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

A

a - Variable in class Affine
coeff for x2= a*x + b*y1 + c
a0 - Variable in class Affine
inverse coefficient for x2= aO*x1 + bO*y1 + cO
a_count - Variable in class WriteGifEncoder
 
abortFlag - Variable in class Flicker
set true if run into problems when exiting and do not want to write out the state as we may corrupt it.
abortTransform() - Method in class ImageXform
abortTransform() - abort all image transforms in progress.
accum - Variable in class WriteGifEncoder
 
actionPerformed(ActionEvent) - Method in class BuildGUI
actionPerformed() - handle action performed state changed events
actionPerformed(ActionEvent) - Method in class DrawHistogram
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class EventMenu
actionPerformed() - common function to handle action events
actionPerformed(ActionEvent) - Method in class PopupDialogQuery
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupTextFieldDialog
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class PopupYesNoDialogBox
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class ShowReportPopup
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class Spot
actionPerformed() - Handle Control panel button clicks
activeBin - Variable in class DrawHistogram
active bin idx [0:nHist-1] else -1
activeImage - Variable in class DrawHistogram
active image name is "left" or "right"
activeImage - Variable in class Flicker
active image "left", "right", "both" === was both
addButtonsCnt - Variable in class PopupDialogQuery
# of buttons to add.
addCheckboxes(JPanel) - Method in class BuildGUI
addCheckboxes() - add checkboxes to chkboxPanel
addDemoLandmarks(int) - Static method in class Landmark
addDemoLandmarks() - add 3 or 6 demo landmark pairs but only for
addGuardRegion(boolean) - Method in class ImageScroller
addGuardRegion() - set up siCanvas for guard region
addImageParameterStateScrollers(JPanel) - Method in class BuildGUI
addImageParameterStateScrollers() - create image parameter state scrollers and put on right of main frame.
addImageScrollers(JPanel, JPanel) - Method in class BuildGUI
addImageScrollers() - add image scrollers: flicker to pFlicker, and image 1 and Image 2 scrollable images to pImages panels in the frame.
addLandmark() - Method in class Landmark
addLandmark() - "Add LM" add temporary landmarks to landmark list If exist in both I1 and I2 images into permanent landmarks and indicate in images push landmark.
addMenuTree(Frame, MenuBar) - Method in class BuildGUI
addMenuTree() - create pull down menus in menu bar
addOrUpdate(String, String, String, String, String) - Static method in class FlkRecent
addOrUpdate() - add or Update an entry to database FlkRecents[0:nMaps-1].
addOrUpdatePair(String, String, String, String, String, String, String) - Static method in class FlkRecent
addOrUpdatePair() - add or Update an entry pair to DB FlkRecents[0:nMaps-1].
addUniqueSpotToSpotList(int, int, int, int, int, int, int, int, float, boolean, boolean, float, float, float, float, float, float, float, float, float, float, float) - Method in class ImageDataSpotList
addUniqueSpotToSpotList() - add spot if it is unique to the spot list else just update the spot measurement but keep the spot number if it is an existing spot if +- 1 pixel in xC and/or yC
addUserDemoFilesDBbyURL(String) - Method in class Util
addUserDemoFilesDBbyURL() - Add user's demo images to DB by userURL.
addUserImagesMenuTrees() - Method in class BuildGUI
addUserImagesMenuTrees() - build both paired and single menu trees
addUserImagesPairs2UserDB() - Method in class FlkUser
addUserImagesPairs2UserDB() - add "Images//..." data to (File | Open user images | ...subdirectories) menu entries.
adjustmentValueChanged(AdjustmentEvent) - Method in class EventScroller
adjustmentValueChanged() - handle adjustment value changed events
adjustmentValueChanged(AdjustmentEvent) - Method in class ImageScroller
adjustmentValueChanged() - handle ImageScroller scroll events.
aff - Variable in class Flicker
Affine instance
aff - Variable in class ImageXform
Affine xform instance
aff - Variable in class Info
 
Affine - Class in <Unnamed>
The Affine class does affine transform setup and pixel operations.
Affine(Flicker) - Constructor for class Affine
Affine() - constructor which sets up the global links
affine_calcsString - Static variable in class Affine
affine xform calculations
AFFINEWARP - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
affineWarp() - Method in class ImageXform
affineWarp() - compute Affine Warp of left I1 into geometry of right I2.
aH - Variable in class ImageScroller
deals with scroller events
alertColor - Variable in class Flicker
Color to use for background of alert messages
alertDone - Variable in class PopupDialogQuery
button pressed flag
alertTimeout(String) - Method in class PopupDialogQuery
alertTimeout() - update the popup dialog msg - wait for "Continue"
allImgFileList - Static variable in class FlkUser
[0:nDirs-1][0:nFiles(dir)-1] all image file names for all directories
allowXformFlag - Variable in class Flicker
transforms are allowed
allowXformsCheckbox - Variable in class BuildGUI
Allow transforms, so that there is no oImg.
altMod - Variable in class ScrollableImageCanvas
ALT/Mouse
ALWAYS - Static variable in class TiffLoader
Fixed value of true for DEBUGGING
angle - Variable in class ImageXform
state copy: angle factor for pseudo3D
angle - Variable in class SliderState
GUI state: degrees 3D perspective xform
angleBar - Variable in class BuildGUI
scroll bar for angle
angleLabel - Variable in class BuildGUI
GUI label for angle scroll
answer - Variable in class PopupTextFieldDialog
Returned value from text field
appendReportMsg(String) - Static method in class Util
appendReportMsg() - append a report message to the report popup window
appendReportMsg(String, Color) - Static method in class Util
appendReportMsg() - append a report message to the report popup window
appendText(String) - Method in class ShowReportPopup
appendText() - append text in popup window
applyNTSCrgb2grayTransform() - Method in class ImageData
applyNTSCrgb2grayTransform() - optionally convert RGT to grayscale for the iPix[] data.
area - Variable in class Boundary
 
area - Variable in class Spot
spot area in pixels
args - Variable in class Flicker
 
aU - Variable in class ImageXform
Coefficient for u(x,y) poly warp
aU - Variable in class SpatialXform
[MXTERMS][MXTERMS]coefficients
aV - Variable in class ImageScroller
deals with scroller events
AVG8 - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
avg8() - Method in class ImageXform
avg8() - compute 8-neighbor average

B

b - Variable in class Affine
coeff for x2= a*x1 + b*y1 + c
b - Variable in class BrightnessContrastFilter
current BLUE pixel when filter is running
b - Variable in class WriteGifEncoder
 
b0 - Variable in class Affine
inverse coefficient for x2= aO*x1 + bO*y1 + cO
backupSpotList(boolean) - Method in class ImageDataSpotList
backupSpotList() - backup spotList[0:nSpots-1] to spotListBkup[] and nSpotBkup.
baseFlkServer - Static variable in class Flicker
Base URL of Flicker server containing documentation and resources
baseURL - Variable in class FlkMap
file field BaseURL: of the database web site URL: e.g., "http://www.expasy.org/"
basis(int, double, double) - Static method in class SpatialXform
basis() - return (x,y) value of f'th orthogonal basis function.
bCE - Variable in class ImageXform
compute intercept in g'=mCE+bCE
bcImg - Variable in class ImageData
brightness contrast filtered image if used.
bcImgF - Variable in class ImageScroller
Instance of Brightness/Contrast Filter.
bcImgF - Variable in class ScrollableImageCanvas
Instance of Brightness/Contrast Filter.
bgColor - Variable in class PopupYesNoDialogBox
background color
bGui - Variable in class EventMenu
 
bGui - Variable in class Flicker
BuildGUI instance of user interface
bGui - Variable in class ImageIO
BuildGUI instance
bGui - Variable in class ImageXform
Build GUI instance
bGui - Variable in class Info
 
bIntercept - Variable in class BrightnessContrastFilter
brightness intercept is (bS -0.5)*(2*maxGray)
bitpp - Variable in class PpxLoader
bits per pixel (one band)
BITS - Static variable in class WriteGifEncoder
 
bkgrd - Variable in class Spot
total spot mean background density
bkgrdCircleColor - Variable in class Flicker
Adjustable measurement circle color
bkgrdCircleRadius - Variable in class Flicker
"background" circle radius.
bkgrdCircleRadius - Variable in class SliderState
NOT a GUI slider.
bkgrdGrayValue - Variable in class ImageDataMeas
Capture "background" pixel gray or OD value.
bkgrdObjX - Variable in class ImageDataMeas
Capture "background" X coordinate
bkgrdObjY - Variable in class ImageDataMeas
Capture "background" Y coordinate
bkGrdX - Variable in class ScrollableImageCanvas
bk grd X
bkGrdY - Variable in class ScrollableImageCanvas
bk grd Y
blackIsZeroFlag - Variable in class ImageData
Is true if original input image has BLACK as gray value 0, else WHITE is gray value 0
blackIsZeroFlag - Variable in class PpxLoader
1 if BLACK is gray value 0, else 0 if WHITE is gray value 0
blackIsZeroFlag - Variable in class TiffLoader
Black is Zero flag
blkaln - Variable in class PpxLoader
block alignment flag 0 = aligned)
blueBits(int) - Method in class MedianCut
blueBits() - Get 8-bit blue component of a 15-bit color 8-bit pixel with low 3 bits zero.
bLUT - Variable in class MedianCut
[0:255] Blue Color map look up table
bmax - Variable in class MC_Cube
 
bmin - Variable in class MC_Cube
 
bnd - Variable in class Boundary
Boundary of object
bnd - Variable in class ImageData
This boundary boundary is ImageData specific.
bndColor - Variable in class Boundary
color to draw boundary
bndOpenFlag - Variable in class Boundary
boundary is active
Boundary - Class in <Unnamed>
Class Boundary performs boundary operations and its instance exists in the ImageData object.
Boundary(Flicker) - Constructor for class Boundary
Boundary() - constructor.
bPixels - Variable in class PpxLoader
pixels [0:nPixels-1] for the image
brightness - Variable in class SliderState
GUI state: contrast in [MIN_BRIGHTNESS:MAX_BRIGHTNESS]
brightnessBar - Variable in class BuildGUI
scroll bar for brightness
BrightnessContrastFilter - Class in <Unnamed>
Class BrightnessContrastFilter implements RGBFilter for image adjustment to implement a contrast/brightness filter.
BrightnessContrastFilter(Flicker) - Constructor for class BrightnessContrastFilter
BrightnessContrastFilter() - constructor.
brightnessLabel - Variable in class BuildGUI
GUI label for brightness scroll
bScaled - Variable in class BrightnessContrastFilter
scaled current brightness value to range of [0:1.0]
bubbleSort(String[], int) - Static method in class Util
bubbleSort() - Sort String array via bubble sort w/len
bubbleSortIndex(String[], int, boolean) - Static method in class Util
bubbleSortIndex() - sort copy of String[0:len-1] data with bubble sort, return index[].
bubbleSortIndex(float[], int, boolean) - Static method in class Util
bubbleSortIndex() - sort copy of float[0:len-1] data with bubble sort, return index[].
BuildGUI - Class in <Unnamed>
BuildGUI class is used to build the Flicker GUI.
BuildGUI(Flicker, String) - Constructor for class BuildGUI
BuildGUI() - constructor for Class BuildGUI
buildGUI(JFrame) - Method in class BuildGUI
buildGUI() - Build the GUI consisting of pannels and image areas
buildGUI() - Method in class PopupYesNoDialogBox
buildGUI() - Build GUI
buildHistGUI() - Method in class DrawHistogram
buildHistGUI() - build the histogram GUI
bV - Variable in class ImageXform
Coefficient for v(x,y) poly warp
bV - Variable in class SpatialXform
[MXTERMS][MXTERMS] coefficients
bytpp - Variable in class PpxLoader
bytes per pixel (one band)

C

c - Variable in class Affine
coeff for x2= a*x1 + b*y1 + c
c0 - Variable in class Affine
inverse coefficient for x2= aO*x1 + bO*y1 + cO
cal - Variable in class Flicker
Calibrate OD instance
CAL_POPUP_HEIGHT - Static variable in class DrawHistogram
default frame size height of popup
CAL_POPUP_WIDTH - Static variable in class DrawHistogram
default frame size width of popup
calcCalib() - Method in class CalibrateOD
calcCalib() - continuous piecewise linear calibration od(gray)
calcHistFindPeaksAndExtrapolate(ImageData) - Method in class CalibrateOD
calcHistFindPeaksAndExtrapolate() - set up histogram, peaks and extrpolate map for the current ROI.
calcHistogram(int, int, int, int) - Method in class ImageDataMeas
calcHistogram() - compute grayscale histogram under the specified computing window [x1:x2, y1:y2].
calcHistogramROI() - Method in class ImageDataROI
calcHistogramROI() - compute grayscale histogram under the current ROI.
calcInverseAffine() - Method in class Affine
calcInverseAffine() - compute inverse affine coefficients.
calcMaskArea(int[][]) - Static method in class ImageDataMeas
calcMaskArea() - compute the area under the mask
calcMaskTotWeight(int[][]) - Static method in class ImageDataMeas
calcMaskTotWeight() - compute the total weights under the mask
calcSumValuesUnderMask(int, int, int, boolean) - Method in class ImageDataMeas
calcSumValuesUnderMask() - compute sum of pixel values under the mask corresponding to the mask set by the current radius.
calFileDate - Variable in class CalibrateOD
Date associated with the .cal file.
calib - Variable in class DrawHistogram
link to working data related CalibrateOD instance
calib - Variable in class ImageData
calibration data is ImageData specific
calibBKUP - Variable in class DrawHistogram
Backup copy of the initial CalibrateOD instance that can be used for restoring the calibration.
calibChangedFlag - Variable in class DrawHistogram
The calibration peak table changed
calibCtr - Static variable in class CalibrateOD
Master Calibration counter
calibHistFlag - Variable in class DrawHistogram
The histogram is a calibration histogram
calibPeakColor - Variable in class DrawHistogram
calibration peaks on histogram color
CalibrateOD - Class in <Unnamed>
CalibrateOD handles grayscale to OD calibrations for images.
CalibrateOD(Flicker, int) - Constructor for class CalibrateOD
CalibrateOD() - constructor to set up the initial map.
CalibrateOD(CalibrateOD) - Constructor for class CalibrateOD
CalibrateOD() - constructor clone a CalibrateOD instance when you want to save the clone state.
CalibrateOD(int) - Constructor for class CalibrateOD
CalibrateOD() - constructor to set up the initial map.
calImageFile - Variable in class CalibrateOD
Image file associated with the .cal file.
cancelFlag - Variable in class PopupYesNoDialogBox
flag set by cancel button
cancelMsg - Variable in class PopupYesNoDialogBox
Cancel label for dialog box
CANVAS_INCR - Static variable in class Flicker
Canvas change increment size - empirically determined
CANVAS_SIZE - Static variable in class Flicker
canvas size used in all canvas image windows
canvasSize - Variable in class Flicker
size for left and right image canvases.
canvasSizeLabel - Variable in class BuildGUI
GUI label for "Canvas size: xxxx"
captureBackgroundValue() - Method in class ImageDataMeas
captureBackgroundValue() - capture the values under the mask of the selected image if it is left or right and assign it to the background pixel value for the current image.
captureMeasCWvalue() - Method in class ImageDataMeas
captureMeasCWvalue() - capture the pixel values under the computing window of the selected image if it is left or right and assign it to the measurement pixel value for the current image.
captureMeasValue() - Method in class ImageDataMeas
captureMeasValue() - capture the pixel values under the mask of the selected image if it is left or right and assign it to the measurement pixel value for the current image.
centerPt - Variable in class ScrollableImageCanvas
center point
changeCanvasSize(String) - Method in class Flicker
changeCanvasSize() - change the canvas size by the specified + or - increment command.
changedFlag - Variable in class Spot
edited the spot flag
changeImageData(String, Image, Dimension, boolean, float[]) - Method in class ImageData
changeImageData() - change values of this ImageData object
changeImageFromSpec(String, String, boolean, boolean) - Method in class ImageIO
changeImageFromSpec() - load a new image from file.
changeSpotList - Variable in class ImageDataSpotList
 
char_init() - Method in class WriteGifEncoder
char_init() - Set up the 'byte output' routine
char_out(byte, FileOutputStream) - Method in class WriteGifEncoder
char_out() - add char to end of current packet, and if it is 254 characters, flush the packet to disk.
checkAndMakeIpix(boolean) - Method in class ImageData
checkAndMakeIpix() - check & make iData.iPix if !exists.
checkAndMakeIpix(String, boolean) - Method in class ImageData
checkAndMakeIpix() - check & make iData.iPix if it does not exist.
checkIfSaveFlkFile() - Method in class Flicker
checkIfSaveFlkFile() - test if need to save the .flk file If so, ask them if they want to do it.
cHeight - Variable in class DrawHistogram
working canvas height
cHeight - Variable in class ScrollableImageCanvas
canvas height
chkBoxMenuItemList - Static variable in class BuildGUI
[MAX_CHKBOX_CMDS] list of ALL checkboxItem cmds menu items corresponding to names
chkBoxMenuLabelList - Static variable in class BuildGUI
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu labels
chkDoneWithTransform() - Method in class Flicker
chkDoneWithTransform() - called by run() thread when xform completed and the xformThreadCtr was incremented by softDoneWithTransform().
chkIfClickableDB(boolean) - Method in class Flicker
chkIfClickableDB() - check if currently selected image is a clickable active map data base in that it has a valid url.
circleMask - Variable in class Flicker
"measurement" circle mask of size nCirMask X nCirMask
circleRadius - Variable in class Spot
he radius of the circlular mask
circleX - Variable in class ScrollableImageCanvas
img X coords for circle
circleY - Variable in class ScrollableImageCanvas
img Y coords for circle
cl_block(FileOutputStream) - Method in class WriteGifEncoder
cl_block() - table clear for block compress Clear out the hash table.
cl_hash(int) - Method in class WriteGifEncoder
cl_hash() - reset code table
clean() - Method in class Boundary
clean() - clean up before init or when kill instance before GC
clean() - Method in class CalibrateOD
clean() - clean up before init or when kill instance before GC
clean() - Method in class ImageDataMeas
clean() - init the image data measurement state
clean() - Method in class ImageDataSpotList
clean() - cleanup the instance.
clean() - Static method in class Landmark
clean() - reinitialize the landmarks data structures
cleanup() - Method in class ImageXform
cleanup() - destroy data structures
cleanup() - Method in class ScrollableImageCanvas
cleanup() - destroy data structures
cleanup() - Method in class SpatialXform
cleanup() - destroy data structures
clear() - Static method in class FlkDemo
clear() - clear database flkDemos[0:nMaps-1].
clear() - Static method in class FlkMap
clear() - clear database flkMaps[0:nMaps-1].
clear() - Static method in class FlkRecent
clear() - clear database FlkRecents[0:nMaps-1].
clear() - Static method in class FlkUser
clear() - clear database flkUsers[0:nMaps-1].
clear_flg - Variable in class WriteGifEncoder
80% occupancy
clearButton - Variable in class ShowReportPopup
"Clear" button
ClearCode - Variable in class WriteGifEncoder
 
clearLandmarkTextListToDraw() - Method in class ImageScroller
clearLandmarkTextListToDraw() - disable text list of things to draw in canvas.
clearLandmarkTextListToDraw() - Method in class ScrollableImageCanvas
clearLandmarkTextListToDraw() - disable text list of landmarks to draw in canvas.
clearReportMsg() - Method in class Util
clearReportMsg() - clear text in report popup window
clearSpotList() - Method in class ImageDataSpotList
clearSpotList() - prompt "are you sure" and clear spot list if 'yes'.
clearText() - Method in class ShowReportPopup
clearText() - clear text in popup window
clickableCGIbaseURL1 - Variable in class Flicker
is clickable to get DB entry
clickableCGIbaseURL1pix - Variable in class Flicker
is clickable to get DB entry
clickableCGIbaseURL2 - Variable in class Flicker
is clickable to get DB entry
clickableCGIbaseURL2pix - Variable in class Flicker
is clickable to get DB entry
clickableCheckbox - Variable in class BuildGUI
enable clickable images
clickableURL - Variable in class FlkMap
file field ClickableURL: is the clickable map URL added to the BaseURL: e.g., "cgi-bin/map3/big/PLASMA_HUMAN?"
clickableURL1 - Variable in class FlkDemo
ClickableURL1: is the clickable map URL for image 1: e.g., "http://www.expasy.org/cgi-bin/map3/big/PLASMA_HUMAN?"
clickableURL1 - Variable in class FlkRecent
is the clickable map URL for image 1: e.g., "http://www.expasy.org/cgi-bin/map3/big/PLASMA_HUMAN?"
clickableURL2 - Variable in class FlkDemo
ClickableURL2: is the clickable map URL for image 2: e.g., ""
clickableURL2 - Variable in class FlkRecent
is the clickable map URL for image 2: e.g., "http://www.expasy.org/cgi-bin/map3/big/PLASMA_HUMAN?"
clone(SliderState) - Method in class SliderState
clone() - clone a copy of the src SliderState
close() - Method in class DrawHistogram
close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e.
close() - Method in class PopupTextFieldDialog
close() - close this popup
close() - Method in class PopupYesNoDialogBox
close() - close this popup
close() - Method in class ShowReportPopup
close() - close this popup and reset flags if needed
close() - Method in class Spot
close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e.
closeButton - Variable in class ShowReportPopup
"Close" button
cm - Variable in class PpxLoader
 
cm - Variable in class TiffLoader
 
cMapMode - Variable in class PpxLoader
color map flag.
cnt - Variable in class MC_Cube
 
codetab - Variable in class WriteGifEncoder
 
coef(int, int, double[], double[], double[], double[], double[][]) - Static method in class SpatialXform
coef() - Find kth mapping function coefficient (Eq.
colinearityLSQerr(int) - Method in class Affine
colinearityLSQerr() - compute colinearity of 3 landmarks as LSQ error.
COLOR2GRAY - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
color_text - Variable in class ScrollableImageCanvas
text list items colors
colorLM - Static variable in class Landmark
 
colorMax - Variable in class MedianCut
# of non-zero bins in hist15[]
colorMode - Variable in class BrightnessContrastFilter
method to use when filter RBG: (NORM_COLOR, PSEUDO_COLOR, RGB_TO_GRAY_COLOR)
colorMode - Variable in class Flicker
method to use when filter RBG in ImageScroller
colSize - Variable in class PopupDialogQuery
# of columns to display
COMPLEMENT - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
complement() - Method in class ImageXform
complement() - compute grayscale complement of gI
componentHidden(ComponentEvent) - Method in class Flicker
 
componentMoved(ComponentEvent) - Method in class Flicker
 
componentResized(ComponentEvent) - Method in class Flicker
componentResized() - resize canvases to proper sizes when frame is resized.
componentShown(ComponentEvent) - Method in class Flicker
 
composeXformCheckbox - Variable in class BuildGUI
xform previous oImg Image
composeXformFlag - Variable in class Flicker
Replace(Preserve) orig imgs w/ xforms
compress(int, FileOutputStream) - Method in class WriteGifEncoder
compress() - GIF Image compression - modified 'compress'.
computeCircularMaskList(int) - Method in class Util
computeCircularMaskList() - create a list of (x,y) point offsets for use later in convolution types of operations.
computeGrayHistStatistics() - Method in class ImageXform
computeGrayHistStatistics() - compute grayscale histogram statistics
computeSurfaceWarp(int, int, double[], double[], double[], double[][], double, int, int, double[]) - Method in class SpatialXform
computeSurfaceWarp() - compute surface warp from data.
CONSOLE_FLAG - Static variable in class Flicker
Debugging flag - Always TRUE
CONTR_ENHANCE - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
contrast - Variable in class SliderState
GUI state: contrast in [MIN_CONTRAST:MAX_CONTRAST]
contrastBar - Variable in class BuildGUI
scroll bar for contasrt
contrastEnhance() - Method in class ImageXform
contrastEnhance() - compute grayscale contrast pixel enhancement compute grayscale contrast enhanced image.
contrastLabel - Variable in class BuildGUI
GUI label for contrast scroll
copy(ScrollableImageCanvas) - Method in class ScrollableImageCanvas
copy() - destroy data structures
copy(SliderState, SliderState) - Method in class SliderState
copy() - copy src SliderState to dst SliderState
copyFile(String, String, String, int) - Method in class Util
copyFile() - binary copy of one file or URL toa local file
copyROI2CW() - Method in class ImageDataROI
copyROI2CW() - copy C-U/C-L ROI to Computing Window (CW)
count - Static variable in class ImageIO
counter to print '.' every NLINES lines
count - Static variable in class TiffLoader
instance # of TiffLoader
count - Variable in class WriteGifEncoderHashitem
 
createFlkDemoMenuTree(Menu) - Method in class BuildGUI
createFlkDemoMenuTree() - create the FlkDemo menu tree from the FlkDemo database "FlkDemoDB.txt" file
createFlkMapMenuTree(Menu) - Method in class BuildGUI
createFlkMapMenuTree() - create the FlkMap menu tree from the FlkMap database "DB/FlkMapDB.txt" file
createFlkRecentMenuTree(Menu) - Method in class BuildGUI
createFlkRecentMenuTree() - create the FlkRecent menu tree from the FlkRecent database "FlkRecentDB.txt" file
createFlkUserPairsMenuTree(Menu) - Method in class BuildGUI
createFlkUserPairsMenuTree() - create the paired FlkUser menu tree from analyzing the Images/* directories and setup the database of pairs of user directory images
createFlkUserSingleMenuTree(Menu) - Method in class BuildGUI
createFlkUserSingleMenuTree() - create the single image FlkUser menu tree from analyzing the Images/* directories and setup the database of user directory single images
createMaskDatabase(int) - Static method in class ImageDataMeas
createMaskDatabase() - create the set of circular masks of size NrxNr stored in a 3D array [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)
createZoomedImage() - Method in class ImageXform
createZoomedImage() - create zoomed image using getScaledInstance.
createZoomedImage(int[]) - Method in class ImageXform
createZoomedImage() - convert pixel array argument into zoomed image using getScaledInstance.
cScaled - Variable in class BrightnessContrastFilter
scaled current contrast value to range of [0:1.0]
ctrlMod - Variable in class ScrollableImageCanvas
CTRL/Mouse
ctrlShiftMod - Variable in class ScrollableImageCanvas
CTRL-SHIFT/Mouse
cubeList - Variable in class MedianCut
list of cubes
cur_accum - Variable in class WriteGifEncoder
 
cur_bits - Variable in class WriteGifEncoder
 
curIS - Variable in class ImageXform
current ImageScroller right or left
curPos - Variable in class ScrollableImageCanvas
keep track of current "+" where last clicked in 1.0 (mag) state
currentIS - Variable in class ScrollableImageCanvas
right or left IS that is being flickered
currentPRIbaseURL - Variable in class Flicker
Base URL for currently selected PIR server for accessing spot data using the previously looked up SWISS-PROT ID.
curSpot - Variable in class ImageDataMeas
Current spot set with showMeasValue if being measured.
curState - Variable in class Flicker
This is the working SliderState instance which will be either the "base-state" or the I1 or I2 instance.
cvByte2Int(byte) - Method in class PpxLoader
cvByte2Int() - convert unsigned byte [0:255] to int in range [0:255]
cvByteToChar(byte) - Method in class BrightnessContrastFilter
cvByteToChar() - convert signed byte [-128:+127] to unsigned char in range [0:255]
cvByteToChar(byte) - Method in class Util
cvByteToChar() - convert signed byte [-128:+127] to unsigned char in range [0:255]
cvByteToInt(byte) - Method in class BrightnessContrastFilter
cvByteToInt() - convert signed byte [-128:+127] to unsigned int in range [0:255]
cvByteToInt(byte) - Method in class Util
cvByteToInt() - convert signed byte [-128:+127] to unsigned int in range [0:255]
cvColor2ColorValue(Color) - Method in class Util
cvColor2ColorValue() - convert Color.xxx to color code
cvColorValue2Color(int) - Method in class Util
cvColorValue2Color() - convert color code to Color.xxx
cvd2s(double, int) - Static method in class Util
cvd2s() - convert double to string with precision # of digits If precision > 0 then limit # of digits in fraction
cvf2s(float, int) - Static method in class Util
cvf2s() - convert float to string with exact precision # of digits.
cvf2sVariable(float, int) - Static method in class Util
cvf2sVariable() - convert float to string with precision # of digits.
cvFeatures2str(String) - Method in class Boundary
cvFeatures2str() - cvt object features to printable string
cvFeatures2str(String) - Method in class ImageScroller
cvFeatures2str() - cvt object features to printable string
cvi2hexs(int) - Static method in class Util
cvi2hexs() - convert integer number to hex string
cvi2os(int) - Static method in class Util
cvi2os() - convert integer number to octal string with leading 0.
cvInt2Byte(int) - Method in class PpxLoader
cvInt2Byte() - convert unsignged int [0:255] to signed byte [-128:+127]
cvIntToByte(int) - Method in class BrightnessContrastFilter
cvIntToByte() - convert int in range [0:255] to signed byte in range of [-128:+127].
cvIntToByte(int) - Method in class Util
cvIntToByte() - convert int in range [0:255] to signed byte in range of [-128:+127].
cvMaskToStr(int[][], String) - Static method in class ImageDataMeas
cvMaskToStr() - convert a mask to a printable string
cvP2Ihdr(byte[]) - Method in class PpxLoader
cvP2Ihdr() - Convert portable header byteData[0:511] into PpxLoader state.
cvs2Array(String, int, String) - Static method in class Util
cvs2Array() - cvt arg list "1,4,3,6,..." to "," - delim String[].
cvs2f(String, float) - Static method in class Util
cvs2f() - convert String to float with default value
cvs2i(String, int) - Static method in class Util
cvs2i() - convert String to int with default value
cvSpot2Str(String, String) - Method in class Spot
cvSpot2Str() - convert spot to printable string
cvtGrayValueToODstr(int) - Method in class ImageDataMeas
cvtGrayValueToODstr() - convert gray value to OD string if the map has been defined for the ImageData instance
cvtImg24toImg8(int) - Method in class MedianCut
cvtImg24toImg8() - Uses Heckbert's median-cut algorithm to divide the color space defined by "hist15[]" into "maxcubes" cubes.
cvtRGBvalToNTSCgrayVal(int) - Static method in class ImageData
cvtRGBvalToNTSCgrayVal() - convert RGB value to NTSC grayscale value.
cvtZoomMagScr2Str(int) - Static method in class SliderState
cvtZoomMagScr2Str() - convert a zoomMag scroller value to a prettyprint string with 2 digits.
cvtZoomMagScr2ZoomMagVal(int) - Static method in class SliderState
cvtZoomMagScr2ZoomMagVal() - convert a zoomMag scroller value to a zoom mag value.
cWidth - Variable in class DrawHistogram
working canvas width
cWidth - Variable in class ScrollableImageCanvas
canvas width
cwx1 - Variable in class ImageDataROI
generic ULHC computing window set when both (C-U) and (C-L) were performed.
cwx2 - Variable in class ImageDataROI
generic LRHC computing window when both (C-U) and (C-L) were performed.
cwy1 - Variable in class ImageDataROI
generic ULHC computing window set when both (C-U) and (C-L) were performed.
cwy2 - Variable in class ImageDataROI
generic LRHC computing window when both (C-U) and (C-L) were performed.

D

d - Variable in class Affine
coeff for y2= d*x1 + e*y1 + f
d0 - Variable in class Affine
inverse coefficient for y2= dO*x1 + eO*y1 + fO
data - Variable in class PopupDialogQuery
for returning data back to caller
databaseName - Variable in class FlkMap
file field DatabaseName: is the Web database name (used to create a sub-menu): "Swiss-2DPAGE"
databaseName - Variable in class FlkRecent
is name of the database: e.g., "SWISS-2DPROT Human"
dataType - Variable in class TiffLoader
data type from sampleModel.getDataType() The types are defined as DataBuffer.TYPE_xxxx where xxxx is (BYTE, DOUBLE, FLOAT, INT, SHORT, UNDEFINED, USHORT)
DATE - Static variable in class Flicker
 
dateStr() - Static method in class Util
dateStr() - return a new Date string of the current day and time
dbMenuName - Variable in class FlkRecent
is the name of the database+menuName: e.g., "SWISS-2DPROT Human Plasma"
DBUG_CALIB - Static variable in class CalibrateOD
Local debugging flag set in CalibrateOD.main() test code
DBUG_NTSC_RGB2GRAY - Variable in class Flicker
DEBUGGING convert color RGB image to grayscale using NTSC algor.
dbugCtr - Static variable in class BrightnessContrastFilter
 
dbugFlag - Variable in class Flicker
true if debug printout, set by GUI
dbugFlag - Static variable in class TiffLoader
debugging flag
DE_ZOOM - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
decoder - Variable in class TiffLoader
Tiff Image Decoder
DEF_ANGLE - Static variable in class SliderState
rotation angle 10 degrees
DEF_BRIGHTNESS - Static variable in class SliderState
default brightness
DEF_CIRCLE_MASK_RADIUS - Variable in class Flicker
The radius is used to determine the size of the circle mask circleMask[nCirMask][nCirMask].
DEF_COL_SIZE - Static variable in class PopupDialogQuery
default # of columns
DEF_CONTRAST - Static variable in class SliderState
default contrast
DEF_ESCALE - Static variable in class SliderState
default eScale 20 percent
DEF_THRESHOLD1 - Static variable in class SliderState
MIN gray
DEF_THRESHOLD2 - Static variable in class SliderState
MAX gray
DEF_ZOOM - Static variable in class SliderState
default zoom X magnificationAWT
DEF_ZOOM_MAG_SCR - Static variable in class SliderState
default zoomMag X magnification scroller value
DEF_ZSCALE - Static variable in class SliderState
default zScale 5 percent
DEFAULT_DELAY - Static variable in class BuildGUI
0.30 sec default delay if not flickering
DEFAULT_FLICKER_DELAY - Static variable in class BuildGUI
default flicker delay0.20 sec
DEFAULT_TARGET_SIZE - Static variable in class Flicker
NOTE: set to 512 to enable if do image resizing
defaultFlickerDelay - Variable in class Flicker
default delay if not flickering
defTxtFile - Variable in class ShowReportPopup
 
delay - Variable in class SliderState
opt.
delayBar - Variable in class ImageScroller
opt.
delayLabel - Variable in class ImageScroller
opt.
delete() - Method in class FlkDemo
delete() - rmv entry from database flkDemos[0:nMaps-1].
delete() - Method in class FlkMap
delete() - rmv entry from database flkMaps[0:nMaps-1].
delete() - Method in class FlkRecent
delete() - rmv entry from database FlkRecents[0:nMaps-1].
delete() - Method in class FlkUser
delete() - rmv entry from database flkUsers[0:nMaps-1].
deleteLandmark() - Method in class Landmark
deleteLandmark() - "Delete LM" undo the last landmark if any
deleteLastLandmark() - Method in class Landmark
deleteLastLandmark() - delete last landmark
deleteLocalFile(String) - Method in class Util
deleteLocalFile() - delete local file.
deleteOldestEntry() - Static method in class FlkRecent
deleteOldestEntry() - delete the oldest entry
demo_setDefaultWedgeData_LeukemiaGels(ImageData) - Method in class CalibrateOD
demo_setDefaultWedgeData_LeukemiaGels() - setup the ND wedge data for the 4 demo GELLAB-II PPX leukemia gels release with Flicker.
density - Variable in class Boundary
 
density - Variable in class Spot
total density uncorrected for background computed as the sum of the gray value or calibrated gray value (i.e.
densPrime - Variable in class Spot
total density corrected for background by computed as: densPrime = (density - mnBkgrd*area)
densRaw - Variable in class Boundary
 
dialogQuery(String, String) - Method in class PopupDialogQuery
dialogQuery() - query String variable requested
dialogQuery(String, String, String[], int) - Method in class PopupDialogQuery
dialogQuery() - query String variable int requested
dirList - Static variable in class FlkUser
[0:nDirs-1] user image directories names if any
dirListPath - Static variable in class FlkUser
[0:nDirs-1] user image directory paths if any
disableXformMenuCmds - Static variable in class BuildGUI
[MAX_CMDS] list of [0:nXformMenuCmds-1] disabled Transform menuItems
displayInfoFlag - Variable in class Flicker
if TRUE then display enter/exit info
dMax - Variable in class Spot
spot MAX OD
dMaxBkgrd - Variable in class Spot
background for spot MAX OD or gray value
dMin - Variable in class Spot
spot MIN OD
dMinBkgrd - Variable in class Spot
background for spot MIN OD or gray value
doFullRepaint() - Method in class Flicker
doFullRepaint() - repaint flkIS, i1IS, i2IS and their canvases as well as flk.repaint().
doingAlertFlag - Static variable in class Util
flag to enforce an atomic alerts
doingTransform - Variable in class ImageData
set by doXform, cleared by doneWithXform
doingXformFlag - Variable in class Flicker
doing the transform
domain - Variable in class PpxLoader
0 = optical density, 1 = transmittance 2 = gray value ...
doMeasureProtIDlookupAndPopupFlag - Variable in class Flicker
Do spot measurement adding it to the spotList, protein lookup for that spot, and popup current access server Web page in one operation when the user clicks on a spot in an active image.
doTiffLoad(String, boolean) - Method in class TiffLoader
doTiffLoad() - load the image and array grab of TIFF files
doXform(ImageData) - Method in class ImageXform
doXform() - transform iPix[] into oPix[] image data by legal transform Then create the oImg.
dPanel - Variable in class ImageScroller
opt.
drawBackgroundCircleInImage(Graphics, Image) - Method in class ScrollableImageCanvas
drawBackgroundCircleInImage() - draw background circle in window if visible.
drawBoundary(Graphics) - Method in class Boundary
drawBoundary() - draw boundary backwards
drawBoundaryInImage(Graphics) - Method in class Boundary
drawBoundaryInImage() - redraw boundary in window if visible.
drawCircleAroundSpot(Graphics, int, int, Color, int, int) - Method in class ScrollableImageCanvas
drawCircleAroundSpot() - draw a circle around spot if visible.
drawFilledBox(Graphics, int, int, int, Color) - Static method in class DrawHistogram
drawFilledBox() - draw plus sign at the specified color.
drawGifFile(String) - Method in class DrawHistogram
drawGifFile() - draw plot into Gif image file if in stand-alone mode.
drawHistInCanvas(Graphics) - Method in class DrawHistogram
drawHistInCanvas() - draw histogram of hist[].
DrawHistogram - Class in <Unnamed>
The DrawHistogram class is used to draw an image intensity histogram in a popup frame.
DrawHistogram(Flicker, String, String, String, int) - Constructor for class DrawHistogram
DrawHistogram() - create a histogram plot for left or right selected image.
drawImageTitle() - Method in class ImageScroller
drawImageTitle() - draw title in image.
drawImageTitle() - Method in class ScrollableImageCanvas
drawImageTitle() - draw title in image.
drawIntoImageFlag - Variable in class DrawHistogram
set if draw plot to GIF file
drawLandmarksTextInImage(Graphics, int, int) - Method in class ScrollableImageCanvas
drawLandmarksTextInImage() - redraw landmark text[] in the image at (x,y)[] locs with the specified color and fonts.
drawMeasCircleInImage(Graphics, Image) - Method in class ScrollableImageCanvas
drawMeasCircleInImage() - draw measurement circles in window if visible.
drawPlus(Graphics, int, int, Color) - Static method in class DrawHistogram
drawPlus() - draw plus sign at the specified color.
drawRoiInImage(Graphics, Image) - Method in class ScrollableImageCanvas
drawRoiInImage() - draw region of interest in window if visible.
drawSpotMeasurementsInImage(Graphics, Image) - Method in class ScrollableImageCanvas
drawSpotMeasurementsInImage() - Draw spot measurements in image if valid and is visible.
drawTargetOverlay(Graphics, ImageScroller, ImageScroller) - Method in class ScrollableImageCanvas
drawTargetOverlay() - Draw Target Overlay in the ImageScroller window.
drawTrialObjInImage(Graphics) - Method in class ScrollableImageCanvas
drawTrialObjInImage() - redraw xyObj in window if visible.
dwCalHist - Variable in class ImageData
generic Calibration popup histogram for image
dwHist - Variable in class ImageData
generic ROI popup histogram for image
dX_P3D - Variable in class ImageXform
fast (width * sin(thetaRad)

E

e - Variable in class Affine
coeff for y2= d*x1 + e*y1 + f
e0 - Variable in class Affine
inverse coefficient for y2= dO*x1 + eO*y1 + fO
editMenu - Variable in class BuildGUI
"Edit" pull down Menu list
editPanel - Variable in class DrawHistogram
Array of TextFields used in constructing the editable Peak Calibration Table.
editSpotFromSpotList(Spot, boolean) - Method in class ImageDataSpotList
editSpotFromSpotList() - edit the spot from the spot list if found
editSpotFromSpotList(Spot, Spot, boolean) - Method in class ImageDataSpotList
editSpotFromSpotList() - edit the spot from the spot list if found
ef1 - Static variable in class PluginMgr
 
ef2 - Static variable in class PluginMgr
 
ef3 - Static variable in class PluginMgr
 
efInfo - Static variable in class PluginMgr
opt.
efIsActive - Static variable in class PluginMgr
if external function is used
efMnuName - Variable in class Flicker
what appears in menu
efMnuName - Static variable in class PluginMgr
which external functions appears in menu
efName - Variable in class Flicker
name of command
efName - Static variable in class PluginMgr
name of external function command
efNbr - Variable in class Flicker
function number 1 to MAX_EXTERN_FCTS
efNbr - Static variable in class PluginMgr
external function number 1 to n
ekb - Variable in class Flicker
get kbd event handler
endDataDict - Variable in class PpxLoader
(unsigned int) if non-zero, then byte # of file where data dictionary ends.
endTime - Variable in class ImageData
ending time of last transform
EOF - Static variable in class WriteGifEncoder
 
EOFCode - Variable in class WriteGifEncoder
 
EP97PAPER_FILE - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
eraseBoundary() - Method in class Boundary
eraseBoundary() - erase boundary backwards one at a time.
errMsg - Variable in class Affine
accumulated error messages
errorLoadingImageFlag - Variable in class Flicker
set by ImageObserver imageUpdate()
errStr - Variable in class Flicker
error string if not ""
errStr - Variable in class ImageData
last error message associated with obj
eScale - Variable in class ImageXform
state copy: scale factor for sharpening xform
eScale - Variable in class SliderState
GUI state: scale factor for image sharpening xform
eScaleBar - Variable in class BuildGUI
scroll bar for eScale
eScaleLabel - Variable in class BuildGUI
GUI label for eScale scroll
evalPoly(int, int, int, double[][]) - Method in class SpatialXform
evalPoly() - eval f_n(x,y)
EventKbd - Class in <Unnamed>
EventKbd class supports keyboard event handling for Flicker top level GUI.
EventKbd(Flicker) - Constructor for class EventKbd
EventKbd() - constructor
EventMenu - Class in <Unnamed>
EventMenu class supports menu item event handling for Flicker top level GUI.
EventMenu(Flicker, BuildGUI) - Constructor for class EventMenu
EventMenu() - constructor
EventMenu(String, int) - Constructor for class EventMenu
EventMenu() - constructor assigns name and id to object.
EventScroller - Class in <Unnamed>
EventScroller class supports scroller event handling for Flicker top level GUI.
EventScroller(Flicker) - Constructor for class EventScroller
EventScroller() - constructor
EventScroller(String, int, Flicker) - Constructor for class EventScroller
EventScroller() - constructor
evMu - Static variable in class BuildGUI
event handler
evMu - Variable in class Flicker
 
evs - Variable in class Flicker
instance of event scroller handler
externFctNbr - Variable in class ImageXform
external fct number if > 0
extFctNbr - Static variable in class PluginMgr
function number
extrapolateNDwedgeMap() - Method in class CalibrateOD
extrapolateNDwedgeMap() - extrapolate the maxNDsteps ND wedge peaks in ndWedgeODvalues[0:maxNDsteps-1] with corresponding gray values ndWedgeGrayValues[0:maxNDsteps-1] into a piecewise linear mapGrayToOD[0:maxGray] array.
extrapolateNDwedgeMap(int, int, int, int[], float[]) - Method in class CalibrateOD
extrapolateNDwedgeMap() - extrapolate the maxNDsteps ND wedge peaks in ndWedgeODvalues[0:maxNDsteps-1] with corresponding gray values ndWedgeGrayValues[0:maxNDsteps-1] into a piecewise linear mapGrayToOD[0:maxGray] array.

F

f - Variable in class Affine
coeff for y2= d*x1 + e*y1 + f
f - Variable in class PopupTextFieldDialog
Frame where dialog box is added
f - Variable in class PopupYesNoDialogBox
Frame where dialog box is added
f0 - Variable in class Affine
inverse coefficient for y2= dO*x1 + eO*y1 + fO
fatalMsg - Variable in class TiffLoader
Msg why failed if not null
fatalReportMsg(String, int) - Method in class Util
fatalReportMsg() - display a fatal report message to the report popup window, then wait for before return.
fBoth - Static variable in class Spot
Frame to create and popup when you edit
fctCalc(Flicker, ImageData, int[]) - Method in class Plugin1
fctCalc() - called to perform the image function
fctCalc(Flicker, ImageData, int[]) - Method in class Plugin2
fctCalc() - called to perform the image function
fctCalc(Flicker, ImageData, int[]) - Method in class Plugin3
fctCalc() - called to perform the image function
fctCalc(Flicker, int, ImageData, int[]) - Static method in class PluginMgr
fctCalc() - called to perform the image function
fDemo - Variable in class Flicker
FlkDemo database
fDemoMenuStub - Variable in class BuildGUI
last fDemo menu tree stub for use if rebuild it
fileDialog - Variable in class Popup
for use in popup FileDialog
FileIO - Class in <Unnamed>
Class FileIO is used to read file I/O from local disk or URL CGI server.
FileIO(Flicker) - Constructor for class FileIO
FileIO() - constructor
fileMenu - Variable in class BuildGUI
"File" pull down Menu list
fileName - Variable in class TiffLoader
filename path of image file
fileSeparator - Static variable in class Flicker
File separator
filterRGB(int, int, int) - Method in class BrightnessContrastFilter
filterRGB() - 1:1 pixel filtering required for RGBFilter class.
filtyp - Variable in class PpxLoader
type of file.
finalize() - Method in class Flicker
finalize() - total stop and kill Flicker threads.Write out the "Flicker.properties" file to save user preferences.
findMedian(int[]) - Method in class ImageXform
findMedian() - compute median of 9 values.
findPeaks(int, int, int[], int, int, int, int, float, int, boolean, boolean) - Method in class CalibrateOD
findPeaks() - Find the peaks in the histogram sHist[].
findPeakTableSizes() - Method in class CalibrateOD
findPeakTableSizes() - find the current maxPeaks and maxNDvalues from non-zero values in the peaks table.
finished1 - Variable in class Flicker
flag that finished transform 1
finished2 - Variable in class Flicker
finished transform 2
finishMeasurement(int, int, int[], int) - Method in class Boundary
finishMeasurement() - finish measurement and compute features
finishMeasurement() - Method in class ImageScroller
finishMeasurement() - finish measurement and compute features
fio - Variable in class Flicker
FileIO utilities
fio - Static variable in class Spot
FileIO utilities
fio - Static variable in class Windump
FileIO utilities
firstTimeThruFlag - Variable in class Flicker
first time to load img at start up, need to fix bug in ImgMeasure
fitWarpLSQ(int, double[], double[], double[], double[][], double) - Method in class SpatialXform
fitWarpLSQ() - weighted LSQ spatial transform w/ orthogonal polynomials Based on algorithm described by Ardeshir Goshtasby in "Image resgistration by local approximation methods", Image and Vision computing, Vold 6, No.
Flicker - Class in <Unnamed>
 
Flicker() - Constructor for class Flicker
Flicker() - constructor for Class Flicker
FLICKER_HOME - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
flickerCheckbox - Variable in class BuildGUI
Toggle flicker on/off
flickerFlag - Variable in class Flicker
enable flickering, set by GUI also from if set
FLIPHORIZ - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
flipHoriz() - Method in class ImageXform
flipHoriz() - compute horizontal flip image Compute 32-bit RGBA pixels from iPix[(x2*height + x2)] in oPix[]
flipLMS() - Method in class Affine
flipLMS() - flip the local copy of the 3 landmarks
FLIPVERT - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
flipVert() - Method in class ImageXform
flipVert() - compute Vertical flip image Compute 32-bit RGBA pixels from iPix[(x2*height + x2)] in oPix[]
flk - Variable in class Affine
Global instance
flk - Variable in class Boundary
 
flk - Static variable in class BrightnessContrastFilter
flicker instance
flk - Variable in class BuildGUI
Flicker instance
flk - Variable in class CalibrateOD
Global instances
flk - Static variable in class DrawHistogram
link to global Flicker instance
flk - Variable in class EventKbd
 
flk - Variable in class EventMenu
instances of global classes
flk - Variable in class EventScroller
 
flk - Variable in class FileIO
instance of Flicker
flk - Static variable in class FlkDemo
Instance of Flicker
flk - Static variable in class FlkMap
Instance of Flicker
flk - Variable in class FlkObserver
Global instances
flk - Static variable in class FlkRecent
Instance of Flicker
flk - Static variable in class FlkUser
Instance of Flicker
flk - Static variable in class ImageData
Flicker global classes
flk - Static variable in class ImageDataMeas
Flicker global classes
flk - Static variable in class ImageDataSpotList
Flicker global classes
flk - Variable in class ImageIO
Flicker class
flk - Variable in class ImageScroller
 
flk - Variable in class ImageXform
main class instance
flk - Variable in class Info
 
flk - Static variable in class Landmark
 
flk - Static variable in class PluginMgr
global instance
flk - Variable in class Popup
 
flk - Variable in class PopupTextFieldDialog
 
flk - Variable in class ScrollableImageCanvas
 
flk - Variable in class ShowReportPopup
link to global Flicker instance
flk - Static variable in class SliderState
 
flk - Static variable in class SpatialXform
Global instance
flk - Static variable in class Spot
instance of Flicker
flk - Static variable in class Util
Instance of Flicker
flk - Static variable in class Windump
instance of Flicker
FLK_BASE_URL - Static variable in class Flicker
Flicker server Base URL
flkCanvasSize - Variable in class Flicker
size for flicker canvas which does not include scrollbars etc.
flkCurPos - Variable in class ScrollableImageCanvas
 
FlkDemo - Class in <Unnamed>
FlkDemo contains methods to maintain the DB/FlkDemoDB.txt database used by Flicker.
FlkDemo(Flicker) - Constructor for class FlkDemo
FlkDemo() - constructor for Class FlkDemo
FlkDemo(String, String, String, String, String, String, String) - Constructor for class FlkDemo
FlkDemo() - constructor to add a new FlkDemo entry NOTE: to do add of an entry, use 'new FlkDemo()' method
FlkDemoDBfile - Static variable in class FlkDemo
name of the database file
flkDemos - Static variable in class FlkDemo
FlkDemo database [0:nMaps]
flkIS - Variable in class Flicker
(non-scrollable) image canvas for drawing flicker images.
FlkMap - Class in <Unnamed>
FlkMap contains methods to maintain the DB/FlkMapDB.txt database used by Flicker.
FlkMap(Flicker) - Constructor for class FlkMap
FlkMap() - constructor for Class FlkMap
FlkMap(String, String, String, String, String) - Constructor for class FlkMap
FlkMap() - constructor to add a new FlkMap entry NOTE: to do add of an entry, use 'new FlkMap()' method
flkMapDBfile - Static variable in class FlkMap
name of the database file
flkMaps - Static variable in class FlkMap
FlkMap database [0:nMaps]
FlkObserver - Class in <Unnamed>
FlkObserver implements our own (rather than default) image observer
FlkObserver(Flicker, ImageIO) - Constructor for class FlkObserver
FlkObserver() - Constructor
FlkRecent - Class in <Unnamed>
FlkRecent contains methods to maintain the FlkRecentDB.txt database used by Flicker.
FlkRecent(Flicker) - Constructor for class FlkRecent
FlkRecent() - constructor for Class FlkRecent
FlkRecent(String, String, String, String, String) - Constructor for class FlkRecent
FlkRecent() - constructor to add a new FlkRecent entry NOTE: to do add of an entry, use 'new FlkRecent()' method
FlkRecent(String, String, String, String, String, String, String) - Constructor for class FlkRecent
FlkRecent() - constructor to add a new FlkRecent entry pair NOTE: to do add of an entry, use 'new FlkRecent()' method
flkRecentChangedFlag - Static variable in class FlkRecent
flat that is set true if we edit the file (add/delete) since we loaded it from the disk.
FlkRecentDBfile - Static variable in class FlkRecent
name of the database file
flkRecents - Static variable in class FlkRecent
FlkRecent database [0:nMaps]
flkStateFile - Variable in class Flicker
current Flicker .flk state file that lives in "DB/".
flkStateHT - Variable in class Util
Hash table of .flk values read
FlkUser - Class in <Unnamed>
FlkUser contains methods to maintain the internal FlkUserDB database created by analyzing the user's image directories they have placed in the Images/ folder.
FlkUser(Flicker) - Constructor for class FlkUser
FlkUser() - constructor for Class FlkUser
FlkUser(String, String, String, String) - Constructor for class FlkUser
FlkUser() - constructor to add a new FlkUser entry NOTE: to do add of an entry, use 'new FlkUser()' method
flkUsers - Static variable in class FlkUser
FlkUser database [0:nMaps]
flush_char(FileOutputStream) - Method in class WriteGifEncoder
flush_char() - flush packet to disk, and reset the accumulator
flushImageResources(Image) - Static method in class ImageIO
flushImageResources() - flush image resources of no-longer needed image.
fm - Variable in class Flicker
FlkMap database
fMapMenuStub - Variable in class BuildGUI
last fMap menu tree stub for use if rebuild it
fNames - Static variable in class Spot
names of the spot fields
fOne - Static variable in class Spot
Frame to create and popup when you edit
font_text - Variable in class ScrollableImageCanvas
text list fonts
fontFamily - Variable in class DrawHistogram
Font family
fontLM - Static variable in class Landmark
color of the landmark
forceClearSpotList() - Method in class ImageDataSpotList
forceClearSpotList() - clear spot list and do NOT prompt if not empty.
forceReportWindowPopup() - Static method in class Util
forceReportWindowPopup() - force the append Report Window to popup
forceROIUpperAndLowerCorners() - Method in class ImageDataROI
forceROIUpperAndLowerCorners() - reorder the ROI so that (roiX1,roiY1) < (roiX2,roiY2)
frame - Variable in class PopupDialogQuery
popup frame instance
FRAME_HEIGHT - Static variable in class Flicker
Frame height
FRAME_INCR - Static variable in class Flicker
Frame change increment size - empirically determined
FRAME_WIDTH - Static variable in class Flicker
Frame width
frameHeight - Variable in class Flicker
main frame height
frameSize - Variable in class DrawHistogram
size of frame
frameWidth - Variable in class Flicker
main frame width
fRecent - Variable in class Flicker
FlkRecent database
fRecentMenuStub - Variable in class BuildGUI
last fRecent menu tree stub for use if rebuild it
free_ent - Variable in class WriteGifEncoder
 
fUser - Variable in class Flicker
FlkUser database
fUserMenuStub - Variable in class BuildGUI
last fUser menu tree stub for use if rebuild it
fversn - Variable in class PpxLoader
(unsigned short) Set to PPX_VRSION by program creating header

G

g - Variable in class BrightnessContrastFilter
current GREEN pixel when filter is running
g - Variable in class WriteGifEncoder
 
g_init_bits - Variable in class WriteGifEncoder
 
GC_MEMORY_DBUG - Variable in class Flicker
Enable pretty-printing GC Memory debugging
gcAndMemoryStats(String) - Method in class Util
gcAndMemoryStats() - String garbage collect & print memory statistics.
gcImageXform(String) - Method in class ImageXform
gcImageXform() - G.C.
genNdwvalues - Variable in class PpxLoader
ND (od) or CPM wedge step values
genPeaksFromMeasSpotList() - Method in class DrawHistogram
genPeaksFromMeasSpotList() - get the peak list from the circular mask measurement spot list using the mean circle measurement grayscale values.
get_aU() - Method in class SpatialXform
get_aU() - get aU[MXTERMS][MXTERMS] array this is solution to:
get_bV() - Method in class SpatialXform
get_bV() - get bV[MXTERMS][MXTERMS] array this is solution to:
get_sWorking() - Method in class ImageIO
get_sWorking() - get the working image progress string
getAffineCalcsString() - Method in class Affine
 
getAffineCoef() - Method in class Affine
getAffineCoef() - return array with [a,b,c,d,e,f]
getAffineMLSQcolinearity(int) - Method in class Affine
getAffineMLSQcolinearity() - get landmark colinearity.
getAnnotationFromServer(ImageData, Spot) - Method in class Util
getAnnotationFromServer() - get the gel iData spot s data from proteomic web server
getBaseFlkPropertiesStr(StringBuffer) - Method in class Util
getBaseFlkPropertiesStr() - add generate tab-delim base Flicker properties State string to the string buffer The format is tab-delimited (name \t value \n) with one entry/line.
getBoundary() - Method in class Boundary
getBoundary() - return boundary
getBoundaryLength() - Method in class Boundary
getBoundaryLength() - return nPoints for boundary
getColorText() - Method in class ImageScroller
getColorText() - text list items colors
getCurDateStr() - Static method in class Util
getCurDateStr() - return date string in the format of YYMMDDHHMMSS.
getDelay() - Method in class ImageScroller
getDelay() - get the Image delay time
getFastNgh(int, int) - Method in class ImageXform
getFastNgh() - get 3x3 8-bit neighborhood at (x,y)
getFileName(String) - Method in class Util
getFileName() - get the file name after last '/' if any
getFileNameFromPath(String) - Method in class Util
getFileNameFromPath() - extract the filename from the path
getFilesInDir(String, String) - Method in class FileIO
getFilesInDir() - get list of files in directory the specified file extension
getFilesWithLegalExtnInDir(String, String[]) - Method in class FileIO
getFilesWithLegalExtnInDir() - get list of files in directory with one of the specified file extensions
getFontText() - Method in class ImageScroller
getFontText() - get text list fonts
getFullCalFilePath(ImageData) - Method in class Util
getFullCalFilePath() - compute the .cal file from the qualified imageFile If there is a subdirectory before the baseFile, then strip out the directory name and add it before the actual base file.
getGrayValueTable() - Method in class CalibrateOD
getGrayValueTable() - get Wedge calibration grayscale[0:maxPeaks-1]
getGuardRegionDimension(double) - Method in class ImageScroller
getGuardRegionDimension() - return guard size
getHasODmapFlag() - Method in class CalibrateOD
getHasODmapFlag() - return the status of the Gray to OD map.
getID() - Method in class Spot
getID() - get the spot ID
getImage() - Method in class PpxLoader
getImage() - get pixels from the raster
getImage() - Method in class TiffLoader
getImage() - get pixels from the raster
getImageForBCInput() - Method in class ImageData
getImageForBCInput() - get image for input to Brightness/Contrast filter.
getImageForDisplayInput() - Method in class ImageData
getImageForDisplayInput() - get image for input to display painting.
getImageForXformInput() - Method in class ImageData
getImageForXformInput() - get the image for input to image transform.
getImageForZoomInput() - Method in class ImageData
getImageForZoomInput() - get image for input to ZoomMag filter.
getImgCursor() - Method in class ImageScroller
getImgCursor() - get the (x,y) scrollable cursor for this image If there is no cursor, then return (0,0).
getImgCursorMax() - Method in class ImageScroller
getImgCursorMax() - get the (x,y) scrollable cursor Maximum for image If there is no cursor, then return (0,0).
getImgPosition() - Method in class ImageScroller
getImgPosition() - get the Image position.
getImgPosition() - Method in class ScrollableImageCanvas
getImgPosition() - get the Image position.
getImgType() - Method in class ImageData
getImgType() - get image type from IMG_TYPE_xxx
getINVAffineCoef() - Method in class Affine
getINVAffineCoef() - return array with [aO,bO,cO,dO,eO,fO]
getLastMsgColor() - Method in class Util
getLastMsgColor() - get the last message color
getLastMsgStr() - Method in class Util
getLastMsgStr() - get the last message string
getLMstr() - Method in class Affine
getLMstr() - return the 3 landmark values for I1 and I2
getMapGrayToOD() - Method in class CalibrateOD
getMapGrayToOD() - return the mapGrayToOD[0:maxGray-1].
getMaxScrollBarHeight() - Method in class ImageScroller
getMaxScrollBarHeight() - return scroll max height
getMaxScrollBarWidth() - Method in class ImageScroller
getMaxScrollBarWidth() - return scroll max width
getMinimumSize() - Method in class DrawHistogram
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class Spot
getMinimumSize() - get the minimum preferred size
getNbrRGBpixels(int[], int) - Method in class TiffLoader
getNbrRGBpixels() - test if red==green==blue for all pixels
getNbrTextItems() - Method in class ImageScroller
getNbrTextItems() - return actual number of text items to display
getNewImageCenterPoint() - Method in class ScrollableImageCanvas
getNewImageCenterPoint() - Calc new center point in image based on scrollers
getNgh(int, int) - Method in class ImageXform
getNgh() - get 3x3 least significant 8-bit neighborhood data at (x,y)
getNgh3x3(int, int) - Method in class ImageXform
getNgh3x3() - get 3x3 least significant 8-bit neighborhood data at (x,y)
getNghInt(int, int) - Method in class ImageXform
getNghInt() - get 3x3 32-bit neighborhood at (x,y)
getNghInt3x3(int, int) - Method in class ImageXform
getNghInt3x3() - get 3x3 32-bit neighborhood at (x,y)
getObjPosition() - Method in class ImageScroller
getObjPosition() - get the object position.
getObjPosition() - Method in class ScrollableImageCanvas
getObjPosition() - get the object position.
getODtable() - Method in class CalibrateOD
getODtable() - get Wedge calibration odTable[0:maxNDsteps-1] OD values
getPeaksByMeasFlag - Variable in class DrawHistogram
Get the peaks from the circular mask measurement spot list using the mean circle measurement grayscale values not corrected for background (since we do not know what background is).
getPixelDataFromImage(Image, int, int) - Static method in class ImageData
getPixelDataFromImage() - get the pixel data from the image
getPixelValue(int, int) - Method in class ImageDataMeas
getPixelValue() - get the pixel value for the image at (x,y).
getPixelValueStr(int, int) - Method in class ImageDataMeas
getPixelValueStr() - get the pixel value string for the image where the trial object (xObj,yObj) is located.
getPreferredSize() - Method in class DrawHistogram
getPreferredSize() - getPreferredSize, needed for sizing frame correctly.
getPreferredSize() - Method in class ImageScroller
getPreferredSize() - getPreferredSize, needed for sizing canvas and ScrollPane correctly.
getPreferredSize() - Method in class ScrollableImageCanvas
getPreferredSize() - getPreferredSize, must be implemented for ScrollPane to be displayed correctly.
getPreferredSize() - Method in class Spot
getPreferredSize() - get the preferred size
getProteinIDdataByXYurl(String, int, int, String) - Method in class Util
getProteinIDdataByXYurl() - read data from protein web site and parse {Swiss-Prot-id, protein-name} if found.
getScrollbarHeight() - Method in class ImageScroller
getScrollBarHeight() - return scroll height position
getScrollbarWidth() - Method in class ImageScroller
getScrollBarWidth() - return scroll width position
getScrollerValuesStateStr() - Method in class Util
getScrollerValuesStateStr() - "Report scroller values" button
getScrollPosition() - Method in class ImageScroller
getScrollPosition() - return scroll positions
getStateStr(ImageData, String) - Method in class CalibrateOD
getStateStr() - get this calibration state as a string
getStateStr() - Method in class Landmark
getStateStr() - get this landmark state as a string
getStateStr(ImageData, String) - Method in class SliderState
getStateStr() - get this scroller state as a string
getStateStr() - Method in class Util
getStateStr() - generate a tab-delim Flicker State string for when we write out the .flk state.
getStateValue(String, String) - Method in class Util
getStateValue() - get PARAM and use default if not found.
getStateValue(String, int) - Method in class Util
getStateValue() - get int PARAM and use default if not found.
getStateValue(String, long) - Method in class Util
getStateValue() - get float PARAM and use default if not found.
getStateValue(String, float) - Method in class Util
getStateValue() - get float PARAM and use default if not found.
getStateValue(String, boolean) - Method in class Util
getStateValue() - get boolean PARAM and use default if not found.
getText() - Method in class ImageScroller
getText() - text list items
getTiffPixels(Raster, boolean) - Method in class TiffLoader
getTiffPixels() - get pixels from the raster
getTiffProperties(Raster) - Method in class TiffLoader
getTiffProperties() - get properties of the Tiff image
getUnits() - Method in class CalibrateOD
getUnits() - get Wedge units, e.g.
getUnitsAbbrev() - Method in class CalibrateOD
getUnitsAbbrev() - get Wedge units abbreviation, e.g.
getUnitsManufacturerPartNbr() - Method in class CalibrateOD
getUnitsManufacturerPartNbr() - get Wedge manufacturerPartNbr
getValBySpotFieldName(String) - Method in class Spot
getValBySpotFieldName() - get spot value string by spot field name
getValidFeaturesFlag() - Method in class Boundary
getValidFeaturesFlag() - get the valid features set after measurement
getValidFeaturesFlag() - Method in class ImageScroller
getValidFeaturesFlag() - get the valid features set after measurement
getXObjPosition() - Method in class ImageScroller
getXObjPosition() - get the X object position.
getXText() - Method in class ImageScroller
getXText() - x text list items positions
getYObjPosition() - Method in class ImageScroller
getYObjPosition() - get the X object position.
getYText() - Method in class ImageScroller
getYText() - y text list items positions
GIFEncode(FileOutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class WriteGifEncoder
GIFEncode() - encode the image Adapted from ppmtogif, which is based on GIFENCOD by David Rowley .
GIFNextPixel() - Method in class WriteGifEncoder
GIFNextPixel() - Return the next pixel from the image
gLUT - Variable in class MedianCut
[0:255] Green Color map look up table
gMax - Variable in class ImageXform
compute max grayscale of iPix
gmax - Variable in class MC_Cube
 
gMean - Variable in class ImageXform
mean of grayscale histogram
gMin - Variable in class ImageXform
compute min grayscale of iPix
gmin - Variable in class MC_Cube
 
gMode - Variable in class ImageXform
mode of grayscale histogram
GOOGLE_2D_SEARCH - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on the Internet
GRAD - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
grad() - Method in class ImageXform
grad() - compute 4-neighbor gradient
gray2OD - Variable in class TiffLoader
[FUTURE] grayscale to OD lookup table [0:maxGray-1] if supplied as additional TIFF tags.
grayCalWedge - Variable in class PpxLoader
(16-bit unsigned) gray scale peaks calibration corresponding to step wedge values.
greenBits(int) - Method in class MedianCut
greenBits() - Get 8-bit green component of a 15-bit color 8-bit pixel with low 3 bits zero.
gToRGB - Variable in class ImageXform
table lookup[256] grayvalue to RGB pixel
guardHeight - Variable in class ImageScroller
size of top & bottom guard region
guardHeight - Variable in class ScrollableImageCanvas
size of top & bottom guard region
guardImgHeight - Variable in class ImageScroller
size of img with guard region
guardImgHeight - Variable in class ScrollableImageCanvas
size of img with guard region
guardImgWidth - Variable in class ImageScroller
size of img with guard region
guardImgWidth - Variable in class ScrollableImageCanvas
size of img with guard region
guardRegionColor - Variable in class Flicker
Adjustable guard region color
guardRegionCorrection(Point) - Method in class ScrollableImageCanvas
guardRegionCorrection() - return guard region location
guardRegionFlag - Variable in class ImageScroller
guard region flag
guardRegionFlag - Variable in class ScrollableImageCanvas
guard region flag
guardWidth - Variable in class ImageScroller
size of right & left guard region
guardWidth - Variable in class ScrollableImageCanvas
size of right & left guard region
gValue - Variable in class ScrollableImageCanvas
gray value of (x,y) pixel object

H

hasODmapFlag - Variable in class CalibrateOD
Indicates that there is an valid mapGrayToOD map else if it was set to 1:1 the flag is set false.
hasODmapFlag - Variable in class ImageData
Indicates that there is an valid mapGrayToOD map else if it was set to 1:1 the flag is set false.
hasPrevCALflag - Variable in class CalibrateOD
Had a valid ND wedge ROI when came into the wizard
height - Variable in class Affine
Image height
height - Variable in class ImageXform
 
height - Variable in class MedianCut
width size of image
height - Variable in class PopupDialogQuery
size of frame
height - Variable in class WriteGifEncoder
 
Height - Variable in class WriteGifEncoder
 
helpMenu - Variable in class BuildGUI
"Help" pull down Menu list
highlightActiveIS() - Method in class ScrollableImageCanvas
highlightActiveIS() - highlight ScrollableImageCanvas.
hist - Variable in class CalibrateOD
histogram of pixel data in ND computing window of [0:255]
hist - Variable in class DrawHistogram
freq hist[0:nHist-1].
hist - Variable in class ImageData
Histogram of data [0:maxGray]
hist - Variable in class ImageXform
histogram of iPix[] if needed
hist15 - Variable in class MedianCut
[0:32K] 15-bit RGB hist.
HIST_EQUAL - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
histColor - Variable in class DrawHistogram
 
histEq - Variable in class ImageXform
equalized histogram of iPix[] if needed
histMode - Variable in class DrawHistogram
The histogram mode is either: MODE_CW_ROI_HIST, MODE_CALIB_ND_ROI_HIST, or MODE_CALIB_SPOTLIST_HIST
histogramEqualization() - Method in class ImageXform
histogramEqualization() - compute grayscale histogram equalization xform for 8-bit pixels
histPtr - Variable in class MedianCut
[0:colorMax-1] points to colors in "hist15[]"
histTopColor - Variable in class DrawHistogram
 
horizCaption - Variable in class DrawHistogram
horizontal caption
HSIZE - Static variable in class MedianCut
max size of image histogram
HSIZE - Static variable in class WriteGifEncoder
 
hsize - Variable in class WriteGifEncoder
 
hsv2rgb(float, float, float, int[]) - Method in class BrightnessContrastFilter
hsv2rgb() - convert (hue,saturation,value) color model to (red,green,blue) color model.
htab - Variable in class WriteGifEncoder
 
hue - Variable in class BrightnessContrastFilter
current hue pixel value when HSV filtering

I

i0 - Variable in class ImageXform
8-neighbor pixels
i1 - Variable in class ImageXform
8-neighbor pixels
i1IS - Variable in class Flicker
scrollable image 1 scrollable image (left)
i2 - Variable in class ImageXform
8-neighbor pixels
i2IS - Variable in class Flicker
scrollable image 2 scrollable image (right)
i3 - Variable in class ImageXform
8-neighbor pixels
i4 - Variable in class ImageXform
8-neighbor pixels
i5 - Variable in class ImageXform
8-neighbor pixels
i6 - Variable in class ImageXform
8-neighbor pixels
i7 - Variable in class ImageXform
8-neighbor pixels
i8 - Variable in class ImageXform
8-neighbor pixels
iabs(int) - Method in class ImageXform
iabs(a) - compute fastABS of two ints
icm - Variable in class ImageData
Index Color map
id - Variable in class EventMenu
 
id - Variable in class EventScroller
event scroller id
id - Variable in class ImageDataMeas
Instance of ImageData for extended classes
id - Variable in class ImageDataROI
Instance of ImageData for extended classes
id - Variable in class ImageDataSpotList
Instance of ImageData for extended classes
id - Variable in class MC_Cube
 
id - Variable in class Spot
Optional associated identifier string if not null.
iData - Variable in class DrawHistogram
link to data related ImageData instance
iData - Static variable in class EventMenu
 
iData - Variable in class EventScroller
ImageData instance of current data sample being processed
iData - Variable in class ImageScroller
Image data for mapGraytoOD[] that will be set later...
iData - Variable in class ImageXform
Image data instance to use we get data from either iImg or oImg
iData1 - Variable in class Flicker
image 1 picture data associated with ImageScroller i1IS (left)
iData2 - Variable in class Flicker
image 2 picture data associated with ImageScroller i2IS (right)
idM - Variable in class ImageData
Current measured circular mask spot for this image
idROI - Variable in class ImageData
Region(s) Of Interest (ROI).
idSL - Variable in class ImageData
Spot list (measured spots) for this image
idxID - Static variable in class Spot
index of "id" field in fNames table.
iHeight - Variable in class Boundary
height of image to measure
iHeight - Variable in class ImageData
height of original input image
iImg - Variable in class ImageData
input image.
IMAGE_FILE1 - Static variable in class Flicker
default left image1 file
IMAGE_FILE2 - Static variable in class Flicker
default right image2 file
ImageData - Class in <Unnamed>
ImageData class supports image data object access.
ImageData(String, Image, Dimension, boolean, float[], Flicker) - Constructor for class ImageData
ImageData() - Constructor.
ImageData() - Constructor for class ImageData
ImageData() - Constructor for extensions
ImageDataMeas - Class in <Unnamed>
ImageDataMeas class supports image data spot measurement object access.
ImageDataMeas(ImageData) - Constructor for class ImageDataMeas
ImageData() - Constructor for spot measurement extension
ImageDataMeas() - Constructor for class ImageDataMeas
ImageData() - Constructor for creating spot masks Defaults to Flicker.MAX_CIRCLE_RADIUS # of masks
ImageDataMeas(int) - Constructor for class ImageDataMeas
ImageData() - Constructor for creating spot masks of size 1x1 to (maxRadiusToCreate X maxRadiusToCreate)
ImageDataROI - Class in <Unnamed>
ImageDataROI class supports image data ROI object access.
ImageDataROI(ImageData) - Constructor for class ImageDataROI
ImageDataROI() - Constructor.
ImageDataSpotList - Class in <Unnamed>
ImageDataSpotList class supports image data spot list object access.
ImageDataSpotList(ImageData) - Constructor for class ImageDataSpotList
ImageDataSpotList() - Constructor for Spot Lists
imageFile - Variable in class DrawHistogram
current image file name
imageFile - Variable in class ImageData
full-path input image file name
imageFile1 - Variable in class Flicker
full path of image 1 (left) file or URL
imageFile2 - Variable in class Flicker
full path of image 2 (right) file or URL
imageFont - Variable in class Flicker
image font for overlay
ImageIO - Class in <Unnamed>
ImageIO class is used to do Flicker image I/O and conversion functions.
ImageIO(Flicker, String) - Constructor for class ImageIO
ImageIO() - Constructor
imageLoadErrorFlag - Variable in class Flicker
true if image loading error
ImageScroller - Class in <Unnamed>
ImageScroller class supports a scrollable image for the Left and right images.
ImageScroller(Flicker, String, String, ImageData, int, int, int, int, int, boolean) - Constructor for class ImageScroller
ImageScroller() - constructor.
imagesToProcess - Variable in class Flicker
CountDown to determine if finished.
imageUpdate(Image, int, int, int, int, int) - Method in class FlkObserver
imageUpdate() - called when loading reporting progress by printing "..." Set by ImageObserver.
imageURL - Variable in class FlkMap
file field ImageURL: is the Image URL added to the BaseURL: e.g.
imageURL1 - Variable in class FlkDemo
ImageURL1: is the Image URL for image 1: e.g.
imageURL1 - Variable in class FlkRecent
ImageURL: is the Image URL for image: e.g.
imageURL1 - Variable in class FlkUser
ImageURL1: is the Image URL for image 1: e.g.
imageURL2 - Variable in class FlkDemo
imageURL2: is the Image URL for image 2: e.g.
imageURL2 - Variable in class FlkRecent
ImageURL: is the Image URL for image: e.g.
imageURL2 - Variable in class FlkUser
imageURL2: is the Image URL for image 2: e.g.
ImageXform - Class in <Unnamed>
ImageXform class supports image transforms.
ImageXform() - Constructor for class ImageXform
ImageXform() - dummy Construct ImageXform object.
ImageXform(Flicker, String, ImageData, String, int) - Constructor for class ImageXform
ImageXform() - Construct ImageXform object.
imax(int, int) - Method in class ImageXform
imax(a,b) - compute fast MAX of two ints
imEncode - Variable in class 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 PpxLoader
Image structure required for Flicker
img - Variable in class TiffLoader
Image structure required for Flicker
img - Variable in class WriteGifEncoder
Image if specified
img_selectedFlag - Variable in class ImageScroller
set if xObj,yObj is set
IMG_TYPE_GIF - Variable in class ImageData
GIF image type
IMG_TYPE_J2K - Variable in class ImageData
[FUTURE] JPEG2000 image type.
IMG_TYPE_JPG - Variable in class ImageData
JPEG image type
IMG_TYPE_PPX - Variable in class ImageData
GELLAB-II PPX image type
IMG_TYPE_TIF - Variable in class ImageData
TIFF image type
IMG_TYPE_UNKNOWN - Variable in class ImageData
Unknown image type
imgFile - Static variable in class EventMenu
 
imgFile - Variable in class EventScroller
file name of current data sample being processed
imgIO - Variable in class EventMenu
 
imgIO - Variable in class Flicker
Flicker image I/O and conversion functions
imgIO - Variable in class FlkObserver
 
imgPos - Variable in class Flicker
position of the image for flickering
imgRoiX1 - Variable in class ScrollableImageCanvas
The true position of ROI with respect to the image not canvas
imgRoiX2 - Variable in class ScrollableImageCanvas
The true position of ROI with respect to the image not canvas
imgRoiY1 - Variable in class ScrollableImageCanvas
The true position of ROI with respect to the image not canvas
imgRoiY2 - Variable in class ScrollableImageCanvas
The true position of ROI with respect to the image not canvas
imgType - Variable in class ImageData
image type is one of IMG_TYPE_xxx
imgXform - Variable in class Flicker
current image transform if any
imin(int, int) - Method in class ImageXform
imin(a,b) - compute fast MIN of two ints
imOrientation - Variable in class PpxLoader
Image orientation bits where: Default 00==>011: 01 = left to right 02 = bottom to top 04 = right to left 010= top to bottom
index - Variable in class WriteGifEncoderHashitem
 
info - Variable in class EventKbd
 
info - Variable in class Flicker
Info status region
Info - Class in <Unnamed>
Info class supports updating the "Info" area on the Flicker GUI displaying messages on the status of Flicker.
Info(Flicker, JPanel) - Constructor for class Info
Info() - constructor
info - Variable in class PluginMgr
optional help message for function
info - Variable in class ScrollableImageCanvas
 
info1Label - Variable in class Info
 
info2Label - Variable in class Info
 
info3Label - Variable in class Info
 
info4Label - Variable in class Info
 
info5Label - Variable in class Info
 
info6Label - Variable in class Info
 
inheritNDwedgeODvalues(ImageData) - Method in class CalibrateOD
inheritNDwedgeODvalues() - if current calibration does NOT have ND wedge OD values, but the paired gel DOES, then inherit its OD wedge values and units to avoid having to type it.
init(String[]) - Method in class Flicker
init() - init Flicker state variables.
init(Flicker, String) - Method in class SliderState
init() - set state to default values.
init_alpha(int, int, int, double[], double[], double[], double[][]) - Static method in class SpatialXform
init_alpha() - compute parameter alpha(j,k) (EQ.
initAffine(float, int, int) - Method in class Affine
initAffine() - init the affine instance for another transform.
initDefaultState() - Method in class Affine
initDefaultState() - Initialize affine state to no transform present.
initialImageLoad() - Method in class Flicker
initialImageLoad() - load the initial images when first enter run().
initialMaxPeaks - Variable in class CalibrateOD
the value of maxPeaks BEFORE running the peak finder
initl - Variable in class PpxLoader
initials of person doing scan
initState(String[]) - Method in class Flicker
initState() - init Flicker state variables.
interlace - Variable in class WriteGifEncoder
80% occupancy
Interlace - Variable in class WriteGifEncoder
80% occupancy
interpolatePoints(int, int, int, int) - Method in class Boundary
interpolatePoints() - interpolate (xOld,yOld) to (xNew,yNew) into list of x,y coordinates of maximum size maxN which are pushed onto the bnd[] point list.
iPix - Variable in class ImageData
For ImageXform and display - input image pixel data for display.
iPix - Variable in class ImageXform
 
IPROCLASS - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on \ the Internet
IPROLINK - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on \ the Internet
is - Variable in class BrightnessContrastFilter
The Image Scroller for the image data to compute filter on
is - Variable in class ScrollableImageCanvas
Parent class
isActive - Static variable in class PluginMgr
set if this instance is active
isCalibFlag - Variable in class Spot
measurements are in calibrated OD rather than grayscale
isClickableDBflag - Variable in class Flicker
flag set if currently selected image is clickable
isClickableDBflag - Variable in class ImageData
flag set if currently selected image is clickable
isColorImgFlag - Variable in class ImageData
Is true if it is a color image where red!=green or red!=blue or when it is read in.
isComponentCMflag - Variable in class TiffLoader
set if has ComponentColorModel
isComponentSMflag - Variable in class TiffLoader
set if has ComponentSampleModel
isFlipLMSflag - Variable in class Affine
flip left and right landmarks after copy to local [FUTURE]
isHeight - Variable in class ImageScroller
height of image from iData.iHeight or zoomed data
isLeftFlag - Variable in class EventScroller
LEFT image is selected
isLoadedFlag - Variable in class ImageIO
set after loaded
isMultiplePixelPackedSMflag - Variable in class TiffLoader
set if has a MultiplePixelPackedSampleModel
isName - Variable in class ScrollableImageCanvas
name of ImageScroller parent
isPackedCMflag - Variable in class TiffLoader
set if PackedColorModel
isPackedFlag - Variable in class TiffLoader
set if pixel can be packed into a byte array
isptsz - Variable in class PpxLoader
(unsigned short) s.s.d in microns*1024
isRGBcolorImage() - Method in class ImageData
isRGBcolorImage() - test if red!=green!=blue for any pixels
isRGBcolorImageFlag - Variable in class TiffLoader
set if this is a RGB color image
isRightFlag - Variable in class EventScroller
RIGHT image is selected
isSinglePixelPackedSMflag - Variable in class TiffLoader
set if has a SinglePixelPackedSampleModel
isSuspendedFlag - Variable in class Flicker
Threads were suspended by stop()
istpx - Variable in class PpxLoader
(unsigned short) X step sizes in microns*1024
istpy - Variable in class PpxLoader
(unsigned short) Y step sizes in microns*1024
isTransparent - Variable in class WriteGifEncoderHashitem
 
isValidCW() - Method in class ImageDataROI
isValidCW() - check if current Computing Window (CW) is valid
isValidLMSflag - Variable in class Affine
Landmark DB has 3 valid landmarks.
isValidNDcalibCW() - Method in class ImageDataROI
isValidNDcalibCW() - check if current Calibration Computing Window is valid
isValidROI() - Method in class ImageDataROI
isValidROI() - check if current region of interest (ROI) is valid
isValidWedgeROI() - Method in class CalibrateOD
isValidWedgeROI() - check if Wedge ROI is valid
isVisibleFlag - Variable in class DrawHistogram
If the Histogram is visible
isWidth - Variable in class ImageScroller
width of image from iData.iWidth or zoomed data
itemStateChanged(ItemEvent) - Method in class BuildGUI
itemStateChanged() - handle item state changed events.
itemStateChanged(ItemEvent) - Method in class EventMenu
itemStateChanged() - handle menu item state changed events
itemStateChanged(ItemEvent) - Method in class PopupDialogQuery
itemStateChanged() - event handler for Choices
itemStateChanged(ItemEvent) - Method in class ShowReportPopup
itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
iWidth - Variable in class Boundary
width of image to measure
iWidth - Variable in class ImageData
width of original input image
ix - Variable in class Flicker
image transform
ixf1 - Variable in class Flicker
image transform for image 1 if any
ixf2 - Variable in class Flicker
image transform for image 2 if any

K

keyPressed(KeyEvent) - Method in class EventKbd
keyPressed() - handle key down events
keyPressed(KeyEvent) - Method in class ScrollableImageCanvas
keyPressed() - handle key pressed events
keyReleased(KeyEvent) - Method in class EventKbd
 
keyReleased(KeyEvent) - Method in class ScrollableImageCanvas
keyReleased() - handle key down events
keyTyped(KeyEvent) - Method in class EventKbd
 
keyTyped(KeyEvent) - Method in class ScrollableImageCanvas
keyTyped() - handle key down events

L

label - Variable in class PopupDialogQuery
for data label
labelColor - Variable in class DrawHistogram
 
Landmark - Class in <Unnamed>
Landmark class supports landmark data structures and operations.
Landmark(Flicker, Font, int) - Constructor for class Landmark
Landmark() - Constructor.
landmarkSimilarity() - Method in class Landmark
landmarkSimilarity() - compute landmark similarity for >=3 LMs.
LAPLACIAN - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
laplacian() - Method in class ImageXform
laplacian() - compute 8-neighbor laplacian
largeFont - Variable in class DrawHistogram
medium font used for labeling
lastIS - Static variable in class EventMenu
 
lastIS - Variable in class EventScroller
Image Scroller for current data sample being processed
lastIS - Variable in class Flicker
last selected image canvas - used in an operation and is selected by clicking on either throws left or right (I1 or I2) images.
lastISName - Variable in class Flicker
last IS that was clicked on
lastISName - Static variable in class ImageScroller
last image scroller - used in new operation "flicker", "left", "right"
lastlastISName - Variable in class ScrollableImageCanvas
from time before...
lastMsgColor - Variable in class Flicker
save last message color state
lastMsgColor - Variable in class Util
 
lastMsgStr - Variable in class Flicker
save last message state
lastMsgStr - Variable in class Util
 
leftFillWithSpaces(String, int) - Static method in class Util
leftFillWithSpaces() - left fill the string with spaces to size n.
leftOrRightSelectedFlag - Static variable in class EventMenu
Flag that indicates the currently selected image is either left or right.
leftOrRightSelectedFlag - Variable in class EventScroller
current data sample being processed is LEFT or RIGHT image
legalImageFileExtensions - Static variable in class ImageIO
list of legal image file extensions
lightWhite - Variable in class DrawHistogram
 
LINES_REPORT_STATUS - Static variable in class Flicker
# lines to compute before status report
listener - Variable in class PopupDialogQuery
Tried this instead of "this"
listPairedSpotListDataTabDelim(boolean) - Static method in class Spot
listPairedSpotListDataTabDelim() - generate a tab-delimited string table of the paired spots (by matching spot id's) in the spot list.
listSpotListData(String, String, Spot[], int) - Static method in class Spot
listSpotListData() - generate a string list of the spots in the spot list
listSpotListDataTabDelim(String, String, Spot[], int) - Static method in class Spot
listSpotListDataTabDelim() - generate a tab-delimited string table of of the spots in the spot list.
listUserImageDirs() - Static method in class FlkUser
listUserImageDirs() - List user's images by directory
lm1 - Variable in class Affine
indices of three landmarks
lm2 - Variable in class Affine
indices of three landmarks
lm3 - Variable in class Affine
indices of three landmarks
lms - Variable in class EventKbd
 
lms - Variable in class EventMenu
 
lms - Variable in class Flicker
list of landmarks
lms - Variable in class ImageXform
landmark data
lms - Variable in class Info
 
lms - Static variable in class SpatialXform
landmarks to use
lmsColor - Variable in class Flicker
Adjustable landmark color
lmsFont - Static variable in class Landmark
font for drawing LMS overlay
lmsMenu - Variable in class BuildGUI
"Landmark" pull down Menu list
loadBlankImageData(String, int, int) - Method in class ImageData
loadBlankImageData() - create and return a blank ImageData object [NOTE] This code has a bug since it does not create the empty window correctly.
loadGifOrJpegPixIntoImageData(String, ImageData, int, boolean) - Method in class ImageIO
loadGifOrJpegPixIntoImageData() - read GIF or JPEG pix file into ImageData object which includes an iPix[] of the data.
loadJpeg2000PixIntoImageData(String, ImageData, int, boolean) - Method in class ImageIO
loadJpeg2000PixIntoImageData() - read JPEG 2000 pix file into ImageData object which includes a iPix[] of the data.
loadPixIntoImageData(String, ImageData, int, boolean) - Method in class ImageIO
loadPixIntoImageData() - read pix file into ImageData obj.
loadPPXpixIntoImageData(String, ImageData, int, boolean) - Method in class ImageIO
loadPPXpixIntoImageData() - read GELLAB-II PPX pix file into ImageData object which includes a iPix[] of the data.
loadTiffPixIntoImageData(String, ImageData, int, boolean) - Method in class ImageIO
loadTiffPixIntoImageData() - read Tiff pix file into ImageData object which includes a iPix[] of the data.
lookup(FlkDemo) - Static method in class FlkDemo
lookup() - lookup entry to database flkDemos[0:nMaps-1].
lookup(FlkMap) - Static method in class FlkMap
lookup() - lookup entry to database flkMaps[0:nMaps-1].
lookup(FlkRecent) - Static method in class FlkRecent
lookup() - lookup entry to database FlkRecents[0:nMaps-1].
lookup(FlkUser) - Static method in class FlkUser
lookup() - lookup entry to database flkUsers[0:nMaps-1].
lookupByDbMenuName(String) - Static method in class FlkRecent
lookupByDbMenuName() - lookup entry by dbMenuName in FlkRecents[0:nMaps-1].
lookupByFileName(String, String) - Static method in class FlkDemo
lookupByFileName() - lookup entry by file name to flkDemos[0:nMaps-1].
lookupByFileName(String, String) - Static method in class FlkUser
lookupByFileName() - lookup entry by file name to flkUsers[0:nMaps-1].
lookupByImageURL(String) - Static method in class FlkRecent
lookupByImageURL() - lookup entry by dbMenuName in FlkRecents[0:nMaps-1].
lookupByImageURL(String, String) - Static method in class FlkRecent
lookupByImageURL() - lookup oair entry by dbMenuName in FlkRecents[0:nMaps-1].
lookupByMenuName(String) - Static method in class FlkMap
lookupByMenuName() - lookup entry by menu name in flkMaps[0:nMaps-1].
lookupBySubmenu(String) - Static method in class FlkDemo
lookupBySubmenu() - lookup entry by submenu name to flkDemos[0:nMaps-1].
lookupBySubmenu(String) - Static method in class FlkUser
lookupBySubmenu() - lookup entry by submenu name to flkUsers[0:nMaps-1].
lookupBySubMenuNameAndEntry(String, String) - Static method in class FlkDemo
lookupBySubMenuNameAndEntry() - lookup entry by matching BOTH the SubMenuName and SubMenuEntry in the flkDemos[0:nMaps-1].
lookupCanvasPtrAndName() - Method in class EventMenu
lookupCanvasPtrAndName() - lookup current image base on activeImage.
lookupCanvasPtrAndName() - Method in class EventScroller
lookupCanvasPtrAndName() - lookup current image base on activeImage.
lookupCurrentImageData() - Method in class Flicker
lookupCurrentImageData() - lookup the current active ImageData if it is left or right
lookupCurrentImageScroller() - Method in class Flicker
lookupCurrentImageScroller() - lookup the current active ImageData if it is left or right
lookupProtIDandNameToSpotList(ImageData) - Method in class ImageDataSpotList
lookupProtIDandNameToSpotList() - if the gel is clickable and the user enabled the clickable DB checkbox, then search the clickableCGIbaseURL protein database for all spots in the spot list and for those that have matches, update the Spot.id and Spot.name.
lookupSpotInSpotListByXY(int, int) - Method in class ImageDataSpotList
lookupSpotInSpotListByXY() - lookup the spot in the spotList[0:nSpots-1] if the (xC,yC) are +- 1 pixel in x and/or y.
low - Variable in class MC_Cube
 
lvl - Variable in class MC_Cube
 

M

mag - Variable in class ImageData
magnification factor
mag - Variable in class ImageXform
magnification
magnificationAWT - Variable in class SliderState
GUI state: zoom mangification in range [1X:MAX_ZOOM]
magVal - Variable in class ImageData
 
main(String[]) - Static method in class CalibrateOD
main() - for testing and optimizing parameters for findPeak method using preset data from GELLAb-II Leukemia-AML gel image (gel 0324.1).
main(String[]) - Static method in class Flicker
main() - for Flicker application CMD LINE: java Flicker [image1] [image2]
main(String[]) - Static method in class ImageDataMeas
main() - createMaskDatabase function for debugging...
main(String[]) - Static method in class TiffLoader
main() - test loader.
make8BitImage() - Method in class MedianCut
make8BitImage() - Generate 8-bit image from interla 15-bit image.
makeChkBoxMenuItem(Menu, String, String, int, boolean) - Method in class BuildGUI
makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list.
makeInverseMap(int[], int) - Method in class MedianCut
makeInverseMap() - for all cubes, compute centroid of colors in cube.
makeMenuItem(Menu, String, String, int, boolean) - Method in class BuildGUI
makeMenuItem() - make menuItem entry in menu list.
makePPXimage() - Method in class PpxLoader
makePPXimage() - make img and pixels[] from the byte bPixels[] data
makeSubMenu(Menu, String, String, int) - Method in class BuildGUI
makeSubMenu() - make submenu entry in menu list.
makeTransformMenuItem(Menu, String, String, int, boolean) - Method in class BuildGUI
makeTransformMenuItem() - make transform menuItem entry in menu list.
manufacturerPartNbr - Variable in class CalibrateOD
optional manufacturer part number for the step wedge
mapGrayToOD - Variable in class Boundary
gray scale to OD map
mapGrayToOD - Variable in class CalibrateOD
 
mapGrayToOD - Variable in class ImageData
mapGrayToOD data if not null
mapRelCircleCoordstoImageCoords(int, int, int, int, Image) - Method in class ScrollableImageCanvas
mapRelCircleCoordstoImageCoords() - remap circle center and background (x,y) coords in current canvas to img coords (x,y).
mapRelRoiCoordstoImageCoords(int, int, int, int, Image) - Method in class ScrollableImageCanvas
mapRelRoiCoordstoImageCoords() - remap ROI(x,y) in current canvas to img ROI(x,y).
mapRelXYtoImage(MouseEvent, int, int) - Method in class ScrollableImageCanvas
mapRelXYtoImage() - map (x,y) Mouse in current canvas to (xImg,yImg) as well as updating the parent.(xImg,yImg) values which are RELATIVE to the current image.
mapSPIDtoPIRURL(String, String, int, int) - Method in class ImageDataSpotList
mapSPIDtoPIRURL() - if using a PIR server database AND we have either looked up the Swiss-Prot ID for the spot, then map the dataURL to the PRI site by adding the SP ID to the currentPRIbaseURL.
mapStateToZoom(Point) - Method in class ImageData
mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal.
mapXYtoAffineIdx(int, int) - Method in class Affine
mapXYtoAffineIdx() - Compute Affine transform (x',y') idx from f(x,y) where idx is the index of the pixel in the input image to be used for the output image.
mapXYtoAffineX(int, int) - Method in class Affine
mapXYtoAffineX() - Compute Affine transform x' from f(x,y) to be used for the output image.
mapXYtoAffineY(int, int) - Method in class Affine
mapXYtoAffineY() - Compute Affine transform y' from f(x,y) to be used for the output image.
mapXYtoInvAffineX(int, int) - Method in class Affine
mapXYtoInvAffineX() - Compute Inverse Affine transform x'= f(x,y) to be used for the output image.
mapXYtoInvAffineY(int, int) - Method in class Affine
mapXYtoInvAffineY() - Compute Inverse Affine transform y' from f(x,y) to be used for the output image.
mapXYtoPolyPoint(int, int) - Method in class ImageXform
mapXYtoPolyPoint() - map PolyWarp xform (xPrime,yPrime) from f(x1,y1) Verifies that (xPrime,yPrime) in width * height else returns (0,0).
mapXYtoPseudo3DPoint(int, int) - Method in class ImageXform
mapXYtoPseudo3DPoint() - map Pseud3D transform Point(x',y')= f(x,y) Verifies that (x2,y2) in width * height else returns (0,0).
mapZoomToState(Point, int, int) - Method in class ImageData
mapZoomToState() - map zoom point to state point with Guard Region factored in.
mapZoomToState(Point) - Method in class ImageData
mapZoomToState() - map zoom point to state point based on zoomMagVal.
maskArea - Static variable in class ImageDataMeas
List of areas under each mask index by the mask radius
maskNxN - Static variable in class ImageDataMeas
Array of masks [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)
maskRadius - Static variable in class ImageDataMeas
Array of mask radius size where Nr is (2*radius+1)
masks - Variable in class WriteGifEncoder
 
maskTotWeight - Static variable in class ImageDataMeas
List of total weights under each mask index by the mask radius
MAX8 - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
max8() - Method in class ImageXform
max8() - compute max of 8-neighbor pixels for 8-bit data
MAX_ANGLE - Static variable in class SliderState
max degrees
MAX_BND - Variable in class Boundary
Max boundary size
MAX_BRIGHTNESS - Static variable in class SliderState
max brightness baseline
MAX_CANVAS_SIZE - Static variable in class Flicker
Maximum canvas size used in all canvas image windows
MAX_CHKBOX_CMDS - Static variable in class BuildGUI
max number of menu checkbox items allowed
MAX_CIRCLE_RADIUS - Static variable in class Flicker
maximum circle mask radius.
MAX_CMDS - Static variable in class BuildGUI
max number of menu items allowed.
MAX_CONTRAST - Static variable in class SliderState
max constrast x 0.10 slope
MAX_DATABASES - Static variable in class FlkDemo
MAX # of demo databases
MAX_DATABASES - Static variable in class FlkMap
Maximum number of Web clickable databases
MAX_DATABASES - Static variable in class FlkUser
MAX # of user databases
MAX_DELAY - Static variable in class BuildGUI
maximum delay 10000 mSec= 10.0 Sec
MAX_DEMOS - Static variable in class FlkDemo
Max # of demo images
MAX_ESCALE - Static variable in class SliderState
max eScale percent
MAX_EXTERN_FCTS - Static variable in class Flicker
maximum # of external Fcts (10 or 20 is nice)
MAX_EXTERN_FCTS - Static variable in class PluginMgr
max # of external functions alloc'ed
MAX_FLICKER_DELAY - Static variable in class BuildGUI
maximum flicker delay1000 mSec= 1.0 Sec
MAX_GRAY - Static variable in class CalibrateOD
Maximum gray value possible in 8-bits
MAX_GRAY - Static variable in class DrawHistogram
# gray values in a pixel
MAX_KEEPALIVE_TIME - Static variable in class Flicker
5 min.
MAX_MAPS - Static variable in class FlkMap
Max # of clickable image maps on the Web
MAX_ND_STEPS - Static variable in class CalibrateOD
Maximum # of OD and peak values in the peak table
MAX_ND_STEPS - Static variable in class DrawHistogram
default # of peak wedge calibration table steps
MAX_RECENTS - Static variable in class FlkRecent
Max # of recent images
MAX_SPOTS - Static variable in class Flicker
Maximum # of spots that can be measured/gel image and saved in .spt file
MAX_TARGET_SIZE - Static variable in class Flicker
max target size if do initial image resizing
MAX_TEXT - Variable in class ScrollableImageCanvas
max # of text items
MAX_THRESHOLD1 - Static variable in class SliderState
max GRAY threshold 1
MAX_THRESHOLD2 - Static variable in class SliderState
max GRAY threshold 2
MAX_USER_IMAGES - Static variable in class FlkUser
Max # of images since can have LOTS of combinations of user data
MAX_ZOOM - Static variable in class SliderState
max X magnificationAWT
MAX_ZOOM_MAG_SCR - Static variable in class SliderState
max zoomMag (zoom/dezoom) X magnification mapped to [-1/10X : 10X]
MAX_ZOOM_MAG_VAL - Static variable in class SliderState
max zoomMag value (zoom/dezoom) X magnification
MAX_ZSCALE - Static variable in class SliderState
max zScale percent
MAXBINS - Static variable in class DrawHistogram
# of histogram into bins
maxbits - Variable in class WriteGifEncoder
 
maxBkgrdGrayValue - Variable in class ImageDataMeas
Capture max "background" pixel gray or OD value
maxBnd - Variable in class Boundary
Max size of boundary array
maxCanvasDim - Variable in class ScrollableImageCanvas
Maximum canvas size
maxcode - Variable in class WriteGifEncoder
 
MAXCODE(int) - Method in class WriteGifEncoder
MAXCODE() - return n bits
MAXCOLORS - Static variable in class MedianCut
maximum # of output colors
maxColsToPrint - Variable in class Flicker
WinDump window size in pixels
maxd - Variable in class Boundary
 
maxG - Variable in class BrightnessContrastFilter
maximum Gray value seen in the original inputpixels[].
maxG - Variable in class ImageData
maximum Gray value seen in the original iPix[].
maxGray - Variable in class BrightnessContrastFilter
 
maxGray - Variable in class TiffLoader
maximum gray value
maxGrayValue - Variable in class CalibrateOD
max gray value found in the image and it is <= 255
maxGrayValue - Variable in class ImageDataMeas
Capture max pixel gray or OD value within mask
MAXLMS - Static variable in class Landmark
3 for affine, but 10x10 for warp
maxLMS - Static variable in class Landmark
max # of landmarks allowed
maxmaxcode - Variable in class WriteGifEncoder
 
maxMeasGrayValue - Variable in class ImageDataMeas
Capture max "measurement" pixel gray or OD value
maxMsgSize - Variable in class BuildGUI
max text length that can be put into msg1 or msg2
maxNDsteps - Variable in class CalibrateOD
eg.
maxPeaks - Variable in class CalibrateOD
eg.
maxSlopeC - Variable in class BrightnessContrastFilter
maximum contrast needed to cover the maximum dynamic range compute as: maxSlopeC= maxGray/(maxG-minG));
mbar - Variable in class BuildGUI
menu bar
MC_Cube - Class in <Unnamed>
 
MC_Cube() - Constructor for class MC_Cube
MC_Cube() - constructor
mCE - Variable in class ImageXform
compute slope in g'=mCE+bCE
meanBkgrdGrayValue - Variable in class ImageDataMeas
Capture mean "background" pixel gray or OD value.
meanGrayValue - Variable in class ImageDataMeas
Capture mean pixel gray or OD value within mask
meanMeasGrayValue - Variable in class ImageDataMeas
Capture mean "measurement" pixel gray or OD value.
measCircleColor - Variable in class Flicker
Adjustable measurement circle color
measCircleRadius - Variable in class Flicker
"measurement" circle radius.
measCircleRadius - Variable in class ImageXform
state: measurement circle radius
measCircleRadius - Variable in class SliderState
GUI state radius of circle mask size used for flk.measCircleRadius
measCircleRadiusBar - Variable in class BuildGUI
scroll bar for measCircleRadius
measCircleRadiusLabel - Variable in class BuildGUI
GUI label for measCircleRadius scroll
measCtr - Variable in class ImageDataSpotList
"Measurement counter" in measurements for this image
measGrayValue - Variable in class ImageDataMeas
Capture "measurement" pixel gray or OD value.
measObjX - Variable in class ImageDataMeas
Capture "background" X coordinate
measObjY - Variable in class ImageDataMeas
Capture "background" Y coordinate
measType - Variable in class Boundary
"Quant" or "Bkgrd"
measurementNbr - Variable in class Boundary
measurement #
measureRegion(int[], int) - Method in class Boundary
measureRegion() - compute image features for object inside boundary.
MEDIAN - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
median8() - Method in class ImageXform
median8() - compute median of 8-neighbors compute pixels in range of [0:255].
MedianCut - Class in <Unnamed>
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 MedianCut
MedianCut() - Constructor Then call cvtImg24toImg8() to get the 8-bit image.
mediumFont - Variable in class DrawHistogram
medium font used for labeling
menuActionCmdList - Static variable in class BuildGUI
[MAX_CMDS] list of menuItem (short-form) cmds for event handler
menuActionLabelList - Static variable in class BuildGUI
[MAX_CMDS] list of menuItem commands labels
menuItemMustSelect - Static variable in class BuildGUI
[0:nMImustSelect-1] list of MenuItems that must be selected else they are disabled (grayed out).
menuName - Variable in class FlkMap
file field MenuName: is the menu image name: e.g., "Expasy Plasma (3-7)"
merx1 - Variable in class Boundary
 
merx2 - Variable in class Boundary
 
mery1 - Variable in class Boundary
 
mery2 - Variable in class Boundary
 
mi_autoMeasProtLookupPopupCB - Variable in class BuildGUI
Auto measure, protein lookup in active server and Web page popup
mi_dbugCB - Variable in class BuildGUI
View DEBUGGING menu item checkbox
mi_DispGrayValsCB - Variable in class BuildGUI
View display gray level in image title menu item checkbox
mi_flickerCB - Variable in class BuildGUI
View menu checkbox item linked with flickerCheckbox
mi_GangBCImgsCB - Variable in class BuildGUI
View gang brightness/contrast menu item checkbox
mi_GangScrollImgsCB - Variable in class BuildGUI
View gang scrolling menu item checkbox
mi_GangZoomImgsCB - Variable in class BuildGUI
View gang scrolling menu item checkbox
mi_MeasCtrCB - Variable in class BuildGUI
Use measurement counters checkbox
mi_MultPopupsCB - Variable in class BuildGUI
View multiple browser popups menu item checkbox
mi_Quant_UseLeukemiaDemoCalibCB - Variable in class BuildGUI
Use demo leukemia gels ND wedge calibration preloads item checkbox
mi_QuantSpotListModeCB - Variable in class BuildGUI
 
mi_QuantTotDensityCB - Variable in class BuildGUI
Quant menu to compute total integrated density for spot else the mean item checkbox
mi_saveOimagesWhenSaveStateCB - Variable in class BuildGUI
 
mi_showReportPopupCB - Variable in class BuildGUI
View Report Popup item checkbox
mi_thresholdInsideCB - Variable in class BuildGUI
Quant threshold Inside menu item checkbox
mi_useGuardImgsCB - Variable in class BuildGUI
 
mi_useLogTIFFfilesCB - Variable in class BuildGUI
Use log of TIFF file else scale to 8-bit data
mi_useNTSCrgbTograyCvtCB - Variable in class BuildGUI
Convert RGB image to grayscale using NTSC transform if needed checkbox.
mi_usePIRiProClassServerCB - Variable in class BuildGUI
Use PIR iProClass DB (IPROCLASS) access checkbox.
mi_usePIRiProLinkServerCB - Variable in class BuildGUI
Use PIR uProLink DB (IPROLINK) access checkbox.
mi_usePIRUniprotServerCB - Variable in class BuildGUI
Use PIR UniProt DB (UNIPROT) access checkbox.
mi_useProteinDBbrowserCB - Variable in class BuildGUI
 
mi_useSwiss2DpageServerCB - Variable in class BuildGUI
Use Swiss-2DPAGE DB (SWISS-2DPAGE) access checkbox.
mi_ViewAnnSpotIdCB - Variable in class BuildGUI
View measured spot annotation {ann} as "spot.id" menu item checkbox
mi_ViewAnnSpotNbrCB - Variable in class BuildGUI
View measured spot annotation {ann} as "spot.nbr" menu item checkbox
mi_ViewBoundaryCB - Variable in class BuildGUI
View boundaries menu item checkbox
mi_ViewLastMeasSpotAsCircleCB - Variable in class BuildGUI
[FUTURE] View last measured spot location as "circle"{ann} menu item checkbox
mi_ViewLastMeasSpotAsPlusCB - Variable in class BuildGUI
View last measured spot location as "+"{ann} menu item checkbox
mi_ViewLmsCB - Variable in class BuildGUI
View landmarks menu item checkbox
mi_ViewMeasCircleCB - Variable in class BuildGUI
View measurement circles menu item checkbox
mi_ViewMeasSpotLocAsCircleCB - Variable in class BuildGUI
View measured spot location as "circle"{ann} menu item checkbox.
mi_ViewMeasSpotLocAsPlusCB - Variable in class BuildGUI
View measured spot location as "+"{ann} menu item checkbox.
mi_ViewRoiCB - Variable in class BuildGUI
View ROI rectangle menu item checkbox
mi_ViewTargetCB - Variable in class BuildGUI
View target menu item checkbox
mi_ViewTrialObjCB - Variable in class BuildGUI
View trial object menu item checkbox
mi_WinDmpRadixDecCB - Variable in class BuildGUI
Quant menu WinDmp radix decimal mode checkbox
mi_WinDmpRadixHexCB - Variable in class BuildGUI
Quant menu WinDmp radix hex mode checkbox
mi_WinDmpRadixOctCB - Variable in class BuildGUI
Quant menu WinDmp radix octal mode checkbox
mi_WinDmpRadixODCB - Variable in class BuildGUI
Quant menu WinDmp radix optical density mode checkbox
mi_WinDmpSize10x10CB - Variable in class BuildGUI
Quant menu WinDmp size 10x10 checkbox
mi_WinDmpSize15x15CB - Variable in class BuildGUI
Quant menu WinDmp size 15x15 checkbox
mi_WinDmpSize20x20CB - Variable in class BuildGUI
Quant menu WinDmp size 20x20 checkbox
mi_WinDmpSize25x25CB - Variable in class BuildGUI
Quant menu WinDmp size 25x25 checkbox
mi_WinDmpSize30x30CB - Variable in class BuildGUI
Quant menu WinDmp size 30x30 checkbox
mi_WinDmpSize35x35CB - Variable in class BuildGUI
Quant menu WinDmp size 35x35 checkbox
mi_WinDmpSize40x40CB - Variable in class BuildGUI
Quant menu WinDmp size 40x40 checkbox
mi_WinDmpSize5x5CB - Variable in class BuildGUI
Quant menu WinDmp size 5x5 checkbox
MIN8 - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
min8() - Method in class ImageXform
min8() - compute min of 8-neighbor pixels for 8-bit data
MIN_ANGLE - Static variable in class SliderState
min degrees
MIN_BRIGHTNESS - Static variable in class SliderState
min brightness baseline
MIN_CANVAS_SIZE - Static variable in class Flicker
Minimum canvas size used in all canvas image windows
MIN_CIRCLE_RADIUS - Static variable in class Flicker
maximum circle mask radius.
MIN_CONTRAST - Static variable in class SliderState
min constrast x 0.10 slope
MIN_DELAY - Static variable in class BuildGUI
minimum delay 0.10 sec
MIN_ESCALE - Static variable in class SliderState
min eScale percent
MIN_FLICKER_DELAY - Static variable in class BuildGUI
minimum flicker delay0.01 sec
MIN_TARGET_SIZE - Static variable in class Flicker
min target size if do initial image resizing
MIN_THRESHOLD1 - Static variable in class SliderState
min GRAY threshold 1
MIN_THRESHOLD2 - Static variable in class SliderState
min GRAY threshold 2
MIN_ZOOM - Static variable in class SliderState
min X magnificationAWT
MIN_ZOOM_MAG_SCR - Static variable in class SliderState
min zoomMag (zoom/dezoom) X magnification mapped to [-1/10X : 10X]
MIN_ZOOM_MAG_VAL - Static variable in class SliderState
min zoomMag value (zoom/dezoom) X magnification
MIN_ZSCALE - Static variable in class SliderState
min zScale percent
minBkgrdGrayValue - Variable in class ImageDataMeas
Capture min "background" pixel gray or OD value
mind - Variable in class Boundary
 
minG - Variable in class BrightnessContrastFilter
minimum Gray value seen in the original inputpixels[].
minG - Variable in class ImageData
minimum Gray value seen in the original iPix[].
minGrayValue - Variable in class ImageDataMeas
Capture min pixel gray or OD value within mask
minLSQcolinearity1 - Variable in class Affine
LSQ colinearity err for I1 lms wrt I1
minLSQcolinearity1 - Variable in class Flicker
for image 1 w.r.t landmarks
minLSQcolinearity2 - Variable in class Affine
LSQ colinearity error for I2 lms wrt I2
minLSQcolinearity2 - Variable in class Flicker
for image 2 w.r.t landmarks
minMeasGrayValue - Variable in class ImageDataMeas
Capture min "measurement" pixel gray or OD value
minX - Variable in class TiffLoader
X upper left hand corner of image origin
minY - Variable in class TiffLoader
Y upper left hand corner of image origin
mnbackground - Variable in class Boundary
 
mnBkgrd - Variable in class Spot
mean spot mean background density
mnDens - Variable in class Spot
mean density
mnDensPrime - Variable in class Spot
mean density corrected for background (mnDensPrime - mnBkgrd)
mnuName - Variable in class PluginMgr
what appears in menu
MODE_CALIB_ND_ROI_HIST - Static variable in class DrawHistogram
Draw histogram mode - draw calibration ND wedge histogram based on ND ROI region.
MODE_CALIB_SPOTLIST_HIST - Static variable in class DrawHistogram
Draw histogram mode - draw calibration histogram based on spot list data.
MODE_CW_ROI_HIST - Static variable in class DrawHistogram
Draw histogram mode - draw CW ROI histogram
mouseClicked(MouseEvent) - Method in class DrawHistogram
 
mouseClicked(MouseEvent) - Method in class ScrollableImageCanvas
 
mouseDragged(MouseEvent) - Method in class DrawHistogram
mouseDragged() - process mouse event
mouseDragged(MouseEvent) - Method in class ScrollableImageCanvas
mouseDragged() - update (xImg,yImg) with relative position in canvas by adding (x,y) to paint ULHC base address (xBase,yBase).
mouseEntered(MouseEvent) - Method in class DrawHistogram
 
mouseEntered(MouseEvent) - Method in class ScrollableImageCanvas
 
mouseExited(MouseEvent) - Method in class DrawHistogram
 
mouseExited(MouseEvent) - Method in class ScrollableImageCanvas
 
mouseHandler(int, int) - Method in class DrawHistogram
mouseHandler() - search for the active bin if any
mouseMoved(MouseEvent) - Method in class DrawHistogram
 
mouseMoved(MouseEvent) - Method in class ScrollableImageCanvas
 
mousePressed(MouseEvent) - Method in class DrawHistogram
 
mousePressed(MouseEvent) - Method in class ScrollableImageCanvas
mousePressed() - update (xImg,yImg) with relative position in canvas by adding (x,y) to paint ULHC base address (xBase,yBase).
mouseReleased(MouseEvent) - Method in class DrawHistogram
mouseReleased() - process mouse event
mouseReleased(MouseEvent) - Method in class ScrollableImageCanvas
mouseReleased() - update (xImg,yImg) with relative position in canvas by adding (x,y) to paint ULHC base address (xBase,yBase).
msg - Variable in class PopupTextFieldDialog
Message to display
msg - Variable in class PopupYesNoDialogBox
Message for dialog box
msgPanel - Variable in class Info
 
MXTERMS - Variable in class SpatialXform
Maximum number of terms in spatial transform

N

n_bits - Variable in class WriteGifEncoder
 
N_PCT_PROLOGUE - Static variable in class DrawHistogram
default # of initial rows in the peak wedge calibration table
name - Variable in class EventMenu
 
name - Variable in class EventScroller
event scroller name
name - Variable in class ImageScroller
obj name "left", "right" or "both".
name - Variable in class PluginMgr
name of command
name - Variable in class PpxLoader
name of the picture - was [16]
name - Variable in class SliderState
 
name - Variable in class Spot
Optional associated protein string if not null.
nameLM - Static variable in class Landmark
font of the landmark
nameLR - Variable in class ImageXform
Image name: "left" or "right" image
nbands - Variable in class PpxLoader
# of scanning bands (colors)
nBands - Variable in class TiffLoader
# of samples/pixel
nBitsPerPixel - Variable in class ImageData
# of bits/pixel.
nBitsPerPixel - Variable in class TiffLoader
# bits/pixel is sampleModel.sampleSize[0]
nbr - Variable in class CalibrateOD
Calibration instance counter.
nbr - Variable in class Spot
measurement number of spot unique to the associated gel
nbrUniqueAFT - Variable in class Flicker
set to # of unique non-colinear affine transform
nCBcmds - Static variable in class BuildGUI
# of menu CheckBoxMenuItem item cmds [0:nCBcmds-1]
nCirMask - Variable in class Flicker
The radius determines the size of circle mask circleMask[nCirMask][nCirMask].
nCirMask - Variable in class Spot
circular mask diameter = 2*circleRadius+1
nCmds - Static variable in class BuildGUI
# of menu item commands [0:nCmds-1]
ncols - Variable in class PpxLoader
(unsigned short) full image size # columns in pixels
nCols - Variable in class ShowReportPopup
# of character cols to show
nCols - Variable in class TiffLoader
# of columns in the image
ncubes - Variable in class MedianCut
# of color cubes
ndcwx1 - Variable in class CalibrateOD
ULHC Neutral Density calibration strip computing window
ndcwx2 - Variable in class CalibrateOD
LRHC Neutral Density calibration strip computing window
ndcwy1 - Variable in class CalibrateOD
ULHC Neutral Density calibration strip computing window
ndcwy2 - Variable in class CalibrateOD
LRHC Neutral Density calibration strip computing window
nDirs - Static variable in class FlkUser
# of user image directories
ndWedgeGrayValues - Variable in class CalibrateOD
Gray value for corresponding wedge point [0:maxPeaks-1].
ndWedgeODvalues - Variable in class CalibrateOD
od value for corresponding wedge point [0:maxNDsteps-1].
nEntries - Variable in class Util
# of hash table entries after call readNameValuesHashTableFromFile()
NEVER - Static variable in class Flicker
Debugging flag - Always FALSE
NEVER - Static variable in class TiffLoader
Fixed value of false for DEBUGGING
newHeight - Variable in class ImageXform
new magnification size of image for IS
newRGBpixel - Variable in class BrightnessContrastFilter
current new RGB pixel when filter is running
newWidth - Variable in class ImageXform
new magnification size of image for IS
nexcpt - Variable in class PpxLoader
(unsigned int) number of exception entries
nExtFcts - Static variable in class PluginMgr
# of external functions
nextID - Static variable in class MC_Cube
 
nGel - Variable in class Spot
Gel# (1 or 2) for "left" or "right" image.
NLINES - Static variable in class ImageIO
# of lines to read before update status
nLM - Static variable in class Landmark
highest landmark #
nMaps - Static variable in class FlkDemo
# of FlkDemos[] map entries
nMaps - Static variable in class FlkMap
 
nMaps - Static variable in class FlkRecent
 
nMaps - Static variable in class FlkUser
# of flkUsers[] map entries
nMasks - Static variable in class ImageDataMeas
number of masks [0:nMasks-1][0:Nr][0:Nr]
nMImustSelect - Static variable in class BuildGUI
 
noMsg - Variable in class PopupYesNoDialogBox
No label for dialog box
nOptions - Variable in class PopupDialogQuery
optionValues[0:nOptions]
NORM_COLOR - Static variable in class Flicker
normal color mapping, no change
normalColor() - Method in class ImageXform
normalColor() - restore output image to original input image
NORMCOLOR - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
NOT_AVAIL_YET - Variable in class Flicker
This is not available yet if it is set to -1, for DEBUGGING, set it to 0.
notDoneFlag - Variable in class Flicker
Set to kill the run loop
nPairs - Static variable in class FlkUser
# of user data pairs added
nPixels - Variable in class ImageXform
 
nPixels - Variable in class PpxLoader
# of pixels for the image is (nrows*ncols)
nPixels - Variable in class TiffLoader
# of pixels/image (is nRows*nCols)
nPluginsFound - Static variable in class PluginMgr
# of active plugins found
nPoints - Variable in class Boundary
# points drawn so far
nrows - Variable in class PpxLoader
(unsigned short) full image size # rows in pixels
nRows - Variable in class ShowReportPopup
# of character rows to show
nRows - Static variable in class Spot
# of names for the spot fields
nRows - Variable in class TiffLoader
# of rows in the image
nSpots - Variable in class ImageDataSpotList
# of measured spots used in SpotList[]
nSpotsBackup - Variable in class ImageDataSpotList
# of measured spots used in SpotListBkup[]
nStateEntries - Variable in class Util
# of .flk hash table entries
nTextItems - Variable in class ScrollableImageCanvas
actual # text items to display
nU - Variable in class SpatialXform
# of CTRL points in x1[], y2[], zU[]
numDataElements - Variable in class TiffLoader
# raster DataBuffer data elements/pixel
numPages - Variable in class TiffLoader
# of TIFF pages
numPixels - Variable in class WriteGifEncoder
 
nV - Variable in class SpatialXform
# of CTRL points in y1[], y2[], zV[]
nWedgeSteps - Variable in class PpxLoader
will contain WEDGE_PPX to be set by user
nx - Variable in class PpxLoader
(unsigned short) X size of region of interest
nxfCmds - Static variable in class ImageXform
# of transform commands
nXformMenuCmds - Static variable in class BuildGUI
# of Transform menuItems
ny - Variable in class PpxLoader
(unsigned short) Y size of region of interest

O

objPos - Variable in class Flicker
position of the object for flickering
odColor - Variable in class DrawHistogram
 
odmn - Variable in class PpxLoader
Min Pixel value.
odmx - Variable in class PpxLoader
Max Pixel value.
oGifFileName - Variable in class DrawHistogram
full Gif file path name
oGifFileName - Variable in class ImageScroller
Name of GIF file used in "SaveAs" of oImg to local GIF file
oImg - Variable in class ImageData
output image generated by ImageXform.
ok - Variable in class WriteGifEncoder
80% occupancy
okFlag - Variable in class PopupTextFieldDialog
Returned true if pressed DONE
okFlag - Variable in class PopupYesNoDialogBox
flag set by the yes button (no or cancel button set to false)
OLD_FLICKER_HOME - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
oldIHeight - Variable in class ImageScroller
calc ScrollPostions
oldIWidth - Variable in class ImageScroller
calc ScrollPostions
oPix - Variable in class ImageXform
 
optBkgrdColor - Variable in class DrawHistogram
 
optionChoice - Variable in class PopupDialogQuery
opt.
optionPanel - Variable in class PopupDialogQuery
for options
optionValues - Variable in class PopupDialogQuery
list of option values if present
origHeight - Variable in class ImageXform
original size of image, for zoom
origWidth - Variable in class ImageXform
original size of image, for zoom
osName - Static variable in class Flicker
name of this operating system
output(int, FileOutputStream) - Method in class WriteGifEncoder
output() - Output the given code.
ox1 - Static variable in class Landmark
X coordinates in left output image 1
ox2 - Static variable in class Landmark
X coordinates in right output image 2
oy1 - Static variable in class Landmark
Y coordinates in left output image 1
oy2 - Static variable in class Landmark
Y coordinates in right output image 2

P

pagestep - Variable in class ImageScroller
thickness of scroller
paint(Graphics) - Method in class BuildGUI
paintComponent() - repaint scroll bars
paint(Graphics) - Method in class DrawHistogram
paint() - draw the histogram
paint(Graphics) - Method in class ImageScroller
paintComponent() - repaint scrollable canvas in region defined by scroll bars
paint(Graphics) - Method in class ScrollableImageCanvas
paint() - repaint scrollable canvas in region defined by scroll bars
paintComponent(Graphics) - Method in class Flicker
paintComponent() - paint Flicker
paintSiCanvas() - Method in class ImageScroller
paintSiCanvas() - paint the scrollable canvas using thread safe method in one place.
parseAndAddEntry(String) - Static method in class FlkDemo
parseAndAddEntry() - parse and add entry to global to flkDemos[0:nMaps-1] if the data is well formed.
parseBaseFlkProperties() - Method in class Util
parseBaseFlkProperties() - parse the base Flicker State properties in the current hash table.
pBlack - Static variable in class ImageXform
 
pdq - Variable in class BuildGUI
generic popup dialog
PEAK_CAL_TBL_COLS - Static variable in class DrawHistogram
default # of editPanel cols
PEAK_CAL_TBL_ROWS - Static variable in class DrawHistogram
default # of editPanel rows
peakCalTblTF - Variable in class DrawHistogram
Array of TextFields used in constructing the Peak Calibration Table editPanel.
peakNbrColor - Variable in class DrawHistogram
peak number color
peakNbrFontSize - Variable in class DrawHistogram
font size for peak number labels
perim - Variable in class Boundary
 
pi - Variable in class TiffLoader
List of PixelAccessors from the RenderedImages'
pImages - Variable in class BuildGUI
+++++++ Gui stuff +++++++
piMgr - Variable in class Flicker
Plugin manager
pixelIndex - Variable in class WriteGifEncoder
 
pixelMask - Variable in class ImageData
bit mask to get the pixel (1 << nBitsPerPixel) -1
pixels - Variable in class PpxLoader
pixels [0:nPixels-1] for the image
pixels - Variable in class TiffLoader
image of size nRows of nCols pixels.
pixels - Variable in class WriteGifEncoder
 
pixels32 - Variable in class MedianCut
32-bit image[width*height] (Alpha,Red,Green,Blue) pixels
pixels8 - Variable in class MedianCut
8-bit image[width*height] using LUTs
Plugin1 - Class in <Unnamed>
Plugin1 External Function object class for Flicker.
Plugin1() - Constructor for class Plugin1
Plugin1() - constructor
Plugin2 - Class in <Unnamed>
Plugin2 External Function object class for Flicker.
Plugin2() - Constructor for class Plugin2
Plugin2() - constructor
Plugin3 - Class in <Unnamed>
Plugin3 External Function object class for Flicker.
Plugin3() - Constructor for class Plugin3
 
PLUGIN_FCT - Static variable in class ImageXform
generic plugin transform number is 1 past the last builtin transform
pluginMenu - Variable in class BuildGUI
"Plugins" pull down Menu list
PluginMgr - Class in <Unnamed>
PluginMgr base class is used for managing user Plugin{n}'s for Flicker.
PluginMgr() - Constructor for class PluginMgr
PluginMgr() - constructor
PluginMgr(Flicker) - Constructor for class PluginMgr
PluginMgr() - constructor called from main to initialize things
poly(int, double, double, double[][]) - Static method in class SpatialXform
poly() - compute k'th polynomial function at point (x,y).
POLYWARP - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
polyWarp() - Method in class ImageXform
polyWarp() - compute Polynomial warp of I1 into I2 as determined by the Polynomial transform warping Xform of iData.
popup - Variable in class EventMenu
 
Popup - Class in <Unnamed>
Popup class supports various popup windows including:
Popup(Flicker) - Constructor for class Popup
Popup() - constructor
POPUP_HEIGHT - Static variable in class Spot
default frame size height of popup
POPUP_WIDTH - Static variable in class Spot
default frame size width of popup
popupAlertMsg(String) - Static method in class Util
popupAlertMsg() - display the msg in msg1 and popup up an Alert message.
popupAlertMsg(String, Color) - Static method in class Util
popupAlertMsg() - display the msg in msg1 and popup up an Alert message
PopupDialogQuery - Class in <Unnamed>
The PopupDialogQuery class is a generic popup query dialog window.
PopupDialogQuery(Frame, int) - Constructor for class PopupDialogQuery
PopupDialogQuery() - Constructor
popupFileDialog(String, String, boolean) - Method in class Popup
popupFileDialog() - popup file dialog and get file name.
popupSpotEdit(boolean) - Method in class Spot
popupSpotEdit() - popup a spot editing function to change the spot.
popupSpotEditBoth(Spot, Spot, boolean) - Method in class Spot
popupSpotEditBoth() - popup a spot editing function to let you edit two selected (putatively paired) spots together Edit the data in 3 columns with the field name on the left column the left image data in the middle column and the right image data in the right column.
popupTextAreaViewer(String, int, int) - Method in class Popup
popupTextAreaViewer() - popup text area viewer [TODO] needs work
popupTextField() - Method in class PopupTextFieldDialog
popupTextField() - popup text field
PopupTextFieldDialog - Class in <Unnamed>
The PopupTextFieldDialog class provides a popup text field with a Done and Cancel buttons.
PopupTextFieldDialog(Flicker, String, String) - Constructor for class PopupTextFieldDialog
PopupTextFieldDialog () - constructor
popupViewer(String, String) - Method in class Popup
popupViewer() - Display URL file in system Web browser.
popupWindowName - Variable in class Flicker
default name of popup window
PopupYesNoDialogBox - Class in <Unnamed>
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 PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup YES/NO/CANCEL modal dialog.
PopupYesNoDialogBox(Frame, String, String, String, String) - Constructor for class PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup YES/NO/CANCEL modal dialog.
PopupYesNoDialogBox(Frame, String, String, String, Color) - Constructor for class PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup YES/NO modal dialog.
PopupYesNoDialogBox(Frame, String, String, String) - Constructor for class PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup YES/NO modal dialog.
PopupYesNoDialogBox(Frame, String, String, Color) - Constructor for class PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup OK modal dialog.
PopupYesNoDialogBox(Frame, String, String) - Constructor for class PopupYesNoDialogBox
PopupYesNoDialogBox() - Constructor for popup OK modal dialog.
positionHistWindow() - Method in class DrawHistogram
positionHistWindow() - position histogram window on the screen
positionReportWindow() - Method in class ShowReportPopup
positionReportWindow() - position report window on the screen
positionWindow(Frame) - Method in class Spot
positionWindow() - position window on the screen
POSTER_FILE1 - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
POSTER_FILE2 - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
POSTER_FILE3 - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
POSTER_FILE4 - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
PPX_VRSION - Static variable in class PpxLoader
Code version 3.5 as 35
ppxFileName - Variable in class PpxLoader
full path of PPX input file
PpxLoader - Class in <Unnamed>
 
PpxLoader() - Constructor for class PpxLoader
PpxLoader() - constuctor()
PpxLoader(byte[]) - Constructor for class PpxLoader
PpxLoader() - constuctor to parse the PPX header and set up the state
pra - Variable in class BuildGUI
generic popup report
preferredHeight - Variable in class ImageScroller
preferred height of canvas
preferredHeight - Variable in class ScrollableImageCanvas
preferred size of canvas
preferredHeight - Variable in class Spot
preferred canvas height
preferredWidth - Variable in class ImageScroller
preferred width of canvas
preferredWidth - Variable in class ScrollableImageCanvas
preferred size of canvas
preferredWidth - Variable in class Spot
preferred canvas width
prettyPrintDateStr(String) - Static method in class Util
prettyPrintDateStr() - pretty-print date string.
prevFlickerFlag - Variable in class Flicker
previous state of flickerFlag saved when start ain ImageXform
printCurrentMemoryUsage(String) - Static method in class Util
printCurrentMemoryUsage() - print: %free, total memory usage and time of day to stdout.
printImgDebugState(String) - Method in class ImageData
printImgDebugState() - Debugging print (iImg,oImg,zImg) object Java pointers.
printProperties(String, Image, Image) - Method in class ImageData
printProperties() - Debugging print (iImg,oImg,zImg) object Java pointers, and img width & height.
processBCimage(ImageData) - Method in class ImageScroller
processBCimage() - process colormap image by running the filter.
processBCimage(ImageData) - Method in class ScrollableImageCanvas
processBCimage() - process colormap image by running the filter.
processBoundaryMode(int, int, boolean) - Method in class Boundary
processBoundaryMode() - process drawing mouse event if boundaryMode
processTransform(String, String, int) - Method in class EventMenu
processTransform() - process the specified transform
PSEUDO3D - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
pseudo3D() - Method in class ImageXform
pseudo3D() - compute Pseudo 3D by scaling (x',y') by g and angle.
PSEUDO_COLOR - Static variable in class Flicker
Pseudo color hsv2rgb mapping
PSEUDOCOLOR - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
pseudoColor() - Method in class ImageXform
pseudoColor() - compute pseudocolor from grayscale Map 255 to blue and green at 1/2 way, and red 0 for 32-bit pixels
pseudoColorFlag - Variable in class BrightnessContrastFilter
true if pseudo color else grayscale.
pushBoundary(int, int) - Method in class Boundary
pushBoundary() - push unique boundary points from last point to current
pushEFentry(String, String, String, boolean, int) - Static method in class PluginMgr
pushEFentry() - push extern fuctnion ef into list.
pushLandmark(int, int, int, int) - Static method in class Landmark
pushLandmark() - push (x1,y1,x2,y2) and return nLM.
Putbyte(byte, FileOutputStream) - Method in class WriteGifEncoder
Putbyte() - Write out a byte to the GIF file
Putword(int, FileOutputStream) - Method in class WriteGifEncoder
Putword() - Write out a word to the GIF file
pWhite - Static variable in class ImageXform
pixel definitions of white and black

Q

quantMenu - Variable in class BuildGUI
"Quantify" pull down Menu list
QUICK_START - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
quickSort(int[], int, int) - Method in class 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 Util
quickSort() - sort the int[] array.
quit() - Method in class ShowReportPopup
quit() - closing down the window, get rid of the frame.

R

r - Variable in class BrightnessContrastFilter
current RED pixel when filter is running
r - Variable in class WriteGifEncoder
 
r1 - Variable in class DrawHistogram
extra sample data
r2 - Variable in class DrawHistogram
extra sample data
r3 - Variable in class DrawHistogram
extra sample data
ras - Variable in class TiffLoader
Raster image read
read() - Static method in class FlkDemo
read() - read database from FlkDemoDB.txt file to flkDemos[0:nMaps-1].
read() - Static method in class FlkMap
read() - read database from DB/FlkMapDB.txt file to flkMaps[0:nMaps-1].
read() - Static method in class FlkRecent
read() - read database from FlkRecentDB.txt file to FlkRecents[0:nMaps-1].
readBaseFlkPropertiesFile(String) - Method in class Util
readBaseFlkPropertiesFile() - read the base "Flicker.properties" file if it exists.
readBytesFromURL(String, String) - Method in class Util
readBytesFromURL() - read binary data from URL
readCalibrationFile(ImageData) - Method in class Util
readCalibrationFile() - read the image calibration from the "cal/{image file base}.cal" file or "cal/{image subdirectory}-DIR-{image file base}.cal" file.
readData(String, String) - Method in class FileIO
readData() - read data from URL or file depending on prefix.
readData(String, String, boolean) - Method in class FileIO
readData() - read data from URL or file depending on prefix.
readFileFromDisk(String) - Method in class FileIO
readFileFromDisk() - Will read file from disk & returns as String Allow popup error messages.
readFileFromDisk(String, boolean) - Method in class FileIO
readFileFromDisk() - Will read file from disk & returns as String
readFileFromUrl(String) - Method in class FileIO
readFileFromUrl() - read data from http URL, using JavaCGIBridge If the code has "\r\n", then map them to "\n".
readFlkState(String, boolean) - Method in class Util
readFlkState() - read the Flicker State file stateFile with a .flk file extension.
readFlkStateFile(String, boolean) - Method in class Util
readFlkStateFile() - read a .flk state file and change the state
readNameValuesHashTableFromFile(String, String, int) - Method in class Util
readNameValuesHashTableFromFile() - read a hashtable of tab-delimited name-value pairs from a file.
readNameValuesHashTableFromFile(String, String, int, boolean) - Method in class Util
readNameValuesHashTableFromFile() - read a hashtable of tab-delimited name-value pairs from a file.
readPPXfile(String) - Method in class PpxLoader
readPPXfile() - read loca PPX file or PPX file URL.
readState() - Method in class CalibrateOD
readState() - Read calibration state from .cal state file for this image.
readState() - Method in class Landmark
readState() - Read state from .flk startup state file.
readState(String) - Method in class SliderState
readState() - Read scroller state from .flk startup state file.
readState(String, String) - Static method in class Spot
readState() - Read spotList[] "spt/.spt" file
readTiff(String) - Method in class TiffLoader
readTiff() - read a tiff image file
readyFlag - Variable in class Flicker
finished reading images.
redBits(int) - Method in class MedianCut
redBits() - Get 8-bit red component of a 15-bit color 8-bit pixel with low 3 bits zero.
reExtrapolateCalibration() - Method in class DrawHistogram
reExtrapolateCalibration() - regenerate the mapGrayToOD[] from the peak table
REF_MAN_ADDUSERIMAGES - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_CHECKBOX - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_KEYSTROKES - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_MENUS - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_MOUSE - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_PUTATIVESPOTID - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_SLIDERS - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_SPOTLISTS_ANNOTATE - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_SPOTLISTS_CREATE - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_TRANSFORMS - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MAN_UPDATING - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_MANUAL - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
REF_VERSION_NBR - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
refreshPeakTable(boolean) - Method in class DrawHistogram
refreshPeakTable() - refresh the peak table from the TextFields...
regrowBoundary(int) - Method in class Boundary
regrowBoundary() - increase boundary size
reInitStateVars() - Method in class Flicker
reInitStateVars() - reinitialize the state variables
remapLMS(String, int) - Method in class ImageXform
remapLMS() - remap LMS if transform changed their positions.
remapLMSafterAffine() - Method in class ImageXform
remapLMSafterAffine() - remap LMS since Affine transform changed their positions.
reorderColors(int[], int, int, int) - Method in class MedianCut
reorderColors() - Change ordering of 5-bit colors in each word of int[] so we can sort on the 'longDim' color
repackFlag - Variable in class ImageScroller
 
repaintLockFlag - Variable in class Flicker
xForm sync
reportErrorMsgsFlag - Static variable in class ImageData
report errors on loading else ignore messages
reset() - Method in class SliderState
reset() - reset state to default values.
resetDefaultView() - Method in class Flicker
resetDefaultView() - Reset default state of views, colors, etc.
resetImageData(boolean) - Method in class ImageData
resetImageData() - reset this ImageData object.
resizeFrameFlag - Variable in class Flicker
allow dragging the frame to cause it to resize
resizeImageCanvas(Image, int, int, double) - Method in class ImageScroller
resizeImageCanvas() - Reset Image, used in zoom and dezoom.
resizeImageToTargetSize(Image, int, int, int, int, int) - Static method in class ImageData
resizeImageToTargetSize() - resize image to target size if the w or h is outside the range [minTargetSize : maxTargetSize].
resizeLAXfileData() - Method in class Util
resizeLAXfileData() - resize Flicker.lax file data for Flicker.
restoreColorOrder(int[], int, int, int) - Method in class MedianCut
restoreColorOrder() - Restore the 5-bit colors to original order
restoreFromClone(CalibrateOD) - Method in class CalibrateOD
restoreFromClone() - restore this.
restoreImage(ImageData, boolean) - Method in class ImageIO
restoreImage() - restore images from original copy (iPix) that was first read in.
restoreSpotList() - Method in class ImageDataSpotList
restoreSpotList() - retore spotList[0:nSpots-1] from spotListBkup[] and nSpotBkup.
rgb - Variable in class WriteGifEncoderHashitem
 
rgb15(int) - Method in class MedianCut
rgb15() - convert from 24-bit (ignore alpha) to 15-bit color.
rgb2gray() - Method in class ImageXform
rgb2gray() - convert color image to NTSC gray value image using NTSC transform gray= red*0.33 + green*0.50 + blue*0.17 NOTE: don't apply this transform more than once or it will have bogus results.
rgb3 - Variable in class BrightnessContrastFilter
array hold return values (R,G,B) for hsv2rgb(H,S,V)
RGB_TO_GRAY_COLOR - Static variable in class Flicker
RGB to gray color using .33*r+.5*g+.17*b
rgbToGrayFlag - Variable in class BrightnessContrastFilter
cvt RGB to grayscale.
ri - Variable in class TiffLoader
List of Rendered images that was read in the tiff file
rix - Variable in class PpxLoader
(unsigned short) X top left corner of region of interest (0,0) is U.L.H.C.
riy - Variable in class PpxLoader
(unsigned short) X top left corner of region of interest (0,0) is U.L.H.C.
rLUT - Variable in class MedianCut
[0:255] Red Color map look up table
rmax - Variable in class MC_Cube
 
rmin - Variable in class MC_Cube
 
rmvFileExtension(String) - Method in class Util
rmvFileExtension() - remove ".tif", ".jpg", ".gif", ".ppx" from file name and ignore the case.
rmvRtnChars(String) - Static method in class Util
rmvRtnChars() - remove return chars.
rmvSpecifiedChar(String, char) - Static method in class Util
rmvSpecifiedChar() - remove specified chararcter
rmvSpotFromSpotList(Spot) - Method in class ImageDataSpotList
rmvSpotFromSpotList() - remove the spot from the spot list if found If the spot is at the end of the list, the reuse the spot number.
rmvSpotListFile(String, String) - Static method in class Spot
rmvSpotListFile() - clear the .spt file from the spt/ directory by moving the spt/.spt file into spt/.spt.bkup andclearing the .bkup file if it previously existed first.
ROI_POPUP_HEIGHT - Static variable in class DrawHistogram
default frame size height of popup
ROI_POPUP_WIDTH - Static variable in class DrawHistogram
default frame size width of popup
roiColor - Variable in class Flicker
 
roiX1 - Variable in class ImageDataROI
ULHC ROI window set by (C-U).
roiX2 - Variable in class ImageDataROI
LRHC ROI window set by (C-L).
roiY1 - Variable in class ImageDataROI
ULHC ROI window set by (C-U).
roiY2 - Variable in class ImageDataROI
LRHC ROI window set by (C-L).
run() - Method in class Flicker
run() - Flicker method to run threads and perform timing dependent operators.
run() - Method in class ImageXform
run() - Transform the pixels in iPix[] into oPix[] image data by legal transform 'useXform'.
runT - Variable in class Flicker
Flicker thread
runTimeMsec - Variable in class ImageData
# of milli-seconds to process last transform

S

s1 - Variable in class Spot
Left Spot 1 if editing both spots
s2 - Variable in class Spot
Right Spot 2 if editing both spots
sampleModel - Variable in class TiffLoader
Tiff sample model name
sampleSizes - Variable in class TiffLoader
bits/pixel is sample sizes [0:nBands-1] from sampleModel.getSampleSize()
saturation - Variable in class BrightnessContrastFilter
current saturation pixel value when HSV filtering
saveAsButton - Variable in class ShowReportPopup
"SaveAs" .txt button
saveAsImgFile - Variable in class ScrollableImageCanvas
Name of GIF file to save the next repaint.
saveAsOverlayFile(String) - Method in class ImageScroller
saveAsOverlayFile() - save repainted image as GIF file
savedMsg - Variable in class ShowReportPopup
message after Saved Txt into file
saveOimagesWhenSaveStateflag - Variable in class Flicker
Save oImgs when do a "Save(As) state" if they exist and allowXformFlag is enabled.
saveOImgAsGifFile(String, boolean) - Method in class ImageScroller
saveOImgAsGifFile() - save the oImg into a Gif image file in the < userDir >/tmp/.
scaleFactor - Variable in class ImageXform
scale factor for pseudo3D
scprog - Variable in class PpxLoader
name of scanning program
scpvrs - Variable in class PpxLoader
version of scanning program
scrHeight - Variable in class Flicker
min (FRAME_HEIGHT, screenHeight)
ScrollableImageCanvas - Class in <Unnamed>
ScrollableImageCanvas class supports a scrollable canvas Define a scrollable image canvas.
ScrollableImageCanvas(Image, ImageScroller, Flicker, boolean) - Constructor for class ScrollableImageCanvas
ScrollableImageCanvas() - constructor.
scrollPos - Variable in class ImageScroller
keep track of ScrollPostions
scrollPos - Variable in class ScrollableImageCanvas
current scroll position
scrWidth - Variable in class Flicker
min (FRAME_WIDTH, screenWidth)
scsys - Variable in class PpxLoader
ID of the scanning system
sdate - Variable in class PpxLoader
date of scan
sdDensity - Variable in class Boundary
 
selectedComponent - Variable in class BuildGUI
from Mouse Adapters
selectedImageColor - Static variable in class ScrollableImageCanvas
selected image title color
serialVersionUID - Static variable in class BuildGUI
for JFrame
set(String, String, String, String, String, String, boolean) - Method in class FlkDemo
set() - set entry to database flkDemos[0:nMaps-1].
set(String, String, String, String, String) - Method in class FlkMap
set() - set entry to database flkMaps[0:nMaps-1].
set(String, String, String, String, String) - Method in class FlkRecent
set() - set entry to database FlkRecents[0:nMaps-1].
set(String, String, String, String, String, String, String) - Method in class FlkRecent
set() - set entry pair to database FlkRecents[0:nMaps-1].
set(String, String, String, String) - Method in class FlkUser
set() - set entry to database flkUsers[0:nMaps-1].
set(int, int, String, String, int, int, int, int, int, int, float, boolean, boolean, float, float, float, float, float, float, float, float, float, float, float) - Method in class Spot
set() - set the data for a spot with new data
set_sWorking(String) - Method in class ImageIO
set_sWorking() - set the working image progress string
setAccessServerDBcheckbox(CheckboxMenuItem) - Method in class EventMenu
setAccessServerDBcheckbox() - set checkbox radio button afor server access DB
setBndColor(Color) - Method in class Boundary
setBndColor() - set the boundary drawing color
setBndState(boolean) - Method in class Boundary
setBndState() - set the boundary state in the imageCanvas
setBndState(boolean) - Method in class ImageScroller
setBndState() - set the boundary state in the imageCanvas
setBrCt(ImageScroller, int, int, int, int, boolean) - Method in class BrightnessContrastFilter
setBrCt() - set parameters for the filter when it is invoked by pressing or dragging the mouse with the Shift key pressed.
setByImageURL(String, String, String, String, String) - Static method in class FlkRecent
setByImageURL() - set entry to database FlkRecents[0:nMaps-1].
setCanvasAndFrameSize(int, int, int) - Method in class Flicker
setCanvasAndFrameSize() - change the canvas and frame sizes
setCanvasSize(int) - Method in class ImageScroller
setCanvasSize() - change the size of this Canvas.
setCanvasSize(int, int) - Method in class ImageScroller
setCanvasSize() - change the size of this Canvas.
setCanvasSize(int) - Method in class ScrollableImageCanvas
setCanvasSize() - change the size of this Canvas.
setCanvasSize(int, int) - Method in class ScrollableImageCanvas
setCanvasSize() - change the size of this Canvases.
setCircleMaskRadius(int, ImageData) - Static method in class ImageDataMeas
setCircleMaskRadius() - set the circle radius for measurement and background, as well as the circle mask given the radius.
setColorAll(Color) - Static method in class Landmark
setColorAll() - set the landmark color for all landmarks
setcurrentIS(ImageScroller) - Method in class ImageScroller
setcurrentIS() - set the currentIS, used when flickering
setDbugFlag(boolean) - Method in class TiffLoader
setDbugFlag() - flag
setDefaultGrayscaleIndexColorMap(byte[], byte[], byte[]) - Method in class ImageData
setDefaultGrayscaleIndexColorMap() - set the RGB IndexColorMap from (r,g,b) maps Note: see Hacking Java, pg 90 on cycling color palette [TODO] Update the display...
setDefaultGrayscaleIndexColorMap() - Method in class ImageData
setDefaultGrayscaleIndexColorMap() - set the default grayscale colormap to a RGB IndexColorMap with all colors the same
setDefaultUnits() - Method in class CalibrateOD
setDefaultUnits() - set the default to units to "Optical density", unitsAbbrev to "od" and unitsManufacturerPartNbr to "< opt.
setEnabled(boolean) - Method in class EventScroller
setEnabled() - Enable/disable for ImageXform scrollers
setEventScrollers(SliderState) - Method in class EventScroller
setEventScrollers() - set Event scrollers for Flicker top level GUI.
setExtraInfo(String, String, String) - Method in class DrawHistogram
setExtraInfo() - set the extra info fields (r1,r2,f3)
setFlickerGUI(boolean) - Method in class Util
setFlickerGUI() - set the Flicker GUI state
setFlickerState(boolean) - Method in class Util
setFlickerState() - enable/disable flicker and the checkbox and save the flickerFlag while doing Xform.
setGuardRegion(int, int, double) - Method in class ImageScroller
setGuardRegion() - force siCanvas to create guard region
setGuiEnable(boolean) - Method in class BuildGUI
setGuiEnable() enable/disable GUI operations
setHorizCaption(String) - Method in class DrawHistogram
setHorizCaption() - set the horizontal caption
setID(String) - Method in class Spot
setID() - set the spot ID
setImageData(ImageData) - Method in class ImageScroller
setImageData() - change the ImageData for the panel.
setImageData(ImageData, Point) - Method in class ImageScroller
setImageData() - change the ImageData for the panel.
setImageToImageData(String, Image, boolean, ImageData, float[], int) - Method in class ImageIO
setImageToImageData() - set the Image and associated parameters to the ImageData object imgData.
setImgPosition(Point) - Method in class ImageScroller
setImgPosition() - set the Image position.
setImgPosition(int, int) - Method in class ImageScroller
setImgPosition() - set the Image position.
setImgPosition(int, int) - Method in class ScrollableImageCanvas
setImgPosition() - set the Image position.
setInfo1Text(String) - Method in class Info
setInfo1Text() - set text for info1 field (used for last landmark)
setLandmarksTextListToDraw(int, Color[], String[], Font[], int[], int[]) - Method in class ImageScroller
setLandmarksTextListToDraw() - set text list including color and position.
setLandmarksTextListToDraw(int, Color[], String[], Font[], int[], int[]) - Method in class ScrollableImageCanvas
setLandmarksTextListToDraw() - set text list including color and position.
setLastMsgColor(Color) - Method in class Util
setLastMsgColor() - set the last message color
setLMSindexes(int, int, int, boolean) - Method in class Affine
setLMSindexes() - set the 3 landmark indexes (lm1,lm2,lm3) into the landmark stack where nLM should be >=3.
setMapGrayToOD(float[]) - Method in class Boundary
setMapGrayToOD() - set the MapGrayToOD[] table
setMapGrayToOD(float[], int) - Method in class CalibrateOD
setMapGrayToOD() - change the mapGrayToOD to the specified Gray to OD map.
setMustSelectImageMenuItemsEnable(boolean) - Method in class BuildGUI
setMustSelectImageMenuItemsEnable() - enable/disable GUI menu items that must have an image selected to be enabled
setNDwedgeTable(int[], float[], int, int, int) - Method in class 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_ND_STEPS-1].
setObjPosition(Point) - Method in class ImageScroller
setObjPosition() - set the object position.
setObjPosition(int, int) - Method in class ImageScroller
setObjPosition() - set the object position.
setObjPosition(int, int) - Method in class ScrollableImageCanvas
setObjPosition() - set the object position.
setOrigInputPixels(int[], int, boolean) - Method in class ImageData
setOrigInputPixels() - set the original image iPix[] pixels and associated flags.
setReportMsg(String) - Method in class Util
setReportMsg() - set a report message to the report popup window
setROI(int, int, int, int) - Method in class ImageDataROI
setROI() - set computing window region of interest (ROI)
setROI2CALCW(int, int, int, int) - Method in class ImageDataROI
setROI2CALCW() - set ND wedge computing window region of interest (ROI)
setROI2CW(int, int, int, int) - Method in class ImageDataROI
setROI2CW() - set region of interest (ROI) to Computing Window (CW)
setScrollersToDefault() - Method in class EventScroller
setScrollersToDefault() - set Event scrollers to default values for Flicker top level GUI.
setShow(boolean) - Method in class ShowReportPopup
setShow() - set the show/hide popup status
setStateHashtableForGetValue(Hashtable, int) - Method in class Util
setStateHashtableForGetValue() - set working hash table for next getStateValue calls
setStateHashtableForGetValue(Hashtable) - Method in class Util
setStateHashtableForGetValue() - set working hash table for next getStateValue calls
setStatusMsg(String) - Method in class DrawHistogram
setStatusMsg() - set the status msg
setStatusMsg(String, Color) - Method in class DrawHistogram
setStatusMsg() - set the status msg
setStatusMsg(String) - Method in class Spot
setStatusMsg() - set the status msg
setStatusMsg(String, Color) - Method in class Spot
setStatusMsg() - set the status msg
setSyncLockFlag(boolean) - Method in class ImageXform
setSyncLockFlag() - set the repaintLockFlag to lock Flicker from repainting while this the flag is true
setTitle(String) - Method in class ImageData
setTitle() - change the title for the ImageData instance.
setTitle(String, boolean) - Method in class ImageScroller
setTitle() - change the title for the panel.
setTitleHist(String) - Method in class DrawHistogram
setTitleHist() - set the title
setTransformsEnable(boolean) - Method in class BuildGUI
setTransformsEnable() enable/disable GUI Transforms menu operations
setTrialLMS(int, int) - Method in class ScrollableImageCanvas
setTrialLMS() - set trial landmark in & center image, save object(x,y).
setUnits(String) - Method in class CalibrateOD
setUnits() - set Wedge units, e.g.
setUnitsAbbrev(String) - Method in class CalibrateOD
setUnitsAbbrev() - set Wedge units abbreviation, e.g.
setUnitsManufacturerPartNbr(String) - Method in class CalibrateOD
setUnitsManufacturerPartNbr() - set Wedge manufacturerPartNbr
setupCircularMaskStatistics() - Method in class ImageDataMeas
setupCircularMaskStatistics()- compute the mask area and total weights for each mask.
setupDialogBox(Frame, String, String, String, String, Color) - Method in class PopupYesNoDialogBox
setupDialogBox() - setup for popup yes/no/cancel modal dialog.
setUseLogFlag(boolean) - Method in class TiffLoader
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
setVertCaption(String) - Method in class DrawHistogram
setVertCaption() - set the vertical caption
setVisible(boolean, boolean) - Method in class DrawHistogram
setVisible() - set the histogram as visible or not
setWedgeROI(int, int, int, int) - Method in class CalibrateOD
setWedgeROI() - set ND step Wedge region of interest
setWindmpRadixCheckbox(int) - Method in class EventMenu
setWindmpRadixCheckbox() - set checkbox radio button and process event for windmp radix checkboxes
setWindmpSizeCheckbox(int) - Method in class EventMenu
setWindmpSizeCheckbox() - set checkbox radio button and process event for windmp size checkboxes
SHARPENGRAD - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
sharpenGrad() - Method in class ImageXform
sharpenGrad() - Compute add 4-neighbor gradient to grayscale of pixel data
SHARPENLAPL - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
sharpenLaplacian() - Method in class ImageXform
sharpenLaplacian() - Compute add 8-neighbor Laplacian to grayscale of pixel data.
shiftMod - Variable in class ScrollableImageCanvas
SHIFT/Mouse
sHist - Variable in class DrawHistogram
modified freq sHist[0:nHist-1].
SHOW_DECIMAL - Static variable in class Windump
Window dump OCTAL data mode
SHOW_HEX - Static variable in class Windump
Window dump OCTAL data mode
SHOW_OCTAL - Static variable in class Windump
Window dump OCTAL data mode
SHOW_OD - Static variable in class Windump
Window dump OD data mode
showAffineCalcs() - Method in class Affine
showAffineCalcs() - show affine calculations string report.
showAffineLM(String) - Method in class Affine
showAffineLM() - show affine Landmarks
showBkgrdValue() - Method in class ImageDataMeas
showBkgrdValue() - print the background measurement value.
showI1flag - Variable in class Flicker
flag to indicate that I1 is being displayed in flkIS else I2 is being displayed.
showImageMousePositions(MouseEvent, String, int, int) - Method in class ScrollableImageCanvas
showImageMousePositions() - show the image mouse positions Only report if debugging...
showLandmarkSimilarity() - Method in class Landmark
showLandmarkSimilarity() - show landmark similarity for >=3 LMs
showMeasValue(String) - Method in class ImageDataMeas
showMeasValue() - print the measurement value subtracting the background value.
showMediaTrackerStatusBits(String, URL, String, MediaTracker) - Method in class ImageIO
showMediaTrackerStatusBits() - print the media tracker status bits
showMsg(String, Color) - Method in class Util
showMsg() - show msg in GUI area 1, set the status-line & set color.
showMsg1(String, Color) - Method in class Util
showMsg1() - show msg in GUI area 1, set the status-line & set color.
showMsg2(String, Color) - Method in class Util
showMsg2() - show msg in GUI text area 2, status line and set color.
ShowReportPopup - Class in <Unnamed>
The ShowReportPopup class creates and displays scrollable string text area in a popup window.
ShowReportPopup(Flicker, String, int, int, String, String, boolean) - Constructor for class ShowReportPopup
ShowReportPopup() - Constructor.
showScrollCoords(boolean) - Method in class Info
showScrollCoords() - show the scroll bar coordinates
showStatus(String, Color) - Method in class Util
showStatus() - show msg in GUI area 1, set the status-line & set color.
showStatusFlag - Variable in class ShowReportPopup
 
shrinkCube(MC_Cube) - Method in class MedianCut
shrinkCube() - Encloses "cube" with a tight-fitting cube by updating the (rmin,gmin,bmin) and (rmax,gmax,bmax) members of "cube".
shutOffGuardRegion() - Method in class EventMenu
shutOffGuardRegion() - turn off guard region
siCanvas - Variable in class ImageScroller
pointer to the associated image canvas
sicHeight - Variable in class ScrollableImageCanvas
image height
sicWidth - Variable in class ScrollableImageCanvas
image width
sid - Variable in class PpxLoader
further identification - (sample ID)
sleepFlag - Variable in class PopupDialogQuery
wait for button to be pushed
sleepMsec(int) - Static method in class Util
sleepMsec() - sleep for mSec.
SliderState - Class in <Unnamed>
Class State contains the sliders state for an ImageScroller instance.
SliderState() - Constructor for class SliderState
SliderState() - constructor
slopeC - Variable in class BrightnessContrastFilter
contrast slope is (cS -0.5)*maxSlopeC
smallFont - Variable in class DrawHistogram
small font used for labeling
smoothHistogram(int[], int, int, int) - Method in class CalibrateOD
smoothHistogram() - Compute smoothed histogram of hist[0:maxGray] into hData[0:maxGray] using 'Disaster Analysis'.
softDoneWithTransform(ImageData, String, String) - Method in class ImageXform
softDoneWithTransform() - ImageXform thread calls when xform completed.
solveAffineXform() - Method in class Affine
solveAffineXform() - compute the affine transformation for 3 LM of the 3 landmarks and return a dynamically allocated affine object.
solvePolyXformCoef() - Method in class SpatialXform
solvePolyXformCoef() - solve the aU, bV coefficients from LMS data.
southPanel - Variable in class ImageScroller
opt.
sp - Variable in class ImageScroller
scroller for the canvas, siCanvas
spaces - Variable in class PopupDialogQuery
DEF_COL_SIZE spaces
SpatialXform - Class in <Unnamed>
Class SpatialXform is used for doing non-linear order warping These methods are derived from:
SpatialXform(Flicker) - Constructor for class SpatialXform
SpatialXform() - constructor.
Spot - Class in <Unnamed>
Class Spot contains the spot structure for measured spots.
Spot(Flicker) - Constructor for class Spot
Spot() - setup Spot part of the database
Spot() - Constructor for class Spot
Spot() - Constructor for new Spot
Spot(int, int, String, String, int, int, int, int, int, int, float, boolean, boolean, float, float, float, float, float, float, float, float, float, float, float) - Constructor for class Spot
Spot() - Constructor for new Spot with data
spotList - Variable in class ImageDataSpotList
List of measured spots data if not null [0:nSpots-1].
spotListBkup - Variable in class ImageDataSpotList
Backup list of measured spots data if not null [0:nSpotsBkup-1].
spotsListModeFlag - Variable in class Flicker
C-J Toggle between list-of-spots else trial-spot measurement mode.
spotTable - Static variable in class Spot
spot Editable table [nRows][2]
spotTableBoth - Static variable in class Spot
spot Editable table [nRows][3] that handles spots in s1 [1] and spots in s2 [2].
spt - Variable in class Flicker
Spot structures
start() - Method in class Flicker
start() - start new Flicker threads
startDataDict - Variable in class PpxLoader
(unsigned int) if non-zero, then byte # of file where data dictionary starts.
startImageData - Variable in class PpxLoader
(unsigned int) if non-zero, then byte # of file where image data starts.
startMeasurement(String, int, int) - Method in class Boundary
startMeasurement() - start measurement of object.
startMeasurement(String) - Method in class ImageScroller
startMeasurement() - start measurement of object.
startPopupDialog(String, int) - Method in class PopupDialogQuery
startPopupDialog() - create a hidden dialog panel within a frame.
startTime - Variable in class ImageData
starting time of last transform
startupDataFlag - Variable in class FlkDemo
is TRUE if should be the default startup for Flicker.
startupDate - Variable in class Flicker
 
state - Variable in class ImageData
SliderState threshold parameters associated with the image
state - Variable in class ImageScroller
SliderState threshold parameters associated with the image
stateChanged(ChangeEvent) - Method in class BuildGUI
 
statusLabel - Variable in class DrawHistogram
status Label
statusLabel - Variable in class Spot
status Label
steps - Variable in class ImageScroller
prewired scroller steps
stime - Variable in class PpxLoader
time of scan
stop() - Method in class Flicker
stop() - stop or suspend Flicker threads
stopAnnotationUpdateFlag - Variable in class Flicker
Flag to stop spot list annotation lookup from proteomics Web server.
subMenuEntry - Variable in class FlkDemo
is the menu image name: e.g., "(Swiss2DPAGE vs Merril) gels - clickable"
subMenuEntry - Variable in class FlkUser
is the menu image name: e.g., "(Swiss2DPAGE vs Merril) gels - clickable"
subMenuName - Variable in class FlkDemo
is the menu image name: e.g., "Human Plasma"
subMenuName - Variable in class FlkUser
is the menu image name: e.g., "Human Plasma"
SUN_JAI_LICENSE - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
sUserPairTreeMnu - Variable in class BuildGUI
Add directories for paired user images tree
sUserSingleTreeMnu - Variable in class BuildGUI
Add directories for single user images tree
SWISS_2DPAGE - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on the Internet
sWorking - Variable in class Flicker
incremental loading message
sWorking - Variable in class ImageIO
for incremental loading message progress string
sx - Variable in class Boundary
 
sxf - Variable in class Flicker
poly warp spatial transform
sxf - Variable in class ImageXform
poly warp spatial transform
sxy - Variable in class Boundary
 
sy - Variable in class Boundary
 
syncGuiWithState() - Method in class BuildGUI
syncGuiWithState() - sync GUI checkboxes and menu checkboxes with the state which may have changed.

T

targetColor - Static variable in class Flicker
adjustable cross-hairs color
tessl - Variable in class PpxLoader
(unsigned int) tesselation code ??? bits???
testAndSetThreadCounter() - Method in class Flicker
testAndSetThreadCounter() - safe test and set of thread counter
text - Variable in class ScrollableImageCanvas
text list items
textarea - Variable in class ShowReportPopup
Text area GUI for main report
textAreaFontSize - Variable in class ShowReportPopup
font size
textField - Variable in class PopupDialogQuery
place text to be edited here
textFont - Variable in class Flicker
text font for messages
textFontFamily - Variable in class ShowReportPopup
Text area font family
textInputColor - Variable in class DrawHistogram
 
textMsgLabel1 - Variable in class BuildGUI
GUI text 1 msg line
textMsgLabel2 - Variable in class BuildGUI
GUI text 2 msg line
textReport - Variable in class ShowReportPopup
copy of text in textArea
textValueChanged(TextEvent) - Method in class EventKbd
textValueChanged() - handle text value changed events
textValueChanged(TextEvent) - Method in class ImageScroller
textValueChanged() - process text change events in image title text area NOTE: this is DEPRICATED!
tf - Variable in class PopupTextFieldDialog
text field
thetaRad - Variable in class ImageXform
pseudo3D angle in radians
THICKNESS - Static variable in class BuildGUI
Thickness of the scrollbar slider control
THR_COLINEARITY - Static variable in class BuildGUI
threshold for LMS colinearity
thrColinearity - Variable in class Affine
threshold for colinearity tests
thrColinearity - Variable in class Flicker
co-linearity threshold for testing LMS
thrColinearity - Variable in class ImageXform
colinearity threshold
threadIsPaintFlag - Variable in class ImageData
Ok to paint ImageScroller
THRESHOLD - Static variable in class ImageXform
Transform number corresponding to the xfCmd[] table entry.
threshold() - Method in class ImageXform
threshold() - compute grayscale threshold of gI gO= (gI<=t2 && gI>=t1) ? gI : pWhite; compute thresholded 8-bit pixel
threshold1 - Variable in class ImageXform
state copy: lower bound threshold for grayscale slicing
threshold1 - Variable in class SliderState
GUI state: lower bound threshold for grayscale slicing
threshold1Bar - Variable in class BuildGUI
scroll bar for threshold1
threshold1Label - Variable in class BuildGUI
GUI label for threshold 1 scroll
threshold2 - Variable in class ImageXform
state copy: upper bound threshold for grayscale slicing
threshold2 - Variable in class SliderState
GUI state: upper bound threshold for grayscale slicing
threshold2Bar - Variable in class BuildGUI
scroll bar for threshold2
threshold2Label - Variable in class BuildGUI
GUI label for threshold 2 scroll
ticX - Variable in class ScrollableImageCanvas
tic mark X
ticY - Variable in class ScrollableImageCanvas
tic mark Y
TiffLoader - Class in <Unnamed>
Class TiffLoader reads Tiff image into the class instance.
TiffLoader() - Constructor for class TiffLoader
TiffLoader() - constructor
TiffLoader(boolean) - Constructor for class TiffLoader
TiffLoader() - constructor where set the debug flag
timeStamp - Variable in class FlkRecent
is the time stamp when it was saved: e.g.
timeStr() - Static method in class Util
timeStr() - return a new daytime HH:MM:SS string of the current time.
title - Variable in class BuildGUI
title for frame
title - Variable in class DrawHistogram
current canvas title
title - Variable in class Flicker
Title of program
title - Variable in class ImageData
current title for image scroller associated with iData
title - Variable in class ImageScroller
current title for image scroller associated with iData
title - Variable in class ShowReportPopup
string for title of frame
toString() - Method in class PpxLoader
toString() - return string representation of this PpxLoader instance
toString() - Method in class TiffLoader
toString() - return string representation of this instance
totDens - Variable in class Spot
total density over the measurement area
totGrayValue - Variable in class ImageDataMeas
Capture total pixel gray or OD value within mask
totMeasGrayValue - Variable in class ImageDataMeas
Capture total "measurement" pixel gray or OD value.
tr - Variable in class Flicker
Tiff image reader
trialObjColor - Variable in class Flicker
Adjustable trial object color
trnsl - Variable in class PpxLoader
translation flag (0 = raw, 1 = done)
tSize - Variable in class ScrollableImageCanvas
target Size
turnOnGuardRegion() - Method in class EventMenu
turnOnGuardRegion() - turn on guard region
TWO_D_HUNT - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on the Internet
txtField - Variable in class ImageScroller
image title placed above canvas

U

UNIPROT - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on \ the Internet
units - Variable in class CalibrateOD
full name units used in the step wedge.
unitsAbbrev - Variable in class CalibrateOD
abbreviation of units name used in the step wedge E.g., "od"
unselectedImageColor - Static variable in class ScrollableImageCanvas
selected image title color
up - Variable in class MC_Cube
 
update(Graphics) - Method in class ImageScroller
update() - update without background the scrollable canvas
update(Graphics) - Method in class ScrollableImageCanvas
update() - update without background the scrollable canvas
updateBothSpotsFromEditedSpotTable() - Method in class Spot
updateBothSpotsFromEditedSpotTable() - set both spots from the spotTableBoth table data
updateClickableCanvas() - Method in class ImageScroller
updateClickableCanvas() - perform canvas update operations invoked by various controls
updateClickableCanvas() - Method in class ScrollableImageCanvas
updateClickableCanvas() - perform clickable canvas update operations invoked by various controls.
updateDemoDBfiles() - Method in class Util
updateDemoDBfiles() - update DB/FlkDemoDB.txt into program install area.
updateFlickerImage() - Method in class Flicker
updateFlickerImage() - update the flicker image.
updateFlickerJarFile() - Method in class Util
updateFlickerJarFile() - update Flicker.jar into program install area.
updateFlkDBfiles(String[]) - Method in class Util
updateFlkDBfiles() - update DB/ files into program install area.
updateHistogramPlot(boolean) - Method in class DrawHistogram
updateHistogramPlot() - set hist state and do repaint to draw it.
updateImageScrollableTitles(boolean) - Method in class ScrollableImageCanvas
updateImageScrollableTitles() - update 1 or 2 scrollable images
updateInfoString() - Method in class Info
updateInfoString() - update Flicker Info string messages.
updateLMSvaluesInImages() - Method in class Util
updateLMSvaluesInImages() - redraw landmarks in images if needed.
updatePeakCalTable() - Method in class DrawHistogram
updatePeakCalTable() - update the peak calibration table with new data from the calib od and gray value arrays.
updatePopupDialog(String, String, String[], int) - Method in class PopupDialogQuery
updatePopupDialog() - display/unhide popup dialog frame and set new values.
updateSaveAsFile(String) - Method in class ShowReportPopup
updateSaveAsFile() - update SaveAs file default file name
updateScrollCanvas() - Method in class ScrollableImageCanvas
updateScrollCanvas() - scroll the image in the scrollable canvas.
updateScrollers() - Static method in class Landmark
updateScrollers() - update LM in both siCanvases and repaint.
updateSpotFromEditedSpotTable() - Method in class Spot
updateSpotFromEditedSpotTable() - set the spot from the table data
updateText(String) - Method in class ShowReportPopup
updateText() - update text in popup window
updateTitle(String) - Method in class ShowReportPopup
updateTitle() - update title in popup window
USE_AWT_ZOOM - Variable in class Flicker
Enable using AWT implemented zoom only does positive integer zoom
USE_DE_ZOOM - Variable in class Flicker
Enable using de_zoom transform over 1/N to NX zoom (-N to +N)
USE_GANG_BC - Variable in class Flicker
DEBUGGING Enable using "View Gang Brightness/Contrast"
USE_GUARD - Variable in class Flicker
Enable guard region in the menu
USE_PLUGINS - Variable in class Flicker
Enable plugins in the menu
useDemoLeukemiaCalPreFlag - Variable in class Flicker
Use demo leukemia gels ND wedge calibration preloads.
useFileSeparatorChar(String, String) - Static method in class Util
useFileSeparatorChar() - use specified file separator chararcter Eg.
useGuardRegionImageFlag - Variable in class Flicker
 
useLogInputFlag - Variable in class Flicker
"Use log of pixels if > 8-bits grayscale image"
useLogInputFlag - Variable in class TiffLoader
"Use log of pixels if > 8-bits grayscale image"
useMeasCtrFlag - Variable in class Flicker
"Use measurement counters" in measurements
useNTSCrgbTograyCvtFlag - Variable in class Flicker
use NTSC RGB to grayscale when read in color image when generate the iData.iPix[] pixel array.
usePIRiProClassServerFlag - Variable in class Flicker
Enable access to the PIR iProClass server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
usePIRiProLinkFlag - Variable in class Flicker
Enable access to the PIR iProLink server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
usePIRUniprotServerFlag - Variable in class Flicker
Enable access to the PIR UniProt server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
useProteinDBbrowserFlag - Variable in class Flicker
Use protein DB browser, else lookup ID and name on active images.
userCalDir - Static variable in class Flicker
User calibration "cal/" directory used for saving .cal files
userClickableImageDBflag - Variable in class Flicker
User enabled image as clickable DB checkbox to get DB entry
userClickableImageDBflag - Variable in class ImageData
User enabled image as clickable DB checkbox to get DB entry
userDir - Static variable in class Flicker
User directory
userImagesProblemFlag - Static variable in class BuildGUI
flag set if the user had too many images in the Images/ subdirectories
userSptDir - Static variable in class Flicker
User spot data "spt/" directory used for saving .spt files
userTmpDir - Static variable in class Flicker
User temporary "tmp/" directory used for misc.
useScrollBarsFlag - Variable in class ImageScroller
create and use scrollers flag
useScrollBarsFlag - Variable in class ScrollableImageCanvas
create and use scrollers flag
useSwiss2DpageServerFlag - Variable in class Flicker
Enable access to the Swiss-2DPAGE server for accessing spot data.
useThresholdInsideFlag - Variable in class Flicker
Use threshold inside/outside filter [t1:t2] else outside of [t1:t2]
useTotDensityFlag - Variable in class Flicker
"Use sum density else mean" in measurements
useTotDensityFlag - Variable in class Spot
measurements total density else mean values
useXform - Variable in class ImageXform
transform to use
util - Variable in class BuildGUI
Util instance
util - Variable in class CalibrateOD
 
util - Static variable in class DrawHistogram
link to global CalibrateOD instance
util - Variable in class EventKbd
 
util - Variable in class EventMenu
 
util - Variable in class EventScroller
 
util - Variable in class FileIO
instance of Util
util - Variable in class Flicker
misc utility methods
util - Static variable in class FlkDemo
Instance of Util
util - Variable in class FlkObserver
 
util - Static variable in class FlkRecent
Util instance
util - Static variable in class FlkUser
Instance of Util
util - Static variable in class ImageData
extended Flicker state variable class
util - Static variable in class ImageDataMeas
extended Flicker state variable class
util - Static variable in class ImageDataSpotList
extended Flicker state variable class
util - Variable in class ImageIO
extended Flicker state variable class
util - Variable in class ImageScroller
 
util - Variable in class ImageXform
Utility instance
util - Variable in class Info
 
util - Static variable in class Landmark
 
util - Variable in class Popup
 
util - Variable in class PopupTextFieldDialog
 
util - Variable in class ScrollableImageCanvas
new boundary state
util - Static variable in class SliderState
 
util - Static variable in class SpatialXform
 
util - Static variable in class Spot
misc utility methods
Util - Class in <Unnamed>
Class Util contains utility methods used by Flicker.
Util(Flicker) - Constructor for class Util
Util() - constructor for Class Util
util - Static variable in class Windump
misc utility methods

V

validAffineFlag - Variable in class Flicker
set when do valid affine xform
validFeaturesFlag - Variable in class Boundary
Set object features as function of input pixels [] and boundary
value - Variable in class BrightnessContrastFilter
current value pixel value when HSV filtering
VERSION - Static variable in class Flicker
Compiled Version constant for use in version comparison etc.
vertCaption - Variable in class DrawHistogram
vertical caption
viewBoundaryFlag - Variable in class Flicker
view boundary overlay
viewDispGrayValuesFlag - Variable in class Flicker
view display image RGB as gray values
viewDrawSpotAnnIdFlag - Variable in class Flicker
view measurement annotation as 'spot nbr' overlay
viewDrawSpotAnnNbrFlag - Variable in class Flicker
view measurement annotation as 'spot nbr' overlay
viewDrawSpotLocCircleFlag - Variable in class Flicker
view measurement location as 'circle'{annotation} overlay
viewDrawSpotLocPlusFlag - Variable in class Flicker
view measurement location as '+'{annotation} overlay
viewGangBCFlag - Variable in class Flicker
gang brightnessContrast both images
viewGangScrollFlag - Variable in class Flicker
gang scroll both images
viewGangZoomFlag - Variable in class Flicker
gang zoom both images
viewLMSflag - Variable in class Flicker
view landmarks overlay
viewMeasCircleFlag - Variable in class Flicker
view measurement circle overlay
viewMenu - Variable in class BuildGUI
"View" pull down Menu list
viewMultPopups - Variable in class Flicker
view multiple popups
viewNormalizedColorFlag - Variable in class Flicker
view normalized color
viewPortSize - Variable in class ScrollableImageCanvas
dimensions of the view port
viewPseudoColorFlag - Variable in class Flicker
view pseudo color display
viewReportPopupFlag - Variable in class Flicker
view Report popup window
viewRGB2GrayFlag - Variable in class Flicker
RGB to gray color .33*r+.5*g+.17*b image display
viewRoiFlag - Variable in class Flicker
view ROI overlay
viewTargetFlag - Variable in class Flicker
view target overlay
viewTrialObjFlag - Variable in class Flicker
view trial objects overlay
VIGNETTES - Static variable in class Flicker
Popup HTML browser documentation for Flicker.
vism - Variable in class PpxLoader
visualization method

W

WALKER_BOOK_CHAPTER_2005 - Static variable in class Flicker
Popup HTML browser additional documentation for related to Flicker.
warpLSQ(int, double[], double[], double[], double[][], double, int, int, double[]) - Method in class SpatialXform
warpLSQ() - weighted LSQ spatial transform with orthogonal polynomials Based on algorithm described by Ardeshir Goshtasby in "Image resgistration by local approximation methods", Image and Vision computing, Vold 6, No.
WEDGE_PPX - Static variable in class PpxLoader
Max number of wedge steps if applicable
wedgeType - Variable in class 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 PpxLoader
(24-bit unsigned) ND*1024 or CPM wedge step values
width - Variable in class Affine
Image width
width - Variable in class ImageXform
iData.iWidth for speedup
width - Variable in class MedianCut
width size of image
width - Variable in class PopupDialogQuery
size of frame
width - Variable in class WriteGifEncoder
 
Width - Variable in class WriteGifEncoder
 
windmp - Variable in class EventMenu
 
windmp - Variable in class Flicker
Window digital data dump
windowActivated(WindowEvent) - Method in class BuildGUI
 
windowActivated(WindowEvent) - Method in class DrawHistogram
 
windowActivated(WindowEvent) - Method in class Flicker
 
windowActivated(WindowEvent) - Method in class PopupDialogQuery
 
windowActivated(WindowEvent) - Method in class PopupTextFieldDialog
 
windowActivated(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowActivated(WindowEvent) - Method in class ShowReportPopup
 
windowActivated(WindowEvent) - Method in class Spot
 
windowClosed(WindowEvent) - Method in class BuildGUI
 
windowClosed(WindowEvent) - Method in class DrawHistogram
 
windowClosed(WindowEvent) - Method in class Flicker
 
windowClosed(WindowEvent) - Method in class PopupDialogQuery
 
windowClosed(WindowEvent) - Method in class PopupTextFieldDialog
 
windowClosed(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowClosed(WindowEvent) - Method in class ShowReportPopup
 
windowClosed(WindowEvent) - Method in class Spot
 
windowClosing(WindowEvent) - Method in class BuildGUI
windowClosing() - close the window
windowClosing(WindowEvent) - Method in class DrawHistogram
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class Flicker
 
windowClosing(WindowEvent) - Method in class PopupDialogQuery
windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupTextFieldDialog
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupYesNoDialogBox
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class ShowReportPopup
windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class Spot
windowClosing() - close down the window.
windowDeactivated(WindowEvent) - Method in class BuildGUI
 
windowDeactivated(WindowEvent) - Method in class DrawHistogram
 
windowDeactivated(WindowEvent) - Method in class Flicker
 
windowDeactivated(WindowEvent) - Method in class PopupDialogQuery
 
windowDeactivated(WindowEvent) - Method in class PopupTextFieldDialog
 
windowDeactivated(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowDeactivated(WindowEvent) - Method in class ShowReportPopup
 
windowDeactivated(WindowEvent) - Method in class Spot
 
windowDeiconified(WindowEvent) - Method in class BuildGUI
 
windowDeiconified(WindowEvent) - Method in class DrawHistogram
 
windowDeiconified(WindowEvent) - Method in class Flicker
 
windowDeiconified(WindowEvent) - Method in class PopupDialogQuery
 
windowDeiconified(WindowEvent) - Method in class PopupTextFieldDialog
 
windowDeiconified(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowDeiconified(WindowEvent) - Method in class ShowReportPopup
 
windowDeiconified(WindowEvent) - Method in class Spot
 
windowIconified(WindowEvent) - Method in class BuildGUI
 
windowIconified(WindowEvent) - Method in class DrawHistogram
 
windowIconified(WindowEvent) - Method in class Flicker
 
windowIconified(WindowEvent) - Method in class PopupDialogQuery
 
windowIconified(WindowEvent) - Method in class PopupTextFieldDialog
 
windowIconified(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowIconified(WindowEvent) - Method in class ShowReportPopup
 
windowIconified(WindowEvent) - Method in class Spot
 
windowOpened(WindowEvent) - Method in class BuildGUI
 
windowOpened(WindowEvent) - Method in class DrawHistogram
 
windowOpened(WindowEvent) - Method in class Flicker
 
windowOpened(WindowEvent) - Method in class PopupDialogQuery
 
windowOpened(WindowEvent) - Method in class PopupTextFieldDialog
 
windowOpened(WindowEvent) - Method in class PopupYesNoDialogBox
 
windowOpened(WindowEvent) - Method in class ShowReportPopup
 
windowOpened(WindowEvent) - Method in class Spot
 
Windump - Class in <Unnamed>
Class Windump is used debug print methods for image neighbohood, windows, etc.
Windump(Flicker) - Constructor for class Windump
Windump() - constructor
winDump(int[], int, int, int, int, int, int, String, int, int, int, ImageData) - Static method in class Windump
winDump() - Draw a window from picture frlo the lower 8-bit/pixel data in an int[] 'pix' at
winDumpRadix - Variable in class Flicker
WinDump data printing radix
wM - Variable in class SpatialXform
(dynamic) weights
WORLD_2DPAGE - Static variable in class Flicker
Popup HTML browser additional documentation for finding 2D gels on the Internet
write() - Static method in class FlkDemo
write() - write database in memory to DB/FlkDemoDB.txt database file.
write() - Static method in class FlkMap
write() - write database in memory to DB/FlkMapDB.txt database file.
write() - Static method in class FlkRecent
write() - write database in memory to FlkRecentDB.txt database file.
writeBaseFlkPropertiesFile(String) - Method in class Util
writeBaseFlkPropertiesFile() - write out "Flicker.properties" file to save user preferences.
writeCalibrationFile(ImageData) - Method in class Util
writeCalibrationFile() - write the image calibration into the "cal/{{demo image file base}.cal" file.
writeFile(String) - Method in class WriteGifEncoder
writeFile() - write the Gif encoded image to output file
writeFileToDisk(String, String) - Method in class FileIO
writeFileToDisk() - write string data to a local disk file.
writeFlkState(String) - Method in class Util
writeFlkState() - write a .flk state file
writeGif(FileOutputStream) - Method in class WriteGifEncoder
writeGif() - Saves the image as a GIF file.
WriteGifEncoder - Class in <Unnamed>
The WriteGifEncoder class writes out an Image object as a named GIF file.
WriteGifEncoder(int, int, byte[], byte[], byte[], byte[]) - Constructor for class WriteGifEncoder
WriteGifEncoder() - Constructs a new WriteGifEncoder.
WriteGifEncoder(Image) - Constructor for class WriteGifEncoder
WriteGifEncoder() - Constructs using 24-bit Image.
WriteGifEncoderHashitem - Class in <Unnamed>
 
WriteGifEncoderHashitem(int, int, int, boolean) - Constructor for class WriteGifEncoderHashitem
WriteGifEncoderHashitem() - constructor
writeState(String, StringBuffer) - Method in class CalibrateOD
writeState() - Write this calibration state to string buffer sBuf
writeState(StringBuffer) - Method in class Landmark
writeState() - Write this landmark state to string buffer sBuf
writeState(String, StringBuffer) - Method in class SliderState
writeState() - Write this scroller state to string buffer sBuf
writeState(String, String, Spot[], int) - Static method in class Spot
writeState() - Write the spotlist[] to "spt/.spt" file
writeString(FileOutputStream, String) - Static method in class WriteGifEncoder
writeString() - write string to the file.

X

x0 - Variable in class PpxLoader
(unsigned short) top left X corner of image in cm*1024
x1 - Static variable in class Landmark
X coordinates in left input image 1
x1 - Variable in class SpatialXform
x1 is list of x coordinates for image 1
x11 - Variable in class Affine
 
x12 - Variable in class Affine
 
x13 - Variable in class Affine
 
x2 - Static variable in class Landmark
X coordinates in right input image 2
x2 - Variable in class SpatialXform
x2 is list of x coordinates for image 2
x21 - Variable in class Affine
 
x22 - Variable in class Affine
 
x23 - Variable in class Affine
 
x_text - Variable in class ScrollableImageCanvas
x text list items positions
X_TRIAL_OBJ_OFFSET - Variable in class ScrollableImageCanvas
offset to draw trial obj
xAbs - Variable in class Boundary
 
xB - Variable in class Spot
background x centroid
xBase - Variable in class ScrollableImageCanvas
+ base address of ULHC of clipped image in image canvas used in last paint
xC - Variable in class Spot
spot X centroid
xCtr - Variable in class ScrollableImageCanvas
center coords of image, for zoom/dezoom
xfCmd - Static variable in class ImageXform
Corresponding builtin transform command names used in the menu action commands.
xformMenu - Variable in class BuildGUI
"Transform" pull down Menu list
xformMenuCmds - Static variable in class BuildGUI
[MAX_CMDS] list of [0:nXformMenuCmds-1] Transform menuItems
xformName - Variable in class Flicker
current transform
xformThreadCtr - Variable in class Flicker
test and set thread counter.
xImg - Variable in class ScrollableImageCanvas
+ image address (x,y)+(xBase,yBase)
xLM1a - Static variable in class Landmark
 
xLM1b - Static variable in class Landmark
 
xLM1c - Static variable in class Landmark
 
xLM2a - Static variable in class Landmark
 
xLM2b - Static variable in class Landmark
 
xLM2c - Static variable in class Landmark
 
xObj - Variable in class ImageData
Image current object mark
xObj - Variable in class ImageScroller
X cursor position mapped to image
xObj - Variable in class ScrollableImageCanvas
 
xPainted - Static variable in class DrawHistogram
active hit coordinates
xPoints - Variable in class Boundary
coordinates for drawing using polyline
xPrime - Variable in class ImageXform
 

Y

y0 - Variable in class PpxLoader
(unsigned short) top left Y corner of image in cm*1024
y1 - Static variable in class Landmark
Y coordinates in left input image 1
y1 - Variable in class SpatialXform
y1 is list of x coordinates for image 1
y11 - Variable in class Affine
 
y12 - Variable in class Affine
 
y13 - Variable in class Affine
 
y2 - Static variable in class Landmark
Y coordinates in right input image 2
y2 - Variable in class SpatialXform
y2 is list of x coordinates for image 2
y21 - Variable in class Affine
 
y22 - Variable in class Affine
 
y23 - Variable in class Affine
 
y_text - Variable in class ScrollableImageCanvas
y text list items positions
Y_TRIAL_OBJ_OFFSET - Variable in class ScrollableImageCanvas
offset to draw label
yAbs - Variable in class Boundary
 
yB - Variable in class Spot
background Y centroid
yBase - Variable in class ScrollableImageCanvas
 
yC - Variable in class Spot
spot Y centroid
yCtr - Variable in class ScrollableImageCanvas
center coords of image, for zoom/dezoom
yesMsg - Variable in class PopupYesNoDialogBox
Yes label for dialog box
yImg - Variable in class ScrollableImageCanvas
+ externally set (x,y) object position
yLM1a - Static variable in class Landmark
 
yLM1b - Static variable in class Landmark
 
yLM1c - Static variable in class Landmark
 
yLM2a - Static variable in class Landmark
 
yLM2b - Static variable in class Landmark
 
yLM2c - Static variable in class Landmark
 
yObj - Variable in class ImageData
Image current object mark
yObj - Variable in class ImageScroller
Y cursor position mapped to image
yObj - Variable in class ScrollableImageCanvas
 
yPainted - Static variable in class DrawHistogram
active y hit coordinates
yPoints - Variable in class Boundary
coordinates for drawing using polyline
yPrime - Variable in class ImageXform
 
yw - Variable in class ImageXform
computed y*width for speedup
ywMw - Variable in class ImageXform
computed yw-width for speedup
ywPw - Variable in class ImageXform
computed yw+width for speedup

Z

z12U - Variable in class SpatialXform
OUTPUT: z[]= f(x[],y[])
z12V - Variable in class SpatialXform
OUTPUT: z[]= f(x[],y[])
zImg - Variable in class ImageData
ZoomMag filtered image if used.
zoomBar - Variable in class BuildGUI
scroll bar for (AWT display zoom)
zoomedHeight - Variable in class ImageData
zoomed height
zoomedWidth - Variable in class ImageData
zoomed width
zoomLabel - Variable in class BuildGUI
GUI label for zoom scroll (AWT zoom)
zoomMagBar - Variable in class BuildGUI
scroll bar for zoom (de_zoom transform over 1/N to NX zoom (-N to +N))
zoomMagLabel - Variable in class BuildGUI
GUI label for zoom scroll de_zoom transform over 1/N to NX zoom (-N to +N))
zoomMagScr - Variable in class ImageData
zoom value
zoomMagScr - Variable in class SliderState
GUI scroller state: dezoom and zoom magnification in range [MIN_ZOOM_MAG_SCR : MAX_ZOOM_MAG_SCR]
zoomMagVal - Variable in class ImageXform
state remapped copy: the zoomMagScr magnification scroller value is mapped using SliderState.cvtZoomMagScr2ZoomMagVal() to this value.
zoomMagVal - Variable in class SliderState
GUI magnification state: dezoom and zoom magnification in range [MIN_ZOOM_MAG_VAL : MAX_ZOOM_MAG_VAL]
zScale - Variable in class ImageXform
state copy: Z axis scale factor for pseudo3D
zScale - Variable in class SliderState
GUI state: % grayscale factor 3D xform
zScaleBar - Variable in class BuildGUI
scroll bar for zScale
zScaleLabel - Variable in class BuildGUI
GUI label for zScale scroll

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