: Class Reval

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Class Reval

java.lang.Object
  |
  +--RevalBase
        |
        +--Reval

public class Reval
extends RevalBase

Class Reval is used to evaluate R scripts with data supplied from MAExplorer 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 class (see addRLO() method for details on the RLO).

This is an instantiation of the RevalBase class where the Client is MAExplorer. When we refer to the Client in this class we mean MAExplorer. If the code were used with another cliet, then this instantiation must be (heavily) modified.

R is an extensible language and envirnment for statistical computing and graphics. R is Open Source (GNU public license) and is available for download at www.r-project.org.

NOTE: This class's methods contain a command interpreter, and support methods and data structures to enable you to execute R program .R scripts using client (MAExplorer) data. The Client-R library used by R is RLORlibr and for MAExplorer is called "MAERlibr".

It is intended to be used when writing MAEPlugins that need to access the R program to execute .R scripts with MAExplorer data. This may generate reports and plots (PDF, JPG, PNG, Postscript, SVG). Some of these reports may be used to pass the R results back into the MAExplorer state (Gene Sets, Filter gene sets, Normalization gene sets, Condition Lists, OCL, etc.).

This class evaluates R scripts with data supplied from the client 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 class. (see class variable definitions and addRLO() method for details on the RLO). The RLOs 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()

The client-R interface library "MAERlibr" (the instance of RLORlibr) is kept in the Client {installation directory}/lib/RLORlibr/ and contains the standard R library format subdirectories including R/ (separate files) and R-ex/ (single file). When an RLO script is evaluated, we copy the .R script with a "tmp-" prefix to the project Temp/ and prepend the following 2 lines: setwd("...Temp/") library(RLORlibr,lib.loc="{installation directory}/lib") which are required for the .R script to access the data generated by the client program and to access the library.

When executed, an R script is allowed to generate multiple output files that may include the following formats: text, tab-delimited text, PDF and JPG. 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.

 1. data is exported from the client to tab-delimited data input files 
   {Project}/Temp/. These will then be read by R when your script is 
   evaluated.
 2. 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 the client if required.
 3. The .R scripts are shared with all instances of the client
    and are kept in {Client installation}/R/
 4. The .rlo files are shared by all instances of the client and are kept
    in {Client installation}/RLO/ directory.
 5. 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 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: 2003/07/07 21:40:40 $ $Revision: 1.66 $
Author:: P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD
See Also:: MAExplorer Home, RevalBase, RLO

Field Summary

private boolean[] activeGeneList
          list [0:maxGenes-1] booleans for genes passing data Filter

(package private) static MAExplorer mae
          Global link

private static int maxGenes
          current active genes lists for generating export data

private static int[] midList
          current active genes lists for generating export data

(package private) static MaeJavaAPI mja
          MaeJavaAPI classes

(package private) MJAcluster mjaCluster


(package private) MJAcondition mjaCondition


(package private) MJAfilter mjaFilter


(package private) MJAgeneList mjaGeneList


(package private) MJAgeometry mjaGeometry


(package private) MJAplot mjaPlot


(package private) MJAproperty mjaProperty


(package private) MJAreport mjaReport


(package private) MJAsampleList mjaSampleList


(package private) MJAsampleList mjaSL


(package private) MJAstate mjaState


(package private) MJAutil mjaUtil


private static int nCondsInOCL
          current active genes lists for generating export data

private static int nFiltered
          current active genes lists for generating export data

private static int nGenes
          current active genes lists for generating export data

private boolean useBkgrdFlag
          status of (a.processBits & lookupProcessBitsDBvalue("Use-background-data"))!=0)

private boolean useF1F2dataFlag
          status of (a.processBits & lookupProcessBitsDBvalue("Use-F1-F2-channels"))!=0)

private boolean useFilterFlag
          status of (a.processBits & lookupProcessBitsDBvalue("Use-filter"))

private boolean useHPsetsFlag


private boolean useMeanHPeListDataFlag


private boolean useRawDataFlag
          status of (a.processBits & lookupProcessBitsDBvalue("Use-raw-data"))

private boolean verticallyStackedFlag
          status of (a.processBits & lookupProcessBitsDBvalue("Use-vert-stacked-data"))!=0)

Fields inherited from class RevalBase

analyses, clientName, clientRlibrBasePath, curAnalysis, dbugFlag, DEFAULT_R_OUTPUT_FILE, fileSeparator, fullRoutputFilePath, fullRscriptInputPath, fullRunRfilePath, inputRscriptFileName, isWindowsFlag, javaHome, MAX_ANALYSES, maxRLO, nAnalyses, NO_R_INSTALLED, nOfileTypes, nProcessBits, nR2ClientActions, nRdataTypes, osName, parseDelimChar, parseName, parseValue, promptDir, promptExt, promptFile, quoteRunPathFlag, r2ClientActionMenu, r2ClientActionName, r2ClientActionVal, r2ClientPrefix, RbasePath, RbinBasePath, rDataTypeMenu, rDataTypeName, rDataTypeVal, REB_DBUG, reportBasePath, reportFileName, rlo, RLO_VERSION, RLObasePath, rloReportLoggingFile, RLORlibr, rOfileTypeMenu, rOfileTypeName, rOfileTypeStdOut, rOfileTypeVal, rPB_useVanillaBit, rProcessBitMenu, rProcessBitName, rProcessBitVal, rReport, RscriptBasePath, rStdout, RuserBasePath, specificCreateInputFileProblem, SPlusBasePath, SPlusBinBasePath, startupRscriptFileName, tempBasePath, timeStampReportDir, userDir, useRLOloggingFlag, useSPlusFlag

Constructor Summary

(package private) Reval(MaeJavaAPI mja, int maxAnalyses)
          Reval() - constructor for initial database allocation

Method Summary

(package private) boolean copyFile(java.lang.String srcName, java.lang.String dstName, java.lang.String optUpdateMsg, int optEstInputFileLth)
          copyFile() - binary copy of one file or URL toa local file

(package private) boolean createInputDataFiles(java.lang.String inputFilesBasePath)
          createInputDataFiles() - create any input data files required for current analysis.

private SimpleTable cvtFloatArrayData2Table(RLO a, SimpleTable st, float[][] xData, float[][] yData, float[][] xBkgrd, float[][] yBkgrd, int nX, int nY, int nFiltered, boolean[] activeGeneList, java.lang.String[] fieldNames, java.lang.String[] classNames)
          cvtFloatArrayData2Table() - convert xData,yData nX,nY expression data for nGenes active genes to SimpleTable.

private SimpleTable cvtStringArrayData2Table(RLO a, SimpleTable st, java.lang.String[][] sData, int nRows, int nCols, java.lang.String[] fieldNames)
          cvtStringArrayData2Table() - convert sData, nS, nRows to SimpleTable.

(package private) boolean deleteLocalFile(java.lang.String fileName)
          deleteLocalFile() - delete local file.

private boolean genCurAnnotationDataFile(RLO a, SimpleTable st)
          genCurAnnotationDataFile() - generate exported input data file for current gene annotation data.

private boolean genCurHPdataFile(RLO a, SimpleTable st)
          genCurHPdataFile() - generate exported input data file for current HP.

private boolean genCurHPsetDataFile(RLO a, SimpleTable st, int inputType)
          genCurHPsetDataFile() - generate exported input data file for current HP set data (including: HP-X set, HP-Y set, HP-E list, current condition list).

private boolean genCurHPXYdataFile(RLO a, SimpleTable st, boolean useHPsetsFlag)
          genCurHPXYdataFile() - generate exported input data file for current HP-X and HP-Y or mean (HP-X set and mean HP-Y set).

private boolean genCurHPXYsetsDataFile(RLO a, SimpleTable st)
          genCurHPXYsetsDataFile() - generate exported input data file for current HP-X and HP-Y sets data.

private boolean genCurOCLdataFile(RLO a, SimpleTable st)
          genCurOCLdataFile() - generate exported input data file for current Ordered Condition List data.

private boolean genCurStateThresholdsFile(RLO a, SimpleTable st)
          genCurStateThresholdsFile() - generate exported input data file for current state thresholds data.

private boolean genCurStateValuesFile(RLO a, SimpleTable st)
          genCurStateValuesFile() - generate exported input data file for current state flags and names values data.

(package private) java.lang.String popupDialog(java.lang.String promptMsg, java.lang.String defaultAnswer)
          popupDialog() prompt with message and return response.

(package private) java.lang.String readTextFromFile(java.lang.String textFileName, java.lang.String loadingMsg)
          readTextFromFile() - read text from text file.

(package private) boolean setRoutput2ClientObjects()
          setRoutput2ClientObjects() - copy data for any R2Mae Action entries in the RLO.

void setupNameTypeDB()
          setupNameTypeDB() - setup the RLO (name,type) input, output, action, processBits database

(package private) void setWaitCursor(boolean flag)
          setWaitCursor() - turn wait cursor on and off

(package private) void showMsg(java.lang.String msg)
          showMsg() - display message in client GUI

(package private) java.lang.String toString(int rloID, java.lang.String optGenRbitsStr)
          toString() - create string representing the R LayOut (RLO) of the instance.

private boolean writeRdataTableFile(SimpleTable st, java.lang.String fileName)
          writeRdataTableFile() - write the MAE table data as R input file

(package private) boolean writeTextToFile(java.lang.String textFileName, java.lang.String textReport)
          writeTextToFile() - save text string as text file.

Methods inherited from class RevalBase

accept, addRLO, clearRLOdb, copyTempOutputFilesToReportDir, createRunRscript, createTempRscript, cvRLO2string, cvs2i, cvtBackslash2Fwdslash, cvtEnvPaths2Properties, cvtInputType2Str, cvtOutType2Str, cvtR2ClientType2Str, execRscript, getAllProcessBits, getCurDateStr, getCurrentRLO, getInputDataFileNames, getInputDataTypes, getListofRLOmenuNames, getListofRLOscriptNames, getNbrAnalyses, getNextStrNameValFromLine, getOfileTypeDBmenus, getOfileTypeDBnames, getOfileTypeDBtypes, getOutputDataFileNames, getOutputDataTypes, getProcessBitsDBmenus, getProcessBitsDBnames, getProcessBitsDBvalues, getR2ClientActionDBmenus, getR2ClientActionDBnames, getR2ClientActionDBtypes, getRdataTypeDBmenus, getRdataTypeDBnames, getRdataTypeDBtypes, getRLOidByRscriptName, getSetR2ClientFileNames, getSetR2ClientObjNames, getSetR2ClientObjTypes, getStrValFromLine, lookupOfileTypeDBmenu, lookupOfileTypeDBmenu, lookupOfileTypeDBvalue, lookupProcessBitsDBmenu, lookupProcessBitsDBvalue, lookupR2ClientActionDBMenu, lookupR2ClientActionDBMenu, lookupR2ClientActionDBtype, lookupR2ClientActionDBvalue, lookupRdataTypeDBmenu, lookupRdataTypeDBmenu, lookupRdataTypeDBvalue, newRLO, promptFileName, readPermanentRLOdatabase, readRLOfile, rmvRLO, rmvRtnChars, runRscriptWithR, setAllProcessBits, setCurrentRLO, setDbugFlag, setInputFilesData, setOfileTypeDB, setOutputFilesData, setProcessBitsDB, setR2ClientActionDB, setR2ClientFilesData, setRdataTypeDB, setRLO, setRLOreportLoggingFlag, setupAllBasePaths, setupRbinPath, simpleLookupRprogramPath, simpleLookupSPLUSprogramPath, sortArray, toString, writePermanentRLOdatabase, writeRLOfile

Methods inherited from class java.lang.Object

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

Field Detail

mae

static MAExplorer mae

Global link

mja

static MaeJavaAPI mja

MaeJavaAPI classes

mjaCluster

MJAcluster mjaCluster

mjaCondition

MJAcondition mjaCondition

mjaFilter

MJAfilter mjaFilter

mjaGeneList

MJAgeneList mjaGeneList

mjaGeometry

MJAgeometry mjaGeometry

mjaPlot

MJAplot mjaPlot

mjaProperty

MJAproperty mjaProperty

mjaReport

MJAreport mjaReport

mjaSampleList

MJAsampleList mjaSampleList

mjaSL

MJAsampleList mjaSL

mjaState

MJAstate mjaState

mjaUtil

MJAutil mjaUtil

useFilterFlag

private boolean useFilterFlag

status of (a.processBits & lookupProcessBitsDBvalue("Use-filter"))

useRawDataFlag

private boolean useRawDataFlag

status of (a.processBits & lookupProcessBitsDBvalue("Use-raw-data"))

verticallyStackedFlag

private boolean verticallyStackedFlag

status of (a.processBits & lookupProcessBitsDBvalue("Use-vert-stacked-data"))!=0)

useBkgrdFlag

private boolean useBkgrdFlag

status of (a.processBits & lookupProcessBitsDBvalue("Use-background-data"))!=0)

useF1F2dataFlag

private boolean useF1F2dataFlag

status of (a.processBits & lookupProcessBitsDBvalue("Use-F1-F2-channels"))!=0)

useHPsetsFlag

private boolean useHPsetsFlag

useMeanHPeListDataFlag

private boolean useMeanHPeListDataFlag

activeGeneList

private boolean[] activeGeneList

list [0:maxGenes-1] booleans for genes passing data Filter