/** File: SearchGUI.java */
 
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.Hashtable;
import java.util.StringTokenizer;

import javax.swing.*;
import javax.swing.event.*;

import O2PlibSS.gui.*;


/**
 * Class SearchGUI is used to create a popup GUI to run the converter.
 * <PRE>
 * <B>List of Methods</B><BR>
 * ===================
 * SearchGUI() - Constructor
 * initGUI() - create the popup GUI
 * addMenuTree() - create pull down menus in menu bar for the GUI
 * clearGuiProcessingState() - clear the GUI state
 * processGuiStateData() - Process data specified by the GUI state
 * resetGuiState() - reset the GUI state so nothing is specified.
 * setCancelFlag() - set the Cancel flag value
 * getCancelFlag() - get the Cancel flag value
 * setDemoParameters() - set the Search Terms list for demo state.
 * setUserTermListFromFile() - set  user search term-list state from a file.
 * setGUItoSGstate() - set GUI to instance of SGstate.
 * getGUItoSGstate() - get additional SGstate variables from GUI.
 * setEnableSearchParamsButtonsAndMenus() - set Search Params GUI &  state
 * setEnableCancelButtonsAndMenus() - when are able to do processing state
 * setEnableViewingButtonsAndMenus() - enable view processed HTML files state
 * positionReportWindow() - position report window on the screen
 * setShow() - set the show/hide popup status
 * updateReportStatusLine() - clear text in popup window
 * clearText() - clear text in popup window
 * getDBgeneList() - get printable text list of genes in the database.
 * getEGsampleList() - get printable text list of EG samples in the database.
 * matchEGsampleBySearchTerms() - test sGSPID if match searchTerms list.
 * getReportText() - get the text from the Report popup window
 * setReportText() - update text in popup window
 * setGUItitle() - update title in popup window
 * setSaveAsFile() - set SaveAs file default file name
 * close() - close this popup and reset flags if needed
 * testAndSetProjDir() - test and set project directory cvt.userDir.
 * actionPerformed() - Handle menu actions and button clicks
 * resetInitialGuiProcessingState() - reset search terms & samples GUI state
 * quit() - closing down the window, get rid of the frame.
 * updateSearchGUIjarFile() - update SearchGui.jar from URL_HOME web server.
 * itemStateChanged() - handle item state changed events
 * viewHTMLfile() - popup browser on guiActiveHTMLfile file.
 * windowClosing() - closing down the window, get rid of the frame.
 * 
 * Class SGstate - holds SearchGui GUI data that can be read/write by methods
 * -------------
 * SGstate() - constructor
 * copyStateFromCvt() - copy the partial state from cvt Globals
 * copySGstateInstance() - copy from SGstate instance values to this.
 * cvtSGstateToStr() - convert SGstate vars. to .sgs state string to write to file.
 * copyGlobalsToSGstate() - copy Globals instance in SGstate variables.
 * readSGstateFile() - read the SearchGUI State file stateFile
 * parseHTtoSGstate() - parse .sgs state hashtable to SGstate variables.
 * writeSGstate() - write SearchGUI state to .sgs SGstate file.
 * readNameValuesHashTableFromFile() - read hashtable tab-delim  name-value pairs
 * setStateHashtableForGetValue() - set working hash table for next getStateValue calls
 * getStateStr() - generate  tab-delim SGstate string for writing .sgs state.
 * getStateValue() - get PARAM and use default if not found. 
 *</PRE>
 *<P> 
 * This code is available at the HTMLtools project on SourceForge at
 * <A HREF="http://htmltools.sourceforge.net/">http://htmltools.sourceforge.net/</A>
 * under the "Common Public License Version 1.0" 
 * <A HREF="http://www.opensource.org/licenses/cpl1.0.php">
 * http://www.opensource.org/licenses/cpl1.0.php</A>.<P></P>
 * <P>
 * It was derived and refactored from the open source
 * MAExplorer (http://maexplorer.sourceforge.net/), and
 * Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules.
 * <P>
 * $Date: 2009/12/16 11:45:56 $ $Revision: 1.42 $
 * <BR> 
 * Copyright 2008, 2009 by Peter Lemkin 
 * E-Mail: lemkin@users.sourceforge.net  
 * <A HREF="http://lemkingroup.com/">http://lemkingroup.com/</A>
 * <BR>
 */

public class SearchGUI extends JFrame
       implements ItemListener, ActionListener, WindowListener 
{ /* SearchGUI */ 
  
  public final static long
    serialVersionUID= 0;

  /** Home URL for server */
  public final static String
    URL_HOME= "http://jak-stat.nih.gov/"; 
  
  /** Home URL for DB on server */
  public final static String
    URL_HOME_DB= "***NOT AVAILABLE***"; 

  /** URL for SearchGui.jar if update from the server */
  public final static String
    //URL_JAR_FILE= URL_HOME+"Prospector/jar/SearchGui.jar";
    URL_JAR_FILE= "file:///C:/tmp/SearchGui.jar";  /* [DEBUG] */
    
  /* Note all global variables are in Globals.java except the help 
   * messages which are in HelpMsgs.java.
   */
  public HTMLtools 
    cvt;
  
  /* Primary GUI for use with InvokeLater */
  public SearchGUI
    sGui;
  
  /** SearchGUI state variables that can be saved/imported from .sgs files. */
  public SGstate 
    sgs= null;

  /** string for title of frame */
  private String
    title;  
  /** The name of the program */
  private String
    programName; 
  /** version number of the program */
  private String
    version; 

  
  /* --------- SearchGUI components ----- */
  
  /** menu bar for the frame */
  private MenuBar
    mbar;

  /** "File" pull down Menu list */
  private Menu 
    fileMenu;
  /** "View" pull down Menu list */
  private Menu 
    viewMenu;
  /** "List" pull down Menu list */
  private Menu 
    listMenu;
  /** "Help" pull down Menu list */
  private Menu 
    helpMenu;
  
  /** Menu support functions using Hashtables to track what is active */ 
  private MenuSupport
    ms;

  /** Menu checkbox item for Verbose reporting */
  private CheckboxMenuItem 
    verboseMCB= null;

  /** Menu checkbox item for "Report Fold Change of 2 sample subsets" */
  private CheckboxMenuItem
    foldChangeMCB= null;
  
  /** Menu checkbox item for 
   * "Only keep genes/probes with |fold-change| >= threshold"
   * This pops up a dialog to enter the threshold value between 0.0 and 
   * some large number and saves it in sgs.foldChangeThr. The associated flag
   * is sgs.foldChangeThrFlag. */
  private CheckboxMenuItem
    foldChangeThrMCB= null;
  
  /** MenuItem "Restore previously saved search .sgs parameters from file" */
  private MenuItem 
    lastRestoreSGstateMI= null; 
  
  /** MenuItem "Restore previously saved search .sgs parameters from file" */
  private MenuItem 
    restoreSGstateMI= null; 

  /** MenuItem "SaveAs current search .sgs parameters to file" */
  private MenuItem 
    saveSGstateMI= null;

  /** MenuItem "Assign EG samples to Class A" */
  private MenuItem 
    classAMI= null; 
  
  /** MenuItem "Assign EG samples to Class A" */
  private MenuItem 
    classBMI= null; 
  
  /** Menu checkbox item for "Show data heat-map in View HTML Results" */
  private CheckboxMenuItem 
    showDataHeatmapFlipTableMCB= null; 
    
  /* showStatusFlag for setVisible(): show (true), hide (false) 
   * set by calling program... */
  public boolean 
    showStatusFlag;   
  
  /** font size */
  private int
    textAreaFontSize= 12;
  /** Text area font family */
  private String   
    textFontFamily= "Helvetica";
  
  /** Optional Big popup text viewer for Report-Log */
  public PopupTextViewer
    bptv= null;
  
  /** Text area GUI for main Report-Log. Data is also kept int textReport and
   * can be saved in reportFile. */             
  private JTextArea 
    reportTextarea;   
  
  /** Text area GUI for entering list of search terms */             
  private JTextArea 
    searchTermTextArea;
  
  /* List of Sample groups  for search */
  private JList
    samplesList;

  /** button for "Process" button - may enable/disable button */
  public JButton
    processButton;
  /** button for "Cancel" button - may enable/disable button  */
  public JButton
    cancelButton;
  /** button for "ViewHTML" button - may enable/disable button  */
  public JButton
    viewHTMLButton;
  /** button for "Reset" converter button */
  private JButton
    resetButton;
  
  /** Status line label updated with UtilCM.updateReportStatusLine() */
  private JLabel
    statusLineLabel; 

  /* Optional Expression Group filter by GSP ID substring */
  private JTextField 
    filterRowTextField;
  
  /** SearchResults filename Prefix text field */
  private JTextField 
    searchResultsFilenamePrefixTF;

  /** Exact match radio button for search-term specification,
   * button grouped with matchSearchStrTermRB. 
   * Sets sgs.flipTableUseExactMatchFlag.
   */
  private JRadioButton 
    matchGeneTermRB= null;
  
  /** Substring match radio button for search-term specification,
   * button grouped with matchGeneTermRB. 
   * Clears sgs.flipTableUseExactMatchFlag.
   */
  private JRadioButton 
    matchSubStrTermRB= null; 

  /** AND match radio button for EG sample list specification,
   * button grouped with orEGnamesRB. 
   * Sets sgs.evalSearchANDbooleanFlag.
   */
  private JRadioButton 
    andEGnamesRB= null; 

  /** OR match radio button for EG sample list specification,
   * button grouped with andEGnamesRB.  
   * Clears sgs.evalSearchANDbooleanFlag.
   */
  private JRadioButton 
    orEGnamesRB= null;
  
  
  /* ------ Report-Log state ----- */
  
  /** Copy of text in Report-Log reportTextarea */
  private String
    textReport= "";

  /** Default SAVE AS .txt file for Report-Log textReport data used in
   * reportTextarea. */
  private String  
    reportFile= null;
  
  
  /* ------ Default -search 'Term' switches and GUI search term state. ----- 
   * ------ Read from the ParamsSearchDefault.map file.                -----
   */ 

  /** Switch supplied search Terms filter prompt for searchTermTextArea
   * Set by -searchTermsFilterPrompt:{...}.
   */
  private String 
    searchTermsFilterPrompt= null;
  

  /* List of search term lists from searchTermTextArea GUI
   * searchTermFilter[0:nSearchTermNames-1][]. The list is created
   * from the searchTermTextArea GUI associated 
   * sgs.searchTermFilterStr String;
   */
  private String
    searchTermFilter[][]= null;
  
  /* List of search term names. Set by 
   * '-searchTermNames:{t1,t2,...,tn}'.
   */
  private String
    searchTermNames[]= null;      
  
  /* Size of list of search term lists from searchTermTextArea GUI
   * searchTermFilter[0:nSearchTermNames-1][].
   * Set by '-searchTermNames:{t1,t2,...,tn}'
   */
  private int
    nSearchTermNames= 0;
      
  
  /* -------------- Database Table and Index Map files ------ */

  /** Name of database Table file that we will use to verify search terms.
   * We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
   */
  public String 
    flipTableDataFile= null;
  
  /** Name of Index Map file that we will use to verify search terms.
   * We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
   * This is used to read the ftIM FileTable.
   */
  public String 
    flipTableIndexMapFile= null;

  /** Index Map FileTable that we will use to verify search terms.
   * We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
   */
  public FileTable 
    ftIM= null;

  /** Header-only Data FileTable that we will use to get the list of 
   * EG Samples.We get this from
   *  '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
   */
  public FileTable 
    ftData= null;
  
  /** This is the list of ftData Data Table columns starting with "EG" 
   * and is the list of EG GSP IDs in the database.
   */
  private String dbGSPIDlist[]= null;
  
  /** The Index Map file into ftIM has been read successfully
   * by the ProcessLoadIndexMapData Thread. */
  public volatile boolean
    indexMapReadyFlag= false;
  
  /** There has been a problem reading the Index Map file into ftIM 
   * by the ProcessLoadIndexMapData Thread. */
  public volatile boolean
    indexMapProblemFlag= false;

  /* --------- User supplied GUI samples list ------- */

  /** The name of the sample list Table file. It is a 2 column array where 
   * used for the sample Choice GUI where the choice Object value is [][0], 
   * and the viewable choice name is [][1].
   * Set by '-searchsearchSampleChoiceFile:{sample choice Table file}'.
   */
  private String
    searchSampleChoiceFile= null;
 
  /** The sample list is a 2 column array where 
   * the Object value is [][0], and the viewable choice
   * name is [][1].
   */
  private String
    sampleChoiceData[][]= null;
  
  
  /* ----- User supplied GUI labels and prompts from switches ----- */

  /** Switch supplied search sample groups filter name for 
   * sampleExprGroupsTextArea. Set by -searchRowFilterName:{...}.
   */
  private String
    searchRowFilterName= null;
  
  /** Switch supplied search samples group filter prompt for 
   * sampleExprGroupsTextArea. Set by -searchRowFilterPrompt:{...}.
   */
  private String
    searchRowFilterPrompt= null;
    

  /* ---------- Process Data state ----------- */ 
  
  /** Thread for converter processing */
  public ProcessDataSearch 
    pds= null;
  
  /** "Processing" data in the GUI */
  public volatile boolean
    processFlag= false;
  /** "Process was ok" if true. Set to false if any problems. */
  public volatile boolean
    processedOKflag= false;
  /** "Done" processing data in the GUI */
  public volatile boolean
    doneFlag= false; 
  /** "Close" the GUI */
  public volatile boolean
    closeGuiFlag= false; 
  /** "Cancel" the processing in the GUI */
  public volatile boolean
    cancelFlag= false;
  
  /** GUI FSM state */
  public volatile String 
    guiFSMstate= "reset"; 

  /** The subtitle for generated Web page by mapping to the preface
   * "$$DATA_SOURCE_SUBTITLE$$" */
  private String
    dataSource= "";
  
  /* ---- These are the default parameters used in the param .map 
   * script generator ------
   */
 
  /** Param .map default input Dir */
  public volatile String
    inputSearchDir= null;
  /** Param .map default output Dir */
  public volatile String
    outputSearchDir= null;
  /** Param .map default table Dir */
  public volatile String
    tableSearchDir= null;
  
  /** GUI Converter params map file */
  public volatile String
    guiParamsMapFile= null;
  /** GUI Converter params map default file path */
  public volatile String
    guiParamsMapDefaultPath= null;
  
  /* GUI Converter active HTML file that was selected for viewing. */
  public volatile String
    guiActiveHTMLfile= null;
  
  /* GUI Converter active TXT excel compatible file generated. */
  public volatile String
    guiActiveTXTfile= null;
  
  /* -----------   ----------- */

  /** Command line string created to use when running the converter
   * used by ProcessDataSearch */
  public volatile String
    sGuiArgV= null;
  
  /** Command line string array created to use when running the 
   * converter used by ProcessDataSearch */
  public volatile String
    guiArgV[]= null;
  
      
  /**
   * SearchGUI() - Constructor
   * @param cvt is an instance of the CvtTabDelim2HTML class
   * @param programName name of the program
   * @param version - of program
   * @param textReport is initial text string for buffer. 
   * @param title of the window
   * @param String reportFile is default SAVE AS .txt file. Default
   *        "log.txt"
   * @param guiParamsMapDefaultFile is default params. map file if not null,
   *        else it uses "paramsSearchDefault.map".
   */
  public SearchGUI(HTMLtools cvt, String programName, 
                   String version, String textReport, String title, 
                   String reportFile, String paramsMapDefaultFile)
  { /* SearchGUI */
    super("SearchGUI");   

    /* [1] Setup copies of args */
    this.sGui= this;         /* may need for InvokeLater method calls */

    this.cvt= cvt;
    this.programName= programName;
    this.version= version;
    this.title= title;
    this.textReport= ((textReport==null)
                        ? "" : textReport);
    this.reportFile= (reportFile!=null)
                        ? reportFile : programName+"-Report.txt";
    this.showStatusFlag= true;   
    
    /* [1.1] Set up SearchGUI state instance */    
    sgs= new SGstate(this);   
    
    /* [1.1.1] Set up SearchGUI state instance */   
    if(!sgs.copyStateFromCvt(cvt))
      UtilCM.logMsg("DRYROT - problem creating SGstate instance.\n");
    
    /* [1.2] Setup defaults used when generate Params .map script */
    sgs.showDataHeatmapFlipTableFlag= true;
                                        /* Force -showDataHeatmapFlipTables */
   
    closeGuiFlag= false;          /* Only set true by "Close" menu or button */
  
    inputSearchDir= "data.search";
    outputSearchDir= "data.search";
    tableSearchDir= "data.Table";
    guiParamsMapFile= "paramSearchFlip.map"; 
                                        /* use same name & create it each time */
    
    /* [1.3] This will contain the additional search parameters parsed by 
     * getOtherSearchParams().
     */
    if(paramsMapDefaultFile!=null)
      guiParamsMapDefaultPath= inputSearchDir + cvt.fileSep +
                               paramsMapDefaultFile;
    else
      guiParamsMapDefaultPath= inputSearchDir + cvt.fileSep +
                               "paramsSearchDefault.map";  /* default */   
    if(!getOtherSearchParams(guiParamsMapDefaultPath))
    {
      closeGuiFlag= false;
      return;
    }

    /* [2] Reset the GUI state flags to initial "Search Params" data state. */
    clearGuiProcessingState();  /* clear the GUI state */     

    /* [3] Create and startup the popup GUI */
    initGUI();
  } /* SearchGUI */   
  

  /**
   * getOtherSearchParams() - get search information for GUI for prompts and menus
   * These terms are found in the default search params .map file. The following
   * must be defined:
   *<PRE>
   * E.g.,
   *   -flipTableByIndexMap:{dataSet.txt,dataSet.idx}
   *   -searchTermNames:"Gene,Feature ID"
   *   -searchRowFilterName:"Sample Experiment Groups"
   *   -searchSampleChoiceFile:sampleExperimentGroupsChoices.txt
   *   -searchTermsDemoData:"Stat5a Stat5b 1438470_at 1441476_at 1446085_at"
   *   -searchUserTermList:"LitRefGeneList.txt,Gene,Literature Review"
   *   -searchTermsFilterPrompt:"'Gene' and/or 'Probe' names. E.g., Stat5a, Stat5b, 1449109_at, etc."
   *   -searchRowFilterPrompt:"'Sample Experiment Groups'. E.g., select one or more Experiment Groups"
   *</PRE>
   * @return true if succeed, false if do not find all of the search terms
   */
  public boolean getOtherSearchParams(String paramsSearchDefaultPath)
  { /* getOtherSearchParams */ 
    /* [1] Read the default parameter file to get additional args */
    String psdf= cvt.fio.readFileAsString(paramsSearchDefaultPath);
    if(psdf==null)
    {
      UtilCM.logMsg("Problem with missing search parameters .map default file '"+
                    paramsSearchDefaultPath+"'\n");
      return(false);
    }
    
    /* [2] Convert parameter string to parameter list for parsing */
    String
      sParamsM= UtilCM.mapCRLF2space(psdf),
      argList[]= UtilCM.cvs2Array(sParamsM," ");
    
    for(int i=0;i<argList.length;i++)
    { /* look for lines that start with "-search" */
      String 
        sTmp,
        sLine= argList[i];
      
      if(!sLine.startsWith("-search") && !sLine.startsWith("-flipTable"))
        continue;
      
      int idxColon= sLine.indexOf(":");
      if(idxColon==-1)
      {
        UtilCM.logMsg("Problem with missing data for -search arg '"+sLine+
                      "' in parameters .map default file '"+
                      paramsSearchDefaultPath+"'\n");
        return(false);
      }
      
      /* Get the arg list */
      String sArg= sLine.substring(idxColon + 1);

      if(sLine.startsWith("-flipTable"))
      { /* "-flipTableByIndexMap:{dataSet.txt,dataSet.idx}" */
        String sList[]= UtilCM.cvs2Array(sArg,",");
        flipTableDataFile= sList[0];
        flipTableIndexMapFile= sList[1];
        int srbfLth= flipTableIndexMapFile.length()-".txt".length();
        sgs.searchResultsBaseFile= flipTableIndexMapFile.substring(0,srbfLth);
        
        /* Get the header-only Data FileTable that we will use to get the 
         * list of EG Samples. 
         */
        ftData= new FileTable("Data-table-header-only");
        String 
          dataFilePath= inputSearchDir + cvt.fileSep + flipTableDataFile;
        if(!ftData.readAndParseTableFields(dataFilePath))
        { /* Can't find Table file */
          UtilCM.logMsg("Problem reading Data Table fields '" + 
                        dataFilePath + "'\n" + "  "+ 
                        ftData.errMsgLog + "\n");
          return (false);
        }
        else
        { /* make list of EG GSP IDs */
          dbGSPIDlist= new String[ftData.tCols];
          int 
            k= 0;
          for(int c=0;c<ftData.tCols;c++)
          { /* build list of only EG prefaced strings */
            String colStr= ftData.tFields[c];
            if(ftData.tFields[c].startsWith("EG"))
              dbGSPIDlist[k++]= ftData.tFields[c];
          }
          dbGSPIDlist= UtilCM.rightSizeArray(dbGSPIDlist, k, null);
        }
        
        /* Get Index Map FileTable that we will use to verify search terms.
         * We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
         */
        ftIM= new FileTable("Index-Map");
        String indexMapPath= inputSearchDir + cvt.fileSep + 
                             flipTableIndexMapFile;        
        ProcessLoadIndexMapData
          plimd= new ProcessLoadIndexMapData(sGui,indexMapPath, ftIM);
        plimd.start();
      } /* "-flipTableByIndexMap:{dataSet.txt,dataSet.idx}" */
      
      else if(sLine.startsWith("-searchTermNames"))
      { /* "-searchTermNames" */
        searchTermNames= UtilCM.cvs2Array(sArg,",");
        nSearchTermNames= searchTermNames.length;
      }
      
      else if(sLine.startsWith("-searchUserTermList"))
      { /* "-searchUserTermList:{userListTable,colName, title string}" */
        String sTmpList[]= UtilCM.cvs2Array(sArg,",");
        sgs.searchUserTermListFile= sTmpList[0];
        if(sTmpList.length==1)
          sgs.searchUserTermListColName= null;
        else
          sgs.searchUserTermListColName= sTmpList[1];
        sgs.searchUserTermListTitle= (sTmpList.length>2)
                                         ? sTmpList[2]
                                         : "user list";
      }

      else if(sLine.startsWith("-searchTermsDemoData"))
      { /* "-searchTermsDemoData" */
        sgs.searchTermsDemoData= sArg;
      }
            
      else if(sLine.startsWith("-searchRowFilterName"))
      { /* "-searchRowFilterName" */
        searchRowFilterName= sArg;
      }
        
      else if(sLine.startsWith("-searchSampleChoice"))
      { /* "-searchSampleChoiceFile:{table of data}" */
        searchSampleChoiceFile= inputSearchDir+cvt.fileSep+sArg;
        /* Read the data from the Table */
        FileTable ft= new FileTable("Sample Choice Database");
        ft.setHasTableHeaderFlag(cvt.hasTableHeaderRowFlag);
        ft.setRmvTrailingBlankLinesFlag(true);
        ft.setRmvTrailingEmptyColumnsFlag(true);
        if(!ft.readAndParseTable(searchSampleChoiceFile))
        { /* failed*/
          UtilCM.logMsg("Problem reading -searchSampleChoiceFile file '" +
                        searchSampleChoiceFile+"'\n"+ ft.errMsgLog+"\n");
          return(false);
        }
        else if(ft.tRows==0 || ft.tCols!=2)          
        { /* failed - bad table */
          UtilCM.logMsg("Problem -searchSampleChoiceFile file '" +
                        searchSampleChoiceFile+"' - #rows="+ft.tRows+
                        " or #columns="+ft.tCols+
                        " in Table NEQ 2 required.\n");
          return(false);
        }
        sampleChoiceData= ft.tData;  /* Save the data */
      } /* "-searchSampleChoiceFile:{table of data}" */
      
      else if(sLine.startsWith("-searchTermsFilterPrompt"))
      { /* "-searchTermsFilterPrompt" */
        searchTermsFilterPrompt= sArg; 
      }   
      
      else if(sLine.startsWith("-searchRowFilterPrompt"))
      { /* "-searchRowFilterPrompt" */
        searchRowFilterPrompt= sArg; 
      }  
      
      else
      {
        UtilCM.logMsg("\nProblem with undefined -search parameters arg '"+
                      sLine+"'\n");
        return(false);
      }
    } /* look for lines that start with "-search" */
    
    /* Make sure all args are defined */
    if(flipTableDataFile==null || flipTableIndexMapFile==null ||
       searchTermNames==null || searchRowFilterName==null || 
       searchSampleChoiceFile==null || searchTermsFilterPrompt==null ||
       searchRowFilterPrompt==null)
    {
      UtilCM.logMsg("\nProblem with undefined -search switches in "+
                    "parameters .map default file '"+
                    paramsSearchDefaultPath+"'\n");
      return(false);
    }

    return(true);
  } /* getOtherSearchParams */
  
  
  /**
   * initGUI() - create the popup GUI
   * @return true if succeed
   */
  @SuppressWarnings("deprecation")
  public boolean initGUI()
  { /* initGUI */    
    /* [1] Setup the GUI */
    mbar= new MenuBar();
    this.setMenuBar(mbar);       /* activate menu bar even if menus 
                                  * are not active*/    
    Font mbarFont= new Font("Helvetica", Font.PLAIN, 12);
    mbar.setFont(mbarFont);      /* make it a larger font */  
    
    /* [2] Create pull down menus in menu bar */
    addMenuTree(this, mbar);
    
    JPanel middlePanel= new JPanel();
    middlePanel.setLayout(new GridLayout(6,1));
    this.add("Center", middlePanel);

    //textFontFamily= "Helvetica";
    textFontFamily= "Courier";
    textAreaFontSize= 12;  
    int nCols= 115;     
        
    /* [2.1] Add Search term GUI objects including text area for 
     * entering a list of search terms, etc. 
     */ 
    
    /* [2.1.1] Add Panel to put the searchTermsLabel and panel containing the 
     * radio buttons matchGeneTermRB and matchSubStrTermRB.
     */
    JPanel EPtermLblPanel= new JPanel();
    EPtermLblPanel.setLayout(new GridLayout(3,1));
    
    /* [2.1.1.1] Add Top step label for "1." */
    String searchTermsDescr= "1. Enter list of "+searchTermsFilterPrompt+":";
    JLabel searchTermsLabel= new JLabel(searchTermsDescr); 
    EPtermLblPanel.add(searchTermsLabel);      

    /* [2.1.1.2] Create Panel containing the radio buttons matchGeneTermRB 
     * and matchSubStrTermRB.
     */    
    JPanel EPtermRBPanel= new JPanel();
    EPtermRBPanel.setLayout(new GridLayout(1,2));
    EPtermLblPanel.add(EPtermRBPanel);    
       
    /* Set radio buttons group to match Gene Names or Match Substrings
     * of search terms.
     */
    matchGeneTermRB= new JRadioButton("Match list of exact gene/probe names search terms");
    matchSubStrTermRB= new JRadioButton("Match list of sub-strings search terms");
    matchGeneTermRB.setActionCommand("MatchGeneNameTerms");
    matchSubStrTermRB.setActionCommand("MatchSubStrTerms");
    matchGeneTermRB.addActionListener(this);
    matchSubStrTermRB.addActionListener(this);
    matchGeneTermRB.setSelected(true);
    matchSubStrTermRB.setSelected(false);
    final ButtonGroup group1= new ButtonGroup();
    group1.add(matchGeneTermRB);
    group1.add(matchSubStrTermRB);
    sgs.flipTableUseExactMatchFlag= true; 

    EPtermRBPanel.add(matchGeneTermRB);
    EPtermRBPanel.add(matchSubStrTermRB);
    
    /* [2.1.1.3] Add another row with label & SR filename prefix text field */ 
    JPanel SRPanel= new JPanel();
    SRPanel.setLayout(new GridLayout(1,2));
    EPtermLblPanel.add(SRPanel);
    
    JLabel
      SRFNlabel= new JLabel(
                   "Change generated Search-Results files prefix (optional)");
    SRPanel.add(SRFNlabel);
    
    searchResultsFilenamePrefixTF= new JTextField(sgs.searchResultsBaseFile);
    ActionListener srTFlistener=
      new ActionListener()
          { /* ActionListener */
            public void actionPerformed(ActionEvent e)
            { 
              String
                oldSRFNP= sgs.searchResultsBaseFile,
                arg= searchResultsFilenamePrefixTF.getText();
              if(arg!=null)
                sgs.searchResultsBaseFile= arg;
              if(!oldSRFNP.equals(arg))
                UtilCM.logMsg("\nChanging the ");
              else
                UtilCM.logMsg("\nThe current ");
              UtilCM.logMsg("generated filenames prefix to '"+
                            sgs.searchResultsBaseFile+"'.\n");
              printSearchResultsFileNames();  /* Print to log */
            }
          }; /* ActionListener */
    String 
      srfpTT= "Change the generated Search-Results filenames prefix to "+
              "add to '-search' filename."; 
    searchResultsFilenamePrefixTF.setToolTipText(srfpTT);    
    searchResultsFilenamePrefixTF.addActionListener(srTFlistener);
    SRPanel.add(searchResultsFilenamePrefixTF);
    
    /* [2.1.1.4] Add EPtermLblPanel to second slot in middlePanel */
    middlePanel.add(EPtermLblPanel);
            
    /* [2.1.2] Add the search term input text area */
    sgs.searchTermFilterStr= "";
    searchTermTextArea= new JTextArea(5,nCols);  /* was nCols */
    searchTermTextArea.setFont(new Font(textFontFamily,Font.PLAIN,textAreaFontSize));
    searchTermTextArea.setEditable(true);
    searchTermTextArea.setBackground(Color.white);
    searchTermTextArea.setText(sgs.searchTermFilterStr);
    searchTermTextArea.setToolTipText("Enter Gene, Well ID or probe (Feature) "+
                                      "ID search terms.");
    JScrollPane sttaPane= new JScrollPane(searchTermTextArea);
    middlePanel.add(sttaPane);
    
    /* [2.2] Add Sample Choice selector for entering 1 or more search row groups. */
    JPanel EPchoicePanel= new JPanel();
    EPchoicePanel.setLayout(new GridLayout(4,1));
    middlePanel.add(EPchoicePanel);
        
    /* [2.2.1] Add instructions label */
    String searchRowsStr= "2. Select one or more "+searchRowFilterPrompt+":";
    JLabel searchRowLabel= new JLabel(searchRowsStr);
    EPchoicePanel.add(searchRowLabel);
    
    /* [2.2.2] Add EG group filter if not null. */    
    String 
      filterRowsStr= "Filter further by optional AND/OR search sub-strings in matching "+
                     "Expression Groups samples (e.g., '.Stat5 .GH', etc.)";
    JLabel filterRowLabel= new JLabel(filterRowsStr);
    EPchoicePanel.add(filterRowLabel);

    /* Add the search text field */
    sgs.filterRowStr= "";       /* optional overide */
    filterRowTextField= new JTextField(sgs.filterRowStr);
    ActionListener frtfListener=
      new ActionListener()
          { /* ActionListener */
            public void actionPerformed(ActionEvent e)
            { 
              String arg= filterRowTextField.getText();
              if(arg!=null)
              {
                sgs.filterRowStr= arg;
                UtilCM.logMsg("Restricting Expression Groups by '"+arg+
                              "' filter sub-string for GSP ID names.\n");
              }
            }
          }; /* ActionListener */
    filterRowTextField.setToolTipText(
                  "Filter further by optional AND/OR search sub-strings for "+
                  "Expression Groups by matching with GSP ID names "+
                  "(e.g., '.Stat5 .GH', etc.)");
    filterRowTextField.addActionListener(frtfListener);
    
    /* Set radio buttons group for AND/OR of search terms */
    andEGnamesRB= new JRadioButton("AND search terms");
    orEGnamesRB= new JRadioButton("OR search terms");
    andEGnamesRB.setActionCommand("ANDsearchTerms");
    orEGnamesRB.setActionCommand("ORsearchTerms");
    andEGnamesRB.addActionListener(this);
    orEGnamesRB.addActionListener(this);
    final ButtonGroup group2= new ButtonGroup();
    group2.add(andEGnamesRB);
    group2.add(orEGnamesRB);
    andEGnamesRB.setSelected(true);
    orEGnamesRB.setSelected(false);
    sgs.evalSearchANDbooleanFlag= true; 
    
    /* Add space before the EG list */
    /* Panel to put the filterRowTextField and filterRowAndorEGnamesRB  */
    JPanel EPsearchStrPanel= new JPanel();
    EPsearchStrPanel.setLayout(new GridLayout(1,3));
    EPchoicePanel.add(EPsearchStrPanel);
    
    EPsearchStrPanel.add(filterRowTextField);
    EPsearchStrPanel.add(andEGnamesRB);
    EPsearchStrPanel.add(orEGnamesRB);    
    
    JLabel spacerLabel2= new JLabel(" ");
    EPchoicePanel.add(spacerLabel2);

    /* [2.2.3] Build the samplesList Jlist */
    int nSampleChoiceData= sampleChoiceData.length;
    sgs.nEGSelNames= nSampleChoiceData;   
    sgs.egSelNamesFlag= new boolean[sgs.nEGSelNames];    
    String scList[]= new String[nSampleChoiceData];
    /* setup the List GUI and the samples to use */
    for(int i=0;i<nSampleChoiceData;i++)
      scList[i]= sampleChoiceData[i][1];
    samplesList= new JList(scList);
    JScrollPane scPane= new JScrollPane(samplesList);
    middlePanel.add(scPane);
    sgs.egSelNamesFlag[0]= true;
    samplesList.setSelectedIndex(0);
    samplesList.setVisibleRowCount(4);    
    samplesList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
    ListSelectionListener lsListener=
      new ListSelectionListener()
          { /* ListSelectionListener */
            public void valueChanged(ListSelectionEvent lsEvent)
            { updateSampleList(lsEvent); }
          }; /* ListSelectionListener */
    samplesList.setToolTipText(
                      "Select one or more sample groups or All (all groups). "+
                      "Select a range holding SHIFT key. "+
                      "Select a set by holding the CONTROL key.");
    samplesList.addListSelectionListener(lsListener);   
    
    /* [2.3] Create Report TextArea to display the contents of report log string.
     * Should use equi-space font such as courier.
     */
    JLabel reportLabel= new JLabel("Processing Report-Log:");
    middlePanel.add(reportLabel);
    
    reportTextarea= new JTextArea(10,nCols);
    reportTextarea.setFont(new Font(textFontFamily,Font.PLAIN,textAreaFontSize));
    reportTextarea.setEditable(true);
    reportTextarea.setBackground(Color.white);
    JScrollPane rtaPane= new JScrollPane(reportTextarea);
    rtaPane.setWheelScrollingEnabled(true);
    reportTextarea.setToolTipText("Log of results of processing. "+
                                  "You may 'Clear' or 'SaveAs' this log. ");
    middlePanel.add(rtaPane);
    
    /* [2.3.1] Notify UtilCM that the logMsg() text area exists */
    UtilCM.setReportTextArea(reportTextarea);
    reportTextarea.setText(textReport);
    
    /* [2.4] Reset the search terms textarea and the samples ExprGrp GUI. */
    resetInitialGuiProcessingState();
        
    /* [3] Create a bottom panel to hold a couple of buttons */
    FlowLayout cpFlowLayout= new FlowLayout(FlowLayout.LEFT, 6,1);
    JPanel controlSubPanel= new JPanel();
    controlSubPanel.setLayout(cpFlowLayout);

    GridLayout cpGridLayout= new GridLayout(2,1,1,1);
    JPanel controlPanel= new JPanel();
    controlPanel.setLayout(cpGridLayout);
    controlPanel.add(controlSubPanel);
    this.add(controlPanel, "South");
    
    /* Create the buttons and arrange to handle button clicks */
    Font buttonFont= new Font("Helvetica", Font.PLAIN /*BOLD*/, 12);   
    
    JButton b= new JButton("Clear Report-Log");
    b.setActionCommand("ClearReportLog");
    b.addActionListener(this);
    b.setFont(buttonFont);
    b.setToolTipText("Clear the Report-Log data.");    
    controlSubPanel.add(b); 
    
    b= new JButton("Save Report-Log As");
    b.setActionCommand("SaveReportLogAs");
    b.addActionListener(this);
    b.setFont(buttonFont);
    b.setToolTipText("Save the current Report-Log in a text file you specify.");    
    controlSubPanel.add(b);
    
    /* [3.1] Note: we set some button objects to variables so we can
     * enable/disable them.
     */
    processButton= new JButton("Process");
    processButton.setActionCommand("Process");
    processButton.addActionListener(this);
    processButton.setFont(buttonFont);
    processButton.setToolTipText("Start processing after you have specified "+
                                 "search terms (1) and sample groups (2).");
    controlSubPanel.add(processButton);

    cancelButton= new JButton("Cancel");
    cancelButton.setActionCommand("Cancel");
    cancelButton.addActionListener(this);
    cancelButton.setFont(buttonFont);
    cancelButton.setToolTipText("Cancel processing. Normally, the "+
                                "processing takes about 10 seconds.");
    controlSubPanel.add(cancelButton);

    viewHTMLButton= new JButton("View HTML Results");
    viewHTMLButton.setActionCommand("ViewHTML");
    viewHTMLButton.addActionListener(this);
    viewHTMLButton.setFont(buttonFont);
    viewHTMLButton.setToolTipText("View the generated HTML table just "+
                                  "computed in a popup Web browser.");
    controlSubPanel.add(viewHTMLButton);
    
    resetButton= new JButton("Reset");
    resetButton.setActionCommand("resetConverter");
    resetButton.addActionListener(this);
    resetButton.setFont(buttonFont);
    resetButton.setToolTipText("Reset the converter to the initial state. "+
                               "You must then specify search terms (1) and "+
                               "sample groups (2).");
    controlSubPanel.add(resetButton);
        
    /* Add status line on 2nd Grid line of control panel that is 
     * updated with UtilCM.updateReportStatusLine().
     */
    statusLineLabel= new JLabel(programName+" converter program");
    statusLineLabel.setFont(new Font(textFontFamily, Font.PLAIN,10));
    statusLineLabel.setBackground(Color.white);
    statusLineLabel.setToolTipText("Status line show what the converter is "+
                                   "doing or if it is waiting for user input.");
    controlPanel.add(statusLineLabel);
    UtilCM.setReportStatusLineLabel(statusLineLabel);
    
    /* [3.2] Setup the listener thread to "Process" data */
    processButton.addActionListener(new ActionListener() 
       { /* add new listener thread to start ProcessDataSearch */
         public void actionPerformed(ActionEvent evt)
         { /* actionPerformed processButton */
           if(processFlag)
           { 
             UtilCM.logMsg("\nCan't start a new conversion process until "+
                           "the current one is finished or canceled.\n");
             return;
           }
           
           if(indexMapProblemFlag)
           { /* See if problem reading the index map*/
             UtilCM.logMsg("\nFound problem reading the Index Map - unable to "+
                           "do a search.\n");
             return;
           }
           
           if(!indexMapReadyFlag)
           { /* Wait until the index map is finished being read */
             UtilCM.logMsg("\nCan't start the search conversion until the "+
                           "Index Map database is finished being read.\n"+
                           "Waiting while finish reading the Index Map ......\n");
             while(!indexMapReadyFlag)
               UtilCM.sleepMsec(1000);
             UtilCM.logMsg("Finished reading the Index Map - continuing the search.\n");
           }
           
           /* Start the conversion process in a new ProcessDataSearch thread */
           cvt.setAbortProcessingFlag(false); /* clear flag */
           if(!processGuiStateData())
             return;                         /* Don't start processing */
           /* Start Processing */          
           pds= new ProcessDataSearch(sGui,sGuiArgV, guiArgV);
           pds.start();
           processButton.setEnabled(false);                
           cancelButton.setEnabled(true);
           restoreSGstateMI.setEnabled(true);
           saveSGstateMI.setEnabled(true);
           sGui.requestFocus();
         } /* actionPerformed processButton */
       } /* add new listener thread to start ProcessDataSearch */
     );
    
    /* [3.3] Setup the listener thread to "Cancel" ProcessDataSearch */
    cancelButton.addActionListener(new ActionListener() 
       { /* add new listener thread to start ProcessDataSearch */
         public void actionPerformed(ActionEvent evt)
         { /* actionPerformed cancelButton */
           if(!processFlag)
           {
             UtilCM.logMsg("\nCan't cancel conversion since no "+
                           "conversion process is running.\n");
             return;
           }
           pds.interrupt(); 
           /* kill the processing */
           UtilCM.logMsg("\nInterrupting processing....\n");
           UtilCM.updateReportStatusLine("Canceled processing...");
           cvt.setAbortProcessingFlag(true);   /* set flag */ 
           /* clear Generated HTML path List cvt.genHTMLpathList[].
            * Will get list of converted HTML files.
            */
           cvt.clearGenHTMLpathList(true);
           sGui.setEnableSearchParamsButtonsAndMenus();
           sGui.requestFocus();
         } /* actionPerformed cancelButton */
       } /* add new listener thread to start ProcessDataSearch */
     );
        
    /* [3.4] Add listener for window events */
    this.addWindowListener(this);      
    this.setGUItitle(title+" - "+version);

    UtilCM.updateReportStatusLine("Specify search values");
    
    /* [4] Display the GUI */
    this.setCursor(Cursor.DEFAULT_CURSOR);
    
    /* pack it */
    Dimension preferredSize= new Dimension(720,700);
    this.setPreferredSize(preferredSize);
    this.validate();
    this.pack();
    
    /* Center frame on the screen, position report window on the screen */
    positionReportWindow(); 
    
    /* Popup the window */
    this.setVisible(showStatusFlag);
    
    /* Reset the GUI state so no files specified and set Search Params buttons 
     * & menus state. This sets the flags to the initial "Search Params" data 
     * state. 
     */
    setEnableSearchParamsButtonsAndMenus();

    repaint();
    
    return(true);
  } /* initGUI */
       
  
  /**
   * addMenuTree() - create pull down menus in menu bar for the GUI
   * @param f is frame
   * @param mbar is MenuBar
   */
  private void addMenuTree(Frame f, MenuBar mbar)
  { /* addMenuTree */
    Menu smnu= null;
    
    /* Setup menu support hash tables */
    ms= new MenuSupport(); 

    /* [1] Create menus to put in the tree */
    fileMenu= new Menu("File");
    viewMenu= new Menu("View");
    listMenu= new Menu("List");
    helpMenu= new Menu("Help");
    
    /* [1.1] add submenus to menu bar frame */
    mbar.add(fileMenu);    
    mbar.add(viewMenu);    
    mbar.add(listMenu);       
    mbar.add(helpMenu); 

    /* [1.2] T if the last GUI GSstate .sgs file exists, so can recover it 
     * if want on startup.
     */
    int hasLastSGSfile= -1;
    try
    { /* test if file exists */
      String 
        filePath= outputSearchDir+cvt.fileSep+"lastSearchState.sgs";
      File fd= new File(filePath);
      hasLastSGSfile= (fd.exists()) ? 0 : -1;
    }
    catch(Exception e)
    {
      hasLastSGSfile= -1;
    }
        
    /* [2] Add "File" pulldown menu */
    ms.makeMenuItem(this, fileMenu, "Set demo term-list data", "SetDemoData",0);
    ms.makeMenuItem(this, fileMenu, "Import user term-list data from a file", 
                    "GetUserTermListFile",0);
    fileMenu.addSeparator();      /* "__________" */
    ms.makeMenuItem(this, fileMenu, 
                    "Change default Search-Results output directory", 
                    "ChangeSearchResultsOutputDir",-1);    
    fileMenu.addSeparator();      /* "__________" */
    
    saveSGstateMI= ms.makeMenuItem(this, fileMenu, 
                           "SaveAs current search GUI parameters to .sgs file", 
                           "SaveAsSGstate",0); 
    restoreSGstateMI= ms.makeMenuItem(this, fileMenu, 
                           "Restore previously saved search GUI parameters from .sgs file", 
                           "RestoreSGstate",0);
    lastRestoreSGstateMI= ms.makeMenuItem(this, fileMenu, 
                           "Restore last saved search GUI parameters from last session", 
                           "RestoreLastSavedSGstate",hasLastSGSfile);
            
    fileMenu.addSeparator();      /* "__________" */
    
    restoreSGstateMI.setEnabled(true);
    saveSGstateMI.setEnabled(true);
    
    ms.makeMenuItem(this, fileMenu, "ResetConverter", "resetConverter",0);
    ms.makeMenuItem(this, fileMenu, "Quit", "Close", 0);

    /* [4] Add "View" pulldown menu */
    verboseMCB= ms.makeChkBoxMenuItem(this, viewMenu, "Verbose reporting", 
                                      "Verbose", 0, cvt.verboseLoggingFlag);
    ms.makeMenuItem(this, viewMenu, "Show big Report-Log window", 
                    "ShowBigTextViewer",0);
    viewMenu.addSeparator();      /* "__________" */
    
    ms.makeMenuItem(this, viewMenu, 
                    "Sort descending by column data in generated table", 
                    "SortByColData",0);
    showDataHeatmapFlipTableMCB= ms.makeChkBoxMenuItem(this, viewMenu, 
                                       "Show data heat-map in View HTML Results", 
                                       "showDataHeatmapFlipTable", 0, 
                                       sgs.showDataHeatmapFlipTableFlag);

    ms.makeMenuItem(this, viewMenu, 
                    "Set data precision for generated HTML Results", 
                    "SetdataPrecisionHTMLtable",0);  

    viewMenu.addSeparator();      /* "__________" */
    foldChangeMCB= ms.makeChkBoxMenuItem(this, viewMenu, 
                                         "Report Fold Change of 2 sample subsets", 
                                         "ReportFoldChange", 0, 
                                         sgs.reportFoldChangeFlag);

    classAMI= ms.makeMenuItem(this, viewMenu, "Assign EG samples to Class A", 
                              "AssignEGsamplesToClassA",0);    
    classBMI= ms.makeMenuItem(this, viewMenu, "Assign EG samples to Class B", 
                              "AssignEGsamplesToClassB",0);
    foldChangeThrMCB= ms.makeChkBoxMenuItem(this, viewMenu, 
                         "Only keep genes/probes with |fold-change| >= threshold", 
                                         "FoldChangeThr", 0, 
                                         sgs.foldChangeThrFlag);
    sgs.foldChangeThr= 0.0F;
    classAMI.setEnabled(false);
    classBMI.setEnabled(false);
    foldChangeThrMCB.setEnabled(false);

    /* [5] Add "Help" pulldown menu */
    ms.makeMenuItem(this,listMenu,
                    "List all genes in database in the Report window",
                    "ListAllGenes",0);
    ms.makeMenuItem(this,listMenu,
                    "List matching genes in database in the Report window",
                    "ListMatchingGenes",0);    
    listMenu.addSeparator();      /* "__________" */
    ms.makeMenuItem(this,listMenu,"List matching EG samples in Report window",
                    "ListMatchingEGsamples",0);
    ms.makeMenuItem(this,listMenu,
                    "List class A EG samples, if defined, in Report window",
                    "ListClassAsamples",0);
    ms.makeMenuItem(this,listMenu,
                    "List class B EG samples, if defined, in Report window",
                    "ListClassBsamples",0);
    
    /* [6] Add "Help" pulldown menu */
    ms.makeMenuItem(this,helpMenu,"Documentation on using Search GUI",
                    "SearchGUIusage",0);
    ms.makeMenuItem(this,helpMenu,"Jak-Stat.nih.gov Web site",
                    "jakStatWebsite",0);
    ms.makeMenuItem(this,helpMenu,"Jak-Stat.nih.gov Prospector Web site",
                    "jakStatProspectorWebsite",0);
    ms.makeMenuItem(this,helpMenu, "Summary", "Summary",0);
    ms.makeMenuItem(this,helpMenu,"License", "License",0);
    ms.makeMenuItem(this,helpMenu,"About Jak-Stat Database", "AboutJSDB",0);    
    ms.makeMenuItem(this,helpMenu,"About Software", "AboutSoftware",0);    
    helpMenu.addSeparator();      /* "_______" */
    ms.makeMenuItem(this,helpMenu,"Full Converter Reference Manual",
                    "ReferenceManual",0);
    ms.makeMenuItem(this,helpMenu,"Update SearchGUI program",
                    "UpdateSearchGUI",-1);
  } /* addMenuTree */
      
  
  /**
   * processGuiStateData() - Process data specified by the GUI state.
   * This is called from the "Process" event-handler for the button
   * and menu handler.
   * @return true if succeed, false if any problems after write 
   *         err msg to window
   */
  private boolean processGuiStateData()
  { /* processGuiStateData */  
    /* [1] Make sure not currently processing */
    if(processFlag)
    {
      UtilCM.logMsg("\nCan't start a new process until the current "+
                    "one is finished or canceled.\n");
      return(false);
    }
    
    /* [2] Make sure there is a list of search terms to process. Then assign 
     * them to either the searchTermNames[0:nSearchTermNames-1] lists.
     * Parse the data into searchTermFilter[0:nSearchTermNames-1][]
     */
    String sttaStr= searchTermTextArea.getText();
    sgs.searchTermFilterStr= UtilCM.mapCRLF2space(sttaStr);
    if(sgs.searchTermFilterStr==null || sgs.searchTermFilterStr.length()==0)
    { /* make sure they specify at least one search term */
      UtilCM.logMsg(
          "\nProblem: you need to define a list of one or more search terms:");
      for(int k=0;k<nSearchTermNames;k++)
        UtilCM.logMsg(" "+searchTermNames[k]);
      UtilCM.logMsg(".\nSet this list in the search terms window (1.) "+
                    "above and try again.\n");
      return(false);
    }
    else
    { /* get the lists of search terms */
      searchTermFilter= new String[nSearchTermNames][];
      for(int k=0;k<nSearchTermNames;k++)
        searchTermFilter[k]= null;
      String gpList[]= UtilCM.getCleanArgList(sgs.searchTermFilterStr);
      int nList= gpList.length;
      
      /* [2.1] Get a list of Index Map column indices idxIM[]. */
      String imData[][]= ftIM.tData;
      int imRows= ftIM.tRows;      
      int idxIM[]= new int[nSearchTermNames];
      for(int k=0;k<nSearchTermNames;k++)
      { /* get Table indexes of term names */
        String sTerm= searchTermNames[k];
        int idx= ftIM.lookupFieldIdx(sTerm);
        if(idx==-1)
        {
          UtilCM.logMsg("\nBad -searchTermName '"+sTerm+
                        "' - not in Index Map.\n");
          return(false);
        }
        idxIM[k]= idx;
      } /* get Table indexes of term names */
      
      /* [2.2] Save user search terms in separate search terms lists 
       * sorted by corresponding term names specified in the
       * '-searchTermNames:{n1,n2,...nk}' and the corresponding list
       * of legal terms in the database Index Map Table.
       */
      for(int i=0;i<nList;i++)
      { /* Save filters in appropriate list */ 
        String 
          sIM= null,
          s= gpList[i];  /* get next term instance user specified */ 
        int idxIMk= 0;
        boolean foundIt= false;
        for(int k=0;k<nSearchTermNames;k++)
        { /* Search ftIM table for term instance */
          
          /* [2.2.1] Check IM data to see if s in k'th IM term */
          idxIMk= idxIM[k];
          for(int t=0;t<imRows;t++)
          { /* look for match of user term  s with IM DB terms */
            sIM= imData[t][idxIMk];
            if(s.equalsIgnoreCase(sIM) || !sgs.flipTableUseExactMatchFlag)
            { /* found substring match that is not wild-card */
              foundIt= true;
              searchTermFilter[k]= 
                        UtilCM.appendElementToArray(searchTermFilter[k], s);
              break;
            }
          } /* look for match of user term  s with IM DB terms */
          if(foundIt && sgs.flipTableUseExactMatchFlag) 
            break;           /* else search another IM Data term */
        } /* Search ftIM table for term instance */
          
       /* If not found, then it is not in the database, make them fix it
        * and try again. If not doing exact match then don't report this.
        */
       if(!foundIt && sgs.flipTableUseExactMatchFlag) 
       {
         UtilCM.logMsg("\nBad user search term '"+s+"' - not found in the database. "+
             "Edit or remove it and press 'Process' again to continue.\n"+
             "Or, if you want to use search terms to match substrings, then uncheck\n"+
             "   'File menu | Use exact Gene names matching, else match substrings'\n"+
             "and then press 'Process' again to continue.\n");
         return(false);
       }
      } /* Save filters in appropriate list */
    } /* get the list of search terms */
    
    /* [3] Make sure there is a list of sample expression groups. Check if
     * there is a filter substring to search the GSP ID names of the EG's
     * selected. 
     */
    if(sgs.reportFoldChangeFlag)      
    { /* Make sure have two classes */
      /* [3.1] If reporting fold change, then make sure two different 
       * classes are defined.
       */   
      if(sgs.classAsamples==null || sgs.classAsamples.length()==0)
      {
        UtilCM.logMsg("\nCan't Process report fold change since EG Samples for "+
                  "class A was not defined.\n"+
                  "Must define Class A and B samples first, then try Process again.\n");
        return(false);
      }
      else if(sgs.classBsamples==null || sgs.classBsamples.length()==0)
      {
        UtilCM.logMsg("\nCan't Process report fold change since EG Samples for "+
                  "class B was not defined.\n"+
                  "Must define Class A and B samples first, then try Process again.\n");
        return(false);
      }
      else if(sgs.classAsamples.equals(sgs.classBsamples))
      {
        UtilCM.logMsg("\nCan't Process report fold change since EG Samples for "+
                      "classes A and B are the same.\n");
        return(false);
      }
      
      /* Check to make sure that A and B samples are mutually exclusive */
      
      /* Get EG GSPID Samples lists in the class A & B data. */
      String
        samplesInClassA[]= UtilCM.getCleanArgList(sgs.classAsamples),
        samplesInClassB[]= UtilCM.getCleanArgList(sgs.classBsamples); 
      
      /* Get lengths of the lists */
      int
        nA= samplesInClassA.length,
        nB= samplesInClassB.length;
      
      for(int i=0;i<nA;i++)
      { /* Validate samples are unique between A and B */
       for(int j=0;j<nB;j++)
         if(samplesInClassA[i].equals(samplesInClassB[j]))
         {
           UtilCM.logMsg("\nProblem computing fold-change report. "+
                         "Class A and B samples must be unique.\n" +
                         "Sample ["+samplesInClassA[i]+
                         "] was found in both class A and B.\n");
           return(false);
         }
      } /* Validate samples are unique between A and B */
      UtilCM.logMsg("Class A and B samples are unique.\n");
    } /* Make sure have two classes */
    
    else
    { /* Make sure intensity report has some EG samples */
      /* [3.2] Make sure have non-null set of EG samples to process */
      String arg= filterRowTextField.getText();
      if(arg != null && arg.length() > 0)
      { /* restrict the sampleRowFilter[] */
        sgs.filterRowStr= arg;
        UtilCM.logMsg("Restricting Expression Groups by '" + arg
                      + "' filter sub-string for filtering GSP ID names.\n");
      } /* restrict the sampleRowFilter[] */

      /* [3.1] Make sure there is a list of sample expression groups. */
      if(sgs.sampleRowFilter == null || sgs.sampleRowFilter.length == 0)
      { /* problem with sample expression group list */
        UtilCM.logMsg("\nProblem: you need to at least one '"
                      + searchRowFilterName + "'. Set this and try again.\n");
        return (false);
      }
    } /* Make sure intensity report has some EG samples */
    
    /* [4] Set the "Processing" State. */
    this.setEnableCancelButtonsAndMenus("Processing file ...");
    
    /* [5] Build the Param .map processing string. If we can't schedule this
     * now, we will use it later after ensure pd thread is running.
     */
    sGuiArgV= "";
    sGuiArgV= inputSearchDir + cvt.fileSep + guiParamsMapFile;
    
    /* [5.1] Create guiParamsMapFile from default params.map file */
    if(!createParamsMapFile())
    {
      UtilCM.logMsg("\nProblem creating '"+guiParamsMapFile+".\n"+
                    "Set this and try again.\n");
      return(false);
    }

    /* [6] Make it an arg list */
    guiArgV= UtilCM.cvs2Array(sGuiArgV, " ");  
    
    return(true);
  } /* processGuiStateData */
  

  /**
   * createParamsMapFile() -  Create guiParamsMapFile from default params.map file
   * <PRE>
   * Add the following required switches:
   *   -flipOrderHdrColNames:"*LIST*,Stat5a,"
   *   -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
   *   -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at"
   *   -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2"
   *  
   * Add the following optional switches:
   *   -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
   *   -flipAclass:"{classAsamples}"  [if sgs.reportFoldChangeFlag]
   *   -flipBclass:"{classBsamples}"  [if sgs.reportFoldChangeFlag]
   *   -flipFCthreshold:{foldChangeThr} [if foldChangeThrFlag && foldChangeThr>0.0F]
   *   -dataPrecisionHTMLtable:{precision of HTML table}
   *   -sortFlipTableByColumnName:{sort column}
   *   -showDataHeatmapFlipTable
   *   -flipUseExactColumnNameMatch:{sgs.flipTableUseExactMatchFlag}
   *   -flipDirectory:"{outputSearchDir}"
   *   -flipSaveOutputFile:"{searchResultsBaseFile}"
   * </PRE>
   * @return true if created the params .map file
   */
  private boolean createParamsMapFile()
  { /* createParamsMapFile */
    /* [1] Make sure default params .map file exists */
    String 
      paramTemplate= cvt.fio.readFileAsString(guiParamsMapDefaultPath);
    if(paramTemplate==null)
    {
      UtilCM.logMsg("\nCan't find file '"+guiParamsMapDefaultPath+".\n"+
                   "Check the system setup.\n");
      return(false);
    }
    
    /* [2] Create filter comma strings if the data exists.  */
    String searchFilterSW= "";
    
    /* [2.1] Add -flipOrderHdrColNames that is from the list of
     * searchTermNames[] to searchFilterSW list.
     */
    searchFilterSW += "-flipOrderHdrColNames:\"";
    for(int k=0;k<nSearchTermNames;k++)
      searchFilterSW += ((k==0) ? "" : ",") + searchTermNames[k];
    searchFilterSW += "\"\n";
  
    /* [2.2] Add searchTermFilter[k][] for searchTermNames[] as 
     * "-flipColumnName:\"*LIST*," that exist to searchFilterSW list.
     */
    for(int k=0;k<nSearchTermNames;k++)
    { /* process filter k */
      if(searchTermFilter[k]!=null)
      { /* add it to searchFilterSW list */
        searchFilterSW += "-flipColumnName:\"*LIST*,"+searchTermNames[k];
       for(int i=0;i<searchTermFilter[k].length;i++)
          searchFilterSW += ","+searchTermFilter[k][i];
        searchFilterSW += "\"\n";
      }    
    } /* process filter k */

    /* [2.3] Add sampleRowFilter as "-flipRowFilterNames:\"*LIST*" 
     * if sampleRowFilter exists to searchFilterSW list.
     */
    if(sgs.sampleRowFilter!=null && !sgs.sampleRowFilterALLflag)
    { /* add it to searchFilterSW list */
      searchFilterSW += "-flipRowFilterNames:\"*LIST*";
      for(int i=0;i<sgs.sampleRowFilter.length;i++)
        searchFilterSW += ","+sgs.sampleRowFilter[i];
      searchFilterSW += "\"\n";
    }
    
    /* [2.3.1] If !sgs.reportFoldChangeFlag then add filterRowStr as 
     * "-flipRowGSPIDfilterSubstring:"AND/OR,{substring}" 
     * if filterRowStr exists to searchFilterSW list.
     */
    if(!sgs.reportFoldChangeFlag && sgs.filterRowStr!=null && 
        sgs.filterRowStr.length()>0)
    { /* add it to searchFilterSW list */
      /* Normalize the string */
      sgs.flipRowGSPIDfilters= UtilCM.getCleanArgList(sgs.filterRowStr);
      searchFilterSW += "-flipRowGSPIDfilters:\"";
      searchFilterSW += (sgs.evalSearchANDbooleanFlag) ? "AND," : "OR,";
      for(int k=0;k<sgs.flipRowGSPIDfilters.length;k++)
      {
        searchFilterSW += sgs.flipRowGSPIDfilters[k];
        if(k<(sgs.flipRowGSPIDfilters.length-1))
          searchFilterSW +=",";
      }
      searchFilterSW += "\"\n";
    }
    
    /* [2.3.2] If sgs.reportFoldChangeFlag then add report fold change as 
     * "-flipAclass:"{classAsamples}" and "-flipBclass:"{classBsamples}".
     */
    if(sgs.reportFoldChangeFlag)
    { /* only write if report fold-change flag set */
      searchFilterSW += 
        "#\n#\"Set report Fold Change EG samples A and B.\"\n"+
        "-flipAclass:\""+sgs.classAsamples+"\"\n"+
        "-flipBclass:\""+sgs.classBsamples+"\"\n"+
        "#\n";
      if(sgs.foldChangeThrFlag && sgs.foldChangeThr>0.0F)
      { /* only write if report fold-change threshold flag set */
        searchFilterSW += 
          "#\"Set report Fold Change specify |fold-change threshold|.\"\n"+
          "-flipFCthreshold:\""+UtilCM.cvf2s(sgs.foldChangeThr,4)+"\"\n"+
          "#\n";
      }
    } /* only write if report fold-change flag set */
    
    /* [2.4] Add -dataPrecisionHTMLtable:{sgs.dataPrecisionHTMLtable}. */
    searchFilterSW += 
      "#\n#\"Set the data precision for generated HTML.\"\n"+
      "-dataPrecisionHTMLtable:"+sgs.dataPrecisionHTMLtable+"\n"+
      "#\n";
    
    /* [2.5] Add -sortFlipTableByColumnName:{sort column} if doing sorting. */
    if(sgs.sortFlipTableByColumnName!=null)
    { /* sort flip table by column name */
      if(sgs.reportFoldChangeFlag)
      {
        UtilCM.logMsg("\nCan't sort data by header term-name if "+
                      "reporting fold-change. Not sorting report.\n");
        sgs.sortFlipTableByColumnName= null;
      }
      searchFilterSW += 
        "#\n#\"Set the flip-table sort by column name.\"\n"+
        "-sortFlipTableByColumnName:\""+sgs.sortFlipTableByColumnName+"\"\n"+
        "#\n";
    }  /* sort flip table by column name */    
    
    /* [2.6] If the "-showDataHeatmapFlipTable" switch is set, then pass it on. */
    if(sgs.showDataHeatmapFlipTableFlag)   
      searchFilterSW += 
         "#\"Generate heat-map data cells in a HTML conversion if .sidx exists.\"\n"+
         "-showDataHeatmapFlipTable\n"+
         "#\n";
    
    /* [2.7] Set the exact match filter flag. If an exact match, then
     * match flipColNameFilterData[][] exactly with equalsIgnoreCase(),
     * otherwise do lower case IndexOf() comparison to pick up substrings.
     * Set with the -flipUseExactColumnNameMatch:{TRUE | FALSE} switch.
     */
    searchFilterSW += 
         "#\"Generate heat-map data cells in a HTML conversion if .sidx exists.\"\n"+
         "-flipUseExactColumnNameMatch:"+ ((sgs.flipTableUseExactMatchFlag) 
                                              ? "TRUE" : "FALSE")+"\n"+
         "#\n";
    
    /* [2.8] Set the Search-Results base output directory It uses the base name from 
     * the database <idx map file> set by "-flipTableByIndexMap:<idx map file>,..." .
     * Get the new value from JTextField  searchResultsOutputDirTF 
     * and set it to searchResultsOutputDir. Print names to Report-Log.
    */
    searchFilterSW += 
         "#\"Specify Search-Results base output directory for .txt and .html files.\"\n"+
         "-flipDirectory:\""+ outputSearchDir +"\"\n"+
         "#\n";
    
    /* [2.8.1] Set the Search-Results base file name. It uses the base name from 
     * the database <idx map file> set by "-flipTableByIndexMap:<idx map file>,..." .
     * Get the new value from JTextField  searchResultsFilenamePrefixTF 
     * and set it to searchResultsBaseFile. Print names to Report-Log.
    */
    getSearchResultsFilenamePrefix();
    printSearchResultsFileNames();  /* Print to log */
    searchFilterSW += 
         "#\"Specify Search-Results base file name for .txt and .html files.\"\n"+
         "-flipSaveOutputFile:\""+ sgs.searchResultsBaseFile +"\"\n"+
         "#";    
            
    /* [3] Setup and map keywords in the template, and then map template file */
    int 
      nMaps= 0,
      maxMaps= 100;
    String toStrList[]= new String[maxMaps];
    String keyList[]= new String[maxMaps];
    
    keyList[nMaps]= "$$DATE$$";
    toStrList[nMaps++]= cvt.date;
    keyList[nMaps]= "$$INPUT_DATA$$";
    toStrList[nMaps++]= inputSearchDir;
    keyList[nMaps]= "$$OUTPUT_DATA$$";
    toStrList[nMaps++]= outputSearchDir;
    keyList[nMaps]= "$$TABLE_DATA$$";
    toStrList[nMaps++]= tableSearchDir;

    keyList[nMaps]= "$$SEARCH_FILTERS$$";
    toStrList[nMaps++]= searchFilterSW;

    keyList[nMaps]= "$$DATA_SOURCE_SUBTITLE$$";
    toStrList[nMaps++]= dataSource;  
    
    String
      pmData= UtilCM.mapAllkeywords(paramTemplate,keyList,toStrList,nMaps);
    
    /* [4] Write out the created Param .map file */
    String
      pmPath= inputSearchDir + cvt.fileSep + guiParamsMapFile;
    if(!cvt.fio.writeStringToFile(pmPath, pmData))
    {
      UtilCM.logMsg("\nCan't write the created param .map file: '"+pmPath+".\n"+
                    "Check the system setup.\n");
      return(false);
    }
    
    return(true);    
  } /* createParamsMapFile */
  
  
  /**
   * setDemoParameters() - set the Search Terms list for demo state.
   * The demo argument to load into the searchTermTextArea GUI
   * Set by "-searchTermsDemoData:{list of search terms}" 
   * The demo argument to load into the sample list choice GUI
   * and into sampleRowFilter[] data. Set by 
   * "-searchRowsDemoData:{list of sample groups}"
   */
  public void setDemoParameters()
  { /* setDemoParameters */
    /* [1] Set list of Demo Data terms */
    searchTermTextArea.setText(sgs.searchTermsDemoData); 
    UtilCM.logMsg("Setting Demo Search Terms: "+
                  sgs.searchTermsDemoData+"\n");

    /* [2] Set additional title for generated Web page */
    dataSource= "Set to user demo list of search terms.";
    
    repaint();
  } /* setDemoParameters */
    
  
  /**
   * setUserSearchTermFileParameters() - set search term list from user file.
   * The demo argument to load into the searchTermTextArea GUI
   * Set by "-searchUserTermList:{userListTable,colName,title string}".
   * The demo argument to load into the sample list choice GUI.
   */
  public void setUserSearchTermFileParameters()
  { /* setUserSearchTermFileParameters */
   /* [1] Get the user search term file FileTable */
    String sFile= inputSearchDir + cvt.fileSep + sgs.searchUserTermListFile;

    /* [2] Read the Table */
    FileTable ft= new FileTable("User-Term-List");
    ft.setNbrTableHdrLines(1);
    ft.setHasTableHeaderFlag(true);
    ft.setRmvTrailingBlankLinesFlag(true);
    ft.setRmvTrailingEmptyColumnsFlag(true);
    if(!ft.readAndParseTable(sFile))
    {
      UtilCM.logMsg("Can't find "+sgs.searchUserTermListTitle+
                    " term-list data file '"+
                    sgs.searchUserTermListFile+"'\n");
      return;
    }
    String colData[]= ft.getColumnData(sgs.searchUserTermListColName);
    if(colData==null)
    {
      UtilCM.logMsg("Can't set "+sgs.searchUserTermListTitle+
                    " term-list data from Table '"+
                    sgs.searchUserTermListFile+
                    "' - can't find column name '"+
                    sgs.searchUserTermListColName+"'\n");
      return;
    }
    else
    { /* make a string separated by "" */
      sgs.searchUserTermListStr= "";
      for(int i=0;i<colData.length; i++)
        sgs.searchUserTermListStr += colData[i]+" ";
    }
        
    /* [3] Set list of Demo Data terms */
    searchTermTextArea.setText(sgs.searchUserTermListStr);
    
    /* [4] Set the data */
    UtilCM.logMsg("Set "+sgs.searchUserTermListTitle+
                  " search term data from '"+
                  sgs.searchUserTermListFile+"'\n"); 
    UtilCM.logMsg("The '"+sgs.searchUserTermListTitle+"' search terms: "+
                  sgs.searchUserTermListStr+"\n");

    /* [5] Set additional title for generated Web page */
    dataSource= "Set to '"+sgs.searchUserTermListTitle+
                "' list of search terms.";
    
    repaint();
  } /* setUserSearchTermFileParameters */
  
  
  /**
   * setUserTermListFromFile() - set user search term-list state from a file.
   * It pops up a file browser with the default set to
   * {userListTable} which can be a single column list or
   * if a Table, then use the {colName} set by 
   * "-searchUserTermList:{userListTable,colName,title str}".
   * If {colName} is not specified, then assume the data is just delimited
   * search terms. Map all "  ", ",", "\t" and "\n" to single space normalized
   * string.
   * The list is then loaded into the searchTermTextArea GUI
   */
  public boolean setUserTermListFromFile()
  { /* setUserTermListFromFile */
    /* [1] Get the name of the file */
    UtilCM.logMsg("Specify a search term list by file:\n");
    
    String sFile= inputSearchDir + cvt.fileSep + sgs.searchUserTermListFile;
    PopupFileDialog pfd= new PopupFileDialog();
    String 
      fileStr= pfd.popupFileDialog(sFile, null,
                                   "Set term-list file", true);
    if(fileStr==null)
      return(false);
    else
      sgs.searchUserTermListFile= fileStr;
    
    /* [2] Get the list */
    String sData= cvt.fio.readFileAsString(sgs.searchUserTermListFile);
    if(sData==null)
    {
      UtilCM.logMsg("Can't set term-list data from '"+
                    sgs.searchUserTermListFile+"' - can't find file.\n");
      return(false);
    }
    else
    { /* set the data */
      /* Test if first line contains search term names */
      boolean hasSearchTermHeader= false;
      int 
        idxFirstLine= sData.indexOf("\n"),
        nSTN= 0;
      String 
        firstLine= (idxFirstLine==-1) ? "" : sData.substring(0,idxFirstLine),
        stn= null;
      
      for(int i=0;i<searchTermNames.length;i++)
        if(sData.indexOf(searchTermNames[i])!=-1)
        { /* it can be any of the searchTermNames */
          hasSearchTermHeader= true;
          stn= searchTermNames[i];
          nSTN++;
        }
      /* If specified only one search term name, then overide and use it. */
      if (nSTN==1)
        sgs.searchUserTermListColName= stn;
      /* Get and standardize the data */
      if(sgs.searchUserTermListColName==null || !hasSearchTermHeader)
      { /* use list of symbols which should be genes, Well IDs or Feature IDs */
        /* Standardize to space delimited row of symbols by mapping
        /* commas, tabs, "\n" and multiple spaces to single space. */
        sgs.searchUserTermListStr= UtilCM.getCleanSpaceList(sData);
      } /* use list of symbols which should be genes, Well IDs or Feature IDs */
      else
      { /* treat the file string as a Table */
       FileTable ft= new FileTable("User-Term-List");
       ft.setNbrTableHdrLines(1);
       ft.setHasTableHeaderFlag(true);
       ft.setRmvTrailingBlankLinesFlag(true);
       ft.setRmvTrailingEmptyColumnsFlag(true);
       if(!ft.readAndParseTable(sgs.searchUserTermListFile))
       {
         UtilCM.logMsg("Can't set term-list data from Table '"+
                       sgs.searchUserTermListFile+"'\n");
         return(false);
       }
       String colData[]= ft.getColumnData(sgs.searchUserTermListColName);
       if(colData==null)
       {
         UtilCM.logMsg("Can't set term-list data from Table '"+
                       sgs.searchUserTermListFile+
                       "' - can't find column name '"+
                       sgs.searchUserTermListColName+"'\n");
         return(false);
       }
       else
       { /* make a string separated by "" */
         sgs.searchUserTermListStr= "";
         for(int i=0;i<colData.length; i++)
           sgs.searchUserTermListStr += colData[i]+" ";
       }
      } /* treat it as a Table */
    } /* set the data */
    
    /* [3] Set list of user search term Data terms */
    searchTermTextArea.setText(sgs.searchUserTermListStr); 
    UtilCM.logMsg("Set user Search Terms from file '"+
                  sgs.searchUserTermListFile+"'\n");
    
    /* [4] Set additional title for generated Web page */
    String colSrc= (sgs.searchUserTermListColName==null) 
                       ? "" : "'"+sgs.searchUserTermListColName+"'";
    dataSource= "User "+colSrc+" list from '"+sFile+"'";
    
    repaint();
    return(true);
  } /* setUserTermListFromFile */
  
  
  /**
   * setGUItoSGstate() - set GUI to instance of SGstate.
   * Set the GUI to variables in SGstate sg instance.
   * @param sg is instance of SGstate to use (that could be different
   *        than this.sgs
   * @return true if succeed
   */
  private boolean setGUItoSGstate(SGstate sg)
  { /* setGUItoSGstate */
    /* Report Fold-Change GUI options */
    sg.reportFoldChangeFlag= (sg.classAsamples!=null && sg.classBsamples!=null);
    if(sg.reportFoldChangeFlag)
    { /* Set Report Fold-Change GUI menu options */
    }
    else
    { /* Clear Report Fold-Change GUI menu options */
      sg.reportFoldChangeFlag= false;
      sg.classAsamples= null;
      sg.classBsamples= null;
      sg.foldChangeThrFlag= false;
      sg.foldChangeThr= 0.0F;
    }
    
    /* Search-term GUI */
    if(sg.searchTermFilterStr==null)
      sg.searchTermFilterStr= "";
    searchTermTextArea.setText(sg.searchTermFilterStr);
    if(sg.flipTableUseExactMatchFlag)
    { /* Set AND radio button */
      matchGeneTermRB.setSelected(true);
      matchSubStrTermRB.setSelected(false);
    }
    else
    { /* Set OR radio button */
      matchGeneTermRB.setSelected(false);
      matchSubStrTermRB.setSelected(true);
    }

    /* EG Samples GUI */
    samplesList.clearSelection(); 
    samplesList.setSelectedIndex(0);
    int
      ks= 0,
      nToSelect= 0;
    for(int i=0;i<sg.nEGSelNames;i++)
      if(sg.egSelNamesFlag[i])
        nToSelect++;
    if(nToSelect>0)
    { /* make list to select and then select them */
      int toSelectList[]= new int[nToSelect];
      for(int i=0;i<sg.nEGSelNames;i++)
        if(sg.egSelNamesFlag[i])
          toSelectList[ks++]= i; //(i-1);
      samplesList.setSelectedIndices(toSelectList);
    }    
    
    if(sg.filterRowStr!=null)
      filterRowTextField.setText(sg.filterRowStr);
    else
      filterRowTextField.setText("");
    
    if(sg.evalSearchANDbooleanFlag)
    { /* Set AND radio button */
      andEGnamesRB.setSelected(true);
      orEGnamesRB.setSelected(false);
    }
    else
    { /* Set OR radio button */
      andEGnamesRB.setSelected(false);
      orEGnamesRB.setSelected(true);
    }
    
    /* Output file base name */
    searchResultsFilenamePrefixTF.setText(sg.searchResultsBaseFile);
    
    this.repaint();
    
    return(true);
  } /* setGUItoSGstate */
  
  
  /**
   * getGUItoSGstate() - get additional SGstate variables from GUI.
   * Note that most variables are set as the GUI state changes, but
   * some sg variables need to be set. I.e., the TextAreas and TextFields.
   * Set the GUI to variables in SGstate sg instance.
   * @param sg is instance of SGstate to use (that could be different
   *        than this.sgs
   * @return true if succeed
   */
  private boolean getGUItoSGstate(SGstate sg)
  { /* getGUItoSGstate */

    /* Search-term TextArea GUI */    
    sg.searchTermFilterStr= searchTermTextArea.getText();

    /* Search output base file name */
    sg.searchResultsBaseFile= searchResultsFilenamePrefixTF.getText();

    /* EG Samples GUI */
    sg.filterRowStr= filterRowTextField.getText();

    /* Get the list from the Choice list. Code it as list of Table row indices. */
    for(int i=0;i<sg.nEGSelNames;i++)
    { /* setup the List GUI and the samples to use, less ALL */
      sg.egSelNamesFlag[i]= samplesList.isSelectedIndex(i);
    } /* selected some samples that are not ALL */    
    
    return(true);
  } /* getGUItoSGstate */
  

  /**
   * saveGUItoGSstateFile() - save GUI to GSstate .sgs file
   * @param filePath - of .sgs file to save
   * @return true if succeed
   */
  private boolean saveGUItoGSstateFile(String filePath)
  { /* saveGUItoGSstateFile */
    if(!getGUItoSGstate(this.sgs))
    {
      UtilCM.logMsg("Can't set GSstat from GUI.\n"); 
      return(false);
    }      
    if(!sgs.writeSGstate(filePath))
    {
      UtilCM.logMsg("Problem saving last search GUI parameters as a file.\n");
      return(false);
    }
    else
    {
      UtilCM.logMsg("Saved last search GUI parameters as file '"+
                    filePath+"'\n");
      return(true);
    }
  } /* saveGUItoGSstateFile */
    

  /**
   * restoreGUIfromGSstateFile() - restore GUI from GSstate .sgs file
   * @param filePath - of .sgs file to restore
   * @return true if succeed
   */
   private boolean restoreGUIfromGSstateFile(String filePath)
   { /* restoreGUIfromGSstateFile */
    SGstate sg= new SGstate(this);        
    if(!sg.readSGstateFile(filePath)) 
    {
      UtilCM.logMsg("Can't restore search GUI parameters from file '"+
                    filePath+"'.\n");
      return(false);
    }  
    else
    { /* Update the GUI from the imported .sgs file data. */
      UtilCM.logMsg("Restored search GUI parameters from file '"+
                  filePath+"'.\n");        
      if(!setGUItoSGstate(sg))
      {
        UtilCM.logMsg("Can't set GUI parameters from file '"+
                      filePath+"'.\n"); 
        return(false);
      }  
    
      /* If all is well, then copy the SGstate */
      sgs.copySGstateInstance(sg);
      return(true);
    } /* Update the GUI from the imported .sgs file data. */
  } /* restoreGUIfromGSstateFile */  
    
  
  /**
   * setEnableSearchParamsButtonsAndMenus() - set Search buttons & menus state.
   * This sets the flags to the initial "Assign" data state. 
   */
  public void setEnableSearchParamsButtonsAndMenus()
  { /* setEnableSearchParamsButtonsAndMenus */
    processButton.setEnabled(true);
    cancelButton.setEnabled(false);
    viewHTMLButton.setEnabled(false);

    setEnableSearchParamsState();  /* clear the GUI state */
    
    UtilCM.updateReportStatusLine("Enter search terms and select sample groups");

    UtilCM.logMsg(
      "\nTo generate a Gene-Expression Report for a subset of genes and samples:\n"+
      "1. Enter a list of genes and/or probes (case is ignored),\n"+
      "2. Select the sample expression groups to use (default ALL). "+
      "Alternatively, you can enter a set of search terms\n"+
      "    to filter Experiment Group samples by matching part of the "+
      "GSP ID names for each sample.\n"+
      "3. Press the 'Process' button to compute the 'Gene-Expression Report',\n"+
      "4. After it finishes (about 7 to 10 seconds), press 'View HTML' to "+
      "popup a Web browser window with the report.\n\n");
    
    this.repaint();   
  } /* setEnableSearchParamsButtonsAndMenus */
  
  
  /**
   * setEnableCancelButtonsAndMenus() - when are able to do processing state.
   * This sets the flags to the "Process" data state. It also
   * clears the list of generated HTML files.
   * @param statusLabel to use for Report status line.
   */
  public void setEnableCancelButtonsAndMenus(String statusLabel)
  { /* setEnableCancelButtonsAndMenus */
    processButton.setEnabled(false);
    cancelButton.setEnabled(true);
    viewHTMLButton.setEnabled(false);

    setEnableCancelState();

    UtilCM.updateReportStatusLine(statusLabel);    

    UtilCM.logMsg("\nWait until processing is finished or press the "+
                  "'Cancel' button to abort the processing.\n");
    this.repaint();
  } /* setEnableCancelButtonsAndMenus */
  
  
  /**
   * setEnableViewingButtonsAndMenus() - when can view processed HTML files state.
   * This sets the flags to the "Viewing-enable" data state. 
   */
  public void setEnableViewingButtonsAndMenus()
  { /* setEnableViewingButtonsAndMenus */
    processButton.setEnabled(true);   /* [NOTE] allow to reprocess without RESET! */
    cancelButton.setEnabled(false);
    viewHTMLButton.setEnabled(true);    
    
    /* assign the list of HTML files */
    String genHTMLpathList[]= cvt.getGenHTMLpathList();
    guiActiveHTMLfile= (genHTMLpathList!=null)
                     ? genHTMLpathList[0] : null;
    if(guiActiveHTMLfile!=null)
      guiActiveTXTfile= guiActiveHTMLfile.substring(0,
                                     guiActiveHTMLfile.length()-5)+".txt";
    
    setEnableViewingState();
    
    UtilCM.updateReportStatusLine("View HTML file");
    
    this.repaint();
  } /* setEnableViewingButtonsAndMenus */
  
  
  /**
   * positionReportWindow() - position report window on the screen
   */
  public void positionReportWindow()
  { /* positionReportWindow */
    int
      xPos,
      yPos;
       
    /* Center frame on the screen, PC only */
    Dimension
      rptSize= this.getSize(),
      screen= Toolkit.getDefaultToolkit().getScreenSize();
    xPos= (screen.width - rptSize.width +100)/2;
    yPos= (screen.height - rptSize.height)/2;
    if(xPos<0 || yPos<0)
    { /* came up too soon */
      xPos= (screen.width - rptSize.width)/2;
      yPos= (screen.height - rptSize.height)/2;
    }
      
    /* Override X position in upper left hand part of screen */
    xPos= 150;    
    //xPos= 50;    
    
    Point pos= new Point(xPos,yPos);
    this.setLocation(pos);
  } /* positionReportWindow */ 
  
  
  /**
   * setShow() - set the show/hide popup status
   * @param showStatusFlag to show (true), hide(false).
   */
  public void setShow(boolean showStatusFlag)
  { this.setVisible(showStatusFlag);  }
   
  
  /**
   * updateReportStatusLine() - clear text in popup window
   * @param msg to display
   */
  public void updateReportStatusLine(String msg)
  { /* updateReportStatusLine */
    statusLineLabel.setText(msg); 
    this.repaint();
  } /* updateReportStatusLine */
  
  
  /**
   * clearText() - clear text in popup window
   */
  public void clearText()
  { /* clearText */
    textReport= "";    
    reportTextarea.setText(textReport); 
    if(bptv!=null)
      bptv.setText(textReport);
    this.repaint();
  } /* clearText */
  
  
  /**
   * getReportText() - get the text from the Report popup window
   * @return text report
   */
  public String getReportText()
  { /* getReportText */
    textReport= reportTextarea.getText(); 
    return(textReport);
  } /* getReportText */
  

  /**
   * getSearchResultsFilenamePrefix() - get the new value from JTextField
   * searchResultsFilenamePrefixTF and set it to searchResultsBaseFile
   * 
   */
  public void getSearchResultsFilenamePrefix()
  { /* getSearchResultsFilenamePrefix */
    String arg= searchResultsFilenamePrefixTF.getText();
    if(arg!=null && !arg.equals(sgs.searchResultsBaseFile))
    {
      sgs.searchResultsBaseFile= arg;
      UtilCM.logMsg("Changing the generated filenames prefix to '"+arg+
                    "'.\n");
    }
  } /* getSearchResultsFilenamePrefix */
  
  
  /**
   * getDBgeneList() - get printable text list of genes in the database.
   * If there are no search terms, then return the entire list.
   * @param searchTermsStr - list of search terms if not null in which case
   *                return the entire list
   * @param matchSubstringFlag - to match it as a substring of Gene field, else
   *                              use the exact match.
   * @return text if found, else "" if a problem.
   */
  public String getDBgeneList(String searchTermsStr, 
                              boolean matchSubstringFlag)
  { /* getDBgeneList */
    if(ftIM==null || ftIM.tRows<=0 || ftIM.tCols<=0)
      return("");
    
    /* Build the report */
    String 
      searchTerms[]= null,
      sLine,
      sGene,
      sGeneLC,
      sFeatureID,
      tFields[]= ftIM.tFields,
      tData[][]= ftIM.tData,
      tRowData[],
      textReport= "\n"+
                  "List of Gene and Feature IDs      \n"+
                  "#      Gene       Feature ID      \n"+
                  "==================================\n";
    
    if(searchTermsStr!=null && searchTermsStr.length()>0)
    {
      searchTermsStr= searchTermsStr.toLowerCase();
      searchTerms= UtilCM.getCleanArgList(searchTermsStr);
    }
    
    int
      nbr= 0,
      nSearchTerms= (searchTerms==null) ? 0 : searchTerms.length,
      tRows= ftIM.tRows,
      tCols= ftIM.tCols,
      idxGene= ftIM.lookupFieldIdx("Gene"),
      idxFeatureID= ftIM.lookupFieldIdx("Feature ID");
    
    StringBuffer sBuf= new StringBuffer(50000);
    for(int r=0;r<tRows;r++)
    {
      tRowData= tData[r];
      sGene= tRowData[idxGene];
      if(sGene.equals("") || sGene==null)
        sGene= "-NoName-";
      sGeneLC= sGene.toLowerCase();
      sFeatureID= tRowData[idxFeatureID];
      boolean matchIt= false;
      if(searchTerms==null)
        matchIt= true;
      else
      { /* test if match search terms */
        for(int k=0;k<nSearchTerms;k++)
          if(searchTerms[k].equals(sGeneLC) ||
             (matchSubstringFlag && sGeneLC.indexOf(searchTerms[k])!=-1) ||
             searchTerms[k].equalsIgnoreCase(sFeatureID))
          { /* found it */
            matchIt= true;
            break;
          }
      }
      if(matchIt)
      { /* use it */
        sLine= ("#"+((nbr++)+1)) +"    "+ sGene + "    "+ sFeatureID+"\n";
        sBuf.append(sLine);
      }
    }
    textReport += sBuf.toString();
    textReport +=  "==================================\n\n";
    
    return(textReport);
  } /* getDBgeneList */
    
  
  /**
   * getEGsampleList() - get printable text list of EG samples in the database.
   * If there are no search terms, then return the entire list.
   * 
   * [TODO] Read the header from the Database file which contains
   * the sample GSP IDs but omit the leading "Gene, Well ID, Feature ID"
   * @param searchTermsStr - list of search terms if not null in which case
   *                return the entire list,
   * @param egGroupList - is list of the EG groups, if ALL, then all groups
   * @param evalSchANDboolean - is true if AND, false if OR for matching
   *        search terms.
   * @param sTitle optional title if not null
   * @return text if found, else "" if a problem.
   */
  public String getEGsampleList(String searchTermsStr, String egGroupList[],
                                boolean evalSchANDboolean, String sTitle)
  { /* getEGsampleList */
    if(ftIM==null || ftIM.tRows<=0 || ftIM.tCols<=0)
      return("");
    
    /* Build the report */
    String
      searchTerms[]= null,
      sMsg= (sTitle!=null) ? (sTitle+" ") : "",
      textReport= "\n"+
                  "List of "+sMsg+"Sample GSP IDs           \n"+
                  "==================================\n";

    if(searchTermsStr!=null && searchTermsStr.length()>0)
      searchTerms= UtilCM.getCleanArgList(searchTermsStr);    
    int
      nSearchTerms= (searchTerms==null) ? 0 : searchTerms.length;
    
    /* Build list to work from */
    int
      nSamplesInDB= dbGSPIDlist.length,
      nEGlist= egGroupList.length;
    String
      dbGSPIDname,
      egName,
      workingEGlist[]= new String[nSamplesInDB];
    int nSamples= 0;
    for(int d=0;d<nSamplesInDB;d++)
    {
      dbGSPIDname= dbGSPIDlist[d];
      for(int g=0;g<egGroupList.length;g++)
      { /* Build subset if using EG groups selections */
        egName= egGroupList[g];
        if(egName==null || dbGSPIDname.startsWith(egName))
        {
          workingEGlist[nSamples++]= dbGSPIDname;
          break;
        }
      }
    } /* Build subset if using EG groups selections */
    workingEGlist= UtilCM.rightSizeArray(workingEGlist, nSamples, null);    
    
    /* This is the list of ftData Data Table columns starting with "EG" and is
     * the list of EG GSP IDs in the database filtered by the search terms
     * if any. If no search terms, use the workingEGlist.
     */
    String
      sGSPID,
      sLine;
    int k= 0;
    for(int c= 0;c<nSamples; c++)
    { /* Build the list */
      sGSPID= workingEGlist[c];
      if(matchEGsampleBySearchTerms(sGSPID, searchTerms, evalSchANDboolean))
      { /* Found it */
        sLine= ("#"+((k++)+1)) +"    "+ sGSPID+"\n";
        textReport += sLine;
      }
    } /* Build the list */
    
    textReport += "==================================\n\n";
    
    return(textReport);
  } /* getEGsampleList */
  
  
   /**
    * getEGclassSampleList() - get printable text list of class EG samples.
    * @param classSamplesList - set of comma-delim. Class A or B EG samples
    * @param className - (e.g., "A" or "B")
    * @param sTitle - optional title
    * @return printable list else null.
   */
   public String getEGclassSampleList(String classSamplesList, 
                                      String className, String sTitle)
   { /* getEGclassSampleList */
     if(classSamplesList==null || classSamplesList.length()==0)
       return(null);
     
     /* Build the report */
     String
       sGSPID= null,
       sLine= null,
       egList[]= null,
       sMsg= (sTitle!=null) ? (sTitle+" ") : "",
       textReport= "\n"+
                   "List of "+sMsg+"class "+className+" Sample GSP IDs           \n"+
                   "===================================================\n";

     egList= UtilCM.getCleanArgList(classSamplesList);    

     int k= 0;
     for(int c= 0;c<egList.length; c++)
     { /* Build the list */
       sGSPID= egList[c];
       sLine= ("#"+((k++)+1)) +"    "+ sGSPID+"\n";
         textReport += sLine;
     } /* Build the list */
     
     textReport += "==================================\n\n";
     
     return(textReport);
   } /* getEGclassSampleList */
  
  
  /**
   * getEGsamplesString() - get "," separated text string of EG samples in database.
   * If there are no search terms, then return the entire list.
   * 
   * [TODO] Read the header from the Database file which contains
   * the sample GSP IDs but omit the leading "Gene, Well ID, Feature ID"
   * @param searchTermsStr - list of search terms if not null in which case
   *                return the entire list,
   * @param egGroupList - is list of the EG groups, if ALL, then all groups
   * @param evalSchANDboolean - is true if AND, false if OR for matching
   *        search terms.
   * @return text if found, else "" if a problem.
   */
  public String getEGsamplesString(String searchTermsStr, String egGroupList[],
                                  boolean evalSchANDboolean)
  { /* getEGsamplesString */
    if(ftIM==null || ftIM.tRows<=0 || ftIM.tCols<=0)
      return("");
    
    /* Build the report */
    String
      searchTerms[]= null,
      textReport= "";

    if(searchTermsStr!=null && searchTermsStr.length()>0)
      searchTerms= UtilCM.getCleanArgList(searchTermsStr);    
    int
      nSearchTerms= (searchTerms==null) ? 0 : searchTerms.length;
    
    /* Build list to work from */
    int
      nSamplesInDB= dbGSPIDlist.length,
      nEGlist= egGroupList.length;
    String
      dbGSPIDname,
      egName,
      workingEGlist[]= new String[nSamplesInDB];
    int nSamples= 0;
    for(int d=0;d<nSamplesInDB;d++)
    {
      dbGSPIDname= dbGSPIDlist[d];
      for(int g=0;g<egGroupList.length;g++)
      { /* Build subset if using EG groups selections */
        egName= egGroupList[g];
        if(egName==null || dbGSPIDname.startsWith(egName))
        {
          workingEGlist[nSamples++]= dbGSPIDname;
          break;
        }
      }
    } /* Build subset if using EG groups selections */
    workingEGlist= UtilCM.rightSizeArray(workingEGlist, nSamples, null);    
    
    /* This is the list of ftData Data Table columns starting with "EG" and is
     * the list of EG GSP IDs in the database filtered by the search terms
     * if any. If no search terms, use the workingEGlist.
     */
    String
      sGSPID,
      sLine;
    int k= 0;
    for(int c= 0;c<nSamples; c++)
    { /* Build the list */
      sGSPID= workingEGlist[c];
      if(matchEGsampleBySearchTerms(sGSPID, searchTerms, evalSchANDboolean))
      { /* Found it */
        sLine= sGSPID;
        if(c!=(nSamples-1))
          sLine += ",";
        textReport += sLine;
      }
    } /* Build the list */
    
    return(textReport);
  } /* getEGsampleList */
  
  
  /**
   * matchEGsampleBySearchTerms() - test sGSPID if match searchTerms list.
   * Match by evalSearchANDbooleanFlag  true if AND, false if OR for matching
   *  search terms.
   * @param sGSPID - EG sample GSP ID name
   * @param searchTerms - list of search terms to test
   * @param evalSchANDboolean - is true if AND, false if OR for matching
   *        search terms.
   * @return true if match successful.
   */
  private boolean matchEGsampleBySearchTerms(String sGSPID, 
                                             String searchTermList[],
                                             boolean evalSchANDboolean)
  { /* matchEGsampleBySearchTerms */
    if(searchTermList==null)
      return(true);
   
    boolean 
      matchFlag= false;
    int 
      matches= 0,
      nSearchTermList= searchTermList.length;
    String 
      sGSPIDLC= sGSPID.toLowerCase(),
      searchTermLC= null;
    
    for(int k=0;k<nSearchTermList;k++)
    { /* Test if AND of search terms */
      searchTermLC= searchTermList[k].toLowerCase();
      matchFlag= (sGSPIDLC.indexOf(searchTermLC)!=-1);
      if(!matchFlag && sgs.evalSearchANDbooleanFlag)
      { /* failed AND */
        break;
      }
      else if(matchFlag)
        matches++;                  /* Used in computing OR */
    } /* Test if AND of search terms */
    
    /* Compute the global AND/OR match */
    boolean 
      foundIt= false;
    if(matches==nSearchTermList && sgs.evalSearchANDbooleanFlag)
      foundIt= true;                /* AND */
    if(matches>=1 && !sgs.evalSearchANDbooleanFlag)
      foundIt= true;                /* OR */
    
    return(foundIt);
  } /* matchEGsampleBySearchTerms */
  
  
  /**
   * setReportText() - update text in popup window
   * @param newText is string to copy into text window
   */
  public void setReportText(String newText)
  { /* setReportText */
    this.textReport= newText;    
    reportTextarea.setText(this.textReport);
    this.repaint(); 
  } /* setReportText */
  
  
  /**
   * setGUItitle() - update title in popup window
   * @param title is new title.
   */
  public void setGUItitle(String title)
  { /* setGUItitle */
    this.title= title; 
    this.setTitle(title);
    this.repaint();
  } /* setGUItitle */
  
    
  /**
   * setSaveAsFile() - set SaveAs file default file name
   * @param reportFile is new reportFile.
   */
  public void setSaveAsFile(String reportFile)
  { this.reportFile= reportFile; }
    
  
  /**
   * close() - close this popup and reset flags if needed
   */
  public void close()
  { /* close */ 
    /* Save the last GUI GSstate so can recover it if want on startup */
    String 
      filePath= outputSearchDir+cvt.fileSep+"lastSearchState.sgs";
    boolean ok= saveGUItoGSstateFile(filePath);
    
    if(reportFile!=null)
    { /* flush and kill the output channel */
      textReport= reportTextarea.getText(); /* Get the current value */
      cvt.fio.writeStringToFile(reportFile, textReport);
    }
    
    /* just exit */
    this.setVisible(false);
    this.showStatusFlag= false;
    this.dispose();
    closeGuiFlag= true;  /* This exits the main() loop */
  } /* close */
  
  
  /**
   * testAndSetProjDir() - test and set project directory cvt.userDir. If valid,
   * then save it in cvt.userDir.  
   * [TODO] need to [DEBUG]
   * @param testProjDir project directory
   * @return projDir if succeed in finding the project directory, else null
   */
   public String testAndSetProjDir(String testProjDir, 
                                   boolean fatalFlag)
   { /* testAndSetProjDir */   
     boolean dirOK= false;
     String projDir= testProjDir;
     try
     { /* try it straight */
       File fd= new File(testProjDir);
       dirOK= fd.isDirectory();
       projDir= testProjDir;
     }
     catch(Exception e)
     {
       dirOK= false;
     }
     
     /* Try putting test dir under userdir */
     if(!dirOK)
     { /* try it inside of userDir */
       try
       {
         String testProjDir2= cvt.userDir + testProjDir;
         File fd= new File(testProjDir2);
         dirOK= fd.isDirectory();
         projDir= testProjDir2;
       }
       catch(Exception e)
       {
         dirOK= false;
       }
     } /* try it inside of userDir */
     
     if(fatalFlag & !dirOK)
     {
       UtilCM.logMsg("\nProblem finding project directory ["+
                          testProjDir+" ] - exiting Application.");
       reportFile= null;  /* Don't save it */
       close();
     }
     
     if(projDir!=null && dirOK)
       projDir= null;
     return(projDir);
   } /* testAndSetProjDir */
     
  
  /**
   * actionPerformed() - Handle menu actions and button clicks
   * @param e is action evet
   */
  public void actionPerformed(ActionEvent e)
  { /* actionPerformed */
    /* displayURL("file://c:\\docs\\index.html") */
    String 
      filePrefix= "file://"+((cvt.isWinPCflag) ? "\\" : "")+cvt.userDir;
    String
      cmd= e.getActionCommand();

    if (cmd.equals("SetProjDir"))
    { /* [TODO] File: SetProjDir */   
      String dirStr= FileIO.getDirPathByDirBrowser(cvt.userDir,
                                            "Select project directory");
      /* test if and set project directory or exit */
      String oldPrjDir= cvt.userDir;
      /* [TODO] debug test and set */
      dirStr= testAndSetProjDir(dirStr, false);
      if(dirStr!=null)
      {
        UtilCM.logMsg("\nProject directory changed from ["+
                      oldPrjDir+"] to ["+ dirStr+"].\n");
        cvt.userDir= dirStr;
      }
      else
      {
        UtilCM.logMsg("\nProblem finding project directory ["+
                      dirStr+"] - not changed from ["+oldPrjDir+"]\n.");
        return;
      }      
    } /* File: SetProjDir */  
    
    else if (cmd.equals("SetDemoData"))
    { /* File: SetDemoData */
      /* set the Term and Sample lists for demo state. */
      setDemoParameters();
      return;
    } /* File: SetDemoData */ 

    else if (cmd.equals("GetUserTermListFile"))
    { /* File: SetUserTermList */
      /* Set the search-term list from a file: either a Table
       * file with (Genes, Well ID, Feature ID) or just a list of genes
       * or feature ids. */
      setUserTermListFromFile();
      return;
    } /* File: SetUserTermList */    

    else if (cmd.equals("SaveAsSGstate"))
    { /* File: "SaveAs current search parameters GUI to .sgs file" */
      /* Get the old search parameters from a .map file that we 
       * previously saved. 
       */      
      PopupFileDialog pfd= new PopupFileDialog();
      String 
        filePath= pfd.popupFileDialog(outputSearchDir+cvt.fileSep+
                                      "savedSearchState.sgs", null,
                                      "Name of Search State file to SAVE",
                                      false);
      if(filePath==null)
        return;
      boolean ok= saveGUItoGSstateFile(filePath);
      return;
    } /* File: "SaveAs current search parameters GUI to .sgs file"*/  
    
    else if (cmd.equals("RestoreSGstate"))
    { /* File: "Restore previously saved search GUI from .sgs file" */
      /* Get the old search parameters from a .map file that we 
       * previously saved. 
       */
      PopupFileDialog pfd= new PopupFileDialog();
      String 
        filePath= pfd.popupFileDialog(inputSearchDir+cvt.fileSep+
                                      "savedSearchState.sgs", ".sgs",
                                      "Restore GUI from Search State file",
                                      true);
      if(filePath==null)
        return;      
      boolean ok= restoreGUIfromGSstateFile(filePath);
      return;
    } /* File: "Restore previously saved search GUI from .sgs file" */    

    else if (cmd.equals("RestoreLastSavedSGstate"))
    { /* File: "Restore last saved search GUI from .sgs file" */
      /* Get the last search parameters from a .map file that we 
       * previously saved. 
       */
      /* Test if the last .sgs saved file "lastSearchState.sgs" exists */
      String 
        filePath= outputSearchDir+cvt.fileSep+"lastSearchState.sgs";
      File fd= new File(filePath);
      if(!fd.exists())
      {
        UtilCM.logMsg("No lastSearchState.sgs file exists - ignoring.\n");
        return; 
      }
      boolean ok= restoreGUIfromGSstateFile(filePath);
      return;
    } /* File: "Restore last saved search GUI from .sgs file" */
    
    else if (cmd.equals("ChangeSearchResultsOutputDir"))
    { /* File: "Change default Search-Results output directory" */
      /* Popup Dir browser to set the directory */
      PopupFileDialog pdq= new PopupFileDialog();
      int idxFileSep= outputSearchDir.indexOf(cvt.fileSep);
      String
        fullDir= (idxFileSep==-1) ? cvt.userDir+outputSearchDir : outputSearchDir;
      String
        answer= pdq.popupDirectoryDialog(fullDir,
                                         "Change default Search-Results directory", 
                                         false);
      if(answer!=null)
      {
        outputSearchDir= answer;
        UtilCM.logMsg("Changed the Search-Results output directory to '"+
                      outputSearchDir+"'\n");
      }
      return;
    } /* File: "Change Search-Results output directory" */

    else if (cmd.equals("ClearReportLog"))
    { /* File: ClearReport */
      this.clearText();
      return;
    } /* File: ClearReport */ 

    else if (cmd.equals("SaveReportLogAs"))
    { /* File: SaveReportLogAs */    
      PopupFileDialog pfd= new PopupFileDialog();
      String 
        fileStr= pfd.popupFileDialog(reportFile, null,"reportFile", false);
      if(fileStr==null)
        return;                      /* NO-OP */
      reportFile= fileStr;
      textReport= getReportText();  
      if(cvt.fio.writeStringToFile(reportFile, textReport))      
        UtilCM.logMsg("\nSaved Report-Log as ["+reportFile+"]\n"); 
      else
        UtilCM.logMsg("\nProblem saving Report-Log ["+reportFile+
                         "] - not saved.\n"); 
      return;
    } /* File: SaveReportLogAs */ 

    else if (cmd.equals("resetConverter"))
    { /* File: resetConverter */
      /* Reset the GUI state so no files specified and set initial Search Params
       * buttons and menus state. 
       */
      resetInitialGuiProcessingState(); /* reset search terms & samples GUI state */
      setEnableSearchParamsButtonsAndMenus();
      cvt.clearGenHTMLpathList(true);   /* Clear list */
      UtilCM.logMsg("\nReset the converter. You are ready to do a new search "+
                    "- enter search terms.\n");
      this.repaint();
      return;
    } /* File: resetConverter */

    else if (cmd.equals("Close"))
    { /* File: Close */
      close();
    } /* File: Close */
    
    else if (cmd.equals("ViewHTML"))
    { /* (Button): ViewHTML */
      String genHTMLpathList[]= cvt.getGenHTMLpathList();
      if(genHTMLpathList==null)
      {
        UtilCM.logMsg("\nThere were no HTML files that generated.\n");
        guiActiveHTMLfile= null;
        guiActiveTXTfile= null;
        return;
      }
      else 
      {
        guiActiveHTMLfile= genHTMLpathList[0]; 
        if(guiActiveHTMLfile!=null)
          guiActiveTXTfile= guiActiveHTMLfile.substring(0,
                                             guiActiveHTMLfile.length()-5)+".txt";
      }
      viewHTMLfile(); /* popup browser on guiActiveHTMLfile file. */
    } /* (Button): ViewHTML */  

    
    else if(cmd.equals("ShowBigTextViewer"))
    { /* Show "Big Report Text Area" */
      if(bptv==null)
      {
        String rptStr= reportTextarea.getText();
        bptv= new PopupTextViewer("Report-Log", rptStr, 30,115, false);
        UtilCM.setBigReportTextViewer(bptv);
      }
      else
      { /* make it visible */
        bptv.setVisible(true);
      }
    } /* Show "Big Report Text Area" */

    else if (cmd.equals("SortByColData"))
    { /* view: SortByColData */
      if(sgs.reportFoldChangeFlag)
      {
        UtilCM.logMsg("\nCan't sort data by header term-name if "+
                      "reporting fold-change. Not sorting.\n");
        sgs.sortFlipTableByColumnName= null;
        return;
      }
      String
        defStr= (sgs.sortFlipTableByColumnName==null)
                   ? "" : sgs.sortFlipTableByColumnName,
        msg= "Specify header data term-name to sort generated table rows.";
      PopupTextFieldDialog
        ptfd= new PopupTextFieldDialog(this, msg, defStr);
      if(!ptfd.okFlag || ptfd.answer==null)
      {
        UtilCM.logMsg("\nNo change.\n");       
        return;
      }
      String sAnswer= UtilCM.rmvEnclosingWhitespace(ptfd.answer);
      sgs.sortFlipTableByColumnName= sAnswer;

      UtilCM.logMsg("\nSort row data descending by '"+
                    sgs.sortFlipTableByColumnName+
                    "' in generated table.\n");
    } /* File: SortByColData */
        
    else if (cmd.equals("showDataHeatmapFlipTable"))
    { /* view: showDataHeatmapFlipTable */
      String
        defPrecisionStr= (""+sgs.dataPrecisionHTMLtable),
        msg= "Specify precision for numeric data in generated HTML table as -1 (all) or 0 to 5.";
      PopupTextFieldDialog
        ptfd= new PopupTextFieldDialog(this, msg, defPrecisionStr);
      if(!ptfd.okFlag || ptfd.answer==null)
      {
        UtilCM.logMsg("\nNo change - using HTML data precision="+
                      sgs.dataPrecisionHTMLtable+".\n");       
        return;
      }
      int newPrecision= UtilCM.cvs2i(ptfd.answer, -1);
      newPrecision= Math.max(Math.min(newPrecision,5), -1);
      sgs.dataPrecisionHTMLtable= newPrecision;

      UtilCM.logMsg("\nUsing HTML data precision="+sgs.dataPrecisionHTMLtable+".\n");   
    } /* File: showDataHeatmapFlipTable */

    else if (cmd.equals("SetdataPrecisionHTMLtable"))
    { /* view: SetdataPrecisionHTMLtable */
      String
        defPrecisionStr= (""+sgs.dataPrecisionHTMLtable),
        msg= "Specify precision for numeric data in generated HTML table as -1 (all) or 0 to 5.";
      PopupTextFieldDialog
        ptfd= new PopupTextFieldDialog(this, msg, defPrecisionStr);
      if(!ptfd.okFlag || ptfd.answer==null)
      {
        UtilCM.logMsg("\nNo change - using HTML data precision="+
                      sgs.dataPrecisionHTMLtable+".\n");       
        return;
      }
      int newPrecision= UtilCM.cvs2i(ptfd.answer, -1);
      newPrecision= Math.max(Math.min(newPrecision,5), -1);
      sgs.dataPrecisionHTMLtable= newPrecision;

      UtilCM.logMsg("\nUsing HTML data precision="+
                    sgs.dataPrecisionHTMLtable); 
      if(sgs.dataPrecisionHTMLtable<0)
        UtilCM.logMsg(" using full precision");      
      UtilCM.logMsg("\n");   
    } /* view: setdataPrecisionHTMLtable */    
    
    else if (cmd.equals("AssignEGsamplesToClassA"))
    { /* view: Assign EG samples to Class A */
      if(!sgs.reportFoldChangeFlag)
      {
        UtilCM.logMsg("Command ignored - you must enable "+
                      "'Report Fold Change of 2 sample subsets' checkbox first.\n");
        return;
      }
      sgs.filterRowStr= filterRowTextField.getText();
      sgs.classAsamples= getEGsamplesString(sgs.filterRowStr,sgs.sampleRowFilter,
                                            sgs.evalSearchANDbooleanFlag);
      UtilCM.logMsg("\nAssigning currently specified EG samples to class A: "+
                    sgs.classAsamples+"\n");
      String sR= getEGsampleList(sgs.filterRowStr,sgs.sampleRowFilter,
                                 sgs.evalSearchANDbooleanFlag, "Class A");
      UtilCM.logMsg(sR);                                     
    } /* view: Assign EG samples to Class A */    
    
    else if (cmd.equals("AssignEGsamplesToClassB"))
    { /* view: Assign EG samples to Class B */
      if(!sgs.reportFoldChangeFlag)
      {
        UtilCM.logMsg("Command ignored - you must enable "+
                      "'Report Fold Change of 2 sample subsets' checkbox first.\n");
        return;
      }
      sgs.filterRowStr= filterRowTextField.getText();
      sgs.classBsamples= getEGsamplesString(sgs.filterRowStr,sgs.sampleRowFilter,
                                        sgs.evalSearchANDbooleanFlag);
      UtilCM.logMsg("\nAssigning currently specified EG samples to class B: "+
                    sgs.classBsamples+"\n"); 
      String sR= getEGsampleList(sgs.filterRowStr,sgs.sampleRowFilter,
                                 sgs.evalSearchANDbooleanFlag, "Class B");
      UtilCM.logMsg(sR);
    } /* view: Assign EG samples to Class B */
    
    else if (cmd.equals("ListAllGenes"))
    { /* List: "List all genes in Report window" */
      /* get printable text list of genes in the database.*/
      if(processFlag)
      {
        UtilCM.logMsg("\nCan't list all of the genes until finished reading "+
                      "the database.\n Waiting .");
        int maxCnts= 100;
        while(processFlag)
        {
          UtilCM.sleepMsec(500);
          UtilCM.logMsg(".");
          if(maxCnts-- <=0)
            return;
        }
        UtilCM.logMsg("\n");        
      }
      String sR= getDBgeneList(null,false);
      UtilCM.logMsg("\nList of all genes in the database.\n"+sR);
    }
    
    else if (cmd.equals("ListMatchingGenes"))
    { /* List: "List matching genes in Report window" */
      /* get printable text list of genes in the database.*/
      sgs.searchTermFilterStr= searchTermTextArea.getText();
      sgs.searchTermFilterStr= UtilCM.getCleanSpaceList(sgs.searchTermFilterStr);
      String sR= getDBgeneList(sgs.searchTermFilterStr,
                               !sgs.flipTableUseExactMatchFlag);
      UtilCM.logMsg("\nList of matching genes in the database.\n"+sR);
    }
    
    else if (cmd.equals("ListMatchingEGsamples"))
    { /* List: "List matching EG samples in Report window" */
      /* Get printable text list of EG samples in the database.
       * Also need to use the selected EG groups.
       */
      sgs.filterRowStr= filterRowTextField.getText();
      String sR= getEGsampleList(sgs.filterRowStr,sgs.sampleRowFilter,
                                 sgs.evalSearchANDbooleanFlag, null);
      UtilCM.logMsg("\nList of matching EG samples in the database.\n"+sR);
    } 
    
    else if (cmd.equals("ListClassAsamples"))
    { /* List: "List class A EG samples, if defined, in Report window" */
      /* Get printable text list of EG samples in the database.
       */
      String sR= getEGclassSampleList(sgs.classAsamples,"A",null);
      if(sR!=null)
        UtilCM.logMsg("\nList of class A EG samples in the database.\n"+sR);
      else
        UtilCM.logMsg("\nNeed to define class B EG samples first.\n"+sR);
    }
    
    else if (cmd.equals("ListClassBsamples"))
    { /* List: "List class B EG samples, if defined, in Report window" */
      /* Get printable text list of EG samples in the database.
       */
      String sR= getEGclassSampleList(sgs.classBsamples,"B",null);
      if(sR!=null)
        UtilCM.logMsg("\nList of class B EG samples in the database.\n"+sR);
      else
      UtilCM.logMsg("\nNeed to define class B EG samples first.\n"+sR);
    }

    else if (cmd.equals("SearchGUIusage"))
    { /* Help: SearchGUIusage */
      String
        urlStr= filePrefix+"searchGUIusage.html",
        windowName= programName + " Search Database GUI Usage";
      urlStr= UtilCM.replaceSubstrInString(urlStr,"\\","/");
      PopupHTMLbrowser phb= new PopupHTMLbrowser();
      String phbErrMsg= phb.popupHTMLbrowser(urlStr, windowName);
      if(phbErrMsg!=null)
        UtilCM.logMsg(phbErrMsg);
    } /* Help: SearchGUIusage */    
    
    else if (cmd.equals("jakStatWebsite"))
    { /* List: "Jak-Stat.nih.gov Web site" */
      String
        urlStr= URL_HOME,
        windowName= programName + " Trans-NIH Jak-Stat Initiative";
      urlStr= UtilCM.replaceSubstrInString(urlStr,"\\","/");
      PopupHTMLbrowser phb= new PopupHTMLbrowser();
      String phbErrMsg= phb.popupHTMLbrowser(urlStr, windowName);
      if(phbErrMsg!=null)
        UtilCM.logMsg(phbErrMsg);
    }    
    
    else if (cmd.equals("jakStatProspectorWebsite"))
    { /* List: "Jak-Stat.nih.gov Prospector Web site" */
      String
        urlStr= URL_HOME_DB,
        windowName= programName + "Jak-Stat Prospector";
      urlStr= UtilCM.replaceSubstrInString(urlStr,"\\","/");
      PopupHTMLbrowser phb= new PopupHTMLbrowser();
      String phbErrMsg= phb.popupHTMLbrowser(urlStr, windowName);
      if(phbErrMsg!=null)
        UtilCM.logMsg(phbErrMsg);
    } 
    
    else if (cmd.equals("ReferenceManual"))
    { /* Help: ReferenceManual */
      String
        urlStr= filePrefix+cvt.referenceManual,
        windowName= programName + " Reference Manual";
      urlStr= UtilCM.replaceSubstrInString(urlStr,"\\","/");
      PopupHTMLbrowser phb= new PopupHTMLbrowser();
      String phbErrMsg= phb.popupHTMLbrowser(urlStr, windowName);
      if(phbErrMsg!=null)
        UtilCM.logMsg(phbErrMsg);
    } /* Help: ReferenceManual */    
        
    else if (cmd.equals("Summary"))
      { /* Help: Summary */ 
      String 
         msg= "\n-------------------------------------------------------\n"+
              "\n"+title+
              cvt.programSummary+"\n"+
              cvt.openSourceNotice;      
      UtilCM.logMsg(msg);
    } /* Help: Summary */

    else if (cmd.equals("License"))
    { /* Analyze: License */
      String 
        msg= "\n-------------------------------------------------------\n"+
             "\n" + cvt.openSourceNotice;
     UtilCM.logMsg(msg);
    } /* Analyze: License */

    else if (cmd.equals("AboutJSDB"))
    { /* Help: About Jak-Stat Database*/
      String 
        msg= "\n-------------------------------------------------------\n"+
             "\n"+title+"\n\n"+
             "The microarray data in the database has been generated as part of the\n" +
             "Group Stat Project ("+URL_HOME_DB+") \n" +
             "as part of the Trans-NIH JAK-STAT Initiative (http://jak-stat.nih.gov/).\n\n"+
             "DATA SHARING AGREEMENT\n"+
             "The microarray gene expression profiling experiments that are available\n"+
             "in the \"JAK-STAT Prospector\" have been generated by researchers from\n"+
             "the National Institutes of Health (NIDDK, NIAMS, NHLBI and NIAID) using\n"+
             "Federal funds. The mouse data are freely available to researchers inside\n"+
             "and outside the United States to foster their scientific endeavors. This\n"+
             "Web site only contains the mouse data. For any Human data mentioned in\n"+
             "the GSP Inventory, contact the respective PIs for availability. If information\n" +
             " from this database is to be included in scientific publications or\n" +
             "presentations, the National Institutes of Health and the \"JAK-STAT Prospector\"\n" +
             "(http://jak-stat.nih.gov/) should be acknowledged. If the data are also\n" +
             "available through GEO, the respective accession number should be acknowledged.\n\n"+
             "For more information, contact Dr. Lothar Hennighausen (NIDDK) lotharh@mail.nih.gov\n";
      UtilCM.logMsg(msg);
    } /* Help: About Jak-Stat Database */
    
    else if (cmd.equals("AboutSoftware"))
    { /* Help: About Softare*/
      String 
        msg= "\n-------------------------------------------------------\n"+
             "\n"+title+"\n\n"+
             cvt.openSourceNotice;
      UtilCM.logMsg(msg);
    } /* Help: About Software */
                     
    else if (cmd.equals("UpdateSearchGUI"))
    { /* Help: UpdateSearchGUI */      
      UtilCM.logMsg("\n**********************************************************************\n"+
                      "* Updating the SearchGUI program .jar file from the jak-stat.nih.gov "+
                      "Web site is not available at this time.\n" +
                      "**********************************************************************\n");
      updateSearchGUIjarFile();
    } /* Help: UpdateSearchGUI */   
        
    /* Radio button action commands */
    else if (cmd.equals("MatchGeneNameTerms"))
    { /* "Match gene names" */
      sgs.flipTableUseExactMatchFlag= true; 
      UtilCM.logMsg("Use exact 'gene name' matching for search terms.\n");
    }
    
    else if (cmd.equals("MatchSubStrTerms"))
    { /* "Match sub-strings" */
      sgs.flipTableUseExactMatchFlag= false;    
      UtilCM.logMsg("Use sub-string matching for search terms.\n");
    }
        
    /* Radio button action commands */
    else if (cmd.equals("ANDsearchTerms"))
    { /* "AND search terms" */
      sgs.evalSearchANDbooleanFlag= true;  
      UtilCM.logMsg("Use 'AND' of the search terms.\n");
    }
    
    else if (cmd.equals("ORsearchTerms"))
    { /* "OR search terms" */
      sgs.evalSearchANDbooleanFlag= false;    
      UtilCM.logMsg("Use 'OR' or the search terms.\n");
    }
    
  } /* actionPerformed */ 
      
    
  /**
   * printSearchResultsFileNames() - print Search-Results File Names to log.
   */  
  private void printSearchResultsFileNames()
  { /* printSearchResultsFileNames */
    String 
        srBaseName= sgs.searchResultsBaseFile+"-search",
        srOutputDir= cvt.userDir+outputSearchDir;
    UtilCM.logMsg("\nPressing the Process button will generate a "+
                  "Search-Results Excel compatible file '"+
                  srBaseName+".txt'\n"+
                  "and a HTML file '"+srBaseName+
                  ".html' in the that is viewable in a Web browser.\n"+
                  "These files are in the '"+srOutputDir+
                  "' directory.\n");
  } /* printSearchResultsFileNames */
  
  
  /**
   * printGuiFSM() - print GuiFSM if printFlag set
   */  
  public void printGuiFSM(String preface, boolean printFlag)
  { /* printGuiFSM */
    if(printFlag)
      UtilCM.logMsg(preface+" "+getGuiFSM()+"\n");
  } /* printGuiFSM */ 
  
  
  /**
   * printGuiFSMlf() - print GuiFSM if printFlag set followed by extra line feed
   */  
  public void printGuiFSMlf(String preface, boolean printFlag)
  { /* printGuiFSMlf */
    if(printFlag)
      UtilCM.logMsg(preface+" "+getGuiFSM()+"\n\n");
  } /* printGuiFSMlf */
  
  
  /**
    * getGuiFSM() - Get the GUI FSM state string.
    * @return the current state string
    */
   public String getGuiFSM()
   { /* getGuiFSM */
     String
       sR= "GuiFSM["+guiFSMstate+"] (";     
     sR += "process:"+((processFlag) ? "T" : "F");    
     sR += ", processedOK:"+((processedOKflag) ? "T" : "F");   
     sR += ", done:"+((doneFlag) ? "T" : "F");    
     sR += ", cancel:"+((cancelFlag) ? "T" : "F");   
     sR += ", gui.pd("+sGui.pds+")"; 
     if(sGui.pds!=null)
       sR += ".isAlive():"+sGui.pds.isAlive();
     sR += ")";  
   
   return(sR);
   } /* getGuiFSM */

   
  /**
   * resetInitialGuiProcessingState() - reset the search terms & samples GUI state
   */
  public void resetInitialGuiProcessingState()
  { /* resetInitialGuiProcessingState */
    /* [1] Clear the search term list searchTermTextArea GUI */
    searchTermTextArea.setText(""); 
    /* Clear search term from  */
    sgs.searchTermFilterStr= null;
    searchTermFilter= new String[nSearchTermNames][];
    searchTermFilter[0]= null;
    searchTermFilter[1]= null;
    
    /* [2] Setup the List samplesList to ALL */
    sgs.filterRowStr= "";
    sgs.sampleRowFilterALLflag= true;
    int nsampleChoiceData= sampleChoiceData.length;
    sgs.sampleRowFilter= new String[nsampleChoiceData-1];  /* Default is "ALL" */
    for(int i=0;i<nsampleChoiceData;i++)
    { /* setup the List GUI and the samples to use */
      samplesList.setSelectedIndex(i);
    }
    samplesList.setSelectedIndex(0);    
    
    /* [3] Clear the Filter Row TextField data */
    filterRowTextField.setText("");
    sgs.filterRowStr= "";
  } /* resetInitialGuiProcessingState */

  
  /**
   * clearGuiProcessingState() - clear the GUI state
   */
  public void clearGuiProcessingState()
  { /* clearGuiProcessingState */
    guiActiveHTMLfile= null;
    guiActiveTXTfile= null;
    
    processFlag= false;
    processedOKflag= false;
    doneFlag= false;
    cancelFlag= false;

    if(foldChangeMCB!=null)
    {
      foldChangeMCB.setState(false);
      classAMI.setEnabled(false);
      classBMI.setEnabled(false);
    }
    sgs.reportFoldChangeFlag= false;
    sgs.classAsamples= null;
    sgs.classBsamples= null;
    sgs.foldChangeThrFlag= false;
    sgs.foldChangeThr= 0.0F;
        
    sGuiArgV= null;    
   
    cvt.setAbortProcessingFlag(false); /* clear flag */

    /* [2] Set additional title for generated Web page */
    dataSource= "User specified list of search terms and sample groups";

    if(restoreSGstateMI!=null)
      restoreSGstateMI.setEnabled(true);
    if(saveSGstateMI!=null)
      saveSGstateMI.setEnabled(true);
  } /* clearGuiProcessingState */

         
  /**
   * setCancelFlag() - set the Cancel flag value
   * @param flag value to set the cancelFlag
   */
  public void setCancelFlag(boolean flag)
  { cancelFlag= flag; }
       
  
  /**
   * getCancelFlag() - get the Cancel flag value
   */
  public boolean getCancelFlag()
  { return(cancelFlag); }
  
  
  /**
   * setEnableSearchParamsState() - set Search parameters GUI & menus state.
   * This sets the flags to the initial "SearchParams" data state. 
   */
  public void setEnableSearchParamsState()
  { /* setEnableSearchParamsState */
    guiFSMstate= "SearchParams";    
    clearGuiProcessingState();  /* clear the GUI state */    
  } /* setEnableSearchParamsState */
  
  
  /**
   * setEnableCancelState() - when are able to do processing state.
   * This sets the flags to the "Process" data state. It also
   * clears the list of generated HTML files.
   */
  public void setEnableCancelState()
  { /* setEnableCancelState */
    guiFSMstate= "Processing";    
    processFlag= true;
    processedOKflag= false;
    doneFlag= false;
    cancelFlag= false;
    
    cvt.setAbortProcessingFlag(false);
  } /* setEnableCancelState */
  
  
  /**
   * setEnableViewingState() - when can view processed HTML files state.
   * This sets the flags to the "Viewing-enable" data state. 
   */
  public void setEnableViewingState()
  { /* setEnableViewingState */
    guiFSMstate= "Viewing-enable";    
    processFlag= false;
    processedOKflag= false;
    doneFlag= false;
    cancelFlag= false;
    
    String htmlFilesList[]= cvt.getGenHTMLpathList();
    if(htmlFilesList!=null)
    {
      guiActiveHTMLfile= htmlFilesList[0];
      if(guiActiveHTMLfile!=null)
        guiActiveTXTfile= guiActiveHTMLfile.substring(0,
                                     guiActiveHTMLfile.length()-5)+".txt";
    }
    else
    {
      guiActiveHTMLfile= null;        /* Clear it now. Choice will select it */
      guiActiveTXTfile= null;
    }
  } /* setEnableViewingState */ 
     
  
  /**
   * quit() - closing down the window, get rid of the frame.
   * @see #close
   */
  public void quit()
  { close(); } 
  
  
  /**
   * updateSearchGUIjarFile() - update the SearchGui.jar file from
   * the URL_HOME web server.
   */
  public boolean updateSearchGUIjarFile()
  { /* updateSearchGUIjarFile */
    String
      pgmName= "SearchGui",    
      urlJarFile= URL_JAR_FILE;
    if(!UtilCM.updateJarFile(pgmName, urlJarFile, cvt.userDir))
    {
      UtilCM.logMsg("Problem updating the SearchGui.jar file from the server.\n");
      return(false);
    }
    else
      return(true);
  } /* updateSearchGUIjarFile */
  
  
  /**
   * itemStateChanged() - handle item state changed events
   * NOTE: need to implement CheckboxMenuItems.
   * @param e is ItemEvent
   */
  public void itemStateChanged(ItemEvent e)
  { /* itemStateChanged */
    CheckboxMenuItem bogusMCB= new CheckboxMenuItem();
    
    ItemSelectable  s= e.getItemSelectable();
    Object selected[]= s.getSelectedObjects();
    Object obj= e.getSource();
    CheckboxMenuItem itemMCB= (obj instanceof CheckboxMenuItem)
                                 ? (CheckboxMenuItem)e.getSource() : bogusMCB;
    Choice itemCO= (obj instanceof Choice) ? (Choice)obj : null;

    if(itemMCB==verboseMCB)
    { /* viewMenu: Verbose reporting mode */
      cvt.verboseLoggingFlag= itemMCB.getState();
      if(cvt.verboseLoggingFlag)
        UtilCM.logMsg("\nProcess reporting is set to 'Verbose mode'.\n");
      else
        UtilCM.logMsg("\nProcess reporting is set to 'Quiet mode'.\n");
    }
    
    else if(itemMCB==foldChangeMCB)
    { /* viewMenu: Report Fold Change of 2 sample subsets mode */
      sgs.classAsamples= null;  /* Always clear */
      sgs.classBsamples= null;
      sgs.reportFoldChangeFlag= itemMCB.getState();
      if(sgs.reportFoldChangeFlag)
      {
        UtilCM.logMsg("\nReport Fold Change of 2 sample subsets.\n");
        classAMI.setEnabled(true);
        classBMI.setEnabled(true);
        foldChangeThrMCB.setEnabled(true);
      }
      else
      { /* Disable All foldchange related variables */
        UtilCM.logMsg("\nReport data as intensity values.\n");
        classAMI.setEnabled(false);
        classBMI.setEnabled(false);
        foldChangeThrMCB.setEnabled(false); 
        sgs.foldChangeThrFlag= false;
        sgs.foldChangeThr= 0.0F;
      }
    } /* viewMenu: Report Fold Change of 2 sample subsets mode */
    
    else if(itemMCB==foldChangeThrMCB)
    { /* viewMenu: "Only keep genes/probes with |fold-change| >= threshold" */
      sgs.foldChangeThrFlag= itemMCB.getState();
      if(sgs.foldChangeThrFlag)
      { /* Get the fold-change threshold */
        String
          defStr= UtilCM.cvf2s(sgs.foldChangeThr, 4),
          msg= "Specify Fold-Change Report threshold for '|fold-change| >= threshold'.";
        PopupTextFieldDialog
          ptfd= new PopupTextFieldDialog(this, msg, defStr);
        if(!ptfd.okFlag || ptfd.answer==null)
        {
          UtilCM.logMsg("\nNo change to Fold-Change Reporting fold-change threshold: "+
                        UtilCM.cvf2s(sgs.foldChangeThr,4)+"\n");       
          return;
        }
        float value= UtilCM.cvs2f(ptfd.answer,0.0F);
        if(value>=0.0F)
        { /* Change it */         
          sgs.foldChangeThr= value;
          UtilCM.logMsg("\nSet the Fold-Change Reporting fold-change threshold: "+
                        UtilCM.cvf2s(sgs.foldChangeThr,3)+"\n");
          return;
        }
        UtilCM.logMsg("\nProblem, must specify |fold-change threshold| > or = 0.0.\n");
        foldChangeThrMCB.setEnabled(false);
        sgs.foldChangeThrFlag= false;
        sgs.foldChangeThr= 0.0F;
      } /* Get the fold-change threshold */
      else
      { /* Disable All foldchange related variables */
        sgs.foldChangeThrFlag= false;
        sgs.foldChangeThr= 0.0F;
      }
    } /* viewMenu: "Only keep genes/probes with |fold-change| >= threshold" */
    
    else if(itemMCB==showDataHeatmapFlipTableMCB)
    { /* "Show data heat-map in View HTML Results" */
      sgs.showDataHeatmapFlipTableFlag= itemMCB.getState();
      if(sgs.showDataHeatmapFlipTableFlag)
        UtilCM.logMsg("\nCreate data heat-map when generate View HTML.\n");
      else
        UtilCM.logMsg("\nDon't create data heat-map when generate View HTML.\n");
    }
    
  } /* itemStateChanged */
  
  
  /**
   * updateSampleList() - handle item state changed events
   * NOTE: need to implement radio groups here since AWT only
   * implements radio groups for Checkboxes, and CheckboxMenuItems.
   * @param e is ItemEvent
   */
  public void updateSampleList(ListSelectionEvent lsEvent)
  { /* itemStateChanged */
    boolean isAdjusting= lsEvent.getValueIsAdjusting();
    if(isAdjusting)
    { /* select the samples Experiment Groups to use in the search */
      JList list= (JList)lsEvent.getSource();
      int
        curIdx= list.getSelectedIndex(),
        selIdx[]= list.getSelectedIndices();
      Object listObj[]= list.getSelectedValues();
      if(selIdx==null)
        return;
      int
        nSelected= (selIdx==null) ? 0 : selIdx.length,
        nsampleChoiceData= sampleChoiceData.length;  
                                           /* full data available in list */
      
      if(curIdx!=0 && curIdx!=-1)
      { /* selected some samples that are not ALL */
        int nSampleRowFilter= nSelected;
        if(selIdx[0]==0)
          nSampleRowFilter= nSelected-1;
        sgs.sampleRowFilter= new String[nSampleRowFilter]; 
        UtilCM.logMsg("Using samples filter:");
        int k= 0;
        for(int i=0;i<nSelected;i++)
        { /* setup the List GUI and the samples to use, less ALL */
          int p= selIdx[i];
          if(p==0)
          {
            list.setSelectedIndex(0);  /* Clear everything but ALL */
            list.clearSelection();
            continue;
          }
          String expGrp= sampleChoiceData[p][0];
          sgs.sampleRowFilter[i]= expGrp;
          UtilCM.logMsg(" "+expGrp);
        }
        UtilCM.logMsg("\n");
        sgs.sampleRowFilterALLflag= false;
        return;
      } /* selected some samples that are not ALL */
      
      else if(curIdx==0)
      { /* use ALL */
        UtilCM.logMsg("Using ALL samples filter.\n");
        sgs.sampleRowFilter= new String[nsampleChoiceData-1];  /* Default is "ALL" */
        sgs.sampleRowFilterALLflag= true;
        for(int i=1;i<nsampleChoiceData;i++)
        { /* setup the List GUI and the samples to use */
          sgs.sampleRowFilter[i-1]= sampleChoiceData[i][0];
        }
        if(nSelected>1)
        {
          list.clearSelection();
          list.setSelectedIndex(0);  /* Clear everything but ALL */ 
        }
        return;
      } /* use ALL */
      
      else if(curIdx==-1)
      { /* Handle case where item was unselected */
        UtilCM.logMsg("Using ALL samples filter.\n");
        sgs.sampleRowFilter= new String[nsampleChoiceData-1];  /* Default is "ALL" */ 
        for(int i=1;i<nsampleChoiceData;i++)
        { /* setup the List GUI and the samples to use */
          sgs.sampleRowFilter[i-1]= sampleChoiceData[i][0];
        }
        list.clearSelection();
        list.setSelectedIndex(0);  /* Clear everything but ALL */        
        sgs.sampleRowFilterALLflag= true;
        return;
      }/* Handle case where item was unselected */
      
    } /* select the samples Experiment Groups to use in the search */    
    
  } /* updateSampleList */
  
  
  /**
   * viewHTMLfile() - popup browser on guiActiveHTMLfile file.
   * @return true if succeed
   */
  private boolean viewHTMLfile()
  { /* viewHTMLfile */
    if(guiActiveHTMLfile==null)
    {
      UtilCM.logMsg("There is no HTML file selected. "+
                    "Select one and try again.\n");
      return(false);
   }

    /* displayURL("file://c:\\docs\\index.html") */
   String 
     filePrefix= "file://"+((cvt.isWinPCflag) ? "\\" : "")+cvt.userDir,
     urlStr= filePrefix+guiActiveHTMLfile,
     windowName= guiActiveHTMLfile;
   urlStr= UtilCM.replaceSubstrInString(urlStr,"\\","/");
   PopupHTMLbrowser phb= new PopupHTMLbrowser();
   String phbErrMsg= phb.popupHTMLbrowser(urlStr, windowName);
   
   if(phbErrMsg!=null)
     UtilCM.logMsg(phbErrMsg);
   else
   {
     UtilCM.logMsg("Displaying '"+guiActiveHTMLfile+
                   "' in your Web browser.\n");
     UtilCM.logMsg("Note the '"+guiActiveTXTfile+
                   "' Excel file was also created.\n");
   }
   
   return(true);
  } /* viewHTMLfile */
  
  
  /**
   * windowClosing() - closing down the window, get rid of the frame.
   * @param e is window closing event
   * @see #close
   */
  public void windowClosing(WindowEvent e)
  { this.close(); } 
  
  
  /*Others not used at this time */
  public void windowOpened(WindowEvent e) { this.repaint(); }
  public void windowActivated(WindowEvent e) { this.repaint(); }
  public void windowClosed(WindowEvent e) { }
  public void windowDeactivated(WindowEvent e) { }
  public void windowDeiconified(WindowEvent e) { this.repaint(); }
  public void windowIconified(WindowEvent e) { }

  
  /* @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ */

  /**
   * Class SGstate contains the SearchGUI state as well as functions to maintain
   * the state.
   * List of functions
   * =================
   * copyStateFromCvt() - copy the partial state from cvt Globals
   * readSGstate() - read the state from a saved state file .ssg
   * writeSGstate() - write the state to a saved state file .ssg
   * copyGlobalsToSGstate() - save Globals instance in SGstate variables.
   */
  class SGstate
  { /* SGstate */
    /* SearchGUI instance */
    public SearchGUI 
      sGui= null;
    
    /* Converter instance */
    public HTMLtools 
      cvt= null; 

    /** Hash table of .sgs values read */
    public Hashtable 
      sgStateHT;
    /** # of .sgs hash table entries */
    public int
      nStateEntries= 0;
    /** # of hash table entries after call readNameValuesHashTableFromFile() */
    public int
      nEntries= 0;
    
    /* State -flip variables to SearchGUI variables
     * See createParamsMapFile() for what variables to set.
     */
    /* -flipOrderHdrColNames:"*LIST*,Stat5a," */
    public String
      flipOrderHdrColList[]= null;
    public int
      nFlipOrderHdrColList= 0;
        
    /* [TODO] map to: nSearchTermNames,
     * searchTermNames[0:nSearchTermNames-1] and 
     * searchTermFilter[0:nSearchTermNames-1][nbr of terms if any].
     * -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
     * -flipColumnName:"*LIST*,Well ID,123456,123444"
     * -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at" 
     * */
    public int
      nFlipColumns= 0;
    public String
      flipColumnFile[]= null;
    public String
      flipColumnName[]= null;
    public String
      flipColumnValues[][]= null;
      
    /* -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2" */
    public boolean
      sampleRowFilterALLflag= false;
    public String
      sampleRowFilter[]= null;
        
    /** Flag for "Report Fold Change of 2 sample subsets" set by  */
    public boolean
      reportFoldChangeFlag= false;
    
    /* The flag associated with CheckboxMenuItem foldChangeThrMCB
     * "Only keep genes/probes with |fold-change| >= threshold".
     * When it switches to true it pops up the query for foldChangeThr. */
    /* -flipFCthreshold:{foldChangeThr} 
     * [if foldChangeThrFlag && foldChangeThr>0.0F] */
    public boolean
      foldChangeThrFlag= false;
    
    /** Fold-change threshold value used from the Menu checkbox item 
     * foldChangeThrMCB for 
     * "Only keep genes/probes with |fold-change| >= threshold" 
     * that pops up a dialog to enter the threshold value between 0.0 and 
     * some large number. */
    public float
      foldChangeThr= 0.0F;
    
    /* -dataPrecisionHTMLtable:{precision of HTML table} */
    public int
      dataPrecisionHTMLtable= -1;
    
    /* -sortFlipTableByColumnName:{sort column} */
    public String
      sortFlipTableByColumnName= null;
    
    /* -showDataHeatmapFlipTable */
    public boolean
      showDataHeatmapFlipTableFlag= false;
    
    /* -flipUseExactColumnNameMatch:{flipTableUseExactMatchFlag} */
    public boolean 
      flipTableUseExactMatchFlag= false;
    
    /* -flipDirectory:"{outputSearchDir}" */
    public String
      outputSearchDir= null; 
    
    /** Default Search-Results base file name if not null or "".
     * It is used for "-flipSaveOutputFile:{flipSaveOutputFile}" in 
     * the generated param map file.  */
    public String
      searchResultsBaseFile= null;
    
    /* -------------- GUI demo args ---------------------- */
    
    /** The demo argument to load into the searchTermTextArea GUI
     * Set by "-searchTermsDemoData:{list of search terms}" 
     * */
    public String
      searchTermsDemoData= null;   

    /* -------- GUI user default search terms args ---------------- */

    /* Search terms from user entered data in searchTermTextArea GUI.
     * Note this could have embedded \r or \n or \r\n, so must map
     * if save/restore from .sgs file.
     */
    public String
      searchTermFilterStr= null;
    
    /** The file name to use when reading data from a user
     * term list file Table to load into the the searchTermTextArea GUI.
     * Set by "-searchUserTermList:{userListTable,colName,title string}"
     */
    public String
      searchUserTermListFile= null;    

    /** The user column name to use when reading data from a user
     * term list file Table to load into the the searchTermTextArea GUI.
     * Set by "-searchUserTermList:{userListTable,colName,title string}"
     */
    public String
      searchUserTermListColName= null;

    /** The user title string to use when reading data from a user
     * term list file Table to load into the the searchTermTextArea GUI.
     * Set by "-searchUserTermList:{userListTable,colName,title string}"
     */
    public String
      searchUserTermListTitle= null;
    
    /** The user search terms list string to use when reading data from 
     * a user term list file Table to load into the the 
     * searchTermTextArea GUI.
     * Set by "-searchUserTermList:{userListTable,colName,title string}"
     */
    public String
      searchUserTermListStr= null;
    
    /** Eval the search terms as an AND (if true) else OR (if false).
     * Set by the andEGnamesRB and orEGnamesRB radio buttons and 
     * action commands.
     */
    public boolean
      evalSearchANDbooleanFlag= true; 
    
    /** Optional EG group filter if not null. This is set by the GUI 
     * JTextField filterRowTextField.
     */
    public String
      filterRowStr= "";

    /** Number of EG samples selection Choice List. Used with 
     * boolean egSelNames[] data.
     */
    public int 
      nEGSelNames= 0;

    /** Number of EG samples selection Choice List. Used with 
     * boolean egSelNames[] data.
     */
    public boolean 
      egSelNamesFlag[]= null;   

    /* List of GSPID filters used with 
     * -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
     */
    public String
      flipRowGSPIDfilters[]= null;  
    
    /* Size of flipRowGSPIDfilters[] List of GSPID filters used with 
     * -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
     */
    public int
      nRowGSPIDfilters= 0;    

    /** Currently specified EG samples assigned to class A.
     * -flipAclass:"{classAsamples}"  [if reportFoldChangeFlag]
     */
    public String
       classAsamples= null;

    /** Currently specified EG samples assigned to class B.
     * -flipBclass:"{classBsamples}"  [if reportFoldChangeFlag].
     */
     public String
       classBsamples= null;
    
    /* ------------------------- */
        

    /**
     * SGstate() - Constructor
     * @param sGui is an instance of the SearchGUI class
     */
    public SGstate(SearchGUI sGui)
    { /* SGstate */
      this.sGui= sGui;
      this.cvt= sGui.cvt;
    } /* SGstate */
    
    
    /**
     * copyStateFromCvt() - copy the partial state from cvt Globals
     * @param cvt instance of CvtTabDelim2HTML
     * @return true if succeed 
     */
    public boolean copyStateFromCvt(HTMLtools cvt)
    { /* copyStateFromCvt */
      /* Save to local variables */
      boolean ok= copyGlobalsToSGstate(cvt);
      return(ok);
    } /* copyStateFromCvt */
    
    
    /**
     * copySGstateInstance() - copy from SGstate instance values to this.
     * @param sg - instance to copy FROM
     * @return SGstate string in .sps file format. if succeed.
     */  
    public boolean copySGstateInstance(SGstate sg)
    { /* copySGstateInstance */
      if(sg==null)
        return(false);

      /* Report Fold-Change data */
      this.classAsamples= sg.classAsamples;
      this.classBsamples= sg.classBsamples;
      this.reportFoldChangeFlag= sg.reportFoldChangeFlag;
      this.foldChangeThrFlag= sg.foldChangeThrFlag;
      this.foldChangeThr= sg.foldChangeThr;
      
      /* Search Term data */
      this.searchTermFilterStr= sg.searchTermFilterStr;
      this.flipTableUseExactMatchFlag= sg.flipTableUseExactMatchFlag;    
      
      /* View menu data */
      this.dataPrecisionHTMLtable= sg.dataPrecisionHTMLtable;
      this.showDataHeatmapFlipTableFlag= sg.showDataHeatmapFlipTableFlag; 
      this.sortFlipTableByColumnName= sg.sortFlipTableByColumnName; 
      
      /* EG Samples data */
      this.nEGSelNames= sg.nEGSelNames;
      this.egSelNamesFlag= new boolean[sg.nEGSelNames];
      for(int i=0;i<sg.nEGSelNames;i++)
        this.egSelNamesFlag[i]= sg.egSelNamesFlag[i];
      this.filterRowStr= sg.filterRowStr;
      
      this.evalSearchANDbooleanFlag= sg.evalSearchANDbooleanFlag;      
      this.nRowGSPIDfilters= sg.nRowGSPIDfilters;
      this.flipRowGSPIDfilters= (sg.nRowGSPIDfilters==0)
                           ? ((String[])null) : new String[sg.nRowGSPIDfilters];
      for(int i=0;i<this.nRowGSPIDfilters;i++)
        this.flipRowGSPIDfilters[i]= sg.flipRowGSPIDfilters[i];
      
      /* Output file data */
      this.outputSearchDir= sg.outputSearchDir;
      this.searchResultsBaseFile= sg.searchResultsBaseFile;
      
      return(true);
    } /* copySGstateInstance */
               
    
    /**
     * cvtSGstateToStr() - convert SGstate vars. to .sgs state string to write to file.
     * It makes lists of variables of the form "param=value\n" called the .sgs file
     * format.
     * @return SGstate string in .sps file format. if succeed.
     */  
    public String cvtSGstateToStr()
    { /* cvtSGstateToStr */
      String sR= "";
      
      /* Report Fold-Change GUI options  */
      sR += "classAsamples="+classAsamples+"\n";
      sR += "classBsamples="+classBsamples+"\n";
      sR += "reportFoldChangeFlag="+
                         ((reportFoldChangeFlag)
                             ? "true" : "false")+"\n";
      sR += "foldChangeThrFlag="+
                         ((foldChangeThrFlag) 
                             ? "true" : "false")+"\n";
      sR += "foldChangeThr="+foldChangeThr+"\n";
      
      /* Search-term GUI */
      sR += "searchTermFilterStr="+searchTermFilterStr+"\n";
      sR += "flipTableUseExactMatchFlag="+
            ((flipTableUseExactMatchFlag) ? "true" : "false")+"\n";
      
      /* View menu options */
      sR += "dataPrecisionHTMLtable="+dataPrecisionHTMLtable+"\n";
      sR += "sortFlipTableByColumnName="+sortFlipTableByColumnName+"\n";
      sR += "showDataHeatmapFlipTableFlag="+
                          ((showDataHeatmapFlipTableFlag) 
                              ? "true" : "false")+"\n";
      
      /* EG Samples GUI */
      sR += "nEGSelNames="+nEGSelNames+"\n";
      for(int i=0;i<nEGSelNames;i++)
        sR += "egSelNamesFlag["+i+"]="+egSelNamesFlag[i]+"\n";
      sR += "filterRowStr="+filterRowStr+"\n";
      sR += "evalSearchANDbooleanFlag="+
            ((evalSearchANDbooleanFlag) ? "true" : "false")+"\n";

      sR += "nRowGSPIDfilters="+nRowGSPIDfilters+"\n";
      flipRowGSPIDfilters= new String[nRowGSPIDfilters];
      for(int i=0;i<nRowGSPIDfilters;i++)
        sR += "flipRowGSPIDfilters["+i+"]="+flipRowGSPIDfilters[i]+"\n";
      
      /* Output data file GUI options */
      sR += "outputSearchDir="+outputSearchDir+"\n";
      sR += "searchResultsBaseFile="+searchResultsBaseFile+"\n";
      
      return(sR);
    } /* cvtSGstateToStr */
           
    
    /**
     * copyGlobalsToSGstate() - copy Globals instance in SGstate variables.
     * The file being imported was a previous paramsSearchFlip.map file created by
     * createParamsMapFile().<BR>
     * This method parses and sets following parameters 
     * if the switch exists from the list:
     * <PRE>
     *   -flipOrderHdrColNames:"*LIST*,Stat5a,"
     *   -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
     *   -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at"
     *   -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2"
     *  
     *   -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
     *   -flipAclass:"{classAsamples}"  [if reportFoldChangeFlag]
     *   -flipAclass:"{classBsamples}"  [if reportFoldChangeFlag]
     *   -flipFCthreshold:{foldChangeThr} [if foldChangeThrFlag && foldChangeThr>0.0F]
     *   -dataPrecisionHTMLtable:{precision of HTML table}
     *   -sortFlipTableByColumnName:{sort column}
     *   -showDataHeatmapFlipTable
     *   -flipUseExactColumnNameMatch:{glb.flipTableUseExactMatchFlag}
     *   -flipDirectory:"{outputSearchDir}"
     *   -flipSaveOutputFile:"{searchResultsBaseFile}"
     * </PRE>
     * @param glb Globals instance of parsed data file
     * @return true if succeed.
     */  
    public boolean copyGlobalsToSGstate(Globals glb)
    { /* copyGlobalsToSGstate */      
      /* [1] Copy some of the rms. global -flip variables to SearchGUI variables
       * See createParamsMapFile() for what variables to set.
       */
      /* -flipOrderHdrColNames:"*LIST*,Stat5a," */
      flipOrderHdrColList= glb.flipOrderHdrColList;
      nFlipOrderHdrColList= glb.nFlipOrderHdrColList;
          
      /* [2] [TODO] map to: nSearchTermNames,
       * searchTermNames[0:nSearchTermNames-1] and 
       * searchTermFilter[0:nSearchTermNames-1][nbr of terms if any].
       * -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
       * -flipColumnName:"*LIST*,Well ID,123456,123444"
       * -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at" 
       * */
      nFlipColumns= glb.nFlipColumns;
      flipColumnFile= glb.flipColumnFile;
      flipColumnName= glb.flipColumnName;

      /* [3] -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2" */
      if(glb.flipRowFilterNamesFile!=null &&
         glb.flipRowFilterNamesFile.equals("*LIST*"))
      {
        sampleRowFilterALLflag= false;
        sampleRowFilter= glb.flipRowFilterNames;
      }
      
      /* [4] List of GSPID filters used with
       * -flipRowGSPIDfilterSubstring:"AND,.stat,.GH" */
      nRowGSPIDfilters= (glb.flipRowGSPIDfilters==null)
                          ? 0 : glb.flipRowGSPIDfilters.length;
      flipRowGSPIDfilters= (nRowGSPIDfilters==0)
                              ? ((String[]) null) : new String[nRowGSPIDfilters];
      for(int i=0;i<nRowGSPIDfilters;i++)
        flipRowGSPIDfilters[i]= glb.flipRowGSPIDfilters[i];
      
      /* [5] -flipAclass:"{classAsamples}"  [if reportFoldChangeFlag]
       *     -flipBclass:"{classBsamples}"  [if reportFoldChangeFlag]
       */
      classAsamples= glb.flipAclass;
      classBsamples= glb.flipBclass;
      reportFoldChangeFlag= (classAsamples!=null && classBsamples!=null);
      
      /*[6] -flipFCthreshold:{foldChangeThr}
       *  [if foldChangeThrFlag && foldChangeThr>0.0F]
       */
      foldChangeThrFlag= glb.flipFCthrFlag;
      foldChangeThr= glb.flipFCthreshold;
      
      /* [7] -dataPrecisionHTMLtable:{precision of HTML table} */
      dataPrecisionHTMLtable= glb.dataPrecisionHTMLtable;
      
      /* [8] -sortFlipTableByColumnName:{sort column} */
      sortFlipTableByColumnName= glb.sortFlipTableByColumnName;
      
      /* [9] -showDataHeatmapFlipTable */
      showDataHeatmapFlipTableFlag= glb.showDataHeatmapFlipTableFlag;
      
      /* [10] -flipUseExactColumnNameMatch:{glb.flipTableUseExactMatchFlag} */
      flipTableUseExactMatchFlag= glb.flipTableUseExactMatchFlag;
      
      /* [11] -flipDirectory:"{outputSearchDir}" */
      outputSearchDir= glb.flipDirectory;
      
      /* [12] -flipSaveOutputFile:"{searchResultsBaseFile}" */
      searchResultsBaseFile= glb.flipSaveOutputFile;
      
      return(true);
    } /* copyGlobalsToSGstate */              
          
  
  /**
   * readSGstateFile() - read the SearchGUI State file stateFile 
   * with a .sgs file extension.
   * @param stateFile is the name of the Flicker state file
   * @return true if setup and parsed the .sgs hashtable correctly
   */
  public synchronized boolean readSGstateFile(String stateFile)
  { /* readSGstateFile */ 
    File fd= new File(stateFile);
    if(stateFile==null)
      return(false);
    
    if(!stateFile.endsWith(".sgs"))
    { /* problem - hash file not found */
      UtilCM.logMsg("Bad SearchGUI .sgs state file "+
                     "["+stateFile+"] - file must end with '.sgs'.\n");
      return(false);
    }
    
    if(!fd.exists())
    { /* problem - hash file not found */
      UtilCM.logMsg("Can't find SearchGUI disk .sgs state file "+
                     "["+stateFile+"] - file not found\n");
      return(false);
    }

    UtilCM.logMsg("Importing SearchGUI ["+stateFile+"] state file.\n");
    
    Hashtable ht= readNameValuesHashTableFromFile(stateFile,15101);
    if(ht==null)
    { /* problem - hash file is corrupted */
      UtilCM.logMsg("SearchGui .sgs state file ["+stateFile+"]"+
                    "is corrupted - ignoring importing old data.\n\n");
      return(false);
    }
    setStateHashtableForGetValue(ht, nEntries);
    
    /* Parse the data in the hash table into state variables */
    if(nStateEntries==0)
      return(false);
       
    /* Parse the base .sgs state properties */
    if(!parseHTtoSGstate())
      return(false);
    
    return(true);
  } /* readSGstateFile */
   
  
  /**
   * parseHTtoSGstate() - parse .sgs state hashtable to SGstate variables.
   * It checks for each of the variables and then sets the corresponding
   * SGstate variable.
   * @return set the state variables if succeed and return true.
   */
  public boolean parseHTtoSGstate()
  { /* parseHTtoSGstate */    
    /* Parse the data in the hash table into state variables */
    if(nStateEntries==0)
      return(false); 
    
    /* Report Fold-Change data */
    classAsamples= getStateValue("classAsamples",null);
    classBsamples= getStateValue("classBsamples",null);
    reportFoldChangeFlag= getStateValue("reportFoldChangeFlag", false);
    foldChangeThrFlag= getStateValue("foldChangeThrFlag", false);
    foldChangeThr= getStateValue("foldChangeThr",0.0F);
    
    /* Search Term data */
    searchTermFilterStr= getStateValue("searchTermFilterStr", "");  
    flipTableUseExactMatchFlag= getStateValue("flipTableUseExactMatchFlag",
                                              true);
    
    /* View menu data */
    dataPrecisionHTMLtable= getStateValue("dataPrecisionHTMLtable",-1);
    showDataHeatmapFlipTableFlag= getStateValue("showDataHeatmapFlipTableFlag",
                                                false);
    sortFlipTableByColumnName= getStateValue("sortFlipTableByColumnName",null);

    /* EG Samples data */
    nEGSelNames= getStateValue("nEGSelNames",0);
    egSelNamesFlag= new boolean[nEGSelNames];
    for(int i=0;i<nEGSelNames;i++)
      egSelNamesFlag[i]= getStateValue("egSelNamesFlag["+i+"]",false);
    filterRowStr= getStateValue("filterRowStr",null);
        
    evalSearchANDbooleanFlag= getStateValue("evalSearchANDbooleanFlag",true);    
    nRowGSPIDfilters= getStateValue("nRowGSPIDfilters",0);
    flipRowGSPIDfilters= (nRowGSPIDfilters==0)
                            ? ((String[])null) : new String[nRowGSPIDfilters];
    for(int i=0;i<nRowGSPIDfilters;i++)
      flipRowGSPIDfilters[i]= getStateValue("flipRowGSPIDfilters["+i+"]","");    

    /* Output file data */
    outputSearchDir= getStateValue("outputSearchDir",null);
    searchResultsBaseFile= getStateValue("searchResultsBaseFile",null);
            
    return(true);
  } /* parseHTtoSGstate */
  
  
  /**
   * writeSGstate() - write SearchGUI state to .sgs SGstate file.
   * @param fileStr - name of file to write
   * @return true if succeed.
   */  
  public boolean writeSGstate(String fileStr)
  { /* writeSGstate */
    if(fileStr==null)
      return(false);
    String 
      sData= getStateStr();
    boolean ok= false;
    if(sData!=null)
    {
      ok= cvt.fio.writeStringToFile(fileStr, sData);
    }
    
    return(ok);
  } /* writeSGstate */
  
  
  /** 
   * readNameValuesHashTableFromFile() - read hashtable tab-delim  name-value pairs 
   * from a file. Convert the (name\tvalue\n) data to a hashtable.
   * @param fileName is the name of the file to read
   * @param hashTableSize initial size of hashtable
   * @return hashtable else null if not found. The global variable nEntries
   *         contains the number of entries.
   */
  public Hashtable readNameValuesHashTableFromFile(String fileName, 
                                                   int hashTableSize)
  { /* readNameValuesHashTableFromFile */
    String
      name,
      value,
      delimiter;
     
    String sData= cvt.fio.readFileAsString(fileName);
    sData= UtilCM.rmvRtnChars(sData);       /* make sure no "\r\n" stuff.. */
    
    Hashtable ht= new Hashtable(hashTableSize);
    nEntries= 0;
    if(sData==null)
      return(null);
    
    StringTokenizer parser= new StringTokenizer(sData, "\t\n", false);
    
    while(parser.hasMoreTokens())
    { /* parse (name,value) pairs and save in hash table */
      name= parser.nextToken();
      if(!parser.hasMoreTokens())
        break;
      value= parser.nextToken();
      if(name==null || name.length()==0 || value==null)
        break;
      else
        ht.put(name, value);
      nEntries++;  
    } /* parse (name,value) pairs and save in hash table */
    
    if(nEntries==0)
      return(null); 
  
    return(ht);
  } /* readNameValuesHashTableFromFile */
  
  
  /**
   * setStateHashtableForGetValue() - set working H.T. for next getStateValue calls
   * @param ht is hashtable to use
   * @param nEntriesVal is the number of elements used in the hash table.
   */
  public void setStateHashtableForGetValue(Hashtable ht, int nEntriesVal)
  { /* setStateHashtableForGetValue */
    sgStateHT= ht;
    nStateEntries= nEntriesVal;
  } /* setStateHashtableForGetValue */
  
  
  /**
   * setStateHashtableForGetValue() - set working H.T. for next getStateValue calls
   * @param ht is hashtable to use
   */
  public void setStateHashtableForGetValue(Hashtable ht)
  { /* setStateHashtableForGetValue */
    sgStateHT= ht;
  } /* setStateHashtableForGetValue */

    
  /**
   * getStateStr() - generate  tab-delim SGstate string for writing .sgs state.
   * The format is tab-delimited (name \t value \n) with one entry/line.
   * @return the state string
   */
  public String getStateStr()
  { /* getStateStr*/
    StringBuffer sBuf= new StringBuffer(100000);  /* est. - optimize */
    
    /* Report Fold-Change data */    
    sBuf.append("classAsamples\t"+classAsamples+"\n");
    sBuf.append("classBsamples\t"+classBsamples+"\n");
    sBuf.append("reportFoldChangeFlag\t"+reportFoldChangeFlag+"\n");
    sBuf.append("foldChangeThrFlag\t"+foldChangeThrFlag+"\n");
    
    /* Search Term data */
    sBuf.append("searchTermFilterStr\t"+searchTermFilterStr+"\n"); 
    sBuf.append("flipTableUseExactMatchFlag\t"+flipTableUseExactMatchFlag+"\n"); 
    
    /* View menu data */    
    sBuf.append("dataPrecisionHTMLtable\t"+dataPrecisionHTMLtable+"\n");
    sBuf.append("showDataHeatmapFlipTableFlag\t"+showDataHeatmapFlipTableFlag+"\n");
    sBuf.append("sortFlipTableByColumnName\t"+sortFlipTableByColumnName+"\n");
    
    /* EG Samples data */    
    sBuf.append("nEGSelNames\t"+nEGSelNames+"\n");
    for(int i=0;i<nEGSelNames;i++)      
      sBuf.append("egSelNamesFlag["+i+"]\t"+egSelNamesFlag[i]+"\n");    
    sBuf.append("filterRowStr\t"+filterRowStr+"\n");
    
    sBuf.append("evalSearchANDbooleanFlag\t"+evalSearchANDbooleanFlag+"\n");   
    sBuf.append("nRowGSPIDfilters\t"+nRowGSPIDfilters+"\n");
    for(int i=0;i<nRowGSPIDfilters;i++)      
      sBuf.append("flipRowGSPIDfilters["+i+"]\t"+flipRowGSPIDfilters[i]+"\n"); 
    
    /* Output file data */    
    sBuf.append("outputSearchDir\t"+outputSearchDir+"\n");
    sBuf.append("searchResultsBaseFile\t"+searchResultsBaseFile+"\n");          
    
    String sData= new String(sBuf);
    return(sData);
  } /* getStateStr */  
    
    
  /**
   * getStateValue() - get PARAM and use default if not found.
   */
  public String getStateValue(String key, String def)
  { /* getStateValue */    
    if(sgStateHT==null)
      return(def);
    
    String value= (String)sgStateHT.get(key);
    if(value==null || value.equals("null"))
      value= def;
    return(UtilCM.rmvRtnChars(value));
  } /* getStateValue */
  
  
  /**
   * getStateValue() - get int PARAM and use default if not found.
   */
  public int getStateValue(String key, int def)
  { /* getStateValue */
    String sVal= getStateValue(key, null);
    int val;
    
    if(sVal==null)
      return(def);
    try
    {
      Integer valP= new Integer(sVal);
      val= valP.intValue();
    }
    catch(NumberFormatException e)
    { val= def;}
    
    return(val);
  } /* getStateValue */  
  
  
  /**
   * getStateValue() - get float PARAM and use default if not found.
   */
  public long getStateValue(String key, long def)
  { /* getStateValue */
    String sVal= getStateValue(key, null);    
    long val;
    
    if(sVal==null)
      return(def);
    try
    {
      Long valP= new Long(sVal);
      val= valP.longValue();
    }
    catch(NumberFormatException e)
    { val= def;}
    
    return(val);
  } /* getStateValue */   
  
  
  /**
   * getStateValue() - get float PARAM and use default if not found.
   */
  public float getStateValue(String key, float def)
  { /* getStateValue */
    String sVal= getStateValue(key, null);    
    float val;
    
    if(sVal==null)
      return(def);
    try
    {
      Float valP= new Float(sVal);
      val= valP.floatValue();
    }
    catch(NumberFormatException e)
    { val= def;}
    
    return(val);
  } /* getStateValue */
  
  
  /**
   * getStateValue() - get boolean PARAM and use default if not found.
   */
  public boolean getStateValue(String key, boolean def)
  { /* getStateValue */
    String
      sDef= (def) ? "true" : "false",
      sVal= getStateValue(key, sDef);
    boolean value= (sVal!=null && sVal.equalsIgnoreCase("true"));
    
    return(value);
  } /* getStateValue */ 

  
  } /* SGstate */ 
  
} /* end of class SearchGUI */