDialog

readOnlyFlag - Variable in class O2Plib.gui.PopupTableEditDialog

Flag indicating that table is read only

readPPXfile(String) - Method in class O2Plib.image.PpxLoader

readPPXfile() - read loca PPX file or PPX file URL.

readPropFileToHashtable(String) - Static method in class O2Plib.misc.ParamHash

readPropFileToHashtable() - read the property file to a hash table

readSPFdata(String, String, int) - Method in class O2Plib.db.DbPairSamples

readSPFdata() - Read sample Sample Paired-spotlist Files (SPF) into a linked list data base of DbPair objects.

readSPFpairedSpotsXML(String, DbPairSamples) - Method in class O2Plib.db.DbPairSamples

readSPFpairedSpotsXML() - read SPF sample paired spot-list data from XML file.

readSpfTabDelimTable(String) - Method in class O2Plib.db.DbPairSamples

readSpfTabDelimTable() - read SSF tab-delimited file data.

readSSFdata() - Method in class O2Plib.db.DbSample

readSSFdata() - Read sample Sample Spot-list Files (SSF) into a linked list data base of DbSpot objects.

readSsfEpilogueTable(String) - Method in class O2Plib.db.DbSample

readSsfEpilogueTable() - read SSF epilogue tab-delimited file

readSsfPrefaceTable(String) - Method in class O2Plib.db.DbSample

readSsfPrefaceTable() - read SSF preface tab-delimited file

readSsfSpotlistTable(String) - Method in class O2Plib.db.DbSample

readSsfSpotlistTable() - read SSF data table from tab-delimited data

readSsfSpotlistXML(String) - Method in class O2Plib.db.DbSample

readSsfSpotlistXML() - read SSF spot list, preface and epilogue data from XML file.

readTable(String) - Method in class O2Plib.table.Table

readTable() - read a tab-delimited table from FILE/URL.

readTextFile(String) - Static method in class O2Plib.io.FileIO

readTextFile() - Will read file from disk & returns as String

readTiff(String) - Method in class O2Plib.image.TiffPixelLoader

readTiff() - read a tiff image file

reallocBnd(int, boolean) - Method in class O2Plib.db.DbBoundary

reallocBnd() - grow the MAX boundary arrays for this boundary to a new size.

rebuildChkBoxSubmenu(Frame, Menu, String, String[], String) - Method in class O2Plib.gui.MenuSupport

rebuildChkBoxSubmenu() - rebuild a submenu with a new entry list indicated by menu labels from entryList[], the commands are preface+entryList[].

redBits(int) - Method in class O2Plib.image.MedianCut

redBits() - Get 8-bit red component of a 15-bit color 8-bit pixel with low 3 bits zero.

regrow(int) - Method in class O2Plib.db.CSD.CSDcond

regrow() - grow the condition.

regrow(int) - Method in class O2Plib.db.CSD.CSDexpr

regrow() - increase the size of the expression list

regrow(int) - Method in class O2Plib.db.CSD.CSDexprList

regrow() - increase the size of the expression lists

regrow(int) - Method in interface O2Plib.db.CSD.CSDlistInterface

regrow() - increase the size of the list

regrow(int) - Method in class O2Plib.db.CSD.CSDRmap

regrow() - regrow the Rmap

regrow(int) - Method in class O2Plib.db.CSD.CSDRspot

regrow() - increase the size of the Rspot set

regrow(int) - Method in class O2Plib.db.CSD.CSDRspotList

regrow() - grow the RSL.

regrowExprList(int) - Method in class O2Plib.db.CSD.CSDexprList

regrowExprList() - grow the ExprList.

regrowLMS(int) - Method in class O2Plib.db.CSD.CSDlms

regrowLMS() - grow the condition.

relDistLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] relative distance limits

remove(String) - Method in class O2Plib.db.CSD.CSDcond

remove() - remove sample to condition.

remove(DbSample) - Method in class O2Plib.db.CSD.CSDcond

remove() - remove sample to condition.

remove(CSDRspot) - Method in class O2Plib.db.CSD.CSDRmap

remove() - remove entry to the Rmap [TODO]

remove(String) - Method in class O2Plib.db.CSD.CSDRmap

remove() - remove entry to the Rmap

remove(DbPspot) - Method in class O2Plib.db.CSD.CSDRspot

remove() - remove DbPspot from Rspot set.

remove(int) - Method in class O2Plib.db.CSD.CSDRspot

remove() - remove DbPspot from Rspot set by sample index.

remove(int) - Method in class O2Plib.db.CSD.CSDRspotList

remove() - remove Rspot from RSL.

remove(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspotList

remove() - remove Rspot from RSL.

removeRowFromTable(int) - Method in class O2Plib.table.SimpleTable

removeRowFromTable() - remove row of data from table.

removeSPFandSSFSpotListsCSD() - Method in class O2Plib.db.CSD.CSD

removeSPFandSSFSpotListsCSD() - remove the non-Rsample spotlist[] and spotPairList[] .

removeSpot(DbSpot) - Method in class O2Plib.db.DbSample

removeSpot() - remove spot from spotList[0:nTopSpot-1].

removeSpotPair(DbPspot) - Method in class O2Plib.db.DbSample

removeSpotPair() - remove DbPspot from spotPairList[0:nTopSpotPair-1].

renameCSD(String) - Method in class O2Plib.db.CSD.CSD

renameCSD() - rename the CSD [TODO]

reorderColors(int[], int, int, int) - Method in class O2Plib.image.MedianCut

reorderColors() - Change ordering of 5-bit colors in each word of int[] so we can sort on the 'longDim' color

reorderModeDens - Variable in class O2Plib.db.CSD.CSDnorm

[TODO-REFACTOR]value of modeDensity at time of REORDER

replaceColumnData(String, String[]) - Method in class O2Plib.table.SimpleTable

replaceColumnData() - replace data in a column in the table.

replaceColumnData(int, String[]) - Method in class O2Plib.table.SimpleTable

replaceColumnData() - replace data in a column in the table.

replaceColumnData(String, String) - Method in class O2Plib.table.SimpleTable

replaceColumnData() - replace all data in a column in the table with the same value.

replaceColumnData(int, String) - Method in class O2Plib.table.SimpleTable

replaceColumnData() - replace all data in a column in the table with the same value.

replaceFileInArgList(String[], String) - Static method in class O2Plib.misc.Switches

replaceFileInArgList() - replace the file in the arg list.

replaceNthCommaSeparatedArg(String, int, String) - Static method in class O2Plib.misc.Util

replaceNthCommaSeparatedArg() - replace n'th arg in comma separated argList with sVal

replaceSwitchInArgList(String[], String) - Static method in class O2Plib.misc.Switches

replaceSwitchInArgList() - replace the switch in the arg list.

reset() - Method in class O2Plib.db.DbPairSamples

reset() - reset the DbSPF state for current sample.

reset() - Method in class O2Plib.db.DbSample

reset() - reset the DbSample state for current sample.

resetBnd(boolean) - Method in class O2Plib.db.DbBoundary

resetBnd() - reset a boundary to size 0.

resetImage(Image) - Method in class O2Plib.image.ScrollableImage

resetImage() - set or reset images

resetImage(Image, int, int) - Method in class O2Plib.image.ScrollableImage

resetImage() - set or reset images

resetSampleStats() - Method in class O2Plib.db.DbSample

resetSampleStats() - reset global sample stats

resetStatusData - Variable in class O2Plib.gui.PopupOptions

Default checkbox data [0:nData-1] is set by analyzing the switches.

resetTextFields() - Method in class O2Plib.gui.PopupTableEditDialog

resetTextFields() - reset the text fields from the valueData[]

resizeImageCanvas(float) - Method in class O2Plib.image.ScrollableImage

resizeImageCanvas() - Reset Image, used in zoom and dezoom.

resizeImageCanvas(int, int, float) - Method in class O2Plib.image.ScrollableImage

resizeImageCanvas() - Reset Image, used in zoom and dezoom.

resizeLAXfileData(String, String) - Static method in class O2Plib.io.FileIO

resizeLAXfileData() - resize {applicationName}.lax file data for applicationName.

restoreColorOrder(int[], int, int, int) - Method in class O2Plib.image.MedianCut

restoreColorOrder() - Restore the 5-bit colors to original order

restoreDataOrigCopy() - Method in class O2Plib.gui.PopupTableEditDialog

restoreDataOrigCopy() - restore valueData[] from valueDataOrig[]

rgb - Variable in class O2Plib.image.WriteGifEncoderHashitem

rgb15(int) - Method in class O2Plib.image.MedianCut

rgb15() - convert from 24-bit (ignore alpha) to 15-bit color.

ri - Variable in class O2Plib.image.TiffPixelLoader

List of Rendered images that was read in the tiff file

rightFillWithSpaces(String, int) - Static method in class O2Plib.misc.Util

rightFillWithSpaces() - right fill the string with spaces to size n.

rightSize() - Method in class O2Plib.db.CSD.CSD

rightSize() - "Right-size" all CSD lists if required.

rightSize() - Method in class O2Plib.db.CSD.CSDcond

rightSize() - right-size the size of the Condition list to the size actually used.

rightSize() - Method in class O2Plib.db.CSD.CSDexpr

rightSize() - right-size the size of the expression list to the size actually used.

rightSize() - Method in class O2Plib.db.CSD.CSDexprList

rightSize() - right-size the size of the list of expression lists to the size actually used.

rightSize() - Method in interface O2Plib.db.CSD.CSDlistInterface

rightSize() - right-size the size of the list to the size actually used.

rightSize() - Method in class O2Plib.db.CSD.CSDRmap

rightSize() - right-size the size of the Rmap list to the size actually used.

rightSize() - Method in class O2Plib.db.CSD.CSDRspot

rightSize() - right-size the size of the Rspot set to nSpots.

rightSize() - Method in class O2Plib.db.CSD.CSDRspotList

rightSize() - right-size the size of the RspotList to totRspots.

rightSize(boolean) - Method in class O2Plib.db.CSD.CSDRspotList

rightSize() - right-size the size of the RspotList to totRspots.

rightSize(int[], int) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the int[] array to nSize

rightSize(float[], int) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the float[] array to nSize

rightSize(double[], int) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the double[] array to nSize

rightSize(char[], int) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the char[] array to nSize

rightSize(String[], int) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the String[] array to nSize

rightSize(String[]) - Static method in class O2Plib.misc.Util

rightSize() - right-size the size of the String[] array to the size determined by the first null entry.

rix - Variable in class O2Plib.image.PpxLoader

(unsigned short) X top left corner of region of interest (0,0) is U.L.H.C.

riy - Variable in class O2Plib.image.PpxLoader

(unsigned short) X top left corner of region of interest (0,0) is U.L.H.C.

rLUT - Variable in class O2Plib.image.MedianCut

[0:255] Red Color map look up table

rMapsListDB - Static variable in class O2Plib.db.CSD.CSDglb

Database list of Rmaps of the Rspot indices to foreign spot indices to/from spot annotation IDs and info.

rmax - Variable in class O2Plib.image.MC_Cube

rMaxDens - Variable in class O2Plib.db.DbPspot

max Rsample pixel density seen in spot

rMaxDmax - Variable in class O2Plib.db.DbPairSamples

Maximum Rsample maxD of any spot in DB

rMerx1 - Variable in class O2Plib.db.DbPspot

Rsample Spot minimum enclosing rectangle Left in pixel coords

rMerx2 - Variable in class O2Plib.db.DbPspot

Rsample Spot minimum enclosing rectangle Right in pixel coords

rMery1 - Variable in class O2Plib.db.DbPspot

Rsample Spot minimum enclosing rectangle Top in pixel coords

rMery2 - Variable in class O2Plib.db.DbPspot

Rsample Spot minimum enclosing rectangle Bottom in pixel coords

rmin - Variable in class O2Plib.image.MC_Cube

rMinDens - Variable in class O2Plib.db.DbPspot

min Rsample pixel density seen in spot

rMinDmax - Variable in class O2Plib.db.DbPairSamples

minimum Rsample minD of any spot in DB

rMnBkgdDens - Variable in class O2Plib.db.DbPspot

Mean Background pixel density for the G1 spot.

rmvExpr(CSDexpr) - Method in class O2Plib.db.CSD.CSDexprList

rmvExpr() - remove Rspot from ExprList.

rmvFileExtension(String) - Static method in class O2Plib.misc.Util

rmvFileExtension() - remove ".tif", ".jpg", ".gif", ".ppx", ".j2k" from file name and ignore the case.

rmvFromHashtable(CSDRspot) - Method in class O2Plib.db.CSD.CSDRspotList

rmvFromHashtable() - Remove Rspot from Rspot set hashtable.

rmvLMS(String) - Method in class O2Plib.db.CSD.CSDlms

rmvLMS() - remove LMset name from list of LMsets.

rmvRtnChars(String) - Static method in class O2Plib.misc.Util

rmvRtnChars() - remove return chars.

rmvSpecifiedChar(String, char) - Static method in class O2Plib.misc.Util

rmvSpecifiedChar() - remove specified chararcter

rmvSPFlistsAndTable() - Method in class O2Plib.db.DbPairSamples

rmvSPFlistsAndTable() - remove the SSF and SPF spot lists and Tables if they exist.

rmvSPFlistsAndTable() - Method in class O2Plib.db.DbSample

rmvSPFlistsAndTable() - remove the SSF and SPF spot lists, and Tables if they exist.

rmvSwitch(String) - Static method in class O2Plib.misc.Switches

rmvSwitch() - remove switch from the sw[]list by shrinking the list

rmvTableFromTableList() - Method in class O2Plib.table.Table

rmvTableFromTableList() - remove Table from tblList

rNbrCsamples - Variable in class O2Plib.db.DbPspot

# of samples in Rsample Cspot Csample' estimate if not 0.

Roi - Class in O2Plib.image

Roi(int, int, int, int, String, int) - Constructor for class O2Plib.image.Roi

Roi() - creates a new instance of Roi

Roi(int, int, int, int, String, int, Color, boolean) - Constructor for class O2Plib.image.Roi

Roi() - creates a new instance of Roi

Roi(String, int) - Constructor for class O2Plib.image.Roi

Roi() - creates a new instance of Roi

Roi(String, int, boolean) - Constructor for class O2Plib.image.Roi

Roi() - creates a new instance of Roi

Roi(String) - Constructor for class O2Plib.image.Roi

Roi() - creates a new instance of Roi.

Roi() - Constructor for class O2Plib.image.Roi

Roi() - Creates a new instance of Roi with null values.

roiCode - Variable in class O2Plib.image.Roi

code for type of ROI.

roiIDctr - Static variable in class O2Plib.image.Roi

Unique ROI ID that is used to generate a unqiue ROI each time the constructor is called.

RoiList - Class in O2Plib.image

RoiList(int) - Constructor for class O2Plib.image.RoiList

RoiList() - Constructor where size is specified.

RoiList() - Constructor for class O2Plib.image.RoiList

RoiList() - Constructor using DEF_MAX_ROIS

roiList - Variable in class O2Plib.image.RoiList

Roi list of size [0:nRoi-1]

roiName - Variable in class O2Plib.image.Roi

name of ROI if not null

roiWORKING - Variable in class O2Plib.image.RoiList

Internal "WORKING",ROI_WORKING instance that can be used to set the CW, DBUG or PIXDUMP (not the ND) Rois

rowData - Variable in class O2Plib.db.DbAccession.AccContentHandler

instance of current row of data being assembled.

rowData - Variable in class O2Plib.db.DbLM.LmsContentHandler

instance of current row of data being assembled.

rowToEdit - Variable in class O2Plib.gui.PopupTableEditDialog

Row to edit in the table

rowView - Variable in class O2Plib.image.ScrollableImage

row pixel size rulers

rPerimeter - Variable in class O2Plib.db.DbPspot

Rsample spot perimeter (pixels) for spot

rptStatusLineLabel - Static variable in class O2Plib.misc.Util

Report Label will output updateReportStatusLine if not null.

rptStatusLineTextField - Static variable in class O2Plib.misc.Util

Report text field will output updateReportStatusLine if not null.

rptTextArea - Static variable in class O2Plib.misc.Util

Report text area will output appendPRmsg if not null.

RSAMPLE - Static variable in class O2Plib.db.CSD.CSDglb

The index for the Rsample (Reference Sample)

RSAMPLE - Static variable in class O2Plib.db.DbBaseSpot

The index for the Rsample (Reference Sample)

RSAMPLE - Static variable in class O2Plib.db.DbPairSamples

The index for the Rsample (Reference Sample)

RSAMPLE - Static variable in class O2Plib.db.DbSample

The index for the Rsample (Reference Sample)

RSAMPLE - Static variable in class O2Plib.db.LMset

The index for the Rsample (Reference Sample)

rsampleName - Variable in class O2Plib.db.LMset

rSampleParamsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(1.1) when the begining of the list of parameters is found

rSamplePspot - Variable in class O2Plib.db.CSD.CSDRspot

The DbSpot for the Rsample Rspot.

rSampleSpotNbr2RspotNbr - Variable in class O2Plib.db.CSD.CSDRmap

[0:nRmapSize-1] map of Rsample spot number to the Rspot set idNbr.

rSDarea - Variable in class O2Plib.db.DbPspot

Rsample Csample' S.D.

rSDdPrime - Variable in class O2Plib.db.DbPspot

Rsample Csample' S.D.

rSDxCentroid - Variable in class O2Plib.db.DbPspot

Rsample Csample' S.D.

rSDyCentroid - Variable in class O2Plib.db.DbPspot

Rsample Csample' S.D.

rsetBlocks - Variable in class O2Plib.db.CSD.CSDio

# blocks/Rset - from nSamples, (multiple of #nodes/block).

rspCV - Variable in class O2Plib.db.CSD.CSDRspot

sum of coefficient of variation (COV) density for entire Rspot set.

rspCVsq - Variable in class O2Plib.db.CSD.CSDRspot

Square of sum of COV Density.

RSPOT_DIST_THR - Static variable in class O2Plib.db.CSD.CSDRspot

Default distance threshold for restricting adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.

rspot_Xcalib - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] for [0:nXRspots-1] Rspot# for xCoord[] point

rspot_Ycalib - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] for [0:nYRspots-1] Rspot# for yCoord[] point

rSpotBaseBlock - Variable in class O2Plib.db.CSD.CSDio

Base address of the Rspot Node part of the CSD DB

RSPOTCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Color of the Rspots

rSpotDistThr - Static variable in class O2Plib.db.CSD.CSDRspot

Restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.

rspotListsDB - Static variable in class O2Plib.db.CSD.CSDglb

Database of all RspotLists' objects of size [0:nRrspotListDB-1].

rSpotNbr - Variable in class O2Plib.db.DbPspot

spot Rsample spot number

rspotNbr2Annotation - Variable in class O2Plib.db.CSD.CSDRmap

[0:nRmapSize-1] list of Rspot annotation objects if any.

rspotNbr2Rspot - Variable in class O2Plib.db.CSD.CSDRmap

[0:nRmapSize-1] map of a number Rspot id number to the Rspot set object.

rSpotNext - Variable in class O2Plib.db.DbBaseSpot

Next instance for CSD database Rspot linked list

rSpotNext - Variable in class O2Plib.db.DbSpot

Next instance for CSD database Rspot linked list

rSpotOfGroup - Variable in class O2Plib.db.DbPspot

NOTE: not used - Rspot group to which this spot belongs.

rspotsList - Variable in class O2Plib.db.CSD.CSDRspotList

[0:totRspots-1] list of Rspot objects

rspotsNbrs - Variable in class O2Plib.db.CSD.CSDRspotList

[0:totRspots-1] list of Rspot numbers

rSx - Variable in class O2Plib.db.DbPspot

Std Dev of Rsample density weighted X centroid

rSy - Variable in class O2Plib.db.DbPspot

Std Dev of Rsample density weighted Y centroid

rtLimits - Variable in class O2Plib.db.CSD.CSDlimits

[LB:UB] retention time (2D LC-MS) (x) region limits

run() - Method in class O2Plib.db.xml.xmlLoader

rVolume - Variable in class O2Plib.db.DbPspot

Rsample Spot volume (density corrected for background by subtracting mnBackground*area .

rVolumeMax - Variable in class O2Plib.db.DbPairSamples

Maximum Rsample volume (density) of any spot in DB

rVolumeMin - Variable in class O2Plib.db.DbPairSamples

Minimum Rsample volume (density) of any spot in DB

S

SAMPLE - Static variable in class O2Plib.db.CSD.CSDglb

The index for the Sample to be paired with the Rsample

SAMPLE - Static variable in class O2Plib.db.DbBaseSpot

The index for the Sample to be paired with the Rsample

SAMPLE - Static variable in class O2Plib.db.DbPairSamples

The index for the Sample to be paired with the Rsample

SAMPLE - Static variable in class O2Plib.db.DbSample

The index for the Sample to be paired with the Rsample

SAMPLE - Static variable in class O2Plib.db.LMset

The index for the Sample to be paired with the Rsample

sampleEntryFlag - Variable in class O2Plib.db.DbAccession.AccContentHandler

when the begining of the list of spots is found

sampleEntryFlag - Variable in class O2Plib.db.DbLM.LmsContentHandler

when the begining of the list of spots is found

sampleFileNameA - Variable in class O2Plib.db.DbAccession

Accession sample name (without file extension)

sampleInLmsDBlist - Variable in class O2Plib.db.DbLM

List of samples in the landmark DB that are in the accession DB.

sampleList - Variable in class O2Plib.db.CSD.CSDcond

[0:nSamples-1] list of samples in condition.

sampleModel - Variable in class O2Plib.image.TiffPixelLoader

Tiff sample model name

sampleName - Variable in class O2Plib.db.LMset

sampleNameIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

sampleNames - Variable in class O2Plib.db.CSD.CSDacc

names of the samples [0:nSamples-1]

sampleNames - Variable in class O2Plib.db.CSD.CSDcond

[0:nSamples-1] list of names of samples in condition.

sampleNamesDB - Static variable in class O2Plib.db.CSD.CSDglb

sampleNamesUsedDB - Static variable in class O2Plib.db.CSD.CSDglb

PSL samples used to create DB.

sampleNbr - Variable in class O2Plib.db.DbSample

The sample number is either RSAMPLE (0) or SAMPLE(1)

samplePairList - Variable in class O2Plib.db.DbLM

List of all pairs of samples in the landmark DB.

sampleParamsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(1.2) when the begining of the list of parameters is found

sampleSizes - Variable in class O2Plib.image.TiffPixelLoader

bits/pixel is sample sizes [0:nBands-1] from sampleModel.getSampleSize()

sampleType - Variable in class O2Plib.db.DbSample

The sample type name is either "Rsample" or "Sample" based on sampleNbr value.

sArea - Variable in class O2Plib.db.DbPspot

spot Sample area in pixels

sAreaMax - Variable in class O2Plib.db.DbPairSamples

Maximum Sample area of any spot in DB

sAreaMin - Variable in class O2Plib.db.DbPairSamples

Minimum Sample area of any spot in DB

saveAccDB2DelimFile(String, String, boolean) - Method in class O2Plib.db.DbAccession

saveAccDB2DelimFile() - save the accession database into a delimited string file.

saveAccDB2XMLfile(String, boolean) - Method in class O2Plib.db.DbAccession

saveAccDB2XMLfile() - save the accession database into an XML file.

saveAccDB2XMLfile(String, String, boolean) - Method in class O2Plib.db.DbAccession

saveAccDB2XMLfile() - save the accession database into an XML file.

saveAccEntry(String[], String, String) - Method in class O2Plib.db.DbAccession

saveAccEntry() - save accession row entry data in the accession database.

saveAccRowForSample(String[]) - Method in class O2Plib.db.DbSample

saveAccRowForSample() - save accession row entry data in the accession database table for this sample.

saveCSD() - Method in class O2Plib.db.CSD.CSD

saveCSD() - save the CSD [TODO]

saveLmsDB2DelimFile(String, String, boolean) - Method in class O2Plib.db.DbLM

saveLmsDB2DelimFile() - save the landmark database into a delimited string file.

saveLmsDB2XMLfile(String, boolean) - Method in class O2Plib.db.DbLM

saveLmsDB2XMLfile() - save landmark database into an XML file file.

saveLMsetInDBtable(LMset) - Method in class O2Plib.db.DbLM

saveLMsetInDBtable() - save the LM set in the in-core landmark database table.

saveLMsetInDBtable(LMset, String, String) - Method in class O2Plib.db.DbLM

saveLMsetInDBtable() - save the LM set in the in-core landmark database table.

savePropertiesFile(String, String[], String[], boolean[]) - Static method in class O2Plib.misc.Switches

savePropertiesFile() - save the switches in propertyFile - typically "{application}.properties".

scaledMaxOD - Variable in class O2Plib.misc.CalibrateOD

This is the max value index for cal2gray[] it is computed as cal2gray.length-1

scprog - Variable in class O2Plib.image.PpxLoader

name of scanning program

scpvrs - Variable in class O2Plib.image.PpxLoader

version of scanning program

SCREEN_RESOLUTION - Variable in class O2Plib.image.ScrollableImage.Rule

Screen resolution

ScrollableImage - Class in O2Plib.image

ScrollableImageCanvas class supports a scrollable JPanel

ScrollableImage(Image, int, int, int, int, Object, boolean, boolean) - Constructor for class O2Plib.image.ScrollableImage

ScrollableImageCanvas() - constructor.

ScrollableImage.Corner - Class in O2Plib.image

CLASS CornerCorner Adapted from " The Java Tutorial" book.

ScrollableImage.Corner() - Constructor for class O2Plib.image.ScrollableImage.Corner

ScrollableImage.ImageCanvas - Class in O2Plib.image

ScrollableImage.ImageCanvas(int, int) - Constructor for class O2Plib.image.ScrollableImage.ImageCanvas

ImageCanvas() - constructor.

ScrollableImage.Rule - Class in O2Plib.image

CLASS Rule Adapted from " The Java Tutorial" book.

ScrollableImage.Rule(int) - Constructor for class O2Plib.image.ScrollableImage.Rule

Rule() - constructor

scrollerFlag - Variable in class O2Plib.image.ScrollableImage

create w/ scrollers

scrollPaneHeight - Variable in class O2Plib.image.ScrollableImage

height of image scroller

scrollPaneWidth - Variable in class O2Plib.image.ScrollableImage

width of image scroller

scrollPos - Variable in class O2Plib.image.ScrollableImage

keep track of Scroller Positions

scrPane - Variable in class O2Plib.gui.PopupNameListSelectorDialog

Scroll pane to hold the panel

scrPane - Variable in class O2Plib.gui.PopupOptions

Scroll pane to hold the panel

scsys - Variable in class O2Plib.image.PpxLoader

ID of the scanning system

sdArea - Variable in class O2Plib.db.DbSpot

Csample' S.D.

sdate - Variable in class O2Plib.image.PpxLoader

date of scan

sdDprime - Variable in class O2Plib.db.DbSpot

Csample' S.D.

sDensity - Variable in class O2Plib.db.DbPspot

Sample spot density not corrected for background

sdMnCarea - Variable in class O2Plib.db.CSD.CSDRspot

S.D.

sdMnCdPrime - Variable in class O2Plib.db.CSD.CSDRspot

S.D.

sdMnCnormDensity - Variable in class O2Plib.db.CSD.CSDRspot

S.D.

sdMnXcentroid - Variable in class O2Plib.db.CSD.CSDRspot

S.D.

sdMnYcentroid - Variable in class O2Plib.db.CSD.CSDRspot

S.D.

sDprime - Variable in class O2Plib.db.DbPspot

Sample Spot density in D' (density corrected for background by subtracting mnBackground*area .

sDprimeMax - Variable in class O2Plib.db.DbPairSamples

Maximum Sample dPrime (density) of any spot in DB

sDprimeMin - Variable in class O2Plib.db.DbPairSamples

Minimum Sample dPrime (density) of any spot in DB

sdXcentroid - Variable in class O2Plib.db.DbSpot

Csample' S.D.

sDxLM - Variable in class O2Plib.db.DbPspot

X distance Sample spot (x,y) relative to Sample LM(x,y)

sdYcentroid - Variable in class O2Plib.db.DbSpot

Csample' S.D.

sDyLM - Variable in class O2Plib.db.DbPspot

Y distance Sample spot (x,y) relative to Sample LM(x,y)

secondary_SP_PP_pairRate - Variable in class O2Plib.db.DbPairSamples

Percentage: (50.0F*(hSP2+hPP2))/minNbrLMSspots Where minNbrLMSspots= min(nbrRsampleSpotsInLMS,nbrSampleSpotsInLMS)

secondaryPairingStatsFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(3.3) when the begining of SecondarypairingStats> secondary pairing statistics is found.

selectedNames - Variable in class O2Plib.gui.PopupNameListSelectorDialog

list of previously selected names selected.

serialVersionUID - Static variable in class O2Plib.gui.PopupDialogQuery

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupFileDialog

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupHTMLbrowser

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupNameListSelectorDialog

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupOptions

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupTableEditDialog

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupTextFieldDialog

frame id

serialVersionUID - Static variable in class O2Plib.gui.PopupYesNoDialogBox

frame id

serialVersionUID - Static variable in class O2Plib.image.ScrollableImage.Corner

frame id

serialVersionUID - Static variable in class O2Plib.image.ScrollableImage.ImageCanvas

frame id

serialVersionUID - Static variable in class O2Plib.image.ScrollableImage.Rule

frame id

serialVersionUID - Static variable in class O2Plib.image.ScrollableImage

frame id

set2D(int[], int, int, int, int) - Static method in class O2Plib.image.DrawPix

set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)

set2D(char[], int, int, int, int) - Static method in class O2Plib.image.DrawPix

set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)

set_exposure_correction(float) - Method in class O2Plib.db.CSD.CSDcal

set_exposure_correction() - set the exposure correction factors (eFactor) for all samples in the database.

set_lsq_norm_calib() - Method in class O2Plib.db.CSD.CSDnorm

set_lsq_norm_calib() - If least squares mode 'L' is used where we compute D''j=mj*D'i+bi, then store the slopes 'mj' in lsqMcoef[j].

set_ratio_list(CSDRspot[]) - Method in class O2Plib.db.CSD.CSDnorm

set_ratio_list() - Get a list of Rspots which will serve as a basis to normalize spots in calculations and reporting for ratio-list normalization mode.

setAccessionDB(String, String, DbAccession) - Method in class O2Plib.db.CSD.CSDacc

setAccessionDB() - assign the accession DB

setAnnotation(CSDannotation) - Method in class O2Plib.db.CSD.CSDRspot

setAnnotation() - set annotation to Rspot set.

setAnnotation() - Method in class O2Plib.db.CSD.CSDRspot

getAnnotation() - set annotation for Rspot set.

setApplicationName(String) - Static method in class O2Plib.misc.Util

setBinCSDfile(String) - Method in class O2Plib.db.CSD.CSDio

setBinCSDfile() - change the current CSD

setBkgrdFilterSize(int) - Method in class O2Plib.db.DbSample

setBkgrdFilterSize() - set spot saturated percent threshold state for the current sample.

setBothLandmarksToLMset(int, int, int, int, int) - Method in class O2Plib.db.LMset

setBothLandmarksToLMset() - set landmark lmN to (x1,y1,x2,y2) in the landmark set.

setCalData(float[], float[], float[], float[]) - Method in class O2Plib.db.CSD.CSDcal

setCalData() - set the calibration data lists

setCalDataNames(String, String, String, String) - Method in class O2Plib.db.CSD.CSDcal

setCalDataNames() - set the calibration data names

setCalTable(float[], int) - Method in class O2Plib.misc.CalibrateOD

setCalTable() - set calibration wedgeCalValues[0:maxCalSteps-1] values

setCalValueListCalibAccFields(float[]) - Method in class O2Plib.db.DbSample

setCalValueListCalibAccFields() - set Calibration wedge wedgeCalValues in the accession DB field for this sample.

setChangeTextData(String, String) - Method in class O2Plib.gui.PopupOptions

setChangeTextData() set the changed user data in the text fields if the promptData matches

setCsamplesFlag(boolean) - Method in class O2Plib.db.DbPairSamples

setCsamplesFlag() - use Csample extensions to SPF file.

setCSDnameProj(String, String, String, int) - Method in class O2Plib.db.CSD.CSD

setCSDnameProj() - change the current CSD name and project directory

setCW(int, int, int, int) - Method in class O2Plib.db.DbSample

setCW() - set the computing window state for current sample.

setCWroi(int, int, int, int, String[]) - Method in class O2Plib.db.DbSample

setCWroi() - set region of interest (ROI) to Computing Window (CW)

setCWroi(int, int, int, int) - Method in class O2Plib.db.DbSample

setCWroi() - set region of interest (ROI) to Computing Window (CW).

setDataOrigCopy() - Method in class O2Plib.gui.PopupTableEditDialog

setDataOrigCopy() - copy current valueData[] to valueDataOrig[]

setDbPairSamples(DbPairSamples[]) - Method in class O2Plib.db.CSD.CSD

setDbPairSamples() - set the dbSPFlist of pair-samples for the CSD.

setDbSample(DbSample) - Method in class O2Plib.misc.CalibrateOD

setDbSample() - set the database sample object on this calibration instance.

setDbSampleList(DbSample[], String[]) - Method in class O2Plib.db.CSD.CSD

setDbSamples() - set the list of samples for the CSD.

setDbSampleList(DbSample[]) - Method in class O2Plib.db.CSD.CSD

setDbSamples() - set the list of samples for the CSD.

setDbSamples(DbSample, DbSample) - Method in class O2Plib.db.CSD.CSD

setDbSamples() - set the dbRsample and dbSample objects for this spot.

setDbSamples(DbSample, DbSample) - Method in class O2Plib.db.DbBaseSpot

setDbSamples() - set the dbRsample and dbSample objects for this DbBaseSpot.

setDbSamples(DbSample, DbSample) - Method in class O2Plib.db.DbSpot

setDbSamples() - set the dbRsample and dbSample objects for this spot.

setDbugFlag(boolean) - Static method in class O2Plib.db.DbBoundary

setDbugFlag() - set the debug flag

setDbugFlag(boolean) - Method in class O2Plib.db.DbPairSamples

setDbugFlag() - set the generic dbugFlag

setDbugFlag(boolean) - Method in class O2Plib.db.DbSample

setDbugFlag() - set the dbugFlag

setDbugFlag(boolean) - Method in class O2Plib.image.TiffPixelLoader

setDbugFlag() - flag

setDBwindow(int, int, int, int) - Method in class O2Plib.db.DbSample

setDBwindow() - set debug window of interest to region of interest (ROI).

setDebugConsoleFlag(boolean) - Static method in class O2Plib.misc.Util

setDebugConsoleFlag() - set debugConsoleFlag to send all appendPRmsg() output to console.

setDebugCW(boolean, int, int, int, int) - Method in class O2Plib.db.DbSample

setDebugCW() - enable/disable debug computing window to restrict data read when test if p.(xMom,yMom) in SSF CW for debugging.

setDebugFlag(boolean) - Method in class O2Plib.image.PixReader

setDebugFlag() - flag to track additional loading info

setDebugFlag(boolean) - Method in class O2Plib.image.PixWriter

setDebugFlag() - flag to track additional loading info

setDefaultSizes(int, int) - Static method in class O2Plib.db.DbBoundary

setDefaultSizes() - sets the default sizes.

setDefaultUnits() - Method in class O2Plib.misc.CalibrateOD

setDefaultUnits() - set the default to units to "Optical density", unitsAbbrev to "od" and unitsManufacturerPartNbr to "< opt.

setDefMinAcceptableDist(float) - Method in class O2Plib.db.CSD.CSDRspotList

setDefMinAcceptableDist() - set defMinAcceptableDist

setDocumentLocator(Locator) - Method in class O2Plib.db.DbAccession.AccContentHandler

setDocumentLocator() -Provide reference to Locator which provides information about where in a document callbacks occur.

setDocumentLocator(Locator) - Method in class O2Plib.db.DbLM.LmsContentHandler

setDocumentLocator() -Provide reference to Locator which provides information about where in a document callbacks occur.

setDocumentLocator(Locator) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

setDocumentLocator() -Provide reference to Locator which provides information about where in a document callbacks occur.

setDocumentLocator(Locator) - Method in class O2Plib.db.DbSample.SsfContentHandler

setDocumentLocator() -Provide reference to Locator which provides information about where in a document callbacks occur.

setEditable(boolean) - Method in class O2Plib.gui.PopupTableEditDialog

setEditable() - set editable status

setEnabled(boolean) - Method in class O2Plib.gui.PopupNameListSelectorDialog

setEnabled() - set the enabled flag to edit

setEpilogueDbugFlag(boolean) - Method in class O2Plib.db.DbPairSamples

setEpilogueDbugFlag() - set the epilogue dbugEpilogFlag

setERspotDistanceThr(float) - Static method in class O2Plib.db.CSD.CSDRspot

setERspotDistanceThr() - set threshold to restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.

setERspotFlag(boolean) - Method in class O2Plib.db.CSD.CSDRspot

setERspotFlag() - set the eRspot flag

setFieldData(String[], int) - Method in class O2Plib.table.SimpleTable

setFieldData() - set new field[] list for table

setFieldIdxRowDatum(int, int, String) - Method in class O2Plib.table.SimpleTable

setFieldIdxRowDatum() - set datum by field idx with row index

setFieldRowDatum(int, String, String) - Method in class O2Plib.table.SimpleTable

setFieldRowDatum() - set datum by field name with row index

setGrayValueTable(int[], int) - Method in class O2Plib.misc.CalibrateOD

setGrayValueTable() - get calibration grayscale[0:maxPeaks-1] values

setHelpData(String[]) - Method in class O2Plib.table.SimpleTable

setHelpData() - set tHelp[] list for table

setHelpText(String) - Method in class O2Plib.gui.PopupOptions

setHelpText() - set the help text area

setHorizontalScrollBarVal(int) - Method in class O2Plib.image.ScrollableImage

setHorizontalScrollBarVal() -

setIdxSample(int) - Method in class O2Plib.db.DbSample

setIdxSample() - set the idxSample used in the CSD database

setIncrementAndUnits() - Method in class O2Plib.image.ScrollableImage.Rule

setIncrementAndUnits() - set the incriment and units

setLandmarkDB(DbLM, String, int) - Method in class O2Plib.db.CSD.CSDlms

setLandmarkDB() - assign the landmark DB.

setLMsetDebugging(int) - Method in class O2Plib.db.CSD.CSD

setLMsetDebugging() - set the debug LMset number for the CSD.

setLMsetRsample(int) - Method in class O2Plib.db.CSD.CSDRspot

setLMsetRsample() - set the LMset number associated with this spot for the Rsample

setLMSsetRsampleAndSampleNames(String, String) - Method in class O2Plib.db.LMset

setLMSsetRsampleAndSampleNames() - set the Rsample and Sample names

setLRHC(int, int) - Method in class O2Plib.image.Roi

setLRHC() - set the Lower Right Hand Corner of Region of Interest

setMapGrayToCal(float[], int) - Method in class O2Plib.misc.CalibrateOD

setMapGrayToCal() - change the mapGrayToCal to the specified Gray to OD map.

setMaxNbrStatusTimes(int) - Static method in class O2Plib.misc.Util

setMaxNbrStatusTimes() - setup the status times in maxStatusTimes

setMinCentralCoreSize(int) - Method in class O2Plib.db.DbSample

setMinCentralCoreSize() - set spot minimum central core component area size state in pixels for the current sample.

setNameValueEditGUI(String) - Method in class O2Plib.gui.PopupTableEditDialog

setNameValueEditGUI() - setup and build the name-value wizard.

setNbrAltLMsize(int) - Static method in class O2Plib.db.DbSpot

setNbrAltLMsize() - set the default maximum # of alternate paired landmarks all spots in the database could belong to.

setNDwedgeTable(int[], float[], int, int, int) - Method in class O2Plib.misc.CalibrateOD

setNDwedgeTable() - set ND step wedge calibration set of (grayscale,OD) wedge values, # of steps and max grayvalue [CHECK] we may want to copy the data to fixed size arrays [0:MAX_WEDGE_STEPS-1].

setNewDefaultFlag - Variable in class O2Plib.gui.PopupOptions

pressed "Done"

setNewValueData(String[]) - Method in class O2Plib.gui.PopupTableEditDialog

setNewValueData() - set new valueData[] into the local database and dataTextField.

setNormalization(CSDnorm) - Method in class O2Plib.db.CSD.CSDRspot

setNormalization() - set annotation to Rspot set.

setObjPosition(int, int) - Method in class O2Plib.image.ScrollableImage

setObjPosition() - set the object position in non-zoomed space.

setPairingBit(int) - Method in class O2Plib.db.CSD.CSDfilterState

setPairingBit() - set the search pairing bit

setPairingThresholds(float, float, int) - Method in class O2Plib.db.DbPairSamples

setPairingThresholds() - Set the default pairing thresholds: (dt1Threshold, dt2Threshold, defNbrAltLMs)

setPairSampleNames(DbPairSamples) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

setPairSampleNames() - set the paired sample names

setPairSamples(DbSample, DbSample, DbLM) - Method in class O2Plib.db.DbPairSamples

setPairSamples() - setup DbSPF instance of the database and reset data

setPairsDbugFlag(boolean, int) - Method in class O2Plib.db.DbPairSamples

setPairsDbugFlag() - set the preface dbugPairsFlag

setPercentDensityFlag(int) - Method in class O2Plib.db.DbPairSamples

setShortSPFbyLMnbr() - set flag used when reading SPF files.

setPercentDensityFlag(boolean) - Method in class O2Plib.db.DbPairSamples

setPercentDensityFlag() - set flag used when generating SPF files, use percent of density D' rather than density D'.

setPrefaceDbugFlag(boolean) - Method in class O2Plib.db.DbPairSamples

setPrefaceDbugFlag() - set the preface dbugPrefaceFlag

setPreferredHeight(int) - Method in class O2Plib.image.ScrollableImage.Rule

setPreferredHeight() - set height

setPreferredWidth(int) - Method in class O2Plib.image.ScrollableImage.Rule

setPreferredWidth() - set width

setProjectDirs(String) - Method in class O2Plib.io.FileIO

setProjectDirs() - setup the project sub-directories from the project directory (batch/ cache/ ppx/ rdbms/ tmp/ xml/).

setPspotDebugging(int) - Method in class O2Plib.db.CSD.CSD

setPspotDebugging() - set the debug Pspot number for the CSD.

setRadioSublistChkMenuItemStates(String) - Method in class O2Plib.gui.MenuSupport

setRadioSublistChkMenuItemStates() - Do radio function by clearing all of the checkbox menu items except the one mentioned which is set to true.

setRadioSublistChkMenuItemStates(CheckboxMenuItem) - Method in class O2Plib.gui.MenuSupport

setRadioSublistChkMenuItemStates() - Do radio function by clearing all of the checkbox menu items except the one mentioned which is set to true.

setReportStatus(String) - Static method in class O2Plib.misc.Util

setReportStatus() - setup the status times

setReportStatusLineLabel(Label) - Static method in class O2Plib.misc.Util

setReportStatusLineLabel() - assign report status line label in popup report window.

setReportStatusLineTextField(TextField) - Static method in class O2Plib.misc.Util

setReportStatusLineTextField() - assign report status line text field in popup report window.

setReportTextArea(TextArea) - Static method in class O2Plib.misc.Util

setReportTextArea() - assign report text area in popup report window

setROI(int, int, int, int) - Method in class O2Plib.image.Roi

setROI() - set the Region of Interest.

setROI(Roi) - Method in class O2Plib.image.Roi

setROI() - set the ROI from another ROI srcRoi if it exists.

setROI2CALCW(int, int, int, int) - Method in class O2Plib.db.DbSample

setROI2CALCW() - set Calibration wedge computing window ROI

setROI2CW(int, int, int, int) - Method in class O2Plib.db.DbSample

setROI2CW() - set region of interest (ROI) to Computing Window (CW)

setRoiCode(int) - Method in class O2Plib.image.Roi

setRoiCode() - set the ROI code

setRoiDisplay(boolean) - Method in class O2Plib.image.Roi

setRoiDisplay() - set the ROI flag for display the Roi.

setRoiList(int) - Method in class O2Plib.image.RoiList

setRoiList() - set up Roi list

setRoiName(String) - Method in class O2Plib.image.Roi

setRoiName() - set the ROI name

setRowData(String[], int) - Method in class O2Plib.table.SimpleTable

setRowData() - set new row data[] for specific row in the table where newRowData[] must be the size of the table rows.

setRsampleAndSampleNames(String, String) - Method in class O2Plib.db.DbLM

setRsampleAndSampleNames() - set the Rsample and Sample names

setRsampleEditEnable(boolean) - Method in class O2Plib.db.LMset

setRsampleEditEnable() - enble editing Rsample landmark values.

setRspotDebugging(int) - Method in class O2Plib.db.CSD.CSD

setRspotDebugging() - set the debug Rspot number for the CSD.

setRspotDistanceThr(float) - Static method in class O2Plib.db.CSD.CSDRspot

setRspotDistanceThr() - set threshold to restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.

setRspotsList(CSDRspot[]) - Method in class O2Plib.db.CSD.CSDRspotList

setRspotsList() - set the list of Rspot CSDRspot objects This makes a copy of the Rspots not of the rspotsListData array and assigned the rspotsNbrs[], sets up maxRspots, totRspots, nbrRspots, nbrERspots.

setSampleDebugging(int) - Method in class O2Plib.db.CSD.CSD

setSampleDebugging() - set the debug Sample number for the CSD.

setSampleNames(String, String, String, String, String) - Method in class O2Plib.db.DbSample

setSampleNames() - set the DbSample state for current sample.

setSaturationPercentThresholds(float) - Method in class O2Plib.db.DbSample

setSaturationPercentThresholds() - set spot saturated percent threshold state for the current sample.

setSingleROItoDisplay(int) - Method in class O2Plib.image.RoiList

setSingleROItoDisplay() - set one ROI for display

setSizeLM - Variable in class O2Plib.db.LMset

# of spots in the LM set [0:nbrLandmarks-1][RSAMPLE:SAMPLE]

setSizingBit(int) - Method in class O2Plib.db.CSD.CSDlimits

setSizingBit() - set the search sizing limits bit

setSizingThresholds(float, float, float, float, float, float) - Method in class O2Plib.db.DbSample

setSizingThresholds() - set the spot sizing threshold for the current sample.

setSPFdebugCW(boolean, int, int, int, int) - Method in class O2Plib.db.DbPairSamples

setSPFdebugCW() - enable/disable debug computing window to restrict data read when test if dbRsample/dbSample p.(xMom,yMom) in SPF CW for debugging.

setSPFinputNames(String, String, int) - Method in class O2Plib.db.DbPairSamples

setSPFinputNames() - set the DbPairSamples SPF input file names.

setSPFoutputNames(String, int, String) - Method in class O2Plib.db.DbPairSamples

setSPFoutputNames() - set the DbPairSamples SPF output file names.

setStartTime(long) - Static method in class O2Plib.misc.Util

setStartTime() - set the start time for use with subsequent call to off_timer() without the start time arg.

setStateHashtableForGetValue(Hashtable, int) - Method in class O2Plib.misc.ParamHash

setStateHashtableForGetValue() - set working hash table for next getStateValue calls

setStateHashtableForGetValue(Hashtable) - Method in class O2Plib.misc.ParamHash

setStateHashtableForGetValue() - set working hash table for next getStateValue calls

setStudyFields(String[]) - Method in class O2Plib.db.CSD.CSDacc

setStudyFields() - set the accession database study fields.

setULHC(int, int) - Method in class O2Plib.image.Roi

setULHC() - set the Upper Left Hand Corner of Region of Interest

setUnits(String) - Method in class O2Plib.misc.CalibrateOD

setUnits() - set Wedge units, e.g.

setUnitsAbbrev(String) - Method in class O2Plib.misc.CalibrateOD

setUnitsAbbrev() - set Wedge units abbreviation, e.g.

setUnitsManufacturerPartNbr(String) - Method in class O2Plib.misc.CalibrateOD

setUnitsManufacturerPartNbr() - set Wedge manufacturerPartNbr

setupCalAndGrayMaps(int, float[]) - Method in class O2Plib.misc.CalibrateOD

setupCalAndGrayMaps() - set up the mapGrayToCal, gray2cal, and cal2gray maps.

setupDialogBox(Frame, String, String, String, String, Color) - Method in class O2Plib.gui.PopupYesNoDialogBox

setupDialogBox() - setup for popup yes/no/cancel modal dialog.

setupSpotList(int) - Method in class O2Plib.db.DbSample

setupSpotList() - create or regrow the spot list.

setupSpotPairList(int) - Method in class O2Plib.db.DbSample

setupSpotPairList() - create or regrow the DbPspot paired-spot list.

setUseInternalDTDflag(boolean) - Method in class O2Plib.db.CSD.CSD

setUseInternalDTDflag() - set the use internal DTD flag.

setUseInternalDTDflag(boolean) - Method in class O2Plib.db.DbAccession

setUseInternalDTDflag() - set the use internal DTD flag.

setUseInternalDTDflag(boolean) - Method in class O2Plib.db.DbLM

setUseInternalDTDflag() - set the use internal DTD flag.

setUseInternalDTDflag(boolean) - Method in class O2Plib.db.DbPairSamples

setUseInternalDTDflag() - set the use internal DTD flag.

setUseInternalDTDflag(boolean) - Method in class O2Plib.db.DbSample

setUseInternalDTDflag() - set the use internal DTD flag.

setUseLogFlag(boolean) - Method in class O2Plib.image.TiffPixelLoader

setUseLogFlag() - flag to set the log flag This is used if the data has more than 8-bits of grayscale so the data is transformed by the log over the range of 255*log(10**nBits-1) to 0

setUseXYhashFlag(boolean) - Method in class O2Plib.db.CSD.CSDRspotList

setUseXYhashFlag() - set useXYhashFlag to enable use of xyHash table.

setVerticalScrollBarVal(int) - Method in class O2Plib.image.ScrollableImage

setVerticalScrollBarVal() -

setWedgeCalData(float[], float[], int[], int, int, int, String, String) - Method in class O2Plib.misc.CalibrateOD

setWedgeCalData() - setup gray2cal from either gray to OD map or from wedge calibration (peaks,od) list of values.

setWedgeCWroi(int, int, int, int, String[]) - Method in class O2Plib.db.DbSample

setWedgeCWroi() - set Calibration wedge computing window ROI

setWedgeCWroi(int, int, int, int) - Method in class O2Plib.db.DbSample

setWedgeCWroi() - set Calibration wedge computing window ROI.

setWedgeGrayListData(String, int[]) - Method in class O2Plib.db.DbSample

setWedgeGrayListData() - set Calibration wedge wedgeGrayList in the accession DB field for this sample.

setWedgeROI(int, int, int, int) - Method in class O2Plib.misc.CalibrateOD

setWedgeROI() - set the Wedge Region of Interest

setWedgeROIforce(int, int, int, int) - Method in class O2Plib.misc.CalibrateOD

setWedgeROIforce() - force setting the Wedge Region of Interest reguardless of whether it is valid or not.

setXYeRspotCoords(float, float) - Method in class O2Plib.db.CSD.CSDRspot

setXYeRspotCoords() - set the (xERspot,yERspot) for this eRspot set

setXYrspotCoords(float, float) - Method in class O2Plib.db.CSD.CSDRspot

setXYrspotCoords() - set the (xRspot,yRspot) for this Rspot set

shiftMod - Variable in class O2Plib.image.ScrollableImage

SHIFT/Mouse

shortSPFlmNbr - Static variable in class O2Plib.db.DbPairSamples

Landmark number used for restricting SPF data read to Pspots belonging to Landmark shortSPFlmNbr.

shortSPFlmNbr - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

Landmark number used for restricting SPF data read to Pspots belonging to Landmark shortSPFlmNbr.

SHOW_DECIMAL - Static variable in class O2Plib.misc.Util

Window dump OCTAL data mode

SHOW_HEX - Static variable in class O2Plib.misc.Util

Window dump HEXIDECIMAL data mode

SHOW_OCTAL - Static variable in class O2Plib.misc.Util

Window dump OCTAL data mode

SHOW_OD - Static variable in class O2Plib.misc.Util

Window dump Optical Density data mode

showFullInfo(boolean) - Static method in class O2Plib.misc.Util

showFullInfo() - print full info on the program and exit if exitFlag is set.

showMediaTrackerStatusBits(String, URL, String, MediaTracker) - Method in class O2Plib.image.PixReader

showMediaTrackerStatusBits() - print the media tracker status bits

showMsg(String) - Method in class O2Plib.gui.PopupTableEditDialog

showMsg() - display the msg in text area window

showMsg(String) - Static method in class O2Plib.misc.Util

showMsg() - display the msg in message window

showReportStatus(String) - Static method in class O2Plib.misc.Util

showReportStatus() - display the msg in popup report line display And update the timer for the opr

showRoiFlag - Variable in class O2Plib.image.Roi

Flag indicating that the Roi is to be displayed.

showRoiFlag - Variable in class O2Plib.image.RoiList

flags for displaying roi

showStatus(String) - Static method in class O2Plib.misc.Util

showStatus() - display the msg in status

shrinkCube(MC_Cube) - Method in class O2Plib.image.MedianCut

shrinkCube() - Encloses "cube" with a tight-fitting cube by updating the (rmin,gmin,bmin) and (rmax,gmax,bmax) members of "cube".

sid - Variable in class O2Plib.image.PpxLoader

further identification - (sample ID)

simpleFileNameA - Variable in class O2Plib.db.DbSample

simple sample pix file name of the sample without the leading path.

simpleSampleFileNameA - Variable in class O2Plib.db.DbAccession

Simple sample file name with file extension

SimpleTable - Class in O2Plib.table

Class SimpleTable is the base class for tables.

SimpleTable() - Constructor for class O2Plib.table.SimpleTable

SimpleTable() - constructor for creating empty table.

SimpleTable(String, String, String) - Constructor for class O2Plib.table.SimpleTable

SimpleTable(String, String, int, int) - Constructor for class O2Plib.table.SimpleTable

SimpleTable() - constructor for creating empty table.

SimpleTable(String, String, String[], int, int) - Constructor for class O2Plib.table.SimpleTable

SimpleTable() - constructor for creating empty table.

SimpleTable(String, String, int, int, String[], String[][]) - Constructor for class O2Plib.table.SimpleTable

SimpleTable() - constructor for creating a table popupated with fields and data.

SIZE - Static variable in class O2Plib.image.ScrollableImage.Rule

width/height of Rule

sizingBits - Variable in class O2Plib.db.CSD.CSDlimits

skippedEntity(String) - Method in class O2Plib.db.DbAccession.AccContentHandler

skippedEntity() - This reports an entity that is skipped by the parser.

skippedEntity(String) - Method in class O2Plib.db.DbLM.LmsContentHandler

skippedEntity() - This reports an entity that is skipped by the parser.

skippedEntity(String) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

skippedEntity() - This reports an entity that is skipped by the parser.

skippedEntity(String) - Method in class O2Plib.db.DbSample.SsfContentHandler

skippedEntity() - This reports an entity that is skipped by the parser.

sleepFlag - Variable in class O2Plib.gui.PopupDialogQuery

wait for button to be pushed

sleepMsec(int) - Static method in class O2Plib.misc.Util

sleepMsec() - sleep for mSec.

sliderPanel - Variable in class O2Plib.gui.PopupOptions

smallFont - Variable in class O2Plib.gui.PopupTableEditDialog

sMaxDens - Variable in class O2Plib.db.DbPspot

max Sample pixel density seen in spot

sMaxDmax - Variable in class O2Plib.db.DbPairSamples

Maximum Sample maxD of any spot in DB

sMerx1 - Variable in class O2Plib.db.DbPspot

Sample Spot minimum enclosing rectangle Left in pixel coords

sMerx2 - Variable in class O2Plib.db.DbPspot

Sample Spot minimum enclosing rectangle Right in pixel coords

sMery1 - Variable in class O2Plib.db.DbPspot

Sample Spot minimum enclosing rectangle Top in pixel coords

sMery2 - Variable in class O2Plib.db.DbPspot

Sample Spot minimum enclosing rectangle Bottom in pixel coords

sMinDens - Variable in class O2Plib.db.DbPspot

min Sample pixel density seen in spot

sMinDmax - Variable in class O2Plib.db.DbPairSamples

minimum Sample minD of any spot in DB

sMnBkgdDens - Variable in class O2Plib.db.DbPspot

Mean Background pixel density for the G2 spot.

smoothChainCode() - Method in class O2Plib.db.DbBoundary

smoothChainCode() - smooth the chain code and return it in the same boundary.

smoothedChainCode - Variable in class O2Plib.db.DbBoundary

chain code [0:lth-1]

smoothHistogram(int[], int, int, int) - Method in class O2Plib.misc.CalibrateOD

smoothHistogram() - Compute smoothed histogram of hist[0:maxGray] into hData[0:maxGray] using 'Disaster Analysis'.

smoothingFilterWidth - Static variable in class O2Plib.db.DbBoundary

initial smoothing filter width allocation

sNbrCsamples - Variable in class O2Plib.db.DbPspot

# of samples in Sample Cspot Csample' estimate if not 0.

sort() - Method in class O2Plib.db.CSD.CSDcond

sort() - sort the condition set in ascending order by sample names

sort(int) - Method in class O2Plib.db.CSD.CSDRspot

sort() - sort the Rspot set in ascending order by the feature specified by sortByType.

sort() - Method in class O2Plib.db.CSD.CSDRspotList

sort() - sort the list of Rspot sets in ascending order by Rspot numbers

Sort - Class in O2Plib.misc

Class Sort contains utility sort functions for the 2D Open2Dprot program.

Sort() - Constructor for class O2Plib.misc.Sort

Sort() - Constructor

sortedNamesIdx - Variable in class O2Plib.gui.PopupNameListSelectorDialog

index list of names sorted alphabetically by names[0:nNames-1]

sortSpotList(int, boolean) - Method in class O2Plib.db.DbSample

sortSpotList() - sort spotList[0:nTopSpot-1] by feature SORT_BY_xxxx.

sortSpotPairList(int, int, boolean) - Method in class O2Plib.db.DbSample

sortSpotPairList() - sort spotPairList[0:nTopSpotPair-1] by feature SORT_BY_xxxx.

SP - Static variable in class O2Plib.db.CSD.CSDglb

Sure Pair - pairing program generated label

SP - Static variable in class O2Plib.db.DbBaseSpot

Sure Pair - pairing program generated label

SP - Static variable in class O2Plib.db.DbLM

Sure Pair - pairing program generated label

SP - Static variable in class O2Plib.db.DbPairSamples

Sure Pair - pairing program generated label

spaces - Variable in class O2Plib.gui.PopupDialogQuery

DEF_COL_SIZE spaces

SPCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Sure Pair spot label

sPerimeter - Variable in class O2Plib.db.DbPspot

Sample spot perimeter (pixels) for spot

spf - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

where save the paired data

SPF_VERSION - Static variable in class O2Plib.db.DbPairSamples

The Open2Dprot Sample Paired-spot File (SPF) version

spfCWSwitch - Variable in class O2Plib.db.DbPairSamples

Debugging switch.

spfCWX1 - Variable in class O2Plib.db.DbPairSamples

spfCWX2 - Variable in class O2Plib.db.DbPairSamples

spfCWY1 - Variable in class O2Plib.db.DbPairSamples

spfCWY2 - Variable in class O2Plib.db.DbPairSamples

spfFD - Variable in class O2Plib.db.DbPairSamples

output SPF file stream

spfFieldNames - Variable in class O2Plib.db.DbPairSamples

SPF database fields for these samples if not null

spfFile - Variable in class O2Plib.db.DbPairSamples

full path xml/ Sample Paired-Spotlist Files (SPF) full path input file.

spfInputFile - Variable in class O2Plib.db.DbPairSamples

name of SPF input file from file [FUTURE]

spfInputFormatMode - Variable in class O2Plib.db.DbPairSamples

SPF input file mode: Allowed: FileIO.IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

spfOutputEpilogueFile - Static variable in class O2Plib.db.DbPairSamples

full tab-delim EPILOGUE xml/ (Sample Pairs File) full path

spfOutputFile - Variable in class O2Plib.db.DbPairSamples

SPF either tab-delim xml/ Sample Paired Spot-list File full path

spfOutputFormatMode - Variable in class O2Plib.db.DbPairSamples

SPF output ample Paired Spot-list File mode: Allowed: FileIO.IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

spfOutputPrefaceFile - Static variable in class O2Plib.db.DbPairSamples

full tab-delim PREFACE xml/ (Sample Pairs File) full path

spfRowData - Variable in class O2Plib.db.DbPairSamples

SPF database data for these samples if not null

spID - Variable in class O2Plib.db.CSD.CSDannotation

Swiss-Prot ID

spName - Variable in class O2Plib.db.CSD.CSDannotation

Swiss-Prot Name

SPOT_FEATURE_AREA - Static variable in class O2Plib.db.DbBaseSpot

Spot area feature index

SPOT_FEATURE_DENS_PCT - Static variable in class O2Plib.db.DbBaseSpot

Spot percent density feature index

SPOT_FEATURE_DENS_PRIME - Static variable in class O2Plib.db.DbBaseSpot

Spot density' feature index

SPOT_FEATURE_DENSITY - Static variable in class O2Plib.db.DbBaseSpot

Spot density feature index

SPOT_FEATURE_MAX_DENS - Static variable in class O2Plib.db.DbBaseSpot

Spot mean density feature index

SPOT_FEATURE_MEAN_DENSITY - Static variable in class O2Plib.db.DbBaseSpot

Spot mean density feature index

SPOT_FEATURE_MIN_DENS - Static variable in class O2Plib.db.DbBaseSpot

Spot max density feature index

SPOT_FEATURE_VOLUME - Static variable in class O2Plib.db.DbBaseSpot

Spot volume feature index

spotBoundaryStr - Variable in class O2Plib.db.DbSample

spot boundary string if using boundaries

spotBoundaryStr - Variable in class O2Plib.db.DbSpot

spot boundary string if using boundaries

spotBoundaryStrIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

SPOTBOXCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Color of the selected spot indicated by a spot box

spotFeatureFailureFlag - Variable in class O2Plib.db.DbSample.SsfContentHandler

spotFlag - Variable in class O2Plib.db.DbSample.SsfContentHandler

when the begining of the list of spots is found

spotList - Variable in class O2Plib.db.CSD.CSDRspot

List of DbPspots constituting the Rspot set [0:nSpots-1].

spotList - Variable in class O2Plib.db.DbSample

DbSpot list [0:nTopSpot-1] for DbSpot spots entered by CC #.

spotNumber - Variable in class O2Plib.db.DbBaseSpot

Unique sequential spot number.

spotNumber - Variable in class O2Plib.db.DbSample

Unique sequential spot number.

spotPairFlag - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

(2) when begining of the list of spot-pairs is found

spotPairList - Variable in class O2Plib.db.DbSample

DbPspot list [0:nTopSpotPair-1] for DbPspot spots entered by CC #.

spotTblFields - Static variable in class O2Plib.db.DbSample

Accession table fields

spotTblHelpList - Static variable in class O2Plib.db.DbSample

Accession table help list

ss - Variable in class O2Plib.db.DbPairSamples.SpfContentHandler

instance of current Sample DbPspot which is a DbSpot that is extended to encode both spots data in the spot-pair.

sSDarea - Variable in class O2Plib.db.DbPspot

Sample Csample' S.D.

sSDdPrime - Variable in class O2Plib.db.DbPspot

Sample Csample' S.D.

sSDxCentroid - Variable in class O2Plib.db.DbPspot

Sample Csample' S.D.

sSDyCentroid - Variable in class O2Plib.db.DbPspot

Sample Csample' S.D.

SSF_VERSION - Static variable in class O2Plib.db.DbSample

SSF (Sample Spot-list File) version number

ssfCWSwitch - Variable in class O2Plib.db.DbSample

Debugging switch.

ssfCWX1 - Variable in class O2Plib.db.DbSample

ssfCWX2 - Variable in class O2Plib.db.DbSample

ssfCWY1 - Variable in class O2Plib.db.DbSample

ssfCWY2 - Variable in class O2Plib.db.DbSample

ssfEpilogueFD - Variable in class O2Plib.db.DbSample

output SSF Epilogue file stream

ssfFD - Variable in class O2Plib.db.DbSample

output SSF file stream

ssfFile - Variable in class O2Plib.db.DbSample

full path xml/ Sample Spotlist Files (SSF) full path input file.

ssfInputFile - Variable in class O2Plib.db.DbSample

name of SSF input file from file [FUTURE]

ssfInputFormatMode - Variable in class O2Plib.db.DbSample

SSF input file modes: Allowed: FileIO.IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

ssfOutputEpilogueFile - Variable in class O2Plib.db.DbSample

full tab-delim EPILOGUE xml/ Sample Spot-list File full path

ssfOutputFile - Variable in class O2Plib.db.DbSample

SSF either tab-delim xml/ Sample Spot-list File full path

ssfOutputFormatMode - Variable in class O2Plib.db.DbSample

SSF output file modes: Allowed: FileIO.IO_FORMAT_TAB_DELIM, IO_FORMAT_XML, IO_FORMAT_FULL, IO_FORMAT_GELLAB

ssfOutputPrefaceFile - Variable in class O2Plib.db.DbSample

full tab-delim PREFACE xml/ Sample Spot-list File full path

ssfPrefaceFD - Variable in class O2Plib.db.DbSample

output SSF Preface file stream

sSpotNbr - Variable in class O2Plib.db.DbPspot

spot Sample spot number

sSx - Variable in class O2Plib.db.DbPspot

Std Dev of Sample density weighted X centroid

sSy - Variable in class O2Plib.db.DbPspot

Std Dev of Sample density weighted Y centroid

startDataDict - Variable in class O2Plib.image.PpxLoader

(unsigned int) if non-zero, then byte # of file where data dictionary starts.

startDocument() - Method in class O2Plib.db.DbAccession.AccContentHandler

startDocument() - This indicates the start of a Document parse-this precedes all callbacks in all SAX Handlers with the sole exception of DbAccession.AccContentHandler.setDocumentLocator(org.xml.sax.Locator).

startDocument() - Method in class O2Plib.db.DbLM.LmsContentHandler

startDocument() - This indicates the start of a Document parse-this precedes all callbacks in all SAX Handlers with the sole exception of DbLM.LmsContentHandler.setDocumentLocator(org.xml.sax.Locator).

startDocument() - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

startDocument() - This indicates the start of a Document parse-this precedes all callbacks in all SAX Handlers with the sole exception of DbPairSamples.SpfContentHandler.setDocumentLocator(org.xml.sax.Locator).

startDocument() - Method in class O2Plib.db.DbSample.SsfContentHandler

startDocument() - This indicates the start of a Document parse-this precedes all callbacks in all SAX Handlers with the sole exception of DbSample.SsfContentHandler.setDocumentLocator(org.xml.sax.Locator).

startElement(String, String, String, Attributes) - Method in class O2Plib.db.DbAccession.AccContentHandler

startElement() - This reports the occurrence of an actual element.

startElement(String, String, String, Attributes) - Method in class O2Plib.db.DbLM.LmsContentHandler

startElement() - This reports the occurrence of an actual element.

startElement(String, String, String, Attributes) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

startElement() - This reports the occurrence of an actual element.

startElement(String, String, String, Attributes) - Method in class O2Plib.db.DbSample.SsfContentHandler

startElement() - This reports the occurrence of an actual element.

startImageData - Variable in class O2Plib.image.PpxLoader

(unsigned int) if non-zero, then byte # of file where image data starts.

startPopupDialog(String, int) - Method in class O2Plib.gui.PopupDialogQuery

startPopupDialog() - create a hidden dialog panel within a frame.

startPrefixMapping(String, String) - Method in class O2Plib.db.DbAccession.AccContentHandler

startPrefixMapping() - This indicates the beginning of an XML Namespace prefix mapping.

startPrefixMapping(String, String) - Method in class O2Plib.db.DbLM.LmsContentHandler

startPrefixMapping() - This indicates the beginning of an XML Namespace prefix mapping.

startPrefixMapping(String, String) - Method in class O2Plib.db.DbPairSamples.SpfContentHandler

startPrefixMapping() - This indicates the beginning of an XML Namespace prefix mapping.

startPrefixMapping(String, String) - Method in class O2Plib.db.DbSample.SsfContentHandler

startPrefixMapping() - This indicates the beginning of an XML Namespace prefix mapping.

startTime - Static variable in class O2Plib.misc.Util

he start time for use with subsequent call to off_timer() without the start time arg.

statusData - Variable in class O2Plib.gui.PopupOptions

The values set initially to resetStatusData[] and then modified by the user.

statusMemoryFree - Static variable in class O2Plib.misc.Util

Report status memory Free.

statusMemoryTot - Static variable in class O2Plib.misc.Util

Report status memory Total.

statusName - Static variable in class O2Plib.misc.Util

Report status names saved when do setReportStatus(name) calls.

statusStartTime - Static variable in class O2Plib.misc.Util

Report status starting times entries in epoch msec time Saved when do showReportStatus(name) calls.

stime - Variable in class O2Plib.image.PpxLoader

time of scan

storeDataBufParser(String, String[], boolean) - Method in class O2Plib.table.Table

storeDataBufParser() - Put data into Table tData[r][c] and tFields[c], given a String from the whole file.

stuffPanel - Variable in class O2Plib.gui.PopupNameListSelectorDialog

Panel to put "stuff" and will be put into ScrollPane

stuffPanel - Variable in class O2Plib.gui.PopupOptions

Panel to put "stuff" and will be put into ScrollPane

subDirsOKflag - Variable in class O2Plib.io.FileIO

Flag indicating that subdirectories were ok or created ok.

sumCVdensitySq - Variable in class O2Plib.db.CSD.CSDRspot

sum of squares of all rSpCV

sumDprimeRatioMeanSpots - Variable in class O2Plib.db.CSD.CSDnorm

Sum of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization

sVolume - Variable in class O2Plib.db.DbPspot

Sample Spot volume (density corrected for background by subtracting mnBackground*area .

sVolumeMax - Variable in class O2Plib.db.DbPairSamples

Maximum Sample volume (density) of any spot in DB

sVolumeMin - Variable in class O2Plib.db.DbPairSamples

Minimum Sample volume (density) of any spot in DB

sw - Static variable in class O2Plib.misc.Switches

Command line + Open2Dprot.properties state switches

swapBaseValues() - Method in class O2Plib.db.DbBaseSpot

swapBaseValues() - swap the Rsample and Sample field values

swappedRsampleAndSampleFlag - Variable in class O2Plib.db.DbBaseSpot

Set if swap the Rsample and Sample fields

swapSampleValues() - Method in class O2Plib.db.DbPspot

swapSampleValues() - swap the Rsample and Sample field values

Switches - Class in O2Plib.misc

Class Switches parses and manipulates command line switch lists.

Switches() - Constructor for class O2Plib.misc.Switches

Switches() - Constructor

sx - Variable in class O2Plib.db.DbSpot

spot size weight mean std dev

sxTotIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

sxy - Variable in class O2Plib.db.DbSpot

spot size weight mean std dev

sxyTotIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

sy - Variable in class O2Plib.db.DbSpot

spot size weight mean std dev

syTotIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

T

t1Area - Variable in class O2Plib.db.DbSample

lower threshold of area sizing

t1Density - Variable in class O2Plib.db.DbSample

lower threshold of density' sizing

t1Range - Variable in class O2Plib.db.DbSample

lower threshold of (maxD-minD) sizing

t2Area - Variable in class O2Plib.db.DbSample

upper threshold of area sizing

t2Density - Variable in class O2Plib.db.DbSample

upper threshold of density' sizing

t2Range - Variable in class O2Plib.db.DbSample

upper threshold of (maxD-minD) sizing

ta - Variable in class O2Plib.db.DbAccession

Accession database file table

Table - Class in O2Plib.table

Class Table creates a table object with no data or data read from a tab-delimited file.

Table() - Constructor for class O2Plib.table.Table

Table() - constructor for creating table from file.

Table(String) - Constructor for class O2Plib.table.Table

Table() - constructor for creating table from file.

Table(String, String[], boolean) - Constructor for class O2Plib.table.Table

Table() - constructor for creating table from file.

Table(int, int, String) - Constructor for class O2Plib.table.Table

Table() - constructor for creating empty table of (nRows,nCols).

Table(String, String, String, boolean) - Constructor for class O2Plib.table.Table

Table() - constructor for creating empty table.

Table(String, String, String[], int, int) - Constructor for class O2Plib.table.Table

Table() - constructor for creating empty table.

Table(String, String, int, int, String[], String[][]) - Constructor for class O2Plib.table.Table

SimpleTable() - constructor for creating a table popupated with fields and data.

Table(SimpleTable) - Constructor for class O2Plib.table.Table

Table() - constructor for creating table from a SimpleTable Errors are in (errMsg, errFlag).

tbl - Variable in class O2Plib.gui.PopupTableEditDialog

Table being edited.

tblList - Static variable in class O2Plib.table.Table

List of all Tables's [0:tblListSize-1].

tblListSize - Static variable in class O2Plib.table.Table

size of the tableList.

tblName - Variable in class O2Plib.gui.PopupTableEditDialog

Table name for use in the title

tCols - Variable in class O2Plib.db.DbAccession.AccContentHandler

the number of columns of the row to create

tCols - Variable in class O2Plib.db.DbLM.LmsContentHandler

the number of columns of the row to create

tCols - Variable in class O2Plib.table.SimpleTable

# of columns/row in the table

td - Variable in class O2Plib.db.DbSample

SSF data file table

tData - Variable in class O2Plib.table.SimpleTable

row vectors of data [0:tRows-1][0:tCols-1]

te - Variable in class O2Plib.db.DbSample

SSF epilogue file table

tessl - Variable in class O2Plib.image.PpxLoader

(unsigned int) tesselation code ??? bits???

testLegalFileExtension(String, String[]) - Static method in class O2Plib.io.FileIO

testLegalFileExtension() - test if file has a legal file extension by checking the list legalExtens[]

textAreaFontSize - Variable in class O2Plib.gui.PopupTableEditDialog

font size

textField - Variable in class O2Plib.gui.PopupDialogQuery

place text to be edited here

textFieldFont - Variable in class O2Plib.gui.PopupTableEditDialog

textFont - Variable in class O2Plib.gui.PopupOptions

text font

textFontFamily - Variable in class O2Plib.gui.PopupOptions

text font family

textFontFamily - Variable in class O2Plib.gui.PopupTableEditDialog

font family for message window

textFontSize - Variable in class O2Plib.gui.PopupOptions

font size

tf - Variable in class O2Plib.gui.PopupTextFieldDialog

text field

tFields - Variable in class O2Plib.table.SimpleTable

names of table fields

tHelp - Variable in class O2Plib.table.SimpleTable

names of table help data if any for defining the fields

THICKNESS - Variable in class O2Plib.gui.PopupOptions

tickFlagLRHC - Variable in class O2Plib.image.ScrollableImage

paint lower rt hand corner

tickFlagULHC - Variable in class O2Plib.image.ScrollableImage

paint upper lt hand corner

TiffPixelLoader - Class in O2Plib.image

TiffPixelLoader() - Constructor for class O2Plib.image.TiffPixelLoader

TiffPixelLoader() - constructor

TiffPixelLoader(boolean) - Constructor for class O2Plib.image.TiffPixelLoader

TiffPixelLoader() - constructor where set the debug flag

timerSwitch - Static variable in class O2Plib.misc.Util

timer is enabled

timeStamp - Variable in class O2Plib.db.CSD.CSDcond

timeStamp - Variable in class O2Plib.db.CSD.CSDexprList

timeStamp - Variable in class O2Plib.db.CSD.CSDfilterState

timeStamp - Variable in class O2Plib.db.CSD.CSDRmap

timeStamp - Variable in class O2Plib.db.CSD.CSDRspotList

title - Variable in class O2Plib.db.CSD.CSDcond

title information of condition.

title - Variable in class O2Plib.db.CSD.CSDexprList

title information of expression profile.

title - Variable in class O2Plib.db.CSD.CSDfilterState

title information of data-mining filter state.

title - Variable in class O2Plib.db.CSD.CSDRmap

title information of condition.

title - Variable in class O2Plib.db.CSD.CSDRspotList

title information of list of Rspots.

title - Variable in class O2Plib.gui.PopupOptions

Title for popup

title - Variable in class O2Plib.gui.PopupTableEditDialog

Title of Table being edited.

title - Variable in class O2Plib.table.SimpleTable

Optional title of table

tlm - Variable in class O2Plib.db.DbLM

Landmark database file table

tmpDir - Static variable in class O2Plib.db.CSD.CSDglb

Tmp images directory {projDir}/tmp/

tmpDir - Variable in class O2Plib.io.FileIO

Tmp images directory {projDir}/tmp/

toBriefString() - Method in class O2Plib.db.DbPspot

toBriefString() - get brief DbPspot features string of the spot.

toBriefString() - Method in class O2Plib.db.LMset

toBriefString() - get a brief pretty-print string representation of this instance

toBriefXML() - Method in class O2Plib.db.CSD.CSDexpr

toBriefXML() - get a brief string representation of this instance as XML.

toBriefXML() - Method in class O2Plib.db.CSD.CSDRspot

toBriefXML() - get a brief string representation of this instance as XML.

toBriefXML() - Method in class O2Plib.db.CSD.CSDRspotList

toBriefXML() - get a brief string representation of this instance as XML.

toBriefXML() - Method in class O2Plib.db.DbPspot

toBriefXML() - get a brief string representation of this instance as XML.

toBriefXML() - Method in class O2Plib.db.LMset

toBriefXML() - get a brief string representation of this instance as XML.

toDxyBriefString() - Method in class O2Plib.db.DbPspot

toDxyBriefString() - get brief DbPspot features string of the spot.

toDxyDpDlBriefString() - Method in class O2Plib.db.DbPspot

toDxyDpDlBriefString() - get brief DbPspot features string of the spot.

toFullXML() - Method in class O2Plib.db.CSD.CSDexpr

toFullXML() - get a full string representation of this instance as XML.

toFullXML() - Method in class O2Plib.db.CSD.CSDRspot

toFullXML() - get a full string representation of this instance as XML.

toFullXML() - Method in class O2Plib.db.CSD.CSDRspotList

toFullXML() - get a full string representation of this instance as XML.

toFullXML() - Method in class O2Plib.db.DbPspot

toFullXML() - get a full string representation of this instance as XML.

toFullXML() - Method in class O2Plib.db.LMset

toFullXML() - get a full string representation of this instance as XML.

toString() - Method in class O2Plib.db.CSD.CSDacc

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDannotation

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDcal

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDcond

toString() - print list of DbDsamples in the Condition list.

toString() - Method in class O2Plib.db.CSD.CSDexpr

toString() - print normalized values for the expression list.

toString(boolean) - Method in class O2Plib.db.CSD.CSDexpr

toString() - print values for the expression list - either raw or normalized values.

toString() - Method in class O2Plib.db.CSD.CSDexprList

toString() - print the list of expressions values in the list of expression lists.

toString() - Method in class O2Plib.db.CSD.CSDfilterState

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDio

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDlimits

toString() - get a pretty-print string representation of this instance

toString() - Method in interface O2Plib.db.CSD.CSDlistInterface

toString() - print features of the list.

toString() - Method in class O2Plib.db.CSD.CSDlms

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDnorm

toString() - get a pretty-print string representation of this instance [TODO] add additional state...

toString() - Method in class O2Plib.db.CSD.CSDRmap

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDRspot

toString() - print DbRspot features of the spot.

toString() - Method in class O2Plib.db.CSD.CSDRspotList

toString() - return a list of Rspot data for the List of Rspots.

toString() - Method in class O2Plib.db.CSD.CSDsizes

toString() - get a pretty-print string representation of this instance

toString() - Method in class O2Plib.db.CSD.CSDtotals

toString() - return the totals as a printable string

toString() - Method in class O2Plib.db.DbPspot

toString() - get DbPspot features string of the spot.

toString() - Method in class O2Plib.db.DbSpot

toString() - print SSF features of the spot.

toString() - Method in class O2Plib.db.LMset

toString() - get a full pretty-print string representation of this instance

toString() - Method in class O2Plib.image.PpxLoader

toString() - return string representation of this PpxLoader instance

toString() - Method in class O2Plib.image.TiffPixelLoader

toString() - return string representation of this instance

toStringFull() - Method in class O2Plib.db.CSD.CSDcal

toStringFull() - get a pretty-print string representation of this instance including the expanded calibration data

toStringFull() - Method in class O2Plib.db.CSD.CSDRspot

toStringFull() - print DbRspot full features of the spot.

toStringFull() - Method in class O2Plib.db.CSD.CSDRspotList

toStringFull() - return a list of Rspot data for the List of Rspots.

toStringIDs() - Method in class O2Plib.db.CSD.CSDRspotList

toStringIDs() - return a list of Rspot ID numbers for the list of Rspots.

toStringPointers() - Method in class O2Plib.db.CSD.CSDRspot

toStringPointers() - print DbRspot pointers of the spot.

toStringRsampleOnly() - Method in class O2Plib.db.DbPspot

toStringRsampleOnly() - get only Rsample DbPspot features of the spot.

toStringSample(DbPairSamples) - Method in class O2Plib.db.CSD.CSDtotals

toStringSample() - return the totals as a printable string

toStringSampleOnly() - Method in class O2Plib.db.DbPspot

toStringSampleOnly() - get only Sample DbPspot features of the spot.

toStringStatistics() - Method in class O2Plib.db.CSD.CSDRspot

toStringStatistics() - print DbRspot statistics of the Rspot set.

toTabDelimData() - Method in class O2Plib.db.CSD.CSDtotals

toTabDelimData() - get a string representation of this instance as tab delimited data.

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDacc

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDannotation

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDcal

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDcond

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDexpr

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDexprList

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDfilterState

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDlimits

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDlms

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDnorm

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDRmap

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData(String, boolean, boolean) - Method in class O2Plib.db.CSD.CSDRspot

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values.

toTabDelimitedData() - Method in class O2Plib.db.CSD.CSDsizes

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedData() - Method in class O2Plib.db.DbPspot

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

toTabDelimitedFields() - Method in class O2Plib.db.CSD.CSDexprList

toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

toTabDelimitedFields() - Method in class O2Plib.db.CSD.CSDfilterState

toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

toTabDelimitedFields() - Method in class O2Plib.db.CSD.CSDlimits

toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

toTabDelimitedFields() - Method in class O2Plib.db.CSD.CSDlms

toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

totDensPrime - Variable in class O2Plib.db.CSD.CSDnorm

Total D' (density corrected for background) for a sample for the percent total density normalization.

totNbrSpots - Variable in class O2Plib.db.CSD.CSDnorm

# of spots in this sample used in Percent total density normalization.

totRspots - Static variable in class O2Plib.db.CSD.CSDRspotList

Total number of Rspots in the rspotList[0:totRspots-1].

totSampleArea - Variable in class O2Plib.db.CSD.CSDtotals

totSampleArea - Variable in class O2Plib.db.DbSample

totSampleAreaPrime - Variable in class O2Plib.db.CSD.CSDtotals

totSampleAreaPrime - Variable in class O2Plib.db.DbSample

totSampleDensity - Variable in class O2Plib.db.CSD.CSDtotals

Data statistics read from the SSF files.

totSampleDensity - Variable in class O2Plib.db.DbSample

Data statistics read from the SSF files.

totSampleDensityPrime - Variable in class O2Plib.db.CSD.CSDtotals

Data statistics read from the SSF files.

totSampleDensityPrime - Variable in class O2Plib.db.DbSample

Data statistics read from the SSF files.

totSampleNbrSpots - Variable in class O2Plib.db.CSD.CSDtotals

totSampleNbrSpots - Variable in class O2Plib.db.DbSample

totSampleNbrSpotsPrime - Variable in class O2Plib.db.CSD.CSDtotals

totSampleNbrSpotsPrime - Variable in class O2Plib.db.DbSample

totStats - Variable in class O2Plib.db.DbSample

Global total statistics created at the end of the segmentation

toXML() - Method in class O2Plib.db.CSD.CSD

toXML() - convert database to XML string

toXML() - Method in class O2Plib.db.CSD.CSDacc

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDannotation

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDcal

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDcond

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDexpr

toXML() - get a full string representation of this instance as XML.

toXML(boolean) - Method in class O2Plib.db.CSD.CSDexpr

toXML() - get a string representation of this instance as XML.

toXML() - Method in class O2Plib.db.CSD.CSDexprList

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDfilterState

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDlimits

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDlms

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDnorm

toXML() - get a string representation of this instance as XML [TODO]

toXML() - Method in class O2Plib.db.CSD.CSDRmap

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDRspot

toXML() - get a full string representation of this instance as XML.

toXML(boolean) - Method in class O2Plib.db.CSD.CSDRspot

toXML() - get a string representation of this instance as XML

toXML(boolean) - Method in class O2Plib.db.CSD.CSDRspotList

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDsizes

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.CSD.CSDtotals

toXML() - get a string representation of this instance as XML

toXML() - Method in class O2Plib.db.DbPspot

toXML() - get a full string representation of this instance as XML.

toXML(boolean) - Method in class O2Plib.db.DbPspot

toXML() - get a string representation of this instance as XML.

toXML() - Method in class O2Plib.db.LMset

toXML() - get a full string representation of this instance as XML.

toXML(boolean) - Method in class O2Plib.db.LMset

toXML() - get a string representation of this instance as XML.

tp - Variable in class O2Plib.db.DbSample

SSF prologue file table

trimDelimChars(String, String) - Static method in class O2Plib.misc.Util

trimDelimChars() - trim enclosing delimiter charaters if present.

trimWhitespace() - Method in class O2Plib.table.SimpleTable

trimWhitespace() - trim Table tData[][] and tFields[] data.

trnsl - Variable in class O2Plib.image.PpxLoader

translation flag (0 = raw, 1 = done)

tRows - Variable in class O2Plib.table.SimpleTable

# of rows/Table

tspf - Variable in class O2Plib.db.DbPairSamples

tType - Variable in class O2Plib.table.SimpleTable

Type of table

U

UB - Static variable in class O2Plib.db.CSD.CSDfilterState

Upper bound index constant

UB - Static variable in class O2Plib.db.CSD.CSDlimits

Upper bound index constant

union(CSDcond, CSDcond) - Method in class O2Plib.db.CSD.CSDcond

union() - do the union of two condition lists r3= union(r1,r2).

union(CSDexprList, CSDexprList) - Method in class O2Plib.db.CSD.CSDexprList

union() - do the union of two ExprList lists r3= union(r1,r2).

union(CSDRspotList, CSDRspotList) - Method in class O2Plib.db.CSD.CSDRspotList

union() - do the union of two RSL lists r3= union(r1,r2).

uniprotID - Variable in class O2Plib.db.CSD.CSDannotation

UniProt ID

units - Variable in class O2Plib.image.ScrollableImage.Rule

rule units

units - Variable in class O2Plib.misc.CalibrateOD

full name units used in the step wedge.

unitsA - Variable in class O2Plib.db.DbAccession

calibration units

unitsAbbrev - Variable in class O2Plib.misc.CalibrateOD

abbreviation of units name used in the step wedge E.g., "od"

unitsAbbrevA - Variable in class O2Plib.db.DbAccession

calibration units abbreviation

up - Variable in class O2Plib.image.MC_Cube

update(Graphics) - Method in class O2Plib.gui.PopupTableEditDialog

update() - update without background the scrollable canvas

updateFilesFromServer(String, String, String[], String) - Static method in class O2Plib.io.FileIO

updateFilesFromServer() - update a list of files from the current server into the program install area.

updateLMsetsFromDbLM(String, String[]) - Method in class O2Plib.db.CSD.CSDlms

updateLMsetsFromDbLM() - update the LMset database from the DbLM that was previously setup.

updateOptionsGUI(String[], boolean[], String[], String) - Method in class O2Plib.gui.PopupOptions

updateOptionsGUI() - update the popup selector String swOptData[0:(3*nData)-1] is triples of (optionPrompt, guiBuilderSpec, helpStr) data for all switches.

updatePopupDialog(String, String, String[], int) - Method in class O2Plib.gui.PopupDialogQuery

updatePopupDialog() - display/unhide popup dialog frame and set new values.

updateReportStatusLine(String) - Static method in class O2Plib.misc.Util

updateReportStatusLine() - set status line message if text field and/or Label was assigned.

US - Static variable in class O2Plib.db.CSD.CSDglb

Unresolved Spot - pairing program generated label

US - Static variable in class O2Plib.db.DbBaseSpot

Unresolved Spot - pairing program generated label

US - Static variable in class O2Plib.db.DbLM

Unresolved Spot - pairing program generated label

US - Static variable in class O2Plib.db.DbPairSamples

Unresolved Spot - pairing program generated label

usage(String, boolean) - Static method in class O2Plib.misc.Util

usage() - print command usage.

usageFile(String, boolean) - Static method in class O2Plib.misc.Util

usageFile() - print command usage.

USCOLOR - Static variable in class O2Plib.db.DbBaseSpot

Unresolved spot label

USE_DOM_XML_SPF - Static variable in class O2Plib.db.DbPairSamples

Use DOM/JDOM/...

USE_DOM_XML_SSF - Static variable in class O2Plib.db.DbSample

enable for debugging DOM XML writer

useCalibFlag - Variable in class O2Plib.db.CSD.CSDcal

if calibration was performed for rSampleName.

useCsampleFlag - Variable in class O2Plib.db.DbPairSamples

use Csample extensions to SPF file.

useFileSeparatorChar(String, String) - Static method in class O2Plib.misc.Util

useFileSeparatorChar() - use specified file separator chararcter Eg.

useInternalDTDflag - Static variable in class O2Plib.db.CSD.CSDglb

Use internal "Open2Dprot-CSD.dtd" file in CSD XML output file.

useInternalDTDflag - Variable in class O2Plib.db.DbAccession

Use internal "Open2Dprot-Accession.dtd" file in Accession.xml output file

useInternalDTDflag - Variable in class O2Plib.db.DbLM

Use internal "Open2Dprot-Landmark.dtd" file in Landmark.xml output file

useInternalDTDflag - Variable in class O2Plib.db.DbPairSamples

Use internal "Open2Dprot-SPF.dtd" file in SPF XML output file.

useInternalDTDflag - Variable in class O2Plib.db.DbSample

Use internal "Open2Dprot-SSF.dtd" file in SSF XML output file.

useLM - Variable in class O2Plib.db.LMset

set false if bad landmark [0:nbrLandmarks-1]

useLogInputFlag - Variable in class O2Plib.image.TiffPixelLoader

"Use log of pixels if > 8-bits grayscale image"

usePercentDensitySwitch - Variable in class O2Plib.db.DbPairSamples

When generating SPF files, use percent of density D' rather than density D'.

userData - Variable in class O2Plib.gui.PopupOptions

Prompt user data [0:nData-1] if not null, then make a TextField with this data on the right else empty Label.

userDir - Static variable in class O2Plib.misc.Util

current User directory: getProperty("user.dir")+fileSeparator

useTemplateCB - Variable in class O2Plib.gui.PopupTableEditDialog

the "Use template" checkbox

useTemplateFlag - Variable in class O2Plib.gui.PopupTableEditDialog

set from "Use template" checkbox

useXYhashFlag - Variable in class O2Plib.db.CSD.CSDRspotList

Flag to use xyHashtable for lookup of Rspots by CSDRspot.(xRspot,yRspot).

util - Variable in class O2Plib.image.ScrollableImage

for misc methods

Util - Class in O2Plib.misc

Class Util utilities for Open2Dprot program.

Util(String) - Constructor for class O2Plib.misc.Util

Util() - constructor

V

validDataFlag - Variable in class O2Plib.gui.PopupNameListSelectorDialog

validLM - Variable in class O2Plib.db.DbLM

spot pair labels [nbrLandmarks]: "SM" - same spot in > 1 landmark "NG" - No Good, LM outside either/or Rsample or Sample CW "NL" - spot can't latch to LM (use LM DB coords) "OK" - landmark latched to spot.

valueData - Variable in class O2Plib.gui.PopupTableEditDialog

Value user data [0:nData-1] for a TextField with this data on the right

valueDataOrig - Variable in class O2Plib.gui.PopupTableEditDialog

Original Value user data [0:nData-1] for a TextField with this data on the right.

verifyNotCircularSSFlist(DbBaseSpot, String) - Method in class O2Plib.db.DbBaseSpot

verifyNotCircularSSFlist() - test to see if the spotlist is circular given a pointer into the list.

VERSION - Static variable in class O2Plib.db.CSD.CSD

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDacc

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDannotation

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDcache

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDcal

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDcond

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDexpr

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDexprList

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDfilterState

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDglb

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDio

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDlimits

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDlms

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDnorm

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDRmap

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDRspot

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDRspotList

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDsizes

Version for this module

VERSION - Static variable in class O2Plib.db.CSD.CSDtotals

Version for this module

VERSION - Static variable in class O2Plib.db.DbAccession

Version for this module

VERSION - Static variable in class O2Plib.db.DbBaseSpot

Version for this module

VERSION - Static variable in class O2Plib.db.DbBoundary

Version for this module

VERSION - Static variable in class O2Plib.db.DbLM

Version for this module

VERSION - Static variable in class O2Plib.db.DbPairSamples

Version for this module

VERSION - Static variable in class O2Plib.db.DbPspot

Version for this module

VERSION - Static variable in class O2Plib.db.DbSample

Version for this module

VERSION - Static variable in class O2Plib.db.DbSpot

Version for this module

VERSION - Static variable in class O2Plib.db.LMset

Version for this module

VERSION - Static variable in class O2Plib.image.PixReader

Version for this module

VERSION - Static variable in class O2Plib.image.PixWriter

Version for this module

VERSION - Static variable in class O2Plib.image.PpxLoader

Version for this module

VERSION - Static variable in class O2Plib.image.TiffPixelLoader

Version for this module

VERSION - Static variable in class O2Plib.io.FileIO

Version for this module

VERSION - Static variable in class O2Plib.misc.CalibrateOD

Version for this module

versionSPF - Variable in class O2Plib.db.DbPairSamples

version read from SPF file

VERTICAL - Static variable in class O2Plib.image.ScrollableImage.Rule

vertical orientation

VIEW_HEIGHT - Variable in class O2Plib.gui.PopupOptions

VIEW_HEIGHT - Variable in class O2Plib.gui.PopupTableEditDialog

Height of the frame

VIEW_WIDTH - Variable in class O2Plib.gui.PopupOptions

Size of the frame

VIEW_WIDTH - Variable in class O2Plib.gui.PopupTableEditDialog

Width of the frame

viewHeight - Variable in class O2Plib.gui.PopupTableEditDialog

viewHeight - Variable in class O2Plib.image.ScrollableImage

viewPortSize - Variable in class O2Plib.image.ScrollableImage

dimensions of the view port

viewWidth - Variable in class O2Plib.gui.PopupTableEditDialog

viewWidth - Variable in class O2Plib.image.ScrollableImage

vism - Variable in class O2Plib.image.PpxLoader

visualization method

volume - Variable in class O2Plib.db.DbSpot

percent spot volume

volumeIdx - Variable in class O2Plib.db.DbSample

Spot data Table de column field indices if tab-delimited tables are being used.

volumeMax - Variable in class O2Plib.db.CSD.CSDtotals

Maximum volume (density) of any spot in DB

volumeMin - Variable in class O2Plib.db.CSD.CSDtotals

Minimum volume (density) of any spot in DB

vPosOld - Variable in class O2Plib.image.ScrollableImage

old vertical position

W

warning(SAXParseException) - Method in class O2Plib.db.DbAccession.AccErrorHandler

warning() - This will report a warning that has occurred.

warning(SAXParseException) - Method in class O2Plib.db.DbLM.LmsErrorHandler

warning() - This will report a warning that has occurred.

warning(SAXParseException) - Method in class O2Plib.db.DbPairSamples.SpfErrorHandler

warning() - This will report a warning that has occurred; this indicates that while no XML rules were "broken", something appears to be incorrect or missing.

warning(SAXParseException) - Method in class O2Plib.db.DbSample.SsfErrorHandler

warning() - This will report a warning that has occurred; this indicates that while no XML rules were "broken", something appears to be incorrect or missing.

WEDGE_PPX - Static variable in class O2Plib.image.PpxLoader

Max number of wedge steps if applicable

wedgeCalIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

wedgeCalValues - Variable in class O2Plib.misc.CalibrateOD

Calibration value (could be OD) for corresponding wedge point [0:maxCalSteps-1].

wedgeCalValuesA - Variable in class O2Plib.db.DbAccession

list of calibration wedge calibration values if any

wedgeGrayIdx - Variable in class O2Plib.db.DbAccession

Required accession database Table ta column field indices if tab-delimited tables are being used.

wedgeGrayValues - Variable in class O2Plib.misc.CalibrateOD

Gray value for corresponding wedge point [0:maxPeaks-1].

wedgeGrayValuesA - Variable in class O2Plib.db.DbAccession

list of calibration wedge gray values if any

wedgeRoiOKflag - Variable in class O2Plib.misc.CalibrateOD

Had a valid calibration wedge ROI when came into the wizard

wedgeType - Variable in class O2Plib.image.PpxLoader

Type of step wedge if any in the image: 0 = none 1 = ND, neutral density 2 = CPM, counts per minute 3 = DPM, disintegrations per minute 4 to 255 =

wedgeVal - Variable in class O2Plib.image.PpxLoader

(24-bit unsigned) ND*1024 or CPM wedge step values

width - Variable in class O2Plib.image.MedianCut

width size of image

width - Variable in class O2Plib.image.WriteGifEncoder

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowActivated(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowClosed(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowClosing() - close down the window on PC only.

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowClosing() - close down the window.

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowClosing() - close down the window.

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowClosing() - closing down the window, get rid of the frame.

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowClosing() - close down the window - assume false.

windowClosing(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowClosing() - close down the window - assume false.

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowDeactivated(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowDeiconified(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowIconified(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupDialogQuery

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupNameListSelectorDialog

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupOptions

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupTableEditDialog

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupTextFieldDialog

windowOpened(WindowEvent) - Method in class O2Plib.gui.PopupYesNoDialogBox

WinDump - Class in O2Plib.image

WinDump() - Constructor for class O2Plib.image.WinDump

WinDump() - constructor

winDump(int[], int, int, int, int, int, int, String, int, int, float[], int) - Static method in class O2Plib.image.WinDump

winDump() - Draw a window from picture from the lower 16-bit/pixel data in an int[] 'pix' at

winDump(char[], int, int, int, int, int, int, String, int, int, float[], int) - Static method in class O2Plib.image.WinDump

winDump() - Draw a window from picture from the 16-bit/pixel data in an char[] 'pix' at

wrdsPerBlock - Variable in class O2Plib.db.CSD.CSDsizes

# 32-bit words/disk block in cache buffer

wrdsPerNode - Variable in class O2Plib.db.CSD.CSDsizes

# 32-bit words/Rspot NODE in cache buffer

WRITE_TO_BOTH - Static variable in class O2Plib.misc.Util

code to write to Both StdOut and the disk

WRITE_TO_DISK - Static variable in class O2Plib.misc.Util

code to write to StdOut

WRITE_TO_STDOUT - Static variable in class O2Plib.misc.Util

code to write to StdOut

writeAccessionTable(String, int, boolean) - Method in class O2Plib.db.DbAccession

writeAccessionTable() - write out the landmarks table in the specified format.

writeBriefXML(BufferedWriter) - Method in class O2Plib.db.CSD.CSDRspotList

writeBriefXML() - write a brief representation of this instance as XML.

writeCacheFiles(boolean, boolean) - Method in class O2Plib.db.CSD.CSDio

writeCacheFiles() - Write out the CSD database as cache files into the csdCACHEfile file that should already be set up.

writeEntireDOM_XML(String) - Method in class O2Plib.db.DbPairSamples

writeEntireDOM_XML() - write the entire SPF file into an XML file using DOM/JDOM/...

writeEntireDOM_XML(String) - Method in class O2Plib.db.DbSample

writeEntireDOM_XML() - write the entire SSF file into an XML file using DOM/JDOM/...

writeEntireSPF(String, String, int) - Method in class O2Plib.db.DbPairSamples

writeEntireSPF() - write the entirepaired-spots SPF file.

writeEntireSPF(String, String, String, String, String, int) - Method in class O2Plib.db.DbPairSamples

writeEntireSPF() - write the entirepaired-spots SPF file.

writeEntireSSF(String, String[], String, String, String, int) - Method in class O2Plib.db.DbSample

writeEntireSSF() - write the entire SSF file.

writeFile(String) - Method in class O2Plib.image.WriteGifEncoder

writeFile() - write the Gif encoded image to output file

writeFinish(String) - Method in class O2Plib.db.DbSample

writeFinish() - finish and close the segemented output file.

writeFullXML(BufferedWriter) - Method in class O2Plib.db.CSD.CSDRspotList

writeFullXML() - get a full string representation of this instance as XML.

writeGif(FileOutputStream) - Method in class O2Plib.image.WriteGifEncoder

writeGif() - Saves the image as a GIF file.

WriteGifEncoder - Class in O2Plib.image

WriteGifEncoder(int, int, byte[], byte[], byte[], byte[]) - Constructor for class O2Plib.image.WriteGifEncoder

WriteGifEncoder() - Constructs a new WriteGifEncoder.

WriteGifEncoder(Image) - Constructor for class O2Plib.image.WriteGifEncoder

WriteGifEncoder() - Constructs using 24-bit Image.

WriteGifEncoderHashitem - Class in O2Plib.image

WriteGifEncoderHashitem(int, int, int, boolean) - Constructor for class O2Plib.image.WriteGifEncoderHashitem

WriteGifEncoderHashitem() - constructor

writeLandmarksTable(String, int, boolean) - Method in class O2Plib.db.DbLM

writeLandmarksTable() - write out the landmarks table in the specified format.

writePixFile(int[], boolean, String, int, int) - Static method in class O2Plib.image.PixWriter

writePixFile() - write image buffer pix to a GIF or JPEG file.

writePixFile(char[], boolean, String, int, int) - Static method in class O2Plib.image.PixWriter

writePixFile() - write image buffer pix to a GIF or JPEG file.

writeRDBMS(boolean, boolean) - Method in class O2Plib.db.CSD.CSDio

writeRDBMS() - Write out the CSD database into the RDBMS using the the csdRDBMSfile file that should already be set up.

writeSPFfinish(String) - Method in class O2Plib.db.DbPairSamples

writeSPFfinish() - finish and close the SPF output stream in spfFD.

writeSPFpairedSpots() - Method in class O2Plib.db.DbPairSamples

writeSPFpairedSpots() - dump paired spot list data base into SPF output stream in spfFD.

writeSPFpreface(String, String) - Method in class O2Plib.db.DbPairSamples

writeSPFpreface() - Dump the SPF preface to the SPF output stream in spfFD.

writeSpotsToFile() - Method in class O2Plib.db.DbSample

writeSpotsToFile() - write the linked spot list, spot by spot, into the log file.

writeSSFpreface(String, String[], String, String) - Method in class O2Plib.db.DbSample

writeSSFpreface() - write the SSF preface to the SSF file in ssfFD.

writeStatisticsToSPFfile() - Method in class O2Plib.db.DbPairSamples

writeStatisticsToSPFfile() - Dump the epilogue consisting of the paired spot statistics to the SPF output stream in spfFD.

writeStatisticsToSSFfile() - Method in class O2Plib.db.DbSample

writeStatisticsToSSFfile() - write the segmented spot statistics to the SSF file in ssfFD.

writeString(FileOutputStream, String) - Static method in class O2Plib.image.WriteGifEncoder

writeString() - write string to the file.

writeStrToFileBuffer(String, FileWriter) - Static method in class O2Plib.io.FileIO

writeStrToFileBuffer() - Output a String to the output channel 'fd'.

writeTabDelimitedFiles(boolean, boolean) - Method in class O2Plib.db.CSD.CSDio

writeTabDelimitedFiles() - Write out the database as a set of tab-delimited files used the CSD database name as the prefix followed by the type of data followed by .txt.

writeTableDelim(String, String) - Method in class O2Plib.table.Table

writeTableDelim() - Write the table as a delimited character or string file.

writeTableXML(String, String, String, String, String, String) - Method in class O2Plib.table.Table

writeTableXML() - Write the table as an XML file

writeTableXML(String, String, String, String, String) - Method in class O2Plib.table.Table

writeTableXML() - Write the table as an XML file.

writeTextFile(String, String) - Static method in class O2Plib.io.FileIO

writeTextFile() - write string data to a local disk file.

writeXML(BufferedWriter, boolean) - Method in class O2Plib.db.CSD.CSDRspotList

writeXML() - get a string representation of this instance as XML

writeXMLfile(boolean, boolean) - Method in class O2Plib.db.CSD.CSDio

writeXMLfile() - Write out the CSD database as an XML file into the csdXMLfile file that should already be set up.

wrkAnotation - Static variable in class O2Plib.db.CSD.CSDglb

Working Annotation related data instance.

wrkCalib - Static variable in class O2Plib.db.CSD.CSDglb

Working calibration related data

wrkERspot - Static variable in class O2Plib.db.CSD.CSDglb

Working Rspot related data.

wrkExpr - Static variable in class O2Plib.db.CSD.CSDglb

Working expression profile related data.

wrkSamples - Variable in class O2Plib.db.CSD.CSDfilterState

list of samples in the working set of samples

wrkSetSamples - Static variable in class O2Plib.db.CSD.CSDglb

Working set of samples.

X

x0 - Variable in class O2Plib.db.DbBoundary

First pixel (needed if using chain code)

x0 - Variable in class O2Plib.image.PpxLoader

(unsigned short) top left X corner of image in cm*1024

x1 - Variable in class O2Plib.image.Roi

ROI ULHC X coordinate

x2 - Variable in class O2Plib.image.Roi

ROI LRHC X cooreinate

xb - Variable in class O2Plib.db.DbBoundary

x coordinates[0:lth-1]

xBase - Variable in class O2Plib.image.ScrollableImage

+ base address of ULHC of clipped image in image canvas used in last paint

xCalib - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] corresponding calibration value

xCoord - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] X coordinate for pIe

xCtr - Variable in class O2Plib.image.ScrollableImage

center coords of image, for zoom/dezoom

xERspot - Variable in class O2Plib.db.CSD.CSDRspot

Estimated X centroid coordinate of ERspot mapped to the Rsample coordinate space.This is created only if the Rspot is an ERspot.

xImg - Variable in class O2Plib.image.ScrollableImage

image address (x,y)+(xBase,yBase)

xlm - Variable in class O2Plib.db.LMset

X position of landmarks [0:nbrLandmarks-1][RSAMPLE:SAMPLE].

xmlDate - Variable in class O2Plib.db.DbAccession

XML accession file date "Date"

xmlDate - Variable in class O2Plib.db.DbLM

XML landmark file date "Date"

xmlDBname - Variable in class O2Plib.db.DbAccession

XML accession file database name value for "DatabaseName"

xmlDBname - Variable in class O2Plib.db.DbLM

XML landmark file database name "DatabaseName"

xmlDir - Static variable in class O2Plib.db.CSD.CSDglb

Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.

xmlDir - Variable in class O2Plib.io.FileIO

Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.

xmlLoader - Class in O2Plib.db.xml

Class xmlLoader is used to ...

xmlLoader() - Constructor for class O2Plib.db.xml.xmlLoader

xMom - Variable in class O2Plib.db.DbSpot

spot X density weighted centroid

xName - Variable in class O2Plib.db.CSD.CSDcal

name of X-axis isoelectric point : "pIe" or Retention time "RT"

xObj - Variable in class O2Plib.image.ScrollableImage

image address (x,y)+(xBase,yBase)

xRmom - Variable in class O2Plib.db.DbPspot

X Abs Rsample(x,y) spot centroid

xRsampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

xRspot - Variable in class O2Plib.db.CSD.CSDRspot

X coordinate of Rsample Rspot.

xSampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

xSel - Variable in class O2Plib.db.DbSample

Selected X coordinate, set elsewhere

xSetSamples - Static variable in class O2Plib.db.CSD.CSDglb

X set of samples.

xSmom - Variable in class O2Plib.db.DbPspot

X Abs Sample(x,y) spot centroid

xUnits - Variable in class O2Plib.db.CSD.CSDcal

Scale UNITS of X-axis : "pH" or "seconds"

xyHash - Variable in class O2Plib.db.CSD.CSDRspotList

hashTable for xy coordinate lookup.

xyList - Variable in class O2Plib.db.DbSpot

List of all packed (x<<16 | y) 16-bit pixel coordinates in the spot which is updated by the particular application - optional.

xyPoint - Static variable in class O2Plib.db.DbBoundary

working (x,y) point

Y

y0 - Variable in class O2Plib.db.DbBoundary

First pixel (needed if using chain code)

y0 - Variable in class O2Plib.image.PpxLoader

(unsigned short) top left Y corner of image in cm*1024

y1 - Variable in class O2Plib.image.Roi

ROI ULHC Y coordinate

y2 - Variable in class O2Plib.image.Roi

ROI LRHC Y coordinate

yb - Variable in class O2Plib.db.DbBoundary

y coordinates[0:lth-1]

yBase - Variable in class O2Plib.image.ScrollableImage

yCalib - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] corresponding calibration value

yCoord - Variable in class O2Plib.db.CSD.CSDcal

[0:maxCalibrations-1] Y coordinate for MW

yCtr - Variable in class O2Plib.image.ScrollableImage

center coords of image, for zoom/dezoom

yERspot - Variable in class O2Plib.db.CSD.CSDRspot

Estimated Y centroid coordinate of ERspot mapped to the Rsample coordinate space.

yesMsg - Variable in class O2Plib.gui.PopupYesNoDialogBox

Yes label for dialog box

yImg - Variable in class O2Plib.image.ScrollableImage

image address (x,y)+(xBase,yBase)

ylm - Variable in class O2Plib.db.LMset

Y position of landmarks [0:nbrLandmarks-1][RSAMPLE:SAMPLE].

yMom - Variable in class O2Plib.db.DbSpot

spot Y density weighted centroid

yName - Variable in class O2Plib.db.CSD.CSDcal

name of Y-axis Molecular Mass: "mw" or Mass size "mhz"

yObj - Variable in class O2Plib.image.ScrollableImage

image address (x,y)+(xBase,yBase)

yRmom - Variable in class O2Plib.db.DbPspot

Y Abs Rsample(x,y) spot centroid

yRsampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

yRspot - Variable in class O2Plib.db.CSD.CSDRspot

Y coordinate of Rsample Rspot.

ySampleIdx - Variable in class O2Plib.db.DbLM

Landmark data Table tlm column field indices if tab-delimited tables are being used.

ySel - Variable in class O2Plib.db.DbSample

Selected Y coordinate, set elsewhere

ySetSamples - Static variable in class O2Plib.db.CSD.CSDglb

Y set of samples.

ySmom - Variable in class O2Plib.db.DbPspot

Y Abs Sample(x,y) spot centroid

yUnits - Variable in class O2Plib.db.CSD.CSDcal

Scale UNITS of Y-axis : "Dalton"

Z

zoomValue - Variable in class O2Plib.image.ScrollableImage

zoom/magnification value

zSpot - Variable in class O2Plib.db.CSD.CSDio

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