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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object java.awt.Component java.awt.Container java.awt.Window java.awt.Frame javax.swing.JFrame Flicker
public class Flicker
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JFrame |
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javax.swing.JFrame.AccessibleJFrame |
Nested classes/interfaces inherited from class java.awt.Frame |
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java.awt.Frame.AccessibleAWTFrame |
Nested classes/interfaces inherited from class java.awt.Window |
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java.awt.Window.AccessibleAWTWindow |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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boolean |
abortFlag
set true if run into problems when exiting and do not want to write out the state as we may corrupt it. |
java.lang.String |
activeImage
active image "left", "right", "both" === was both |
Affine |
aff
Affine instance |
java.awt.Color |
alertColor
Color to use for background of alert messages |
boolean |
allowXformFlag
transforms are allowed |
java.lang.String[] |
args
|
static java.lang.String |
baseFlkServer
Base URL of Flicker server containing documentation and resources |
BuildGUI |
bGui
BuildGUI instance of user interface |
java.awt.Color |
bkgrdCircleColor
Adjustable measurement circle color |
int |
bkgrdCircleRadius
"background" circle radius. |
CalibrateOD |
cal
Calibrate OD instance |
static int |
CANVAS_INCR
Canvas change increment size - empirically determined |
static int |
CANVAS_SIZE
canvas size used in all canvas image windows |
int |
canvasSize
size for left and right image canvases. |
int[][] |
circleMask
"measurement" circle mask of size nCirMask X nCirMask |
java.lang.String |
clickableCGIbaseURL1
|
java.lang.String |
clickableCGIbaseURL1pix
|
java.lang.String |
clickableCGIbaseURL2
|
java.lang.String |
clickableCGIbaseURL2pix
|
int |
colorMode
method to use when filter RBG in ImageScroller |
boolean |
composeXformFlag
Replace(Preserve) orig imgs w/ xforms |
(package private) static boolean |
CONSOLE_FLAG
Debugging flag - Always TRUE |
java.lang.String |
currentPRIbaseURL
Base URL for currently selected PIR server for accessing spot data using the previously looked up SWISS-PROT ID. |
SliderState |
curState
This is the working SliderState instance which will be either the "base-state" or the I1 or I2 instance. |
(package private) static java.lang.String |
DATE
|
boolean |
DBUG_NTSC_RGB2GRAY
DEBUGGING convert color RGB image to grayscale using NTSC algor. |
boolean |
dbugFlag
true if debug printout, set by GUI |
int |
DEF_CIRCLE_MASK_RADIUS
The radius is used to determine the size of the circle mask circleMask[nCirMask][nCirMask]. |
static int |
DEFAULT_TARGET_SIZE
NOTE: set to 512 to enable if do image resizing |
int |
defaultFlickerDelay
|
boolean |
displayInfoFlag
if TRUE then display enter/exit info |
boolean |
doingXformFlag
doing the transform |
boolean |
doMeasureProtIDlookupAndPopupFlag
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. |
java.lang.String[] |
efMnuName
what appears in menu |
java.lang.String[] |
efName
name of command |
int[] |
efNbr
function number 1 to MAX_EXTERN_FCTS |
EventKbd |
ekb
get kbd event handler |
static java.lang.String |
EP97PAPER_FILE
Popup HTML browser additional documentation for related to Flicker. |
boolean |
errorLoadingImageFlag
set by ImageObserver imageUpdate() |
java.lang.String |
errStr
error string if not "" |
EventMenu |
evMu
|
EventScroller |
evs
instance of event scroller handler |
FlkDemo |
fDemo
FlkDemo database |
static java.lang.String |
fileSeparator
File separator |
boolean |
finished1
flag that finished transform 1 |
boolean |
finished2
finished transform 2 |
FileIO |
fio
FileIO utilities |
boolean |
firstTimeThruFlag
first time to load img at start up, need to fix bug in ImgMeasure |
static java.lang.String |
FLICKER_HOME
Popup HTML browser documentation for Flicker. |
boolean |
flickerFlag
enable flickering, set by GUI also from |
static java.lang.String |
FLK_BASE_URL
Flicker server Base URL |
int |
flkCanvasSize
size for flicker canvas which does not include scrollbars etc. |
ImageScroller |
flkIS
(non-scrollable) image canvas for drawing flicker images. |
java.lang.String |
flkStateFile
current Flicker .flk state file that lives in "DB/". |
FlkMap |
fm
FlkMap database |
static int |
FRAME_HEIGHT
Frame height |
static int |
FRAME_INCR
Frame change increment size - empirically determined |
static int |
FRAME_WIDTH
Frame width |
int |
frameHeight
main frame height |
int |
frameWidth
main frame width |
FlkRecent |
fRecent
FlkRecent database |
FlkUser |
fUser
FlkUser database |
boolean |
GC_MEMORY_DBUG
Enable pretty-printing GC Memory debugging |
static java.lang.String |
GOOGLE_2D_SEARCH
Popup HTML browser additional documentation for finding 2D gels on the Internet |
java.awt.Color |
guardRegionColor
Adjustable guard region color |
ImageScroller |
i1IS
scrollable image 1 scrollable image (left) |
ImageScroller |
i2IS
scrollable image 2 scrollable image (right) |
ImageData |
iData1
image 1 picture data associated with ImageScroller i1IS (left) |
ImageData |
iData2
image 2 picture data associated with ImageScroller i2IS (right) |
static java.lang.String |
IMAGE_FILE1
default left image1 file |
static java.lang.String |
IMAGE_FILE2
default right image2 file |
java.lang.String |
imageFile1
full path of image 1 (left) file or URL |
java.lang.String |
imageFile2
full path of image 2 (right) file or URL |
java.awt.Font |
imageFont
image font for overlay |
boolean |
imageLoadErrorFlag
true if image loading error |
int |
imagesToProcess
CountDown to determine if finished. |
ImageIO |
imgIO
Flicker image I/O and conversion functions |
private java.awt.Point |
imgPos
position of the image for flickering |
ImageXform |
imgXform
current image transform if any |
Info |
info
Info status region |
static java.lang.String |
IPROCLASS
Popup HTML browser additional documentation for finding 2D gels on \ the Internet |
static java.lang.String |
IPROLINK
Popup HTML browser additional documentation for finding 2D gels on \ the Internet |
boolean |
isClickableDBflag
flag set if currently selected image is clickable |
boolean |
isSuspendedFlag
Threads were suspended by stop() |
ImageXform |
ix
image transform |
ImageXform |
ixf1
image transform for image 1 if any |
ImageXform |
ixf2
image transform for image 2 if any |
ImageScroller |
lastIS
last selected image canvas - used in an operation and is selected by clicking on either throws left or right (I1 or I2) images. |
java.lang.String |
lastISName
last IS that was clicked on |
java.awt.Color |
lastMsgColor
save last message color state |
java.lang.String |
lastMsgStr
save last message state |
static int |
LINES_REPORT_STATUS
# lines to compute before status report |
Landmark |
lms
list of landmarks |
java.awt.Color |
lmsColor
Adjustable landmark color |
static int |
MAX_CANVAS_SIZE
Maximum canvas size used in all canvas image windows |
(package private) static int |
MAX_CIRCLE_RADIUS
maximum circle mask radius. |
static int |
MAX_EXTERN_FCTS
maximum # of external Fcts (10 or 20 is nice) |
static int |
MAX_KEEPALIVE_TIME
5 min. |
(package private) static int |
MAX_SPOTS
Maximum # of spots that can be measured/gel image and saved in .spt file |
static int |
MAX_TARGET_SIZE
max target size if do initial image resizing |
int |
maxColsToPrint
WinDump window size in pixels |
java.awt.Color |
measCircleColor
Adjustable measurement circle color |
int |
measCircleRadius
"measurement" circle radius. |
static int |
MIN_CANVAS_SIZE
Minimum canvas size used in all canvas image windows |
(package private) static int |
MIN_CIRCLE_RADIUS
maximum circle mask radius. |
static int |
MIN_TARGET_SIZE
min target size if do initial image resizing |
float |
minLSQcolinearity1
for image 1 w.r.t landmarks |
float |
minLSQcolinearity2
for image 2 w.r.t landmarks |
int |
nbrUniqueAFT
set to # of unique non-colinear affine transform |
int |
nCirMask
The radius determines the size of circle mask circleMask[nCirMask][nCirMask]. |
(package private) static boolean |
NEVER
Debugging flag - Always FALSE |
static int |
NORM_COLOR
normal color mapping, no change |
int |
NOT_AVAIL_YET
This is not available yet if it is set to -1, for DEBUGGING, set it to 0. |
private boolean |
notDoneFlag
Set to kill the run loop |
private java.awt.Point |
objPos
position of the object for flickering |
static java.lang.String |
OLD_FLICKER_HOME
Popup HTML browser additional documentation for related to Flicker. |
static java.lang.String |
osName
name of this operating system |
PluginMgr |
piMgr
Plugin manager |
java.lang.String |
popupWindowName
default name of popup window |
static java.lang.String |
POSTER_FILE1
Popup HTML browser additional documentation for related to Flicker. |
static java.lang.String |
POSTER_FILE2
Popup HTML browser additional documentation for related to Flicker. |
static java.lang.String |
POSTER_FILE3
Popup HTML browser additional documentation for related to Flicker. |
static java.lang.String |
POSTER_FILE4
Popup HTML browser additional documentation for related to Flicker. |
boolean |
prevFlickerFlag
previous state of flickerFlag saved when start ain ImageXform |
static int |
PSEUDO_COLOR
Pseudo color hsv2rgb mapping |
static java.lang.String |
QUICK_START
Popup HTML browser documentation for Flicker. |
boolean |
readyFlag
finished reading images. |
static java.lang.String |
REF_MAN_ADDUSERIMAGES
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_CHECKBOX
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_KEYSTROKES
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_MENUS
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_MOUSE
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_PUTATIVESPOTID
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_SLIDERS
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_SPOTLISTS_ANNOTATE
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_SPOTLISTS_CREATE
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_TRANSFORMS
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MAN_UPDATING
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_MANUAL
Popup HTML browser documentation for Flicker. |
static java.lang.String |
REF_VERSION_NBR
Popup HTML browser documentation for Flicker. |
boolean |
repaintLockFlag
xForm sync |
boolean |
resizeFrameFlag
allow dragging the frame to cause it to resize |
static int |
RGB_TO_GRAY_COLOR
RGB to gray color using .33*r+.5*g+.17*b |
java.awt.Color |
roiColor
|
java.lang.Thread |
runT
Flicker thread |
boolean |
saveOimagesWhenSaveStateflag
Save oImgs when do a "Save(As) state" if they exist and allowXformFlag is enabled. |
int |
scrHeight
min (FRAME_HEIGHT, screenHeight) |
int |
scrWidth
min (FRAME_WIDTH, screenWidth) |
boolean |
showI1flag
flag to indicate that I1 is being displayed in flkIS else I2 is being displayed. |
boolean |
spotsListModeFlag
C-J Toggle between list-of-spots else trial-spot measurement mode. |
Spot |
spt
Spot structures |
java.util.Date |
startupDate
|
boolean |
stopAnnotationUpdateFlag
Flag to stop spot list annotation lookup from proteomics Web server. |
static java.lang.String |
SUN_JAI_LICENSE
Popup HTML browser additional documentation for related to Flicker. |
static java.lang.String |
SWISS_2DPAGE
Popup HTML browser additional documentation for finding 2D gels on the Internet |
java.lang.String |
sWorking
incremental loading message |
SpatialXform |
sxf
poly warp spatial transform |
(package private) static java.awt.Color |
targetColor
adjustable cross-hairs color |
java.awt.Font |
textFont
text font for messages |
float |
thrColinearity
co-linearity threshold for testing LMS |
(package private) java.lang.String |
title
Title of program |
TiffLoader |
tr
Tiff image reader |
java.awt.Color |
trialObjColor
Adjustable trial object color |
static java.lang.String |
TWO_D_HUNT
Popup HTML browser additional documentation for finding 2D gels on the Internet |
static java.lang.String |
UNIPROT
Popup HTML browser additional documentation for finding 2D gels on \ the Internet |
boolean |
USE_AWT_ZOOM
Enable using AWT implemented zoom only does positive integer zoom |
boolean |
USE_DE_ZOOM
Enable using de_zoom transform over 1/N to NX zoom (-N to +N) |
boolean |
USE_GANG_BC
DEBUGGING Enable using "View Gang Brightness/Contrast" |
boolean |
USE_GUARD
Enable guard region in the menu |
boolean |
USE_PLUGINS
Enable plugins in the menu |
boolean |
useDemoLeukemiaCalPreFlag
Use demo leukemia gels ND wedge calibration preloads. |
boolean |
useGuardRegionImageFlag
|
boolean |
useLogInputFlag
"Use log of pixels if > 8-bits grayscale image" |
boolean |
useMeasCtrFlag
"Use measurement counters" in measurements |
boolean |
useNTSCrgbTograyCvtFlag
use NTSC RGB to grayscale when read in color image when generate the iData.iPix[] pixel array. |
boolean |
usePIRiProClassServerFlag
Enable access to the PIR iProClass server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id. |
boolean |
usePIRiProLinkFlag
Enable access to the PIR iProLink server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id. |
boolean |
usePIRUniprotServerFlag
Enable access to the PIR UniProt server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id. |
boolean |
useProteinDBbrowserFlag
Use protein DB browser, else lookup ID and name on active images. |
static java.lang.String |
userCalDir
User calibration "cal/" directory used for saving .cal files |
boolean |
userClickableImageDBflag
User enabled image as clickable DB checkbox to get DB entry |
static java.lang.String |
userDir
User directory |
static java.lang.String |
userSptDir
User spot data "spt/" directory used for saving .spt files |
static java.lang.String |
userTmpDir
User temporary "tmp/" directory used for misc. |
boolean |
useSwiss2DpageServerFlag
Enable access to the Swiss-2DPAGE server for accessing spot data. |
boolean |
useThresholdInsideFlag
Use threshold inside/outside filter [t1:t2] else outside of [t1:t2] |
boolean |
useTotDensityFlag
"Use sum density else mean" in measurements |
Util |
util
misc utility methods |
boolean |
validAffineFlag
set when do valid affine xform |
(package private) static java.lang.String |
VERSION
Compiled Version constant for use in version comparison etc. |
boolean |
viewBoundaryFlag
view boundary overlay |
boolean |
viewDispGrayValuesFlag
view display image RGB as gray values |
boolean |
viewDrawSpotAnnIdFlag
view measurement annotation as 'spot nbr' overlay |
boolean |
viewDrawSpotAnnNbrFlag
view measurement annotation as 'spot nbr' overlay |
boolean |
viewDrawSpotLocCircleFlag
view measurement location as 'circle'{annotation} overlay |
boolean |
viewDrawSpotLocPlusFlag
view measurement location as '+'{annotation} overlay |
boolean |
viewGangBCFlag
gang brightnessContrast both images |
boolean |
viewGangScrollFlag
gang scroll both images |
boolean |
viewGangZoomFlag
gang zoom both images |
boolean |
viewLMSflag
view landmarks overlay |
boolean |
viewMeasCircleFlag
view measurement circle overlay |
boolean |
viewMultPopups
view multiple popups |
boolean |
viewNormalizedColorFlag
view normalized color |
boolean |
viewPseudoColorFlag
view pseudo color display |
boolean |
viewReportPopupFlag
view Report popup window |
boolean |
viewRGB2GrayFlag
RGB to gray color .33*r+.5*g+.17*b image display |
boolean |
viewRoiFlag
view ROI overlay |
boolean |
viewTargetFlag
view target overlay |
boolean |
viewTrialObjFlag
view trial objects overlay |
static java.lang.String |
VIGNETTES
Popup HTML browser documentation for Flicker. |
static java.lang.String |
WALKER_BOOK_CHAPTER_2005
Popup HTML browser additional documentation for related to Flicker. |
Windump |
windmp
Window digital data dump |
int |
winDumpRadix
WinDump data printing radix |
static java.lang.String |
WORLD_2DPAGE
Popup HTML browser additional documentation for finding 2D gels on the Internet |
java.lang.String |
xformName
current transform |
int |
xformThreadCtr
test and set thread counter. |
Fields inherited from class javax.swing.JFrame |
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accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled |
Fields inherited from class java.awt.Frame |
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CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Fields inherited from interface javax.swing.WindowConstants |
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DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE |
Constructor Summary | |
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Flicker()
Flicker() - constructor for Class Flicker |
Method Summary | |
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boolean |
changeCanvasSize(java.lang.String cmd)
changeCanvasSize() - change the canvas size by the specified + or - increment command. |
boolean |
checkIfSaveFlkFile()
checkIfSaveFlkFile() - test if need to save the .flk file If so, ask them if they want to do it. |
void |
chkDoneWithTransform()
chkDoneWithTransform() - called by run() thread when xform completed and the xformThreadCtr was incremented by softDoneWithTransform(). |
boolean |
chkIfClickableDB(boolean showMsgFlag)
chkIfClickableDB() - check if currently selected image is a clickable active map data base in that it has a valid url. |
void |
componentHidden(java.awt.event.ComponentEvent componentEvent)
|
void |
componentMoved(java.awt.event.ComponentEvent componentEvent)
|
void |
componentResized(java.awt.event.ComponentEvent componentEvent)
componentResized() - resize canvases to proper sizes when frame is resized. |
void |
componentShown(java.awt.event.ComponentEvent componentEvent)
|
void |
doFullRepaint()
doFullRepaint() - repaint flkIS, i1IS, i2IS and their canvases as well as flk.repaint(). |
void |
finalize()
finalize() - total stop and kill Flicker threads.Write out the "Flicker.properties" file to save user preferences. |
void |
init(java.lang.String[] args)
init() - init Flicker state variables. |
private void |
initialImageLoad()
initialImageLoad() - load the initial images when first enter run(). |
private void |
initState(java.lang.String[] args)
initState() - init Flicker state variables. |
(package private) ImageData |
lookupCurrentImageData()
lookupCurrentImageData() - lookup the current active ImageData if it is left or right |
(package private) ImageScroller |
lookupCurrentImageScroller()
lookupCurrentImageScroller() - lookup the current active ImageData if it is left or right |
static void |
main(java.lang.String[] args)
main() - for Flicker application CMD LINE: java Flicker [image1] [image2] |
void |
paintComponent(java.awt.Graphics g)
paintComponent() - paint Flicker |
void |
reInitStateVars()
reInitStateVars() - reinitialize the state variables |
void |
resetDefaultView()
resetDefaultView() - Reset default state of views, colors, etc. |
void |
run()
run() - Flicker method to run threads and perform timing dependent operators. |
boolean |
setCanvasAndFrameSize(int newCanvasSize,
int newFrameWidth,
int newFrameHeight)
setCanvasAndFrameSize() - change the canvas and frame sizes |
void |
start()
start() - start new Flicker threads |
void |
stop()
stop() - stop or suspend Flicker threads |
void |
testAndSetThreadCounter()
testAndSetThreadCounter() - safe test and set of thread counter |
void |
updateFlickerImage()
updateFlickerImage() - update the flicker image. |
void |
windowActivated(java.awt.event.WindowEvent windowEvent)
|
void |
windowClosed(java.awt.event.WindowEvent windowEvent)
|
void |
windowClosing(java.awt.event.WindowEvent windowEvent)
|
void |
windowDeactivated(java.awt.event.WindowEvent windowEvent)
|
void |
windowDeiconified(java.awt.event.WindowEvent windowEvent)
|
void |
windowIconified(java.awt.event.WindowEvent windowEvent)
|
void |
windowOpened(java.awt.event.WindowEvent windowEvent)
|
Methods inherited from class javax.swing.JFrame |
---|
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update |
Methods inherited from class java.awt.Frame |
---|
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated |
Methods inherited from class java.awt.Window |
---|
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront |
Methods inherited from class java.awt.Container |
---|
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree |
Methods inherited from class java.awt.Component |
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action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.awt.image.ImageObserver |
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imageUpdate |
Methods inherited from interface java.awt.MenuContainer |
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getFont, postEvent |
Field Detail |
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static final java.lang.String VERSION
static final java.lang.String DATE
static boolean CONSOLE_FLAG
static boolean NEVER
public int NOT_AVAIL_YET
public final boolean USE_GUARD
public final boolean USE_PLUGINS
public final boolean USE_GANG_BC
public final boolean DBUG_NTSC_RGB2GRAY
public final boolean USE_AWT_ZOOM
public final boolean USE_DE_ZOOM
public final boolean GC_MEMORY_DBUG
public static java.lang.String osName
public static java.lang.String fileSeparator
public static java.lang.String userDir
public static java.lang.String userTmpDir
public static java.lang.String userCalDir
public static java.lang.String userSptDir
public static final java.lang.String FLK_BASE_URL
public static java.lang.String baseFlkServer
public static final java.lang.String FLICKER_HOME
public static final java.lang.String QUICK_START
public static final java.lang.String REF_MANUAL
public static final java.lang.String REF_MAN_KEYSTROKES
public static final java.lang.String REF_MAN_MOUSE
public static final java.lang.String REF_MAN_SLIDERS
public static final java.lang.String REF_MAN_CHECKBOX
public static final java.lang.String REF_MAN_MENUS
public static final java.lang.String REF_MAN_TRANSFORMS
public static final java.lang.String REF_MAN_SPOTLISTS_CREATE
public static final java.lang.String REF_MAN_SPOTLISTS_ANNOTATE
public static final java.lang.String REF_MAN_PUTATIVESPOTID
public static final java.lang.String REF_MAN_UPDATING
public static final java.lang.String REF_MAN_ADDUSERIMAGES
public static final java.lang.String REF_VERSION_NBR
public static final java.lang.String VIGNETTES
public static final java.lang.String WALKER_BOOK_CHAPTER_2005
public static final java.lang.String OLD_FLICKER_HOME
public static final java.lang.String EP97PAPER_FILE
public static final java.lang.String POSTER_FILE1
public static final java.lang.String POSTER_FILE2
public static final java.lang.String POSTER_FILE3
public static final java.lang.String POSTER_FILE4
public static final java.lang.String SUN_JAI_LICENSE
public static final java.lang.String SWISS_2DPAGE
public static final java.lang.String WORLD_2DPAGE
public static final java.lang.String TWO_D_HUNT
public static final java.lang.String GOOGLE_2D_SEARCH
public static final java.lang.String UNIPROT
public static final java.lang.String IPROCLASS
public static final java.lang.String IPROLINK
public static java.lang.String IMAGE_FILE1
public static java.lang.String IMAGE_FILE2
public static final int NORM_COLOR
public static final int PSEUDO_COLOR
public static final int RGB_TO_GRAY_COLOR
public static final int LINES_REPORT_STATUS
public static final int MAX_KEEPALIVE_TIME
public static final int CANVAS_SIZE
public static int MIN_CANVAS_SIZE
public static int MAX_CANVAS_SIZE
public static int CANVAS_INCR
public static final int FRAME_HEIGHT
public static final int FRAME_WIDTH
public static int FRAME_INCR
public static final int DEFAULT_TARGET_SIZE
public static final int MIN_TARGET_SIZE
public static final int MAX_TARGET_SIZE
static final int MAX_CIRCLE_RADIUS
static final int MIN_CIRCLE_RADIUS
public int DEF_CIRCLE_MASK_RADIUS
static final int MAX_SPOTS
public Affine aff
public BuildGUI bGui
public CalibrateOD cal
public EventKbd ekb
public EventScroller evs
public EventMenu evMu
public FileIO fio
public FlkDemo fDemo
public FlkUser fUser
public FlkMap fm
public FlkRecent fRecent
public ImageIO imgIO
public ImageXform ix
public Info info
public Landmark lms
public PluginMgr piMgr
public SpatialXform sxf
public Spot spt
public TiffLoader tr
public Util util
public Windump windmp
public ImageScroller lastIS
public ImageScroller flkIS
public ImageScroller i1IS
public ImageScroller i2IS
public ImageData iData1
public ImageData iData2
public ImageXform imgXform
public ImageXform ixf1
public ImageXform ixf2
public java.lang.Thread runT
private boolean notDoneFlag
public java.lang.String[] args
public java.lang.String flkStateFile
public java.lang.String lastISName
public java.util.Date startupDate
java.lang.String title
public java.lang.String activeImage
public java.lang.String sWorking
public java.lang.String errStr
public int colorMode
public java.awt.Color alertColor
public java.awt.Color lastMsgColor
public java.lang.String lastMsgStr
public java.lang.String popupWindowName
public java.lang.String imageFile1
public java.lang.String imageFile2
public java.lang.String xformName
public java.awt.Font imageFont
public java.awt.Font textFont
public boolean showI1flag
public boolean finished1
public boolean finished2
public int xformThreadCtr
public boolean validAffineFlag
public boolean errorLoadingImageFlag
public boolean displayInfoFlag
public boolean doingXformFlag
public boolean isSuspendedFlag
public boolean readyFlag
public boolean imageLoadErrorFlag
public boolean abortFlag
public boolean stopAnnotationUpdateFlag
public boolean viewLMSflag
public boolean viewTargetFlag
public boolean viewTrialObjFlag
public boolean viewBoundaryFlag
public boolean viewRoiFlag
public boolean viewMeasCircleFlag
public boolean viewDrawSpotLocCircleFlag
public boolean viewDrawSpotLocPlusFlag
public boolean viewDrawSpotAnnNbrFlag
public boolean viewDrawSpotAnnIdFlag
public boolean viewMultPopups
public boolean viewGangScrollFlag
public boolean viewGangZoomFlag
public boolean viewGangBCFlag
public boolean viewDispGrayValuesFlag
public boolean firstTimeThruFlag
public boolean viewNormalizedColorFlag
public boolean viewPseudoColorFlag
public boolean viewRGB2GrayFlag
public boolean viewReportPopupFlag
public boolean useGuardRegionImageFlag
public boolean useNTSCrgbTograyCvtFlag
public boolean doMeasureProtIDlookupAndPopupFlag
public boolean useSwiss2DpageServerFlag
public boolean usePIRUniprotServerFlag
public boolean usePIRiProClassServerFlag
public boolean usePIRiProLinkFlag
public java.lang.String currentPRIbaseURL
public boolean useDemoLeukemiaCalPreFlag
public boolean useThresholdInsideFlag
public boolean saveOimagesWhenSaveStateflag
public boolean useProteinDBbrowserFlag
public boolean userClickableImageDBflag
public boolean allowXformFlag
public boolean composeXformFlag
public boolean dbugFlag
public boolean prevFlickerFlag
public boolean flickerFlag
public java.lang.String clickableCGIbaseURL1
public java.lang.String clickableCGIbaseURL2
public java.lang.String clickableCGIbaseURL1pix
public java.lang.String clickableCGIbaseURL2pix
public boolean isClickableDBflag
public SliderState curState
public int defaultFlickerDelay
public int flkCanvasSize
public int canvasSize
public int frameWidth
public int frameHeight
public int scrWidth
public int scrHeight
public boolean resizeFrameFlag
public int winDumpRadix
public int maxColsToPrint
public boolean useLogInputFlag
public boolean useTotDensityFlag
public boolean useMeasCtrFlag
public boolean spotsListModeFlag
public int bkgrdCircleRadius
public int measCircleRadius
public int[][] circleMask
public int nCirMask
private java.awt.Point imgPos
private java.awt.Point objPos
public int imagesToProcess
public int nbrUniqueAFT
public float thrColinearity
public float minLSQcolinearity1
public float minLSQcolinearity2
public java.awt.Color roiColor
static java.awt.Color targetColor
public java.awt.Color trialObjColor
public java.awt.Color lmsColor
public java.awt.Color bkgrdCircleColor
public java.awt.Color measCircleColor
public java.awt.Color guardRegionColor
public static final int MAX_EXTERN_FCTS
public java.lang.String[] efName
public java.lang.String[] efMnuName
public int[] efNbr
public boolean repaintLockFlag
Constructor Detail |
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public Flicker()
Method Detail |
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public static void main(java.lang.String[] args)
args
- is the command line arg listprivate void initState(java.lang.String[] args)
public void resetDefaultView()
public void reInitStateVars()
public void init(java.lang.String[] args)
public void start()
public void stop()
public void run()
run
in interface java.lang.Runnable
public void chkDoneWithTransform()
ImageXform.softDoneWithTransform(ImageData, java.lang.String, java.lang.String)
public boolean checkIfSaveFlkFile()
public void finalize()
finalize
in class java.awt.Frame
private void initialImageLoad()
public boolean changeCanvasSize(java.lang.String cmd)
public boolean setCanvasAndFrameSize(int newCanvasSize, int newFrameWidth, int newFrameHeight)
newCanvasSize
- newFramWidth
- newFrameHeight
-
public void doFullRepaint()
public void updateFlickerImage()
public void testAndSetThreadCounter()
public boolean chkIfClickableDB(boolean showMsgFlag)
showMsgFlag
- to also report a message if true
ImageScroller lookupCurrentImageScroller()
ImageData lookupCurrentImageData()
public void paintComponent(java.awt.Graphics g)
g
- is graphics contextpublic void windowClosing(java.awt.event.WindowEvent windowEvent)
windowClosing
in interface java.awt.event.WindowListener
public void windowClosed(java.awt.event.WindowEvent windowEvent)
windowClosed
in interface java.awt.event.WindowListener
public void windowActivated(java.awt.event.WindowEvent windowEvent)
windowActivated
in interface java.awt.event.WindowListener
public void windowDeactivated(java.awt.event.WindowEvent windowEvent)
windowDeactivated
in interface java.awt.event.WindowListener
public void windowDeiconified(java.awt.event.WindowEvent windowEvent)
windowDeiconified
in interface java.awt.event.WindowListener
public void windowIconified(java.awt.event.WindowEvent windowEvent)
windowIconified
in interface java.awt.event.WindowListener
public void windowOpened(java.awt.event.WindowEvent windowEvent)
windowOpened
in interface java.awt.event.WindowListener
public void componentHidden(java.awt.event.ComponentEvent componentEvent)
componentHidden
in interface java.awt.event.ComponentListener
public void componentMoved(java.awt.event.ComponentEvent componentEvent)
componentMoved
in interface java.awt.event.ComponentListener
public void componentShown(java.awt.event.ComponentEvent componentEvent)
componentShown
in interface java.awt.event.ComponentListener
public void componentResized(java.awt.event.ComponentEvent componentEvent)
componentResized
in interface java.awt.event.ComponentListener
componentEvent
- event
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