Accession
Class AccReportPopup

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  Accession.AccReportPopup

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

 class AccReportPopup
extends java.awt.Frame
implements java.awt.event.ItemListener, java.awt.event.ActionListener, java.awt.event.WindowListener

Class AccReportPopup creates and displays scrollable string text area in a popup window. Various control buttons are also provided at the bottom of the window that are dependent on the type of text area being displayed.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://open2dprot.sourceforge.net/

Version:

$Date: 2005/10/20 11:19:13 $ $Revision: 1.16 $

Author:

P. Lemkin (LECB/NCI), G. Thornwall (SAIC), Frederick, MD

See Also:

Open2Dprot Home

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

private java.awt.Button	accessionEditButton button for "Accession" button
AccACCwizardPopup	accGUI popup Accession wizard GUI
java.awt.Choice	calibEditChoice Choice pull-down menu for selecting calibration method: "Calibrate wedge" "Calibrate spot list" "Calibrate data" "Calibrate by file"
AccCALIBwizardPopup	calibGUI popup Calibration wizard GUI
Table	calibTbl Calibration table that can be used to sepecify calibration values from a file.
int	calIdx index of field "CAL" in calibTbl
int	calUnitAbbrevIdx index of field "CAL-ABBREV" in calibTbl
int	calUnitIdx index of field "CAL-UNIT" in calibTbl
boolean	cancelFlag pressed sog.
private Accession	cs instance of the main class
boolean	doneFlag pressed sog.
java.awt.Menu	editMenu "Edit" pull down Menu list
private java.awt.Button	editOptionsButton button for "Set startup options" button
private int	enableCalibDBUG Enable calibration while debugging
java.awt.Menu	fileMenu "File" pull down Menu list
int	grayIdx index of field "GRAY" in calibTbl
java.awt.Menu	helpMenu "Help" pull down Menu list
(package private) java.awt.MenuBar	mbar menu bar for the frame
MenuSupport	ms Menu support functions using Hashtables to tack what is active
java.lang.String[]	newArgv new switch options
java.io.FileWriter	oFile File to flush and close on "Kill program" if it is not null
int	peakIdx index of field "PEAK" in calibTbl
java.lang.String	poTitle popup options title
boolean	reanalyzeFlag pressed sog.
private java.lang.String	reportFile
private java.awt.Button	roiEditButton button for "ROI" button
AccROIwizardPopup	roiGUI popup ROI Image wizard GUI
java.awt.Menu	rSampleSubmenu Dynamic submenu list for "Set Rsample" the value is "SetRsample:"sample-name'"
java.awt.Menu	sampleSubmenu Dynamic submenu list for "Open Sample for editing" the value is "OpenSampleForEditing:"sample-name'"
(package private) static long	serialVersionUID frame id
boolean	setNewDefaultFlag pressed sog.
boolean	showStatusFlag
PopupOptions	sog popup options GUI
private java.awt.Label	statusLineLabel Status line label
boolean	stopFlag
boolean[]	swOptCBvalue The swOptcCBvalue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions.
java.lang.String[]	swOptData The swOptData[0:(3*nData)-1] is used by the AccReportPopup that in turn may call PopupOptions.
java.lang.String[]	swOptValue The swOptValue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions.
private java.awt.TextArea	textarea Text area GUI for main report
private int	textAreaFontSize font size
private java.lang.String	textFontFamily Text area font family
private java.lang.String	textReport copy of text in textArea
(package private) java.lang.String	title string for title of frame
java.awt.Menu	viewMenu "View" pull down Menu list

Fields inherited from class java.awt.Frame

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

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

AccReportPopup(Accession cs)
AccReportPopup() - Constructor.

AccReportPopup(Accession cs, java.lang.String programName, java.lang.String textReport, int nRows, int nCols, java.lang.String title, java.lang.String reportFile, boolean showStatusFlag)
AccReportPopup() - Constructor.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
private void	addMenuTree(java.awt.Frame f, java.awt.MenuBar mbar) addMenuTree() - create pull down menus in menu bar
boolean	addSpotToSpotList(DbSpot r) addSpotToSpotList() - add (x,y) spot of size spotDiameter to the spot list for the current sample.
void	appendTextMsg(java.lang.String newText) appendTextMsg() - append text in popup window
void	cleanKillApplication(boolean saveFirstFlag) cleanKillApplication() - close the file if needed and do a clean kill of the application
void	clearSpotList() clearSpotList() - clear the spot list for the current sample.
void	clearText() clearText() - clear text in popup window
void	close() close() - close this popup and reset flags if needed
java.lang.String	getReportText() getReportText() - get the text from the Report popup window
java.lang.String	getSpotListStr(java.lang.String dispName) getSpotListStr() - generate a string report (reduced spot features) of a list of spots in the list for the current sample.
java.lang.String	getSpotStr(DbSpot sp, int n) getSpotStr() - generate a printable string for a spot (reduced features)
boolean	getStopStatus() getStopStatus() - get the stop processing flag set by pressing the "Stop processing" button
void	itemStateChanged(java.awt.event.ItemEvent e) itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
void	popupAccWizard() popupAccWizard() - popup the accession wizard GUI.
boolean	popupCalibWizard(int calDataMode) popupCalibWizard() - popup the image calibration wizard GUI on the current Sample.
boolean	popupRoiWizard() popupRoiWizard() - popup the image viewer on the current Sample.
void	positionReportWindow() positionReportWindow() - position report window on the screen
void	quit() quit() - closing down the window, get rid of the frame.
boolean	readCalibValuesFromFile(java.lang.String calibFile, boolean verifyAllFieldsFlag) readCalibValuesFromFile() - read calibration values from file.
boolean	readSpotListFromAccTable() readSpotListFromAccTable() - If spot measurements exist in the accession DB table, then create the dbSample spot list from this data.
boolean	rebuildOpenSampleSubmenus() rebuildOpenSampleSubmenus() - rebuild the Set Rsample and Open Sample submenus from entries in the accession database.
void	reCalcSpotListMeasures(boolean useCommonSpotSizeFlag, boolean useSpotBkbrdCorrectionFlag) reCalcSpotListMeasures() - Recompute spot list measurements.
boolean	rmvSpotFromSpotList(DbSpot r) rmvSpotFromSpotList() - remove (x,y) spot of from the spot list for the current sample.
void	setEnableButtons(boolean flag) setEnableButtons() - by the flag
void	setEnableMenus(boolean flag) setEnableMenus() - by the flag
void	setOutFileToCloseOnKill(java.io.FileWriter oFile) setOutFileToCloseOnKill() - set the show/hide popup status
void	setSaveAsFile(java.lang.String reportFile) setSaveAsFile() - set SaveAs file default file name
void	setShow(boolean showStatusFlag) setShow() - set the show/hide popup status
private boolean	showPopupOptionWindow(java.lang.String poTitle) showPopupOptionWindow() - popup options window using the csPopupOptions GUI.
void	updateReportStatusLine(java.lang.String msg) updateReportStatusLine() - clear text in popup window
void	updateText(java.lang.String newText) updateText() - update text in popup window
void	updateTitle(java.lang.String title) updateTitle() - update title in popup window
boolean	waitForUserClose() waitForUserClose)() wait for user to press "Close" application.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - closing down the window, get rid of the frame.
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)

Methods inherited from class java.awt.Frame

addNotify, finalize, getAccessibleContext, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, paramString, remove, removeNotify, setCursor, setExtendedState, setIconImage, 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, processWindowEvent, 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, addImpl, 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, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate, validateTree

Methods inherited from class java.awt.Component

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

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

serialVersionUID

static final long serialVersionUID

frame id

See Also:

Constant Field Values

cs

private Accession cs

instance of the main class

title

java.lang.String title

string for title of frame

mbar

java.awt.MenuBar mbar

menu bar for the frame

fileMenu

public java.awt.Menu fileMenu

"File" pull down Menu list

editMenu

public java.awt.Menu editMenu

"Edit" pull down Menu list

viewMenu

public java.awt.Menu viewMenu

"View" pull down Menu list

helpMenu

public java.awt.Menu helpMenu

"Help" pull down Menu list

rSampleSubmenu

public java.awt.Menu rSampleSubmenu

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

sampleSubmenu

public java.awt.Menu sampleSubmenu

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

ms

public MenuSupport ms

Menu support functions using Hashtables to tack what is active

textReport

private java.lang.String textReport

copy of text in textArea

reportFile

private java.lang.String reportFile

textarea

private java.awt.TextArea textarea

Text area GUI for main report

textAreaFontSize

private int textAreaFontSize

font size

textFontFamily

private java.lang.String textFontFamily

Text area font family

editOptionsButton

private java.awt.Button editOptionsButton

button for "Set startup options" button

accessionEditButton

private java.awt.Button accessionEditButton

button for "Accession" button

roiEditButton

private java.awt.Button roiEditButton

button for "ROI" button

calibEditChoice

public java.awt.Choice calibEditChoice

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

statusLineLabel

private java.awt.Label statusLineLabel

Status line label

showStatusFlag

public boolean showStatusFlag

stopFlag

public boolean stopFlag

oFile

public java.io.FileWriter oFile

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

sog

public PopupOptions sog

popup options GUI

newArgv

public java.lang.String[] newArgv

new switch options

poTitle

public java.lang.String poTitle

popup options title

swOptData

public java.lang.String[] swOptData

The swOptData[0:(3*nData)-1] is used by the AccReportPopup that in turn may call PopupOptions. It contains triples of (prompt,user, helpStr) data. If the prompt data has a "-", then make a CheckBox, else it is a Label with the prompt data. If it is a CheckBox, use default value false if it starts with "-no" else true. The 2nd arg of the pair is the user data. If the user data is not null, then make a TextField with this user data on the right else make an empty Label.

swOptCBvalue

public boolean[] swOptCBvalue

The swOptcCBvalue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions. It contains boolean values of switch data use for Checkboxes.

swOptValue

public java.lang.String[] swOptValue

The swOptValue[0:nData-1] is used by the AccReportPopup that in turn may call csPopupOptions. It contains String values of associated switch data.

accGUI

public AccACCwizardPopup accGUI

popup Accession wizard GUI

calibGUI

public AccCALIBwizardPopup calibGUI

popup Calibration wizard GUI

roiGUI

public AccROIwizardPopup roiGUI

popup ROI Image wizard GUI

setNewDefaultFlag

public boolean setNewDefaultFlag

pressed sog. "Set new default"

reanalyzeFlag

public boolean reanalyzeFlag

pressed sog. "Reanalyze"

doneFlag

public boolean doneFlag

pressed sog. "Done"

cancelFlag

public boolean cancelFlag

pressed sog. "Cancel"

calibTbl

public Table calibTbl

Calibration table that can be used to sepecify calibration values from a file. It may have 1 or more of the following fields "PEAK", "CAL", "GRAY", "CAL-UNIT", "CAL-ABBREV".

peakIdx

public int peakIdx

index of field "PEAK" in calibTbl

calIdx

public int calIdx

index of field "CAL" in calibTbl

grayIdx

public int grayIdx

index of field "GRAY" in calibTbl

calUnitIdx

public int calUnitIdx

index of field "CAL-UNIT" in calibTbl

calUnitAbbrevIdx

public int calUnitAbbrevIdx

index of field "CAL-ABBREV" in calibTbl

enableCalibDBUG

private int enableCalibDBUG

Enable calibration while debugging

Constructor Detail

AccReportPopup

public AccReportPopup(Accession cs)

AccReportPopup() - Constructor. placeholder instance

Parameters:

cs - is an instance of the main class

AccReportPopup

public AccReportPopup(Accession cs,
                      java.lang.String programName,
                      java.lang.String textReport,
                      int nRows,
                      int nCols,
                      java.lang.String title,
                      java.lang.String reportFile,
                      boolean showStatusFlag)

AccReportPopup() - Constructor. Display Report Window control panel GUI.

Parameters:

cs - is an instance of the main class

programName - name of the program

textReport - is initial text string for buffer.

nRows - is maximum size of window

nCols, - is maximum size of window

title - of the window

String - reportFile is default SAVE AS .txt file.Default "Accession-Report.txt"

showStatusFlag - to show (true), hide(false).

Method Detail

addMenuTree

private void addMenuTree(java.awt.Frame f,
                         java.awt.MenuBar mbar)

addMenuTree() - create pull down menus in menu bar

Parameters:

f - is frame

mbar - is MenuBar

setEnableButtons

public void setEnableButtons(boolean flag)

setEnableButtons() - by the flag

Parameters:

flag - to set enable buttons

setEnableMenus

public void setEnableMenus(boolean flag)

setEnableMenus() - by the flag

Parameters:

flag - to set enable menus

rebuildOpenSampleSubmenus

public boolean rebuildOpenSampleSubmenus()

rebuildOpenSampleSubmenus() - rebuild the Set Rsample and Open Sample submenus from entries in the accession database. Dynamic submenu list for "Set Rsample" the value is "SetRsample:"sample-name'" Dynamic submenu list for "Open Sample for editing" the value is "OpenSampleForEditing:"sample-name'"

Parameters:

true - if suceed

positionReportWindow

public void positionReportWindow()

positionReportWindow() - position report window on the screen

setOutFileToCloseOnKill

public void setOutFileToCloseOnKill(java.io.FileWriter oFile)

setOutFileToCloseOnKill() - set the show/hide popup status

Parameters:

oFile - to flush and close if use Kill command.

setShow

public void setShow(boolean showStatusFlag)

setShow() - set the show/hide popup status

Parameters:

showStatusFlag - to show (true), hide(false).

getStopStatus

public boolean getStopStatus()

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

Returns:

true if "Stop" button had been pressed.

updateReportStatusLine

public void updateReportStatusLine(java.lang.String msg)

updateReportStatusLine() - clear text in popup window

Parameters:

msg - to display

clearText

public void clearText()

clearText() - clear text in popup window

getReportText

public java.lang.String getReportText()

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

Returns:

text report

updateText

public void updateText(java.lang.String newText)

updateText() - update text in popup window

Parameters:

newText - is string to copy into text window

appendTextMsg

public void appendTextMsg(java.lang.String newText)

appendTextMsg() - append text in popup window

Parameters:

newText - is string to append into text window

updateTitle

public void updateTitle(java.lang.String title)

updateTitle() - update title in popup window

Parameters:

title - is new title.

setSaveAsFile

public void setSaveAsFile(java.lang.String reportFile)

setSaveAsFile() - set SaveAs file default file name

Parameters:

title - is new title.

addSpotToSpotList

public boolean addSpotToSpotList(DbSpot r)

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

Parameters:

r - is spot to add

Returns:

true if succeed

rmvSpotFromSpotList

public boolean rmvSpotFromSpotList(DbSpot r)

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

Parameters:

r - is spot to remove

Returns:

true if succeed

clearSpotList

public void clearSpotList()

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

getSpotStr

public java.lang.String getSpotStr(DbSpot sp,
                                   int n)

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

 Spot #1 (x,y)=(42,20) area=289 totGray=16863 mnGray=58+-4.1 range[47:71]

Parameters:

sp - is spot to convert to string

n - is the spot number

Returns:

string if found, else null

getSpotListStr

public java.lang.String getSpotListStr(java.lang.String dispName)

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

 Spot list for gel-HM-071
 Spot #0 (x,y)=(12,26) area=289 totGray=9799 mnGray=33+-5.0 range[23:47]
 Spot #1 (x,y)=(42,20) area=289 totGray=16863 mnGray=58+-4.1 range[47:71]
 Spot #2 (x,y)=(75,29) area=289 totGray=24095 mnGray=83+-4.2 range[71:95]

Parameters:

dispName - of spot list

Returns:

string

readCalibValuesFromFile

public boolean readCalibValuesFromFile(java.lang.String calibFile,
                                       boolean verifyAllFieldsFlag)

readCalibValuesFromFile() - read calibration values from file. It may have 1 or more of the following fields "PEAK", "CAL", "GRAY", "CAL-UNIT", "CAL-ABBREV". It must have at least 2 values i.e. data rows.

Parameters:

calibFile - which is a tab-delimited file

verifyAllFieldsFlag - will test if all fields are well formed.

Returns:

true if succeed, then calibTbl is set up. Else CalibTbl is set to null if it is not found.

readSpotListFromAccTable

public boolean readSpotListFromAccTable()

readSpotListFromAccTable() - If spot measurements exist in the accession DB table, then create the dbSample spot list from this data. If it exists, the spot size is in table field "SpotMeasSize" and the list of nGrayPeaks spot centroids is in field "SpotXYSlist" as "x1,y1,s2,x2,y2,s2, ...xn,yn,sn" where (xi,yi) is spot i's centroid and si is its size (square of odd size centered at xi,yi).

Returns:

true if spot list data exists and spot list was created.

reCalcSpotListMeasures

public void reCalcSpotListMeasures(boolean useCommonSpotSizeFlag,
                                   boolean useSpotBkbrdCorrectionFlag)

reCalcSpotListMeasures() - Recompute spot list measurements.

Parameters:

useCommonSpotSizeFlag - to recompute the measurements with the a common spot size cs.spotBoxSize, else use individual spot sizes defined as (sp.merx2-sp.merx1+1);

useSpotBkbrdCorrectionFlag - to recompute the measurements with background correction

close

public void close()

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

cleanKillApplication

public void cleanKillApplication(boolean saveFirstFlag)

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

Parameters:

saveFirstFlag - to save any open first first.

showPopupOptionWindow

private boolean showPopupOptionWindow(java.lang.String poTitle)

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

 This uses a new instance of the data contained in data created
 by cs.ini.initSwitchOptionsData(). The data is:

  cs.switchOptData[0:(3*nData)-1] is used by the AccReportPopup 
        that in turn may call csPopupOptions. It contains triples of 
        (optionPrompt, guiBuilderSpec, helpStr) data. If the prompt 
        data has a "-", then make a CheckBox (swOptcCBvalue), 
        else it is a Label with the prompt data. 
        If the user data is not null, then make a TextField with 
        this user (swOptValue) data on the right else make an empty 
        Label.
 cs.switchOptCBvalue[0:nData-1] is used by the AccReportPopup 
        that in turn may call csPopupOptions. It contains boolean values
        of switch data use for Checkboxes.
 cs.switchOptValue[0:nData-1] is used by the AccReportPopup 
        that in turn may call csPopupOptions. It contains String 
        text values of associated switch data arguments.

Parameters:

poTitle - for popup options GUI

Returns:

true if open the window.

waitForUserClose

public boolean waitForUserClose()

waitForUserClose)() wait for user to press "Close" application. Close databases if any were still open.

Returns:

true if continue with the application

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

actionPerformed() - Handle button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is action event

quit

public void quit()

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

See Also:

close()

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

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

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

Parameters:

e - is ItemEvent

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

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

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

close()

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener

popupAccWizard

public void popupAccWizard()

popupAccWizard() - popup the accession wizard GUI.

popupCalibWizard

public boolean popupCalibWizard(int calDataMode)

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

Parameters:

calDataMode - is one of AccCALIBwizardPopup.CAL_WEDGE - uses (NC ROI, cal list, gray list) AccCALIBwizardPopup.CAL_SPOTLIST - uses spot list + opt. cal list AccCALIBwizardPopup.CAL_DATA_FILE - uses file for cal + gray lists AccCALIBwizardPopup.CAL_MANUAL - no requirements

Returns:

true if succeed in launching the wizard, false if a problem

popupRoiWizard

public boolean popupRoiWizard()

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

Returns:

true if succeed, false if any problems.