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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