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

A

acc - Variable in class Accession.AccACCwizardPopup

Accession database instance if opened

acc - Static variable in class Accession.Accglb

AccACCwizardPopup - Class in Accession

Class AccACCwizardPopup implements a popup GUI to create and edit the sample annotation used in the accessioning program.

AccACCwizardPopup(Accession, String) - Constructor for class Accession.AccACCwizardPopup

AccACCwizardPopup() - Constructor

AccCALIBwizardPopup - Class in Accession

The AccCALIBwizardPopupclass implements a popup GUI to create and edit the image grayscale calibration used in the accessioning program.

AccCALIBwizardPopup(Accession, DbSample, int, float[], int[], int, int, String, Table) - Constructor for class Accession.AccCALIBwizardPopup

AccCALIBwizardPopup() - Constructor.

AccData - Class in Accession

Class AccData is used for data output for accession data.

AccData() - Constructor for class Accession.AccData

AccData() - Constructor

accDatabaseFile - Static variable in class Accession.Accglb

full path Accession database file

Accession - package Accession

Accession - Class in Accession

The Accession program is used for adding or accessioning sampless for an Open2Dprot database.

Accession() - Constructor for class Accession.Accession

accessionEditButton - Variable in class Accession.AccReportPopup

button for "Accession" button

accessionURL - Static variable in class Accession.Accglb

Hardwired Open2Dprot server connection Switch to S.F.

accFile - Static variable in class Accession.Accglb

Accession database file without the path.

accFormatMode - Static variable in class Accession.Accglb

Accession DB file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

Accglb - Class in Accession

Class Accglb is the base class that specifies global variables used by all of the other Open2Dprot Accession program classes.

Accglb() - Constructor for class Accession.Accglb

accGUI - Variable in class Accession.AccReportPopup

popup Accession wizard GUI

AccIni - Class in Accession

Class AccIni is used to initialize data structures for the 2Open2Dprot Accession program

AccIni() - Constructor for class Accession.AccIni

AccIni() - Constructor

AccReportPopup - Class in Accession

Class AccReportPopup creates and displays scrollable string text area in a popup window.

AccReportPopup(Accession) - Constructor for class Accession.AccReportPopup

AccReportPopup() - Constructor.

AccReportPopup(Accession, String, String, int, int, String, String, boolean) - Constructor for class Accession.AccReportPopup

AccReportPopup() - Constructor.

AccROIwizardPopup - Class in Accession

AccROIwizardPopup(Accession, DbSample) - Constructor for class Accession.AccROIwizardPopup

AccROIwizardPopup() - Constructor

AccROIwizardPopup.ScrollableImageCanvas - Class in Accession

ScrollableImageCanvas class supports a scrollable canvas

AccROIwizardPopup.ScrollableImageCanvas(AccROIwizardPopup, Image) - Constructor for class Accession.AccROIwizardPopup.ScrollableImageCanvas

ScrollableImageCanvas() - constructor.

actionPerformed(ActionEvent) - Method in class Accession.AccACCwizardPopup

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class Accession.AccCALIBwizardPopup

actionPerformed() - Handle Control panel button clicks

actionPerformed(ActionEvent) - Method in class Accession.AccReportPopup

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class Accession.AccROIwizardPopup

actionPerformed() - Handle button clicks

activeBin - Variable in class Accession.AccCALIBwizardPopup

active bin idx [0:nHist-1] else -1

ADD_WINDUMP - Static variable in class Accession.Accglb

Use the winDump option in the ROI GUI.

additionalInit() - Static method in class Accession.AccIni

additionalInit() - initialize other parameters now that we have the computing window, image size, bits/pixel, OD calibration, etc.

addMenuTree(Frame, MenuBar) - Method in class Accession.AccACCwizardPopup

addMenuTree() - create pull down menus in menu bar

addMenuTree(Frame, MenuBar) - Method in class Accession.AccCALIBwizardPopup

addMenuTree() - create pull down menus in menu bar

addMenuTree(Frame, MenuBar) - Method in class Accession.AccReportPopup

addMenuTree() - create pull down menus in menu bar

addMenuTree(Frame, MenuBar) - Method in class Accession.AccROIwizardPopup

addMenuTree() - create pull down menus in menu bar

addSpotToSpotList(DbSpot) - Method in class Accession.AccReportPopup

addSpotToSpotList() - add (x,y) spot of size spotDiameter to the spot list for the current sample.

adjustmentValueChanged(AdjustmentEvent) - Method in class Accession.AccACCwizardPopup

adjustmentValueChanged() - handle ImageScroller scroll events.

adjustmentValueChanged(AdjustmentEvent) - Method in class Accession.AccROIwizardPopup

adjustmentValueChanged() - handle ImageScroller scroll events.

aH - Variable in class Accession.AccACCwizardPopup

aH - Variable in class Accession.AccROIwizardPopup

ALLOW_CALIBRATION - Static variable in class Accession.Accglb

Allow access to Calibration popup window

ALLOW_SAVE_DB - Static variable in class Accession.Accglb

Allow saving modified Accession database file

altMod - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

ALT/Mouse

appendTextMsg(String) - Method in class Accession.AccReportPopup

appendTextMsg() - append text in popup window

applicationName - Static variable in class Accession.Accglb

name of the application

argsV - Static variable in class Accession.Accglb

Total command list arg list originally set fro main(args)

aV - Variable in class Accession.AccACCwizardPopup

aV - Variable in class Accession.AccROIwizardPopup

B

banner - Static variable in class Accession.Accglb

The full version data banner with todays date

bannerTitle - Static variable in class Accession.Accglb

The short version data banner for popup titles

baseImageFile - Variable in class Accession.AccACCwizardPopup

base name of the image for use in the title

batchDir - Static variable in class Accession.Accglb

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

bkgrdSpot - Static variable in class Accession.Accglb

Sample Background spot used in spot measurements if not null.

buildAccWizardGUI() - Method in class Accession.AccACCwizardPopup

buildAccWizardGUI() - Build the ImageViewer GUI

buildHistGUI() - Method in class Accession.AccCALIBwizardPopup

buildHistGUI() - build the histogram GUI

buildImageGUI() - Method in class Accession.AccROIwizardPopup

buildImageGUI() - Build the ImageViewer GUI

buildListOfSamplesSubmenus(Menu, String, String) - Method in class Accession.AccACCwizardPopup

buildListOfSamplesSubmenus() - rebuild submenus list of samples from entries in the accession database.

buttonFont - Variable in class Accession.AccCALIBwizardPopup

C

cacheDir - Static variable in class Accession.Accglb

Cache database directory {projDir}/cache/

CAL_DATA_FILE - Static variable in class Accession.AccCALIBwizardPopup

get (cal,gray) list calibration from tab-delim data file field names: (PEAK CAL GRAY CAL-UNIT CAL-ABBREV)

CAL_MANUAL - Static variable in class Accession.AccCALIBwizardPopup

Enter calibration manually by typing into the table.

CAL_SPOTLIST - Static variable in class Accession.AccCALIBwizardPopup

Use Spot list values for gray values grayDataList[]

CAL_WEDGE - Static variable in class Accession.AccCALIBwizardPopup

Use ND step wedge ROI for gray values

calDataList - Variable in class Accession.AccCALIBwizardPopup

calDataList is calibration value list if not null

calDataMode - Variable in class Accession.AccCALIBwizardPopup

calDataMode of form CAL_WEDGE, CAL_SPOTLIST

calibEditChoice - Variable in class Accession.AccReportPopup

Choice pull-down menu for selecting calibration method: "Calibrate wedge" "Calibrate spot list" "Calibrate data" "Calibrate by file"

calibGUI - Variable in class Accession.AccReportPopup

popup Calibration wizard GUI

calibPeakColor - Variable in class Accession.AccCALIBwizardPopup

calibration peaks on histogram color

calibTbl - Variable in class Accession.AccCALIBwizardPopup

calibration data file table

calibTbl - Variable in class Accession.AccReportPopup

Calibration table that can be used to sepecify calibration values from a file.

calIdx - Variable in class Accession.AccReportPopup

index of field "CAL" in calibTbl

calTypeStr - Variable in class Accession.AccCALIBwizardPopup

String name of calDataMode.

calUnitAbbrevIdx - Variable in class Accession.AccReportPopup

index of field "CAL-ABBREV" in calibTbl

calUnitIdx - Variable in class Accession.AccReportPopup

index of field "CAL-UNIT" in calibTbl

calUnits - Variable in class Accession.AccCALIBwizardPopup

calUnits is name of calibration units if not null

cancelFlag - Variable in class Accession.AccReportPopup

pressed sog.

changedAccCalibrDataFlag - Variable in class Accession.AccCALIBwizardPopup

Flag indicating that the accession calibration fields were defined or were edited

changedAccDBnameFlag - Static variable in class Accession.Accglb

Flag indicating changed the Accession DB data name

changedAccFieldsDataFlag - Variable in class Accession.AccACCwizardPopup

Flag indicating that the data fields were edited

changedCalCWroiFlag - Static variable in class Accession.AccROIwizardPopup

Flag indicates changed the calibration wedge CW ROI.

changedCWroiFlag - Static variable in class Accession.AccROIwizardPopup

Flag indicates changed the CW ROI.

changedValueData - Variable in class Accession.AccACCwizardPopup

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 Accession.AccACCwizardPopup

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

changeGuiFlag - Variable in class Accession.AccROIwizardPopup

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

cleanKillApplication(boolean) - Method in class Accession.AccReportPopup

cleanKillApplication() - close the file if needed and do a clean kill of the application

clearSpotList() - Method in class Accession.AccReportPopup

clearSpotList() - clear the spot list for the current sample.

clearText() - Method in class Accession.AccReportPopup

clearText() - clear text in popup window

clearWorkingROI() - Method in class Accession.AccROIwizardPopup

clearWorkingROI() - clear the working ROI\ to -1's.

close(boolean) - Method in class Accession.AccACCwizardPopup

close() - get the data into newData, close this popup and reset flags

close(boolean) - Method in class Accession.AccCALIBwizardPopup

close() - close this popup and reset flags

close() - Method in class Accession.AccReportPopup

close() - close this popup and reset flags if needed

close(boolean) - Method in class Accession.AccROIwizardPopup

close() - close this popup and reset flags

colorCALCW - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Overlay color for Calibration Wedge ROI

colorCW - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Overlay color for CW ROI

colorROI - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Overlay color for working ROI

colorSPOT_LIST - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Overlay color for spot list

CONSOLE_FLAG - Static variable in class Accession.Accglb

controlPanel - Variable in class Accession.AccACCwizardPopup

Control panel for the main frame

controlPanel - Variable in class Accession.AccROIwizardPopup

Control panel for the main frame

createNewAccDBfile(String, String) - Method in class Accession.Accession

createNewAccDBfile() - create a new the accession database file with the header but not the data.

cs - Variable in class Accession.AccACCwizardPopup

instance of the main class

cs - Variable in class Accession.AccCALIBwizardPopup

instance of the main class

cs - Static variable in class Accession.Accglb

instance of the main class

cs - Variable in class Accession.AccReportPopup

instance of the main class

cs - Variable in class Accession.AccROIwizardPopup

instance of the main class

cs - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

instance of the main class

csi - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

ctrlMod - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

CTRL/Mouse

ctrlShiftMod - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

CTRL-SHIFT/Mouse

curLMS - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

current landmark set of current spot.

cursorColor - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Overlay color for cursor

cwx1 - Variable in class Accession.AccROIwizardPopup

local ULHC CW ROI window.

cwx2 - Variable in class Accession.AccROIwizardPopup

local LRHC CW ROI window.

cwy1 - Variable in class Accession.AccROIwizardPopup

local ULHC CW ROI window.

cwy2 - Variable in class Accession.AccROIwizardPopup

local LRHC CW ROI window.

D

data - Static variable in class Accession.Accglb

dataLabel - Variable in class Accession.AccACCwizardPopup

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

dataLabelColor - Variable in class Accession.AccACCwizardPopup

Label color [0:nData-1] Colors if used

dataTextField - Variable in class Accession.AccACCwizardPopup

Right [0:nData-1] TextFields if used

DATE - Static variable in class Accession.Accglb

CVS Version date

dbRsample - Static variable in class Accession.Accglb

Rsample state parameters read from files.

dbS - Variable in class Accession.AccACCwizardPopup

Name of sample to display

dbS - Variable in class Accession.AccCALIBwizardPopup

link to active sample

dbS - Variable in class Accession.AccROIwizardPopup

Sample to display.

dbS - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

Sample instance structure

dbSample - Static variable in class Accession.Accglb

Sample state parameters read from files.

DBUG_APPEND - Static variable in class Accession.Accglb

Debugging append text flag

DBUG_CONSOLE - Static variable in class Accession.Accglb

Debugging console text flag

DBUG_FREE_0100 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_01000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_010000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_0100000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_01000000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_020 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_0200 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_02000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_020000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_02000000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_04 - Static variable in class Accession.Accglb

Debug code: compute the landmark sets 1/2 radii

DBUG_FREE_040 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_0400 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_04000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_040000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_FREE_0400000 - Static variable in class Accession.Accglb

Debug code: -free-

DBUG_MAIN - Static variable in class Accession.Accglb

Debug code: main()

DBUG_PRINT_AT - Static variable in class Accession.Accglb

Debug code: -printAt() debugging

DBUG_SWITCH_ANALYSIS - Static variable in class Accession.Accglb

Debug code: analyze command line switches

DBUG_SWITCHES - Static variable in class Accession.Accglb

Debugging switches

dbugBitName - Static variable in class Accession.Accglb

Debug bits name from the parsed Accession.dbug file

dBugBits - Static variable in class Accession.Accglb

-DEBUG:bits

dbugBitsHelpStr - Static variable in class Accession.Accglb

Debug bit options help for error messages

dbugBitValues - Static variable in class Accession.Accglb

Debug bits values from the parsed Accession.dbug file

debugSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

defaultSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

demoFileList - Static variable in class Accession.Accglb

List of demo/ files downloadable from the server

demoSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

dispName - Variable in class Accession.AccACCwizardPopup

Name of image to display

dispName - Variable in class Accession.AccCALIBwizardPopup

Name of image to display

dispName - Variable in class Accession.AccROIwizardPopup

Name of image to display "Rsample" or "Sample"

dispPixC - Variable in class Accession.AccCALIBwizardPopup

Picture buffer char[] of image to display .

dispPixC - Variable in class Accession.AccROIwizardPopup

Picture buffer char[] of image to display .

distLatchThr - Static variable in class Accession.Accglb

minimum distance for spot to latch

docFileList - Static variable in class Accession.Accglb

List of documentation files downloadable from the server

doingCWroiFlag - Static variable in class Accession.AccROIwizardPopup

Flag indicates working on the CW ROI, else on the ND CW ROI

doneFlag - Variable in class Accession.AccReportPopup

pressed sog.

drawCalCWroiCB - Variable in class Accession.AccROIwizardPopup

the "Draw CAL CW ROI" checkbox

drawCalCWroiFlag - Variable in class Accession.AccROIwizardPopup

set from "Draw calibration wedge ROI overlay" checkbox and checkbox menu item.

drawCWroiCB - Variable in class Accession.AccROIwizardPopup

the "Draw CW ROI" checkbox

drawCWroiFlag - Variable in class Accession.AccROIwizardPopup

set from "Draw CW ROI" checkbox

drawFilledBox(Graphics, int, int, int, Color) - Static method in class Accession.AccCALIBwizardPopup

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

drawGifFile(String) - Method in class Accession.AccCALIBwizardPopup

drawGifFile() - draw plot into Gif image file if in stand-alone mode.

drawHistInCanvas(Graphics) - Method in class Accession.AccCALIBwizardPopup

drawHistInCanvas() - draw histogram of hist[].

drawIntoImageFlag - Variable in class Accession.AccCALIBwizardPopup

set if draw plot to GIF file

drawMeasSpotListFlag - Variable in class Accession.AccROIwizardPopup

set from "Draw spot list overlays" checkbox menu item.

drawMeasSpotListLabelsFlag - Variable in class Accession.AccROIwizardPopup

set from "Draw measured spot labels overlays" checkbox menu item

drawRoiCB - Variable in class Accession.AccROIwizardPopup

the "Draw ROI" checkbox

drawRoiFlag - Variable in class Accession.AccROIwizardPopup

set from "Draw ROI" checkbox

drawROIrectangle(Graphics, int, int, int, int, Color) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

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

drawROItic(Graphics, int, int, int, int, Color) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

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

dtdSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

dumpFinish() - Static method in class Accession.AccData

dumpFinish() - finish and report statistics

dynamicColor - Static variable in class Accession.AccACCwizardPopup

Color of dynamic labels

E

editMenu - Variable in class Accession.AccACCwizardPopup

"Edit" pull down Menu list

editMenu - Variable in class Accession.AccCALIBwizardPopup

"Edit" pull down Menu list

editMenu - Variable in class Accession.AccReportPopup

"Edit" pull down Menu list

editOptionsButton - Variable in class Accession.AccReportPopup

button for "Set startup options" button

editPane - Variable in class Accession.AccACCwizardPopup

Scrollable edit pane that holds the gridPanel

enableCalibDBUG - Variable in class Accession.AccReportPopup

Enable calibration while debugging

F

fieldNameData - Variable in class Accession.AccACCwizardPopup

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

fileMenu - Variable in class Accession.AccACCwizardPopup

"File" pull down Menu list

fileMenu - Variable in class Accession.AccCALIBwizardPopup

"File" pull down Menu list

fileMenu - Variable in class Accession.AccReportPopup

"File" pull down Menu list

fileMenu - Variable in class Accession.AccROIwizardPopup

"File" pull down Menu list

fileSeparator - Static variable in class Accession.Accglb

File separator: Property("file.separator")

fio - Static variable in class Accession.Accglb

fontFamily - Variable in class Accession.AccACCwizardPopup

fontFamily - Variable in class Accession.AccCALIBwizardPopup

fontFamily - Variable in class Accession.AccROIwizardPopup

fontFamily - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

forceROIUpperAndLowerCorners() - Method in class Accession.AccROIwizardPopup

forceROIUpperAndLowerCorners() - reorder the ROI so that (roiX1,roiY1) < (roiX2,roiY2)

fourSqrtPi - Static variable in class Accession.Accglb

Constant 4*sqrt(PI) constant used in computing spot volume

G

getMinimumSize() - Method in class Accession.AccCALIBwizardPopup

getMinimumSize() - get the minimum preferred size

getNewValueDataResults() - Method in class Accession.AccACCwizardPopup

getNewValueDataResults() - get changedValueData[] from the text fields.

getPreferredSize() - Method in class Accession.AccACCwizardPopup

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

getPreferredSize() - Method in class Accession.AccCALIBwizardPopup

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

getPreferredSize() - Method in class Accession.AccROIwizardPopup

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

getPreferredSize() - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

getPreferredSize() - getPreferredSize, must be implemented for ScrollPane to be displayed correctly.

getReportText() - Method in class Accession.AccReportPopup

getReportText() - get the text from the Report popup window

getSpotListStr(String) - Method in class Accession.AccReportPopup

getSpotListStr() - generate a string report (reduced spot features) of a list of spots in the list for the current sample.

getSpotStr(DbSpot, int) - Method in class Accession.AccReportPopup

getSpotStr() - generate a printable string for a spot (reduced features)

getStopStatus() - Method in class Accession.AccReportPopup

getStopStatus() - get the stop processing flag set by pressing the "Stop processing" button

grayDataList - Variable in class Accession.AccCALIBwizardPopup

grayDataList is peak gray list if not null.

grayIdx - Variable in class Accession.AccReportPopup

index of field "GRAY" in calibTbl

grayValueListChangedFlag - Variable in class Accession.AccCALIBwizardPopup

Flag indicating that the accession calibration gray value fields were defined or were edited

gridPanel - Variable in class Accession.AccACCwizardPopup

Where put the grid of (Label,TextField) name value pairs

H

helpData - Variable in class Accession.AccACCwizardPopup

Optional help data [0:nData-1] if not null, then this is info on the corresponding fieldNameData.

helpList - Variable in class Accession.AccACCwizardPopup

list of help info for each accession DB field

helpMenu - Variable in class Accession.AccACCwizardPopup

"Help" pull down Menu list

helpMenu - Variable in class Accession.AccCALIBwizardPopup

"Help" pull down Menu list

helpMenu - Variable in class Accession.AccReportPopup

"Help" pull down Menu list

helpMenu - Variable in class Accession.AccROIwizardPopup

"Help" pull down Menu list

hist - Variable in class Accession.AccCALIBwizardPopup

freq hist[0:nHist-1].

histColor - Variable in class Accession.AccCALIBwizardPopup

histTopColor - Variable in class Accession.AccCALIBwizardPopup

I

ini - Static variable in class Accession.Accglb

initAccEditGUI(String) - Method in class Accession.AccACCwizardPopup

initAccEditGUI() - init the accession fields GUI editor

initGlb() - Static method in class Accession.Accglb

initGlb() - intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here...

initSwitchOptionsData() - Static method in class Accession.AccIni

initSwitchOptionsData() - init the switchOptionsData[0:(3*nData)-1] data is used by the AccReportPopup that in turn may call OptionsPopup.

inPixFileRsample - Static variable in class Accession.Accglb

original Rsample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions.

inPixFileSample - Static variable in class Accession.Accglb

original Sample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions.

inputFormatSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

isValidCW() - Method in class Accession.AccROIwizardPopup

isValidCW() - check if current Computing Window (CW) is valid

isValidROI() - Method in class Accession.AccROIwizardPopup

isValidROI() - check if current region of interest (ROI) is valid

isValidROI(int, int, int, int) - Method in class Accession.AccROIwizardPopup

isValidROI() - check if current region of interest (ROI) is valid

isVisibleFlag - Variable in class Accession.AccACCwizardPopup

Set true if window is visible

isVisibleFlag - Variable in class Accession.AccCALIBwizardPopup

If the Histogram is visible

isVisibleFlag - Variable in class Accession.AccROIwizardPopup

Set true if window is visible

itemStateChanged(ItemEvent) - Method in class Accession.AccACCwizardPopup

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 Accession.AccCALIBwizardPopup

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 Accession.AccReportPopup

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 Accession.AccROIwizardPopup

itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.

J

jarFileList - Static variable in class Accession.Accglb

List of program .jar files downloadable from the server

jarLibrFileList - Static variable in class Accession.Accglb

List of library .jar files downloadable from the server

K

keyPressed(KeyEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

keyPressed() - handle key down events

keyReleased(KeyEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

keyTyped(KeyEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

L

labelColor - Variable in class Accession.AccCALIBwizardPopup

largeFont - Variable in class Accession.AccACCwizardPopup

largeFont - Variable in class Accession.AccCALIBwizardPopup

largeFont - Variable in class Accession.AccROIwizardPopup

largeFont - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

legalImageFileExtens - Static variable in class Accession.Accglb

List of legal sample image file extensions

logReportFlag - Variable in class Accession.AccACCwizardPopup

set from "Log report" checkbox menu item

logReportFlag - Variable in class Accession.AccCALIBwizardPopup

set from "Log report" checkbox menu item

logReportFlag - Variable in class Accession.AccROIwizardPopup

set from "Log report" checkbox menu item

lookupSampleEntryInAccDB(String, String, String, DbSample) - Method in class Accession.Accession

lookupSampleEntryInAccDB() - lookup the sample image name in the accession DB.

M

main(String[]) - Static method in class Accession.Accession

main() - for Accession 2D spot-pairing program for Open2Dprot.

makeBkupCopyFlag - Static variable in class Accession.Accglb

The parsed of Command line switches

mapRelXYtoImage(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mapRelXYtoImage() - map (x,y)Mouse in current canvas to (xImg,yImg) as well as updating the parent.(xImg,yImg) values.

MAX_GRAY - Static variable in class Accession.AccCALIBwizardPopup

# gray values in a pixel

MAX_TEXT_FIELD_WIDTH - Variable in class Accession.AccACCwizardPopup

MAX_WEDGE_STEPS - Static variable in class Accession.Accglb

default # of peak wedge calibration table steps

MAXBINS - Static variable in class Accession.AccCALIBwizardPopup

# of histogram into bins

mbar - Variable in class Accession.AccACCwizardPopup

menu bar for the frame

mbar - Variable in class Accession.AccCALIBwizardPopup

menu bar for the frame

mbar - Variable in class Accession.AccReportPopup

menu bar for the frame

mbar - Variable in class Accession.AccROIwizardPopup

menu bar for the frame

mediumFont - Variable in class Accession.AccACCwizardPopup

mediumFont - Variable in class Accession.AccCALIBwizardPopup

mediumFont - Variable in class Accession.AccROIwizardPopup

mediumFont - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseClicked(MouseEvent) - Method in class Accession.AccACCwizardPopup

mouseClicked(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseClicked(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseDragged(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseDragged() - process mouse event

mouseDragged(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseDragged() - display data

mouseEntered(MouseEvent) - Method in class Accession.AccACCwizardPopup

mouseEntered(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseEntered(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseExited(MouseEvent) - Method in class Accession.AccACCwizardPopup

mouseExited(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseExited(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseHandler(int, int) - Method in class Accession.AccCALIBwizardPopup

mouseHandler() - search for the active bin if any

mouseMoved(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseMoved(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseMoved() - display data

mousePressed(MouseEvent) - Method in class Accession.AccACCwizardPopup

mousePressed() - display data

mousePressed(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mousePressed(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mousePressed() - display data

mouseReleased(MouseEvent) - Method in class Accession.AccACCwizardPopup

mouseReleased(MouseEvent) - Method in class Accession.AccCALIBwizardPopup

mouseReleased() - process mouse event

mouseReleased(MouseEvent) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

mouseReleased() - display data

ms - Variable in class Accession.AccACCwizardPopup

Menu support functions using Hashtables to tack what is active.

ms - Variable in class Accession.AccCALIBwizardPopup

Menu support functions using Hashtables to tack what is active.

ms - Variable in class Accession.AccReportPopup

Menu support functions using Hashtables to tack what is active

ms - Variable in class Accession.AccROIwizardPopup

Menu support functions using Hashtables to tack what is active.

msgTextArea - Variable in class Accession.AccACCwizardPopup

Text area GUI for message rporting

msgTextArea - Variable in class Accession.AccCALIBwizardPopup

Text area GUI for message rporting

msgTextArea - Variable in class Accession.AccROIwizardPopup

Text area GUI for message rporting

N

N_PCT_PROLOGUE - Static variable in class Accession.AccCALIBwizardPopup

default # of initial rows in the peak wedge calibration table

nCalSteps - Variable in class Accession.AccCALIBwizardPopup

size of calDataList is calibration value list if not null

NCOLS - Static variable in class Accession.AccACCwizardPopup

NCOLS - Static variable in class Accession.AccCALIBwizardPopup

NCOLS - Static variable in class Accession.AccROIwizardPopup

nData - Variable in class Accession.AccACCwizardPopup

# of name-value pair data items

needToSaveAccessionDataFlag - Static variable in class Accession.Accglb

Flag indicates need to save the Accession DB data

NEVER - Static variable in class Accession.Accglb

NEVER and CONSOLE_FLAG - debugging variables - must not be final!

newArgv - Variable in class Accession.AccReportPopup

new switch options

nGrayPeaks - Variable in class Accession.AccCALIBwizardPopup

size of the grayDataList is peak gray list if not null

nPixels - Variable in class Accession.AccCALIBwizardPopup

The pixWidth*pixHeight

nPixels - Variable in class Accession.AccROIwizardPopup

The pixWidth*pixHeight

NROWS - Static variable in class Accession.AccACCwizardPopup

size of the text area in characters

NROWS - Static variable in class Accession.AccCALIBwizardPopup

size of the text area in characters

NROWS - Static variable in class Accession.AccROIwizardPopup

size of the text area in characters

nSwitches - Static variable in class Accession.Accglb

the number of Command line switches

O

odColor - Variable in class Accession.AccCALIBwizardPopup

oFile - Variable in class Accession.AccReportPopup

File to flush and close on "Kill program" if it is not null

oGifFileName - Variable in class Accession.AccCALIBwizardPopup

Full path of image to "Save image" in

oGifFileName - Variable in class Accession.AccROIwizardPopup

Full path of image to "Save image" in

openAccDBfile(String, boolean) - Method in class Accession.Accession

openAccDBfile() - open the accession database.

optBkgrdColor - Variable in class Accession.AccCALIBwizardPopup

OPTBKGROUND - Static variable in class Accession.Accglb

Shift background grayscale away from 0 so graphics show up better...

osName - Static variable in class Accession.Accglb

name of this operating system: Property("os.name")

P

paint(Graphics) - Method in class Accession.AccACCwizardPopup

paint() - repaint scrollable canvas in region defined by scroll bars

paint(Graphics) - Method in class Accession.AccCALIBwizardPopup

paint() - draw the histogram

paint(Graphics) - Method in class Accession.AccROIwizardPopup

paint() - repaint scrollable canvas in region defined by scroll bars

paint(Graphics) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

paint() - repaint scrollable canvas in region defined by scroll bars

PEAK_CAL_TBL_COLS - Static variable in class Accession.AccCALIBwizardPopup

default # of editPanel cols

PEAK_CAL_TBL_ROWS - Static variable in class Accession.AccCALIBwizardPopup

default # of editPanel rows

peakCalTblCols - Static variable in class Accession.AccCALIBwizardPopup

# of editPanel cols in actual table

peakCalTblRows - Static variable in class Accession.AccCALIBwizardPopup

# of editPanel rows in actual table

peakCalTblTF - Variable in class Accession.AccCALIBwizardPopup

Array of TextFields used in constructing the Peak Calibration Table editPanel.

peakIdx - Variable in class Accession.AccReportPopup

index of field "PEAK" in calibTbl

peakNbrColor - Variable in class Accession.AccCALIBwizardPopup

peak number color

peakNbrFontSize - Variable in class Accession.AccCALIBwizardPopup

font size for peak number labels

pImg - Variable in class Accession.AccROIwizardPopup

Image to display

pix - Static variable in class Accession.Accglb

pixFileExtn - Static variable in class Accession.Accglb

Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer.

pixHeight - Variable in class Accession.AccCALIBwizardPopup

The width of the current image

pixHeight - Variable in class Accession.AccROIwizardPopup

The width of the current image

pixNxNtoStr(int, int, int, int, String) - Method in class Accession.AccROIwizardPopup

pixNxNtoStr() - convert current char[] picture of size nXn to string.

pixWidth - Variable in class Accession.AccCALIBwizardPopup

The width of the current image

pixWidth - Variable in class Accession.AccROIwizardPopup

The width of the current image

popupAccWizard() - Method in class Accession.AccReportPopup

popupAccWizard() - popup the accession wizard GUI.

popupCalibWizard(int) - Method in class Accession.AccReportPopup

popupCalibWizard() - popup the image calibration wizard GUI on the current Sample.

popupRoiWizard() - Method in class Accession.AccReportPopup

popupRoiWizard() - popup the image viewer on the current Sample.

positionHistWindow() - Method in class Accession.AccCALIBwizardPopup

positionHistWindow() - position histogram window on the screen

positionImageWindow() - Method in class Accession.AccACCwizardPopup

positionImageWindow() - position image window on the screen

positionImageWindow() - Method in class Accession.AccROIwizardPopup

positionImageWindow() - position image window on the screen

positionReportWindow() - Method in class Accession.AccReportPopup

positionReportWindow() - position report window on the screen

postProcessSwitches() - Method in class Accession.AccIni

postProcessSwitches() - post process switches

poTitle - Variable in class Accession.AccReportPopup

popup options title

ppxDir - Static variable in class Accession.Accglb

Original sample images directory {projDir}/ppx/

pra - Static variable in class Accession.Accglb

generic popup report

preferredHeight - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

preferred size of canvas

preferredWidth - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

preferred size of canvas

processSamples(String[]) - Method in class Accession.Accession

processSamples() - process the two samples.

projDir - Static variable in class Accession.Accglb

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.

projDirSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

propertiesFile - Static variable in class Accession.Accglb

Current startup properties file containing default switches if it exists.

propertiesFileSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

PUBLISH - Static variable in class Accession.Accglb

NOTE: overide the following debugging options if publishing on net.

Q

quit() - Method in class Accession.AccReportPopup

quit() - closing down the window, get rid of the frame.

R

rdbmsDir - Static variable in class Accession.Accglb

RDBMS database directory {projDir}/rdbms/

readCalibValuesFromFile(String, boolean) - Method in class Accession.AccReportPopup

readCalibValuesFromFile() - read calibration values from file.

readSpotListFromAccTable() - Method in class Accession.AccReportPopup

readSpotListFromAccTable() - If spot measurements exist in the accession DB table, then create the dbSample spot list from this data.

readSsfImage(String, DbSample) - Method in class Accession.Accession

readSsfImage() - read the SSF image and set image status in the dbSample instance

reanalyzeFlag - Variable in class Accession.AccReportPopup

pressed sog.

rebuildOpenSampleSubmenus() - Method in class Accession.AccReportPopup

rebuildOpenSampleSubmenus() - rebuild the Set Rsample and Open Sample submenus from entries in the accession database.

reCalcSpotListMeasures(boolean, boolean) - Method in class Accession.AccReportPopup

reCalcSpotListMeasures() - Recompute spot list measurements.

reExtrapolateCalibration() - Method in class Accession.AccCALIBwizardPopup

reExtrapolateCalibration() - regenerate the mapGrayToCal[] from the peak table

refreshMapFromTable(boolean) - Method in class Accession.AccCALIBwizardPopup

refreshMapFromTable() - refresh the peak table from the TextFields...

reportFile - Variable in class Accession.AccReportPopup

requireColor - Static variable in class Accession.AccACCwizardPopup

Color of require labels

reset() - Method in class Accession.AccData

reset() - reset any resources that must be reset for the next run of the program.

resetGlb() - Static method in class Accession.Accglb

resetGlb() - reset any resources that must be reset for the next run of the program.

resetResources(boolean) - Static method in class Accession.Accession

resetResources() - reset any resources that must be reset for the next run of the program.

REVISION - Static variable in class Accession.Accglb

CVS Revision

rmvSpotFromSpotList(DbSpot) - Method in class Accession.AccReportPopup

rmvSpotFromSpotList() - remove (x,y) spot of from the spot list for the current sample.

roiEditButton - Variable in class Accession.AccReportPopup

button for "ROI" button

roiGUI - Variable in class Accession.AccReportPopup

popup ROI Image wizard GUI

roiMenu - Variable in class Accession.AccROIwizardPopup

"Roi" pull down Menu list

roiX1 - Variable in class Accession.AccROIwizardPopup

ULHC ROI window set by (C-U).

roiX2 - Variable in class Accession.AccROIwizardPopup

LRHC ROI window set by (C-L).

roiY1 - Variable in class Accession.AccROIwizardPopup

ULHC ROI window set by (C-U).

roiY2 - Variable in class Accession.AccROIwizardPopup

LRHC ROI window set by (C-L).

RSAMPLE - Static variable in class Accession.Accglb

The index for the Rsample (Reference Sample)

rsampleName - Static variable in class Accession.Accglb

Name of Rsample that does not include either the file extension or the path.

rSampleSubmenu - Variable in class Accession.AccReportPopup

Dynamic submenu list for "Set Rsample" the value is "SetRsample:"sample-name'"

rsampleSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

S

SAMPLE - Static variable in class Accession.Accglb

The index for the Sample to be paired with the Rsample

sampleName - Static variable in class Accession.Accglb

Name of Sample that does not include either the file extension or the path.

sampleSubmenu - Variable in class Accession.AccReportPopup

Dynamic submenu list for "Open Sample for editing" the value is "OpenSampleForEditing:"sample-name'"

sampleSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

saveAllDBfiles() - Static method in class Accession.AccData

saveAllDBfiles() - save any database files that need to be saved.

serialVersionUID - Static variable in class Accession.AccACCwizardPopup

frame id

serialVersionUID - Static variable in class Accession.AccCALIBwizardPopup

frame id

serialVersionUID - Static variable in class Accession.AccReportPopup

frame id

serialVersionUID - Static variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

frame id

serialVersionUID - Static variable in class Accession.AccROIwizardPopup

frame id

setCalValueListCalibAccFields() - Method in class Accession.AccCALIBwizardPopup

setCalValueListCalibAccFields() - set the accession data calibration values peak list calibration fields

setEnableButtons(boolean) - Method in class Accession.AccReportPopup

setEnableButtons() - by the flag

setEnableMenus(boolean) - Method in class Accession.AccReportPopup

setEnableMenus() - by the flag

setGrayPeakListCalibAccFields() - Method in class Accession.AccCALIBwizardPopup

setGrayPeakListCalibAccFields() - set the accession data gray value peaks list calibration fields

setMeasureSizeGUI(int, boolean, boolean) - Method in class Accession.AccROIwizardPopup

setMeasureSizeGUI() - set checkbox radio button and Choice selected and process event for windmp size checkboxes

setNameValueEditGUI(String) - Method in class Accession.AccACCwizardPopup

setNameValueEditGUI() - show the Image Viewer GUI window

setNewDefaultFlag - Variable in class Accession.AccReportPopup

pressed sog.

setNewValueData(String[]) - Method in class Accession.AccACCwizardPopup

setNewValueData() - set new valueData[] into the local database and dataTextField.

setOutFileToCloseOnKill(FileWriter) - Method in class Accession.AccReportPopup

setOutFileToCloseOnKill() - set the show/hide popup status

setPixDatabase(DbSample) - Method in class Accession.AccROIwizardPopup

setPixDatabase() - setup the picture database sample

setROI(int, int, int, int) - Method in class Accession.AccROIwizardPopup

setROI() - set computing window region of interest (ROI)

setROI2CALCW(int, int, int, int) - Method in class Accession.AccROIwizardPopup

setROI2CALCW() - set Calibration wedge computing window ROI

setROI2CW(int, int, int, int) - Method in class Accession.AccROIwizardPopup

setROI2CW() - set region of interest (ROI) to Computing Window (CW)

setRowLabelColors(Color, Color) - Method in class Accession.AccACCwizardPopup

setRowLabelColors() - assign the required and dynamic label colors.

setRsampleByName(String) - Method in class Accession.Accession

setRsampleByName() - set and load the Rsample data into dbRsample

setSampleByName(String) - Method in class Accession.Accession

setSampleByName() - set and load the Sample data into dbSample

setSampleDatabase(String[], String, DbSample) - Method in class Accession.AccACCwizardPopup

setSampleDatabase() - setup the list of predefined samples available to the GUI.

setSampleToEdit(String) - Method in class Accession.AccACCwizardPopup

setSampleToEdit() - set checkbox radio button and choice selected for sample to edit

setSaveAsFile(String) - Method in class Accession.AccReportPopup

setSaveAsFile() - set SaveAs file default file name

setShow(boolean) - Method in class Accession.AccReportPopup

setShow() - set the show/hide popup status

setTitleHist(String) - Method in class Accession.AccCALIBwizardPopup

setTitleHist() - set the title

setupDebugSwitches(String[]) - Static method in class Accession.Accession

setupDebugSwitches() - setup the debug switches

setupDemoSwitches(String[]) - Static method in class Accession.Accession

setupDemoSwitches() - setup the demo switches for the "gel-HM-019" (HUMAN-AML) and "gel-HM-071" (Human-ALL) samples

setupMinDefaultsSwitches(String[]) - Static method in class Accession.Accession

setupMinDefaultsSwitches() - add the minimum default switches.

setupSampleAccessionFieldData() - Method in class Accession.AccACCwizardPopup

setupSampleAccessionFieldData() - setup the accession DB field data for this sample.

setupSampleROIs() - Method in class Accession.AccROIwizardPopup

setupSampleROIs() - setup the CW ROI and the Calibration Wedge ROI.

setVisible(boolean, boolean) - Method in class Accession.AccCALIBwizardPopup

setVisible() - set the histogram as visible or not

setWindmpSizeGUI(int) - Method in class Accession.AccROIwizardPopup

setWindmpSizeGUI() - set checkbox radio button and Choice selected and process event for windmp size checkboxes

shiftMod - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

SHIFT/Mouse

sHist - Variable in class Accession.AccCALIBwizardPopup

modified freq sHist[0:nHist-1].

showImageMousePositions(MouseEvent, String) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

showImageMousePositions() - show the image mouse positions Only report if debugging...

showImgMsg(String) - Method in class Accession.AccROIwizardPopup

showImgMsg() - display the msg in text area window

showMsg(String) - Method in class Accession.AccACCwizardPopup

showMsg() - display the msg in text area window

showMsg(String) - Method in class Accession.AccCALIBwizardPopup

showMsg() - display the msg in text area window

showMsg(String, Color) - Method in class Accession.AccCALIBwizardPopup

showMsg() - set the status msg

showPopupOptionWindow(String) - Method in class Accession.AccReportPopup

showPopupOptionWindow() - popup options window using the csPopupOptions GUI.

showReportStatus(String) - Static method in class Accession.Accglb

showReportStatus() - display the msg in popup report line display And update the timer for the opr

showROIimageGUI() - Method in class Accession.AccROIwizardPopup

showROIimageGUI() - show the Image Viewer GUI window

showStatusFlag - Variable in class Accession.AccReportPopup

siCanvas - Variable in class Accession.AccROIwizardPopup

ScrollableImageCanvas to hold the image

simplePixFileRsample - Static variable in class Accession.Accglb

Simple Rsample original Rsample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions.

simplePixFileSample - Static variable in class Accession.Accglb

Simple original Sample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions.

smallFont - Variable in class Accession.AccACCwizardPopup

smallFont - Variable in class Accession.AccCALIBwizardPopup

smallFont - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

smallFont - Variable in class Accession.AccROIwizardPopup

sog - Variable in class Accession.AccReportPopup

popup options GUI

sortSpotListFlag - Static variable in class Accession.Accglb

Sort the measured spots in assending order by density

sp - Variable in class Accession.AccACCwizardPopup

Scroll pane to hold the Name-Value scrollable panel

sp - Variable in class Accession.AccROIwizardPopup

Scroll pane to hold the image

spfFormatMode - Static variable in class Accession.Accglb

SPF output file modes: Allowed: IO_FORMAT_FULL, IO_FORMAT_GELLAB, IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

spotBoxSize - Static variable in class Accession.Accglb

spot measurement box size

spotListMenu - Variable in class Accession.AccROIwizardPopup

"Spot list" pull down Menu list

ssfCWX1 - Static variable in class Accession.Accglb

SSF computing window used with -ssfCW: to ignore spots outside of this window for both SSF input files.

ssfCWX2 - Static variable in class Accession.Accglb

SSF computing window used with -ssfCW: to ignore spots outside of this window for both SSF input files.

ssfCWY1 - Static variable in class Accession.Accglb

SSF computing window used with -ssfCW: to ignore spots outside of this window for both SSF input files.

ssfCWY2 - Static variable in class Accession.Accglb

SSF computing window used with -ssfCW: to ignore spots outside of this window for both SSF input files.

ssfFileRsample - Static variable in class Accession.Accglb

SSF input file for G1 sample (i.e., Rsample)

ssfFileSample - Static variable in class Accession.Accglb

SSF input file for G2 sample (i.e., Sample)

ssfFormatMode - Static variable in class Accession.Accglb

SSF input file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML

ssfInputEpilogueFileRsample - Static variable in class Accession.Accglb

full tab-delim G1 EPILOGUE xml/Rsample Spot Segmentation File full path

ssfInputEpilogueFileSample - Static variable in class Accession.Accglb

full tab-delim G2 EPILOGUE xml/Sample Segmentation File full path

ssfInputFileRsample - Static variable in class Accession.Accglb

xml/ Rsample G1 Spot Segmentation File full path

ssfInputFileSample - Static variable in class Accession.Accglb

xml/ Sample G2 Spot Segmentation File full path

ssfInputPrefaceFileRsample - Static variable in class Accession.Accglb

full tab-delim G1 PREFACE xml/Rsample Spot Segmentation File full path

ssfInputPrefaceFileSample - Static variable in class Accession.Accglb

full tab-delim G2 PREFACE xml/Sample Spot Segmentation File full path

startTime - Static variable in class Accession.Accglb

starting time in epoch msec time

statusLineLabel - Variable in class Accession.AccReportPopup

Status line label

stopFlag - Variable in class Accession.AccReportPopup

sw - Static variable in class Accession.Accglb

Command line + Accession.properties state switches

switchAnalysis(String[]) - Method in class Accession.AccIni

switchAnalysis() - Analyze the command line.

switchOptCBvalue - Static variable in class Accession.Accglb

The switchOptcCBvalue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions.

switchOptData - Static variable in class Accession.Accglb

The switchOptData[0:(2*nData)-1] is used by the Report Popup that in turn may call PopupOptions.

switchOptValue - Static variable in class Accession.Accglb

The switchOptValue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions.

swOptCBvalue - Variable in class Accession.AccReportPopup

The swOptcCBvalue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions.

swOptData - Variable in class Accession.AccReportPopup

The swOptData[0:(3*nData)-1] is used by the AccReportPopup that in turn may call PopupOptions.

swOptValue - Variable in class Accession.AccReportPopup

The swOptValue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions.

T

textarea - Variable in class Accession.AccReportPopup

Text area GUI for main report

textAreaFontSize - Variable in class Accession.AccACCwizardPopup

font size

textAreaFontSize - Variable in class Accession.AccCALIBwizardPopup

font size

textAreaFontSize - Variable in class Accession.AccReportPopup

font size

textAreaFontSize - Variable in class Accession.AccROIwizardPopup

font size

textFieldFont - Variable in class Accession.AccACCwizardPopup

textFontFamily - Variable in class Accession.AccACCwizardPopup

font family for message window

textFontFamily - Variable in class Accession.AccCALIBwizardPopup

font family for message window

textFontFamily - Variable in class Accession.AccReportPopup

Text area font family

textFontFamily - Variable in class Accession.AccROIwizardPopup

font family for message window

textReport - Variable in class Accession.AccReportPopup

copy of text in textArea

timerSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

title - Variable in class Accession.AccReportPopup

string for title of frame

tmpDir - Static variable in class Accession.Accglb

Tmp images directory {projDir}/tmp/

U

update(Graphics) - Method in class Accession.AccACCwizardPopup

update() - update without background the scrollable canvas

update(Graphics) - Method in class Accession.AccCALIBwizardPopup

update() - update without background the scrollable canvas

update(Graphics) - Method in class Accession.AccROIwizardPopup.ScrollableImageCanvas

update() - update without background the scrollable canvas

update(Graphics) - Method in class Accession.AccROIwizardPopup

update() - update without background the scrollable canvas

updateAccTableWithSpotList() - Method in class Accession.AccCALIBwizardPopup

updateAccTableWithSpotList() - update accession DB table with spot list data.

updateChangedData() - Method in class Accession.AccACCwizardPopup

updateChangedData() - test if user has changed the table data fields Then copy text fields to changedValueData[[0:nData-1].

updateHistogramPlot(boolean) - Method in class Accession.AccCALIBwizardPopup

updateHistogramPlot() - set hist state and do repaint to draw it.

updatePeakCalTable() - Method in class Accession.AccCALIBwizardPopup

updatePeakCalTable() - update the peak calibration table GUI text field and the dbS.calib cal and gray value arrays with new data from calDataList[] and grayDataList[].

updateReportStatusLine(String) - Method in class Accession.AccReportPopup

updateReportStatusLine() - clear text in popup window

updateSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

updateText(String) - Method in class Accession.AccReportPopup

updateText() - update text in popup window

updateTitle(String) - Method in class Accession.AccReportPopup

updateTitle() - update title in popup window

usageSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

USE_DEMO_DATA - Static variable in class Accession.Accglb

Use the demo data by enabling the -demo flag and data.

useAccFileSwitch - Static variable in class Accession.Accglb

The parsed of Command line switches

useCommonSpotSizeFlag - Static variable in class Accession.Accglb

When recompute all spot measurements in the spot list, use the same square spot size (i.e., spotBoxSize).

useLogCB - Variable in class Accession.AccACCwizardPopup

the "Use log" checkbox

useLogCB - Variable in class Accession.AccCALIBwizardPopup

the "Use log" checkbox

useLogCB - Variable in class Accession.AccROIwizardPopup

the "Use log" checkbox

useLogFlag - Variable in class Accession.AccACCwizardPopup

set from "Use log" checkbox

useLogFlag - Variable in class Accession.AccCALIBwizardPopup

set from "Use log" checkbox

useLogFlag - Variable in class Accession.AccROIwizardPopup

set from "Use log" checkbox

userDir - Static variable in class Accession.Accglb

current User directory: getProperty("user.dir")+fileSeparator

useSaveImageFlag - Variable in class Accession.AccCALIBwizardPopup

set from "Save image" Command

useSaveImageFlag - Variable in class Accession.AccROIwizardPopup

set from "Save image" Command

useSpotBkbrdCorrectionFlag - Static variable in class Accession.Accglb

When recompute all spot measurements in the spot list, do spot density background correction

util - Static variable in class Accession.Accglb

instance of utility class

V

valueData - Variable in class Accession.AccACCwizardPopup

Value user data [0:nData-1] for a TextField with this data on the right

VERSION - Static variable in class Accession.Accglb

Manually define Version number

VIEW_HEIGHT - Variable in class Accession.AccACCwizardPopup

Height of the frame

VIEW_HEIGHT - Static variable in class Accession.AccCALIBwizardPopup

Height of the frame

VIEW_HEIGHT - Variable in class Accession.AccROIwizardPopup

Height of the frame

VIEW_WIDTH - Variable in class Accession.AccACCwizardPopup

Width of the frame

VIEW_WIDTH - Static variable in class Accession.AccCALIBwizardPopup

Width of the frame

VIEW_WIDTH - Variable in class Accession.AccROIwizardPopup

Width of the frame

viewHeight - Variable in class Accession.AccACCwizardPopup

viewHeight - Variable in class Accession.AccCALIBwizardPopup

viewHeight - Variable in class Accession.AccROIwizardPopup

viewMenu - Variable in class Accession.AccCALIBwizardPopup

"View" pull down Menu list

viewMenu - Variable in class Accession.AccReportPopup

"View" pull down Menu list

viewMenu - Variable in class Accession.AccROIwizardPopup

"View" pull down Menu list

viewWidth - Variable in class Accession.AccACCwizardPopup

Size of the viewport in the scrollable window

viewWidth - Variable in class Accession.AccCALIBwizardPopup

viewWidth - Variable in class Accession.AccROIwizardPopup

W

waitForUserClose() - Method in class Accession.AccReportPopup

waitForUserClose)() wait for user to press "Close" application.

windmpSize - Variable in class Accession.AccROIwizardPopup

Code for winDump size.

windowActivated(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowActivated(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowActivated(WindowEvent) - Method in class Accession.AccReportPopup

windowActivated(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowClosed(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowClosed(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowClosed(WindowEvent) - Method in class Accession.AccReportPopup

windowClosed(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowClosing(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowClosing() - closing down the window, get rid of the frame.

windowClosing(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowClosing() - close down the window.

windowClosing(WindowEvent) - Method in class Accession.AccReportPopup

windowClosing() - closing down the window, get rid of the frame.

windowClosing(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowClosing() - closing down the window, get rid of the frame.

windowDeactivated(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowDeactivated(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowDeactivated(WindowEvent) - Method in class Accession.AccReportPopup

windowDeactivated(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowDeiconified(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowDeiconified(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowDeiconified(WindowEvent) - Method in class Accession.AccReportPopup

windowDeiconified(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowIconified(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowIconified(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowIconified(WindowEvent) - Method in class Accession.AccReportPopup

windowIconified(WindowEvent) - Method in class Accession.AccROIwizardPopup

windowOpened(WindowEvent) - Method in class Accession.AccACCwizardPopup

windowOpened(WindowEvent) - Method in class Accession.AccCALIBwizardPopup

windowOpened(WindowEvent) - Method in class Accession.AccReportPopup

windowOpened(WindowEvent) - Method in class Accession.AccROIwizardPopup

X

xBase - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

+ base address of ULHC of clipped image in image canvas used in last paint

xImg - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

image address (x,y)+(xBase,yBase)

xmlDate - Static variable in class Accession.Accglb

XML accession file date "Date"

xmlDBname - Static variable in class Accession.Accglb

XML accession file database name value for "DatabaseName"

xmlDir - Static variable in class Accession.Accglb

Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.

xPainted - Static variable in class Accession.AccCALIBwizardPopup

active hit coordinates

Y

yBase - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

yImg - Variable in class Accession.AccROIwizardPopup.ScrollableImageCanvas

image address (x,y)+(xBase,yBase)

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