Class Rtest

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

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

public class Rtest

extends RtestBase

Class Rtest - evaluate R scripts with data supplied from MAExplorer via the MJA 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()

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

(package private) MaeJavaAPI	mja
(package private) MJAproperty	mjaProperty
(package private) MJAreport	mjaReport
(package private) MJAReval	mjaReval instance of Reval
(package private) MJAutil	mjaUtil
(package private) MJAReval	mr

Fields inherited from class RtestBase

appendTextFlag, BANNER, buttonPanel, clearReportButton, clientBrowserTitle, clientDatabase, clientName, clientPrefixName, clientPrjPath, closeButton, CONSOLE_FLAG, dataBkgrd, dataColor, dataTF, DATE, DBUG_APPEND_REPORT, DBUG_FLAG, dbugCheckbox, dbugFlag, DEF_MAX_ANALSYSES, deleteRLOButton, editRLOButton, EPILOGUE_END, EPILOGUE_START, evalButton, fileSep, guiReadyFlag, helpButton, helpMsg, inputPanel, inputTF, isWindowsFlag, javaHome, MIN_WINDOW_HEIGHT, MIN_WINDOW_WIDTH, msgBkgrd, msgColor, msgFont, msgTF, nAnalyses, nCols, nDemoAnalyses, NEVER, newRLOButton, nRows, osName, pe, preferredHeight, preferredWidth, PROLOGUE_END, PROLOGUE_START, reportText, reportTextArea, REVISION, rgd, rt, saveAllDemoRLOsButton, saveasButton, saveReportAsTextFileFlag, scriptChoice, showDemoRLOsCheckbox, showDemoRLOsFlag, showPlotsButton, showRLOButton, showRscriptButton, spaces, titleFont, topPanel, userDir, 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

Rtest(MaeJavaAPI mja)
Rtest() - Constructor

Method Summary

(package private) 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) void	displayPDF(java.lang.String pdfFile) displayPDF() - Display PDF file in adobe, for use in stand-alone.
(package private) void	displayURL(java.lang.String urlStr) displayURL() - Display URL file in system Web browser, for use in stand-alone mode.
(package private) java.lang.String[]	getListOfMenuStubNames() getListOfMenuStubNames() - get list of menu stub names
(package private) 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) java.lang.String	readTextFromFile(java.lang.String fileName, java.lang.String loadingMsg) readTextFromFile() - read text from text file.
(package private) java.lang.String	rmvRtnChars(java.lang.String str) rmvRtnChars() - remove return chars.
(package private) void	showMsg(java.lang.String msg) showMsg() - display message in client GUI
(package private) boolean	writeTextToFile(java.lang.String textFileName, java.lang.String textReport) writeTextToFile() - save text string as text file.

Methods inherited from class RtestBase

actionPerformed, appendReport, buildGUI, close, drawReportText, extractUserRscript, genEpilogue, genPrologue, getPreferredSize, getUseGenRbit, handleEvent, initializeDataAndGUI, initRtest, itemStateChanged, paint, rebuildScriptChoices, saveTextReport, showCurrentRplots, showData, showGuiMsg, update, updateCurGene, updateFilter, updateLabels, updateSlider, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

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

mja

MaeJavaAPI mja

mjaProperty

MJAproperty mjaProperty

mjaReport

MJAreport mjaReport

mjaUtil

MJAutil mjaUtil

mjaReval

MJAReval mjaReval

instance of Reval

mr

MJAReval mr

Constructor Detail

Rtest

public Rtest(MaeJavaAPI mja)

Rtest() - Constructor

See Also:

MJAproperty.getMaeCurProjectPath(), MJAproperty.getMaeBrowserTitle(), MJAproperty.getMaeDatabaseTitle(), MJAproperty.getMaeDbSubsetTitle(), RtestBase.initializeDataAndGUI(), RtestBase.showData(java.lang.String, java.awt.Color, java.awt.Color), RtestBase.showGuiMsg(java.lang.String, java.awt.Color, java.awt.Color)

Method Detail

showMsg

void showMsg(java.lang.String msg)

showMsg() - display message in client GUI

Overrides:

showMsg in class RtestBase

Parameters:

msg - message to display

readTextFromFile

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

readTextFromFile() - read text from text file.

Overrides:

readTextFromFile in class RtestBase

Parameters:

fileName - full path name of text file

loadingMsg - to display while loading, null if no message

Returns:

text if suceed else null

writeTextToFile

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

writeTextToFile() - save text string as text file.

Overrides:

writeTextToFile in class RtestBase

Parameters:

textFileName - full path name of text file

textReport - text to save in file

Returns:

true if succeed.

popupAlertMsg

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.

Overrides:

popupAlertMsg in class RtestBase

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

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://"). [TODO] Handle the Mac better.

Overrides:

displayURL in class RtestBase

Parameters:

url - to display in popup browser

Returns:

false if error.

displayPDF

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

Overrides:

displayPDF in class RtestBase

Parameters:

pdfFile - file to display in Adobe Acrobat

Returns:

false if error.

cvtSpacesToUnderscores

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

Overrides:

cvtSpacesToUnderscores in class RtestBase

Parameters:

str - to be converted

Returns:

converted string

rmvRtnChars

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

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

Overrides:

rmvRtnChars in class RtestBase

Parameters:

String - str to process

Returns:

String with '\r' removed.

getListOfMenuStubNames

java.lang.String[] getListOfMenuStubNames()

getListOfMenuStubNames() - get list of menu stub names

Overrides:

getListOfMenuStubNames in class RtestBase

Returns:

list of Menu Stub Names