Class RtestBase

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--RtestBase

All Implemented Interfaces:

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

Direct Known Subclasses:

Rtest

public abstract class RtestBase

extends java.awt.Frame

implements java.awt.event.ItemListener, java.awt.event.ActionListener, java.awt.event.WindowListener

Class RtestBase - evaluate R scripts with data supplied from Client program via the MJAReval API. Each R analysis is defined by a R LayOut (RLO). Each RLO is saved in an internal RLO database managed by the mjaReval MJA class. These specify the evaluation environment for the .R script when evaluated by R. The R program is then run as a separate process using a System.exec()

NOTE: this base class is used to create Rtest.java class that implements the declared abstract methods using application dependent methods.

When executed, an R script is allowed to generate multiple output files that may include the following format templateValues: text, tab-delimited text, PDF, JPG, etc. There may be also multiple data input files requested by the R script. These are generated by mjaReval class methods as specified by the RLO database entry. Note: during R execution, all files are read and written from the {project}/Temp directory, the R current working directory. They may be copied to or from this directory from or to other directories as required.

data is exported from MAExplorer to tab-delimited data files {Project}/Temp/. These will then be read by R when your script is evaluated.

The output of R is saved to any number of files into {project}/Temp and then moved to {Project}/Report/ where they may then be displayed or read by MAExplorer if required.

The .R scripts are shared with all instances of MAExplorer and are kept in {MAExplorer installation}/R/

The startup script is generated by an mjaReval method and placed in the {project}/Temp directory where it will be used by a System.exec() call.

This example is under construction, but can serve as a model of some the Open Java API interface and writing a simple MAEPlugin.

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 MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/06/18 19:10:37 $ $Revision: 1.80 $

Author:

P. Lemkin (NCI-Frederick); G. Thornwall (SAIC-Frederick); W.G. Alvord and Lubomirski (CSS/DMS/NCI-Frederick), Frederick, MD; S. Sundaram, SRA/BIMAS/CIT-NIH.

See Also:

MAExplorer Home, Reval, MJAReval, Serialized Form

Inner classes inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Inner classes inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Inner classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Inner classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock

Field Summary

private boolean	appendTextFlag Flag for append text and resetting cursor to end of TextArea
private static java.lang.String	BANNER
private java.awt.Panel	buttonPanel button control panel
private java.awt.Button	clearReportButton "Clear report" to clear the text area
private java.lang.String	clientBrowserTitle Client current browser title for this database
private java.lang.String	clientDatabase Client current database
(package private) java.lang.String	clientName Name of the client
(package private) java.lang.String	clientPrefixName Prefix Name of the client
private java.lang.String	clientPrjPath Client current project path.
private java.awt.Button	closeButton "Close" window button
(package private) static boolean	CONSOLE_FLAG Debug flags
private java.awt.Color	dataBkgrd Text data report background color that may be changed
private java.awt.Color	dataColor Text data report foreground color that may be changed
private java.awt.TextField	dataTF Text data report line
private static java.lang.String	DATE
(package private) static boolean	DBUG_APPEND_REPORT
(package private) boolean	DBUG_FLAG
private java.awt.Checkbox	dbugCheckbox dbug checkbox toggles output being appended to reportText window
(package private) boolean	dbugFlag Flag set debugging - toggled by dbugbox if DBUG_FLAG is set
(package private) static int	DEF_MAX_ANALSYSES Maximum # scripts (may grow over time)
private java.awt.Button	deleteRLOButton "Delete RLO" window button
private java.awt.Button	editRLOButton "Edit RLO" to edit existing RLO
(package private) static java.lang.String	EPILOGUE_END fixed epilogue end string
(package private) static java.lang.String	EPILOGUE_START fixed epilogue start string
private java.awt.Button	evalButton "Evaluate" window button
(package private) java.lang.String	fileSep
private boolean	guiReadyFlag set if GUI is ready for action!
private java.awt.Button	helpButton "Help Msg" window button
private java.lang.String	helpMsg Help text
private java.awt.Panel	inputPanel input panel to hold scriptChoice
private java.awt.TextField	inputTF Text input data line
(package private) boolean	isWindowsFlag Flag set if running on a Windows computer
(package private) java.lang.String	javaHome
private static int	MIN_WINDOW_HEIGHT
private static int	MIN_WINDOW_WIDTH MIN size of scrollable Canvas
(package private) MJAReval	mjaReval instance of Reval
(package private) MJAReval	mr
private java.awt.Color	msgBkgrd Text message background color that may be changed
private java.awt.Color	msgColor Text message foreground color that may be changed
(package private) java.awt.Font	msgFont fonts for labeling subtitle for each panel in image
private java.awt.TextField	msgTF Text message report line
(package private) int	nAnalyses The total number of analyses in the RLO database
private int	nCols # of columns size of text area for reporting
(package private) int	nDemoAnalyses The number of "Demo" analyses in the RLO database.
(package private) static boolean	NEVER Debug flags
private java.awt.Button	newRLOButton "New RLO" to create new RLO
private int	nRows # of rows size of text area for reporting
(package private) java.lang.String	osName
private PopupEditRscript	pe
private int	preferredHeight preferred height size of frame
private int	preferredWidth preferred width size of frame
(package private) static java.lang.String	PROLOGUE_END fixed prologue end string
(package private) static java.lang.String	PROLOGUE_START fixed prologue start string
(package private) java.lang.String	reportText text for TextArea
private java.awt.TextArea	reportTextArea Text area to draw reportText that is returned from performing the eval of the .R script
private static java.lang.String	REVISION
(package private) RgenDemo	rgd R demo code generator
(package private) Rtest	rt
private java.awt.Button	saveAllDemoRLOsButton Save All Demo RLOs button if "Show Demo RLOs" is set.
private java.awt.Button	saveasButton "SaveAs" window button
private boolean	saveReportAsTextFileFlag Flag enabled if doing "SaveAs"
private java.awt.Choice	scriptChoice Choice to select an R script to use from analysis[0:nAnalyses-1].
private java.awt.Checkbox	showDemoRLOsCheckbox Show Demo RLOs checkbox toggles showDemoRLOsFlag.
private boolean	showDemoRLOsFlag Flag show Demo RLOs in menu - toggled by showDemoRLOsCheckbox
private java.awt.Button	showPlotsButton "Show generated plot(s)" window button
private java.awt.Button	showRLOButton "Show RLO" window button
private java.awt.Button	showRscriptButton "Show R script" current R script button
(package private) java.lang.String	spaces Spaces
(package private) java.awt.Font	titleFont fonts for labeling full image title etc.
private java.awt.Panel	topPanel top panel holding the buttonPanel and the msgTA TextField
(package private) java.lang.String	userDir
private static java.lang.String	VERSION

Fields inherited from class java.awt.Frame

base, CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, frameSerializedDataVersion, HAND_CURSOR, icon, ICONIFIED, mbManagement, menuBar, MOVE_CURSOR, N_RESIZE_CURSOR, nameCounter, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, ownedWindows, resizable, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, serialVersionUID, state, SW_RESIZE_CURSOR, TEXT_CURSOR, title, W_RESIZE_CURSOR, WAIT_CURSOR, weakThis

Fields inherited from class java.awt.Window

active, dbg, focusMgr, inputContext, inputContextLock, OPENED, ownedWindowList, showWithParent, warningString, windowListener, windowSerializedDataVersion

Fields inherited from class java.awt.Container

component, containerListener, containerSerializedDataVersion, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads

Fields inherited from class java.awt.Component

accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

RtestBase(MJAReval mjaReval, java.lang.String clientName, java.lang.String clientPrefixName, java.lang.String clientPrjPath, java.lang.String clientBrowserTitle, java.lang.String clientDatabase)
RtestBase() - Constructor

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle Control panel button clicks
(package private) void	appendReport(java.lang.String msg, boolean appendToRptFlag) appendReport() - add text to report text area
private boolean	buildGUI() buildGUI() - build the graphical user interface
void	close(int exitCode) close() - exit with specified exit code.
(package private) abstract java.lang.String	cvtSpacesToUnderscores(java.lang.String str) cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable. : space( ) ; " { } < > = , ? \ / % * ! @ & | ' ` \t
(package private) abstract void	displayPDF(java.lang.String pdfFile) displayPDF() - Display PDF file in adobe, for use in stand-alone.
(package private) abstract void	displayURL(java.lang.String urlStr) displayURL() - Display URL file in system Web browser, for use in stand-alone mode.
private void	drawReportText(java.awt.Graphics g) drawReportText() - repaint report.
java.lang.String	extractUserRscript(java.lang.String completeRscript) extractUserRscript() - extract user R script from center of complete.
(package private) java.lang.String	genEpilogue() genEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.
(package private) java.lang.String	genPrologue() genPrologue() - generate prologue R script to read data commands.
(package private) abstract java.lang.String[]	getListOfMenuStubNames() getListOfMenuStubNames() - get list of menu stub names
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
(package private) int	getUseGenRbit(int genRmethod) getUseGenRbit() - lookup the use R_GENR_xxxx bit specified by method
boolean	handleEvent(java.awt.Event evt) handleEvent() - process special events
private boolean	initializeDataAndGUI() initializeDataAndGUI() - build the GUI, then repaint to build the initial display.
boolean	initRtest(Rtest rt) initRtest() - initialize the Rtest popup and create the GUI
void	itemStateChanged(java.awt.event.ItemEvent e) itemStateChanged() - handle item state changed eventsms.
void	paint(java.awt.Graphics g) paint() - repaint full scrolled text area.
(package private) abstract void	popupAlertMsg(java.lang.String title, java.lang.String msg, int nRows, int nCols) popupAlertMsg() - popup alert message in a scrollable text area.
(package private) abstract java.lang.String	readTextFromFile(java.lang.String fileName, java.lang.String loadingMsg) readTextFromFile() - read text from text file.
(package private) void	rebuildScriptChoices() rebuildScriptChoices() - rebuild the R script choices pull-down menu from the menuNames[] data.
(package private) abstract java.lang.String	rmvRtnChars(java.lang.String str) rmvRtnChars() - remove return chars.
private void	saveTextReport(java.lang.String textFileName) saveTextReport() - Saves reportText to file
private void	showCurrentRplots() showCurrentRplots() - show plots generated if any with last R eval.
(package private) void	showData(java.lang.String data, java.awt.Color fgColor, java.awt.Color bgColor) showData() - draw data in GUI data line
(package private) void	showGuiMsg(java.lang.String msg, java.awt.Color fgColor, java.awt.Color bgColor) showGuiMsg() - draw text in GUI message line
(package private) abstract void	showMsg(java.lang.String msg) showMsg() - display message in client GUI
void	update(java.awt.Graphics g) update() - update window
void	updateCurGene(int mid) updateCurGene() - update any data since current gene has changed.
void	updateFilter() updateFilter() - update any dependent data since Filter has changed.
void	updateLabels() updateLabels() - update any dependent data since global labels have changed.
void	updateSlider() updateSlider() - update any dependent data sincea threshold slider has changed.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - close down the window.
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)
(package private) abstract boolean	writeTextToFile(java.lang.String textFileName, java.lang.String textReport) writeTextToFile() - save text string as text file.

Methods inherited from class java.awt.Frame

, addNotify, addToFrameList, constructComponentName, finalize, getAccessibleContext, getCursorType, getFrames, getIconImage, getMenuBar, getState, getTitle, initIDs, isResizable, paramString, postProcessKeyEvent, readObject, remove, removeFromFrameList, removeNotify, setCursor, setIconImage, setMenuBar, setResizable, setState, setTitle, writeObject

Methods inherited from class java.awt.Window

addOwnedWindow, addWindowListener, adjustListeningChildren, applyResourceBundle, applyResourceBundle, connectOwnedWindow, dispatchEventImpl, dispose, eventEnabled, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isActive, isShowing, nextFocus, ownedInit, pack, postEvent, postWindowEvent, preProcessKeyEvent, processEvent, processWindowEvent, removeOwnedWindow, removeWindowListener, resetGC, setCursor, setFocusOwner, setWarningString, show, toBack, toFront, transferFocus

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventToSelf, doLayout, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getMaximumSize, getMinimumSize, getMouseEventTarget, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paintComponents, paintHeavyweightComponents, postsOldMouseEvents, preferredSize, print, printComponents, printHeavyweightComponents, processContainerEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFont, setLayout, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

DATE

private static final java.lang.String DATE

REVISION

private static final java.lang.String REVISION

VERSION

private static final java.lang.String VERSION

BANNER

private static final java.lang.String BANNER

DEF_MAX_ANALSYSES

static final int DEF_MAX_ANALSYSES

Maximum # scripts (may grow over time)

CONSOLE_FLAG

static final boolean CONSOLE_FLAG

Debug flags

NEVER

static final boolean NEVER

Debug flags

MIN_WINDOW_WIDTH

private static final int MIN_WINDOW_WIDTH

MIN size of scrollable Canvas

MIN_WINDOW_HEIGHT

private static final int MIN_WINDOW_HEIGHT

DBUG_APPEND_REPORT

static final boolean DBUG_APPEND_REPORT

PROLOGUE_START

static final java.lang.String PROLOGUE_START

fixed prologue start string

PROLOGUE_END

static final java.lang.String PROLOGUE_END

fixed prologue end string

EPILOGUE_START

static final java.lang.String EPILOGUE_START

fixed epilogue start string

EPILOGUE_END

static final java.lang.String EPILOGUE_END

fixed epilogue end string

DBUG_FLAG

final boolean DBUG_FLAG

rt

Rtest rt

mjaReval

MJAReval mjaReval

instance of Reval

mr

MJAReval mr

rgd

RgenDemo rgd

R demo code generator

nAnalyses

int nAnalyses

The total number of analyses in the RLO database

nDemoAnalyses

int nDemoAnalyses

The number of "Demo" analyses in the RLO database. Demo analyses use the generated .R script options specified by genRbits.

clientName

java.lang.String clientName

Name of the client

clientPrefixName

java.lang.String clientPrefixName

Prefix Name of the client

clientPrjPath

private java.lang.String clientPrjPath

Client current project path. This path will hold the Temp/ and Report/ directories. E.g., "../MAE" startup for MAExplorer client

clientBrowserTitle

private java.lang.String clientBrowserTitle

Client current browser title for this database

clientDatabase

private java.lang.String clientDatabase

Client current database

javaHome

java.lang.String javaHome

osName

java.lang.String osName

fileSep

java.lang.String fileSep

userDir

java.lang.String userDir

isWindowsFlag

boolean isWindowsFlag

Flag set if running on a Windows computer

dbugFlag

boolean dbugFlag

Flag set debugging - toggled by dbugbox if DBUG_FLAG is set

guiReadyFlag

private boolean guiReadyFlag

set if GUI is ready for action!

showDemoRLOsFlag

private boolean showDemoRLOsFlag

Flag show Demo RLOs in menu - toggled by showDemoRLOsCheckbox

appendTextFlag

private boolean appendTextFlag

Flag for append text and resetting cursor to end of TextArea

preferredHeight

private int preferredHeight

preferred height size of frame

preferredWidth

private int preferredWidth

preferred width size of frame

nRows

private int nRows

# of rows size of text area for reporting

nCols

private int nCols

# of columns size of text area for reporting

spaces

java.lang.String spaces

Spaces

saveReportAsTextFileFlag

private boolean saveReportAsTextFileFlag

Flag enabled if doing "SaveAs"

titleFont

java.awt.Font titleFont

fonts for labeling full image title etc.

msgFont

java.awt.Font msgFont

fonts for labeling subtitle for each panel in image

topPanel

private java.awt.Panel topPanel

top panel holding the buttonPanel and the msgTA TextField

inputPanel

private java.awt.Panel inputPanel

input panel to hold scriptChoice

buttonPanel

private java.awt.Panel buttonPanel

button control panel

saveAllDemoRLOsButton

private java.awt.Button saveAllDemoRLOsButton

Save All Demo RLOs button if "Show Demo RLOs" is set. This generates all RLO/DemoRscript*.rlo and R/DemoRscript*.R files for later use by Client next time it starts up.

evalButton

private java.awt.Button evalButton

"Evaluate" window button

showPlotsButton

private java.awt.Button showPlotsButton

"Show generated plot(s)" window button

showRscriptButton

private java.awt.Button showRscriptButton

"Show R script" current R script button

clearReportButton

private java.awt.Button clearReportButton

"Clear report" to clear the text area

saveasButton

private java.awt.Button saveasButton

"SaveAs" window button

closeButton

private java.awt.Button closeButton

"Close" window button

newRLOButton

private java.awt.Button newRLOButton

"New RLO" to create new RLO

editRLOButton

private java.awt.Button editRLOButton

"Edit RLO" to edit existing RLO

showRLOButton

private java.awt.Button showRLOButton

"Show RLO" window button

deleteRLOButton

private java.awt.Button deleteRLOButton

"Delete RLO" window button

helpButton

private java.awt.Button helpButton

"Help Msg" window button

showDemoRLOsCheckbox

private java.awt.Checkbox showDemoRLOsCheckbox

Show Demo RLOs checkbox toggles showDemoRLOsFlag. This controls the entries in the scriptChoice list.

dbugCheckbox

private java.awt.Checkbox dbugCheckbox

dbug checkbox toggles output being appended to reportText window

msgTF

private java.awt.TextField msgTF

Text message report line

msgColor

private java.awt.Color msgColor

Text message foreground color that may be changed

msgBkgrd

private java.awt.Color msgBkgrd

Text message background color that may be changed

dataTF

private java.awt.TextField dataTF

Text data report line

dataColor

private java.awt.Color dataColor

Text data report foreground color that may be changed

dataBkgrd

private java.awt.Color dataBkgrd

Text data report background color that may be changed

inputTF

private java.awt.TextField inputTF

Text input data line

reportTextArea

private java.awt.TextArea reportTextArea

Text area to draw reportText that is returned from performing the eval of the .R script

reportText

java.lang.String reportText

text for TextArea

helpMsg

private java.lang.String helpMsg

Help text

scriptChoice

private java.awt.Choice scriptChoice

Choice to select an R script to use from analysis[0:nAnalyses-1]. The current script is in curAnalysis

pe

private PopupEditRscript pe

Constructor Detail

RtestBase

public RtestBase(MJAReval mjaReval,
                 java.lang.String clientName,
                 java.lang.String clientPrefixName,
                 java.lang.String clientPrjPath,
                 java.lang.String clientBrowserTitle,
                 java.lang.String clientDatabase)

RtestBase() - Constructor

Parameters:

mjaReval - is the Reval API

clientName - is the string name of the client program

clientPrefixName - for the client

clientPrjPath - path of the client's project directory

clientBrowserTitle - to place a top of the window

clientDatabase - name of the database

Method Detail

initRtest

public boolean initRtest(Rtest rt)

initRtest() - initialize the Rtest popup and create the GUI

Parameters:

rt - is the Rtest instance

Returns:

true if succeed

See Also:

initializeDataAndGUI(), showData(java.lang.String, java.awt.Color, java.awt.Color), showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color)

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Container

Returns:

preferred size of window

initializeDataAndGUI

private boolean initializeDataAndGUI()

initializeDataAndGUI() - build the GUI, then repaint to build the initial display.

See Also:

appendReport(java.lang.String, boolean), buildGUI(), #setupAllBasePaths, showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color), #setupProcessCheckboxesStates, #setupClientDemoRLOdb, MJAReval.getListofRLOmenuNames(), MJAReval.getNbrAnalyses(), MJAReval.setupAllBasePaths(java.lang.String), PopupEditRscript.setupGenRcheckboxesStates()

buildGUI

private boolean buildGUI()

buildGUI() - build the graphical user interface

Returns:

true if suceed

See Also:

PopupEditRscript

rebuildScriptChoices

void rebuildScriptChoices()

rebuildScriptChoices() - rebuild the R script choices pull-down menu from the menuNames[] data. This should be called whenever the menuNames[] is changed.

drawReportText

private void drawReportText(java.awt.Graphics g)

drawReportText() - repaint report.

See Also:

saveTextReport(java.lang.String)

paint

public void paint(java.awt.Graphics g)

paint() - repaint full scrolled text area.

Overrides:

paint in class java.awt.Container

See Also:

drawReportText(java.awt.Graphics)

update

public void update(java.awt.Graphics g)

update() - update window

Overrides:

update in class java.awt.Container

appendReport

void appendReport(java.lang.String msg,
                  boolean appendToRptFlag)

appendReport() - add text to report text area

Parameters:

msg - to be printed

appendToRptFlag - to append msg to reportText as well

showGuiMsg

void showGuiMsg(java.lang.String msg,
                java.awt.Color fgColor,
                java.awt.Color bgColor)

showGuiMsg() - draw text in GUI message line

showData

void showData(java.lang.String data,
              java.awt.Color fgColor,
              java.awt.Color bgColor)

showData() - draw data in GUI data line

showCurrentRplots

private void showCurrentRplots()

showCurrentRplots() - show plots generated if any with last R eval. If there were not plots generated with the last Eval, then it is a no-op. Just say so in the msg area

See Also:

MJAReval#getCurrentRLO, MJAReval.getOutputDataFileNames(), MJAReval.getOutputDataTypes(), MJAReval.getReportBasePath(), MJAUtil#displayPDF, MJAUtil#displayURL, appendReport(java.lang.String, boolean), showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color)

saveTextReport

private void saveTextReport(java.lang.String textFileName)

saveTextReport() - Saves reportText to file

See Also:

MJAreport.writeTextToFile(java.lang.String, java.lang.String), showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color)

handleEvent

public boolean handleEvent(java.awt.Event evt)

handleEvent() - process special events

Overrides:

handleEvent in class java.awt.Component

actionPerformed

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

actionPerformed() - Handle Control panel button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

See Also:

MJAReval.getCurrentRLOid(), MJAReval.getInputRscriptFileName(), MJAReval.getRscriptBasePath(), MJAReval.runRscriptWithR(), MJAutil.cvtSpacesToUnderscores(java.lang.String), MJAreport#readTextToFile, PopupEditRscript.editRLO(int), PopupEditRscript.newRLO(), appendReport(java.lang.String, boolean), saveTextReport(java.lang.String), showCurrentRplots(), showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color)

itemStateChanged

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

itemStateChanged() - handle item state changed eventsms.

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

Parameters:

e - is ItemEvent

See Also:

MJAReval.clearProcessBit(int), MJAReval.getListofRLOmenuNames(), MJAReval.setProcessBit(int), MJAReval.setCurrentRLO(int), PopupEditRscript.resetEditRLObuttons(boolean), PopupEditRscript.changeWizardMenuMode(boolean), PopupEditRscript.setupGenRcheckboxesStates(), PopupEditRscript.setupProcessCheckboxesStates()

windowClosing

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

windowClosing() - close down the window.

Specified by:

windowClosing in interface java.awt.event.WindowListener

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

updateCurGene

public void updateCurGene(int mid)

updateCurGene() - update any data since current gene has changed. This is invoked from the PopupRegistry.
[NOTE] could do re-eval of the .R script if there is a gene dependence.

Parameters:

mid - is the MID (Master Gene ID) that is the new current gene.

updateFilter

public void updateFilter()

updateFilter() - update any dependent data since Filter has changed. This is invoked from the PopupRegistry.
[NOTE] could do re-eval of .R script if there is a Filter dependence.

updateSlider

public void updateSlider()

updateSlider() - update any dependent data sincea threshold slider has changed. This is invoked from the PopupRegistry.
[NOTE] could do re-eval of .R script if there is a slider dependence.

updateLabels

public void updateLabels()

updateLabels() - update any dependent data since global labels have changed. This is invoked from the PopupRegistry.
[NOTE] could do re-eval of the .R script if there is a data label (i.e. class names, X, Y, E, condition, OCL names) dependence.

close

public void close(int exitCode)

close() - exit with specified exit code.

genPrologue

java.lang.String genPrologue()

genPrologue() - generate prologue R script to read data commands. Generate the Rscript. It calls genClientReaderPrologue() to generate the code.

Returns:

Rscript if OK, else null. Then sMsg contains error message

See Also:

#genClientReaderPrologue

genEpilogue

java.lang.String genEpilogue()

genEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.

If tabDelimReportFile exists and an objAction is specified, then it will write out the following R object with write.table().

It calls genClientEpilogue() to generate the code.

Returns:

Rscript if OK, else null. Then sMsg contains error message

See Also:

#genClientEpilogue

extractUserRscript

public java.lang.String extractUserRscript(java.lang.String completeRscript)

extractUserRscript() - extract user R script from center of complete.

 R script. It is defined as the code between
   PROLOGUE_END
 and
   EPILOGUE_START

If no template code is there, just return what is there.

Parameters:

completeRscript - is complete R script with (prologue, userRscript,epilogue)

Returns:

user R script from complete R script

getUseGenRbit

int getUseGenRbit(int genRmethod)

getUseGenRbit() - lookup the use R_GENR_xxxx bit specified by method

Parameters:

genRmethod - to lookup

Returns:

useGenR bit

showMsg

abstract void showMsg(java.lang.String msg)

showMsg() - display message in client GUI

Parameters:

msg - message to display

readTextFromFile

abstract java.lang.String readTextFromFile(java.lang.String fileName,
                                           java.lang.String loadingMsg)

readTextFromFile() - read text from text file.

Parameters:

fileName - full path name of text file

loadingMsg - to display while loading, null if no message

Returns:

text if suceed else null

writeTextToFile

abstract boolean writeTextToFile(java.lang.String textFileName,
                                 java.lang.String textReport)

writeTextToFile() - save text string as text file.

Parameters:

textFileName - full path name of text file

textReport - text to save in file

Returns:

true if succeed.

popupAlertMsg

abstract void popupAlertMsg(java.lang.String title,
                            java.lang.String msg,
                            int nRows,
                            int nCols)

popupAlertMsg() - popup alert message in a scrollable text area. Press close to continue. If the auto popdown is set (Edit menu | Preferences submenut) then popdown the window after a timeout else it requires manually pressing the Close button.

Parameters:

title - is the optional title for the popup window

msg - is the message for the popup window

nRows - is the # of rows for the popup window, 20 if specify 0

nCols - is the # of columns for the popup window, 80 if specify 0

displayURL

abstract void displayURL(java.lang.String urlStr)

displayURL() - Display URL file in system Web browser, for use in stand-alone mode. This assumes that you have added the proper plugin to your browser for this data if required.

 Examples:
 displayURL("http://www.javaworld.com")
 displayURL("file://c:\\docs\\index.html")
 displayURL("file:///user/joe/index.html");
 displayURL("file:///user/joe/image.xml");
 displayURL("file:///user/joe/iimage.svg");

Under Unix, the system browser is hard-coded to be 'netscape'. Netscape must be in your PATH for this to work.
Under Windows, this will bring up the default browser under windows, usually either Netscape or Microsoft IE. The default browser is determined by the OS. adapted from : http://www.javaworld.com/javaworld/javatips/jw-javatip66_p.html NOTE: param url the file's url(the url must start with either "http://" or"file://").

Parameters:

urlStr - to display in popup browser

Returns:

false if error.

displayPDF

abstract void displayPDF(java.lang.String pdfFile)

displayPDF() - Display PDF file in adobe, for use in stand-alone. Under Unix, the system browser is hard-coded to be 'Acrobat'. Acrobat must be in your PATH for this to work. Under Windows, this will bring up Acrobat (if installed). adapted from : http://www.javaworld.com/javaworld/javatips/jw-javatip66_p.html

Parameters:

pdfFile - file to display in Adobe Acrobat

Returns:

false if error.

cvtSpacesToUnderscores

abstract java.lang.String cvtSpacesToUnderscores(java.lang.String str)

cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
: space( ) ; " { } < > = , ? \ / % * ! @ & | ' ` \t

Parameters:

str - to be converted

Returns:

converted string

rmvRtnChars

abstract java.lang.String rmvRtnChars(java.lang.String str)

rmvRtnChars() - remove return chars. Map '\r' or "\r\n" to '\n' chars.

Parameters:

String - str to process

Returns:

String with '\r' removed.

getListOfMenuStubNames

abstract java.lang.String[] getListOfMenuStubNames()

getListOfMenuStubNames() - get list of menu stub names

Returns:

list of Menu Stub Names