Child window of application appears behind parent.

I have configured SSGD 4.4 and after logging in and launching a third party application the first child window appears on top of parent but all subsequent windows will appear behind parent. Is there a configuration setting to force all child windows to appear on top of parent windows?

thank you very much for your reply.
my sgd's application is runned in seamless window mode.
and if Run My application in an Independent Window or started via a standard RDP connection, the problem cannot be seen again. it seems to just happened in seamless windows.
My application is a website(jsp,javabean etc) installed in Application server . and I use Application server's IE to open it via sgd for some reasons.

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              browse6.addActionListener(this);
              ok2.addActionListener(this);
              return cp;
         public void actionPerformed(ActionEvent e)
              if(e.getSource()==ok1)
                   String ncbi = "";
                   String repeat= "";
                   try
                        ncbi = jtf1.getText();
                        repeat = jtf2.getText();
                        System.out.println("NCBI" + ncbi + "www");
                        if( ncbi.equals(" ") && repeat.equals(" "))
                             System.out.println("NCBI333" + ncbi);
                             DisplayInfo di = new DisplayInfo("Sorry!, Please select some file", "");
                             di.setSize(450,100);
                             di.setLocation(600,600);
                             di.setVisible(true);
                             GBFileProp.snpFile = "";
                             GBFileProp.geneFile = "";
                             return;
                   catch(Exception ex)
                   GBFileProp.fileFormat="NCBI";
                   GBFileProp.fileName = ncbi;
                   GBFileProp.repeatFile = repeat;
                   ReadNCBI readFile1 = new ReadNCBI(ncbi);
                   ReadRepeatFile rrf = new ReadRepeatFile(repeat);
                   try
                        gb = new GBMainFrame();
                        gb.setSize(1200,750);
                   catch(Exception ex)
                        DisplayInfo di = new DisplayInfo("Sorry!, Wrong File", "Enter file in \".gbk\" format");
                        di.setSize(450,100);
                        di.setLocation(600,600);
                        di.setVisible(true);
                   setVisible(false);
                   setDefaultCloseOperation(DISPOSE_ON_CLOSE);
              if(e.getSource()==ok2)
                   String sequence= "";
                   String repeat= "";
                   String snp= "";
                   String gene= "";
                   try
                        sequence = jtf3.getText();
                        repeat = jtf4.getText();
                        snp = jtf5.getText();
                        gene = jtf6.getText();
                        if( sequence.equals(" ") && repeat.equals(" ") && snp.equals(" ") && gene.equals(" "))
                                                      DisplayInfo di = new DisplayInfo("Sorry!, Please select some file", "");
                             di.setSize(450,100);
                             di.setLocation(600,600);
                             di.setVisible(true);
                             System.out.println("File " + GBFileProp.repeatFile);
                             return;
                   catch(Exception ex)
                   GBFileProp.fileFormat="Other";
                   GBFileProp.fileName = sequence;
                   GBFileProp.repeatFile = repeat;
                   GBFileProp.snpFile = snp;
                   GBFileProp.geneFile = gene;
                   ReadGeneFile a = new ReadGeneFile(gene);
                   ReadSNPFile rsp = new ReadSNPFile(snp);
                   GCReadFile grf = new GCReadFile(sequence);
                   ReadRepeatFile rrf = new ReadRepeatFile(repeat);
                   try
                        gb = new GBMainFrame();
                        gb.setSize(1200,800);
                   catch(Exception ex)
                        DisplayInfo di = new DisplayInfo("Sorry!, Wrong File", "Enter file in corresponding format");
                        di.setSize(450,100);
                        di.setLocation(600,600);
                        di.setVisible(true);
                   setVisible(false);
                   setDefaultCloseOperation(DISPOSE_ON_CLOSE);
              if(e.getSource()==browse1)
                   String w;
                   Fselect(1);
                   try
                   w=f.toString();
                   jtf1.setText(w);
                   catch(Exception ex)
              if(e.getSource()==browse2)
                   String w;
                   Fselect(4);
                   try
                   w=f.toString();
                   jtf2.setText(w);
                   catch(Exception ex)
              if(e.getSource()==browse3)
                   String w;
                   Fselect(3);
                   try
                   w=f.toString();
                   jtf3.setText(w);
                   catch(Exception ex)
              if(e.getSource()==browse4)
                   String w;
                   Fselect(2);
                   try
                   w=f.toString();
                   jtf4.setText(w);
                   catch(Exception ex)
              if(e.getSource()==browse5)
                   String w;
                   Fselect(4);
                   try
                   w=f.toString();
                   jtf5.setText(w);
                   catch(Exception ex)
              if(e.getSource()==browse6)
                   String w;
                   Fselect(2);
                   try
                   w=f.toString();
                   jtf6.setText(w);
                   catch(Exception ex)
              if(e.getActionCommand().equals("sequence_ncbi"))
                   final JFileChooser chooser = new JFileChooser();
                   FileFilter type1 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
                   chooser.addChoosableFileFilter (type1);
                   chooser.setFileFilter (type1);
                   int returnVal = chooser.showOpenDialog(this);
                   if (returnVal == JFileChooser.APPROVE_OPTION)
                        seqFile = chooser.getSelectedFile();
              else if(e.getActionCommand().equals("sequence_other"))
                   final JFileChooser chooser = new JFileChooser();
                   FileFilter type1 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
                   chooser.addChoosableFileFilter (type1);
                   chooser.setFileFilter (type1);
                   int returnVal = chooser.showOpenDialog(this);
                   if (returnVal == JFileChooser.APPROVE_OPTION)
                        seqFile = chooser.getSelectedFile();
         public void itemStateChanged (ItemEvent e)
              GBFileProp.windowsize = (int)Integer.parseInt(winSize.getSelectedItem().toString());
              GBFileProp.shiftsize = (int)Integer.parseInt(shiftSize.getSelectedItem().toString());
         public void Fselect(int sel)
                   final JFileChooser chooser = new JFileChooser();
         ImageIcon openIcon = new ImageIcon("images/open.gif");
                   FileFilter type1 = new ExtensionFilter ("NCBI File(.gbk)", new String[] {".gbk",".txt"});
                   FileFilter type2 = new ExtensionFilter ("ptt File(.ptt)", new String[] {".ptt",".txt"});
                   FileFilter type3 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
                   FileFilter type4 = new ExtensionFilter ("Text File(.txt)", new String[] {".txt",".txt"});
                   chooser.setCurrentDirectory (new File (System.getProperty ("user.dir")));
                   if(sel == 1)
                        chooser.addChoosableFileFilter (type1);
              chooser.setFileFilter (type1);
                   if(sel == 2)
                        chooser.addChoosableFileFilter (type2);
              chooser.setFileFilter (type2);
                   if(sel == 3)
                        chooser.addChoosableFileFilter (type3);
              chooser.setFileFilter (type3);
                   if(sel == 4)
                        chooser.addChoosableFileFilter (type4);
              chooser.setFileFilter (type4);
         int returnVal = chooser.showOpenDialog(this);
                   if (returnVal == JFileChooser.APPROVE_OPTION)
                        f = chooser.getSelectedFile();
                        //System.out.println("path of open "+ f);
    //GBMainFrame file
    package igib.genebrowser;
    import javax.swing.*;
    import java.awt.event.*;
    import java.awt.*;
    import igib.genebrowser.menu.*;
    import igib.genebrowser.plot.*;
    import igib.genebrowser.util.*;
    public class GBMainFrame extends JFrame
         GBMainMenu gb;
         PlotGraph pg;
         JPanel jf = new JPanel();
         JPanel jf1;
         LineGraph lg, lg1;
         JPanel jp1, jp2;
         JLabel jl;
         public GBMainFrame()
              super("File: " + GBFileProp.fileName + " " + GBFileProp.repeatFile + " " + GBFileProp.snpFile + " " + GBFileProp.geneFile);
              Container cp = this.getContentPane();
              cp.setLayout(new BorderLayout());
              cp.setSize(1024,600);
              Color c1=new Color(255,100,100);
              jf = new JPanel(new GridLayout(1,15));
    cp.add(jf, BorderLayout.NORTH);
              pg = new PlotGraph();
              pg.setBackground(Color.white);
              cp.add(pg, BorderLayout.CENTER);
              GBFileProp.jsb.setUnitIncrement(5);
              cp.add(GBFileProp.jsb, BorderLayout.SOUTH);
              lg1 = new LineGraph();
              lg1.setBackground(Color.white);
              lg1.setSize(50, 1000);
              cp.add(lg1, BorderLayout.EAST);
              lg = new LineGraph();
              lg.setBackground(Color.white);
              cp.add(lg, BorderLayout.WEST);
              gb = new GBMainMenu();
              jf.add(gb);
              setVisible(true);
              repaint();
    //PlotGraph File
    package igib.genebrowser.plot;
    import javax.swing.*;
    import java.awt.event.*;
    import java.awt.*;
    import java.util.*;
    import java.awt.image.*;
    import java.io.*;
    //import Acme.JPM.Encoders.*;
    //import Acme.*;
    import java.awt.print.*;
    import java.awt.Component;
    import java.awt.print.PrinterJob;
    import igib.genebrowser.menu.*;
    import igib.genebrowser.util.*;
    import igib.genebrowser.*;
    public class PlotGraph extends JPanel implements MouseListener,MouseMotionListener
         int xcoordinate;
         JScrollBar scrollBar;
         int mouseX;
         int mouseY;
         String st1 = " ";
         JScrollPane jsp;
         int check;
         int n;
         double base;
         int value;
         String repeatSymbol = "!";
         int position[] = new int[1500];
         public PlotGraph(String st)
              check = 0;
              GBFileProp.check = false;
         setVisible(true);
              ToolTipManager.sharedInstance().setInitialDelay(0);
              addMouseListener(this);
              addMouseMotionListener(this);
         public PlotGraph()
              check = 0;
              //System.out.println(GBFileProp.gcmax + "max y");
              if(GBFileProp.genescore>5)
              GBFileProp.filesize = GBFileProp.readGeneEnd[GBFileProp.genescore - 6];
              //System.out.println(GBFileProp.seqscore + " GBFileProp.seqscore");
              if(GBFileProp.filesize < GBFileProp.seqscore)
                   GBFileProp.filesize = GBFileProp.seqscore;
              if(GBFileProp.snpscore>5)
                   if(GBFileProp.filesize < GBFileProp.readSNPPosition[GBFileProp.snpscore-6])
                        GBFileProp.filesize = GBFileProp.readSNPPosition[GBFileProp.snpscore-6];
              if(GBFileProp.repeatscore>2)
                   if(GBFileProp.filesize < GBFileProp.endRepeatPosition[GBFileProp.repeatscore-2])
                        GBFileProp.filesize = GBFileProp.endRepeatPosition[GBFileProp.repeatscore-2];
              GBFileProp.scrollsize = (int)GBFileProp.filesize/285;
              GBFileProp.check = true;
         setVisible(true);
              addMouseListener(this);
              addMouseMotionListener(this);
              try
              AdjustmentListener lst = new AdjustmentListener()
                   public void adjustmentValueChanged(AdjustmentEvent e)
                        int i = e.getValue();
                        value = i;
                        GBFileProp.defaultStartCoordinate = (int)(e.getValue()*10*base);
                        GBFileProp.defaultEndCoordinate = GBFileProp.defaultStartCoordinate + (int)(10000*base);
                        repaint();
              GBFileProp.jsb.addAdjustmentListener(lst);
              catch(Exception e)
                   System.out.println("error here" + e);
    //******************** For Painting all the graph**********************************//
         public void paintComponent(final Graphics g)
              super.paintComponent(g);
              Font f = new Font("Times-Roman", Font.PLAIN, 16);
              g.setFont(f);
              GBFileProp.scrollsize = (int)GBFileProp.filesize/285;
              base = (double)(100.0/GBFileProp.zoomSize);
              n = (int)(GBFileProp.filesize/base);
              GBFileProp.jsb.setMaximum(n/10);
              if(GBFileProp.checkSave)
                   GBFileProp.checkSave = false;
                   Image img = this.createImage(1200,800);               
                   Graphics gph = img.getGraphics();
                   this.paint(gph);
                   try
                        OutputStream os = new FileOutputStream(GBFileProp.save);
                        GifEncoderTest ge = new GifEncoderTest(img,os);
                        ge.encode();
                        os.close();
                        catch(Exception e){}
              if(GBFileProp.checkPrint)
                   try
                        GBFileProp.checkPrint = false;
                        RepaintManager.currentManager(this).setDoubleBufferingEnabled(false);
                        PrinterJob pj=PrinterJob.getPrinterJob();
                        pj.printDialog();
                        pj.print();
                   catch (Exception PrintException)
                        System.out.println("print error" + PrintException);
                        GBFileProp.checkPrint = false;
              if(SetVisibleClass.isMerge)
                        GBFileProp.snpposition = 500;
                        GBFileProp.geneposition = 500;
                        GBFileProp.repeatposition = 500;
                        GBFileProp.userdefinedpoint = 500;
                   else
                        GBFileProp.snpposition = 450;
                        GBFileProp.geneposition = 400;
                        GBFileProp.repeatposition = 150;
                        GBFileProp.userdefinedpoint = 500;
              if(GBFileProp.check)
                   try
                        if(SetVisibleClass.isSNP)
                        drawSNPPage(g);
                   catch(Exception e)
                        System.out.println("Error in snp plotting");
                   try
                        drawGenePage(g);
                   catch(Exception e)
                        System.out.println("Error in gene plotting");
                   try
                        if(SetVisibleClass.isGC)                    
                        drawGCPage(g);
                   catch(Exception e)
                        //System.out.println("Error in GC plotting");
                   try
                        drawUserDefinedPage(g);
                   catch(Exception e)
                        System.out.println("Error in User Defined plotting");
                   try
                        if(SetVisibleClass.isRepeat)                    
                             drawRepeatPage(g);
                   catch(Exception e)
                        System.out.println("Error in Repeat plotting");
    //******************** For Painting all the graph**********************************//
    //***************************** For Painting Gene**********************************//
         public void drawGenePage(Graphics g1)
              Graphics2D g = (Graphics2D)g1;
              g1.setColor(Color.darkGray);
              g.drawLine(0,650,(int)10000,650);
              //g1.setColor(Color.b);
              BasicStroke pen = new BasicStroke(3.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
    g.setStroke(pen);
    //****************************** X coordinate *************************************//
              for(int i = 0; i < 10000; )
                   int xcor = (GBFileProp.defaultStartCoordinate + (int)(i*base));
                   String xCoordinate = "" + xcor;
                   g.drawLine((int)(i/10),645,(int)(i/10),655);
                   g.drawString(xCoordinate,(int)(i/10),665);
                   i = i + 1000; //+ (int)(1000/base);
    //****************************** X coordinate *************************************//
              if(SetVisibleClass.isGene)
                   g1.setColor(Color.darkGray);
                   g1.drawString("Gene:", 10, (GBFileProp.geneposition - 25));
                   g1.setColor(GBColorSymbol.cGene);
                   for (int i = 0; i < GBFileProp.genescore ; i++) // - 5 to b subtracted from genescore
                        int basestart = (int)((GBFileProp.readGeneStart[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
                        int baseend = (int)((GBFileProp.readGeneEnd[i] - (int)(GBFileProp.defaultStartCoordinate))/base);
                        if(basestart >=0 && baseend <=(int)(10000))
                             checkGenePosition(i);
                             g.drawLine((int)((basestart/10)),GBFileProp.geneposition,(int)((baseend/10)),GBFileProp.geneposition);
                             arrow(true,true,i, g, basestart, baseend);
                        if(basestart >=0 && baseend > (int)(10000))
                             checkGenePosition(i);
                             g.drawLine(basestart/10,GBFileProp.geneposition,1000,GBFileProp.geneposition);
                             arrow(true,false,i, g, basestart, 10000);
                        if(basestart < 0 && baseend <= (int)(10000))
                             checkGenePosition(i);
                             g.drawLine(0,GBFileProp.geneposition,baseend/10,GBFileProp.geneposition);
                             arrow(false,true,i, g, 0, baseend);
                        if(basestart < 0 && baseend > (int)(10000))
                             checkGenePosition(i);
                             g.drawLine(0,GBFileProp.geneposition,1000,GBFileProp.geneposition);
                   //System.out.println("GeneSt: " + GBFileProp.readGeneStart[i] + " GeneEd: " + GBFileProp.readGeneEnd[i] + " No " + i + "GeneScore " + GBFileProp.genescore);     
    //*****************************End For Painting Gene**********************************//
    //*****************************Start For Painting snp**********************************//
         public void drawSNPPage(Graphics g1)
              //System.out.println(GBFileProp.snpscore + "for snp");
              Graphics2D g = (Graphics2D) g1;
              BasicStroke pen = new BasicStroke();
              g.setStroke(pen);
              //g.setColor(Color.Red);
              g.drawString("SNP", 20, GBFileProp.snpposition);
              g.setColor(GBColorSymbol.cSnp);
              for(int i = 0; i < GBFileProp.snpscore; i++)
                   int basePosition = (int)((GBFileProp.readSNPPosition[i] - GBFileProp.defaultStartCoordinate)/base);
                   //System.out.println(" position " + (basePosition/10));
                   //g.drawString("|",(basePosition/10),GBFileProp.snpposition);
                   g.drawString(GBColorSymbol.snpSymValues[GBColorSymbol.snpSym],(basePosition/10),GBFileProp.snpposition);
                                                                                                                  //Line SNP score
              //System.out.println(GBFileProp.snplinescore);
              for(int i = 0; i < GBFileProp.snplinescore-1; i++)
                   int basePosition = (int)((GBFileProp.readSNPStartPosition[i] - GBFileProp.defaultStartCoordinate)/base);
                   //g.drawString("|",(basePosition/10),GBFileProp.snpposition);
                   g.drawString(GBColorSymbol.snpSymValues[GBColorSymbol.snpSym],(basePosition/10),GBFileProp.snpposition);
              for(int i = 0; i < GBFileProp.snplinescore-1; i++)
                   int basestart = (int)((GBFileProp.readSNPStartPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
                   int baseend = (int)((GBFileProp.readSNPEndPosition[i] - (int)(GBFileProp.defaultEndCoordinate))/base);
                   System.out.println(basestart + "     " + baseend);
                   if(basestart >=0 && baseend <=(int)(10000))
                             g.drawLine((int)((basestart/10)),GBFileProp.snpposition,(int)((baseend/10)),GBFileProp.snpposition);
                   if(basestart >=0 && baseend >(int)(10000))
                             g.drawLine((int)((basestart/10)),GBFileProp.snpposition,(int)((1000)),GBFileProp.snpposition);
                   if(basestart < 0 && baseend <=(int)(10000))
                             g.drawLine((int)((0)),GBFileProp.snpposition,(int)((baseend/10)),GBFileProp.snpposition);
                   if(basestart < 0 && baseend > (int)(10000))
                             g.drawLine((int)((0)),GBFileProp.snpposition,(int)((1000)),GBFileProp.snpposition);
    //*****************************Start For Painting GCPlotting**********************************//
         public void drawGCPage(Graphics g1)
              Graphics2D g = (Graphics2D) g1;
              g1.setColor(Color.darkGray);
              g.drawString("GC Percentage", 20, 20);
              BasicStroke pen = new BasicStroke();
              g.setStroke(pen);
              g1.setColor(Color.black);
              //System.out.println(GBFileProp.seqscore + " score");
              for(int i = 0; i < (int)((10000)*base); )
                   //System.out.println(GBFileProp.defaultEndCoordinate + " " i" " + GBFileProp.defaultStartCoordinate);
                        //System.out.println(GBFileProp.gcposition);
                        int firstPosition = (int)GBFileProp.GCPercentage[(int)((((int)(i) + GBFileProp.defaultStartCoordinate)/GBFileProp.shiftsize))] * (3*100)/GBFileProp.gcmax;
                        int secondPosition = (int)GBFileProp.GCPercentage[(int)((((int)((i+GBFileProp.shiftsize)) + GBFileProp.defaultStartCoordinate)/GBFileProp.shiftsize))] * (3*100)/(GBFileProp.gcmax);
                        g.drawLine((int)((i/10)/base), GBFileProp.gcposition - firstPosition, (int)(((i+GBFileProp.shiftsize)/10)/base), GBFileProp.gcposition - secondPosition);
                        i = i + GBFileProp.shiftsize;
              for(int i = 0; i < GBFileProp.seqscore -1; i++)
                   int firstPosition = (int)Integer.parseInt(GBFileProp.GCPoint.elementAt(i).toString()) * 3;
                   int secondPosition = (int)Integer.parseInt(GBFileProp.GCPoint.elementAt(i+50).toString()) * 3;
                   //int secondPosition = (int)GBFileProp.GCPercentage[i+50] * 3;
                   //g.drawString("|",basePosition,300);
                   g.drawLine((int)(i/10), 300 - firstPosition, (int)(i+50)/10, 300 - secondPosition);
                   i = i + 49;
    //*****************************End For Painting GCPlotting**********************************//
    //*****************************Start For Painting Repeat File**********************************//
         public void drawRepeatPage(Graphics g1)
              int check = 0;
              Graphics2D g = (Graphics2D) g1;
              g.setColor(Color.darkGray);
              g.drawString("Repeat", 10, 480);
              for (int i = 0; i < GBFileProp.repeatscore ; i++)//- 1 to b subtracted from repeatscore
                   int basestart = (int)((GBFileProp.startRepeatPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
                   int baseend = (int)((GBFileProp.startRepeatPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base);
                   if(basestart > 0 && basestart < 10000)
                        try
                             if(GBFileProp.repeatFamily.equals("LINE"))
                                  System.out.println(" Line" );
                                  GBFileProp.repeatposition = 575;
                                  repeatSymbol = GBColorSymbol.repeatSymValues[GBColorSymbol.lineSym];
                                  if(GBFileProp.repeatName[i].length() >= 2)
                                       if(GBFileProp.repeatName[i].substring(0,2).equals("L1"))
                                            g.setColor(GBColorSymbol.cL1);
                                            g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);
                                       else if(GBFileProp.repeatName[i].substring(0,2).equals("L2"))
                                            g.setColor(GBColorSymbol.cL2);
                                            g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);
                                       else if(GBFileProp.repeatName[i].substring(0,2).equals("L3"))
                                            g.setColor(GBColorSymbol.cL3);
                                            g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);

  • MDI child window appearance

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    using System.ComponentModel;
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    using System.Linq;
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    You could download it form http://1drv.ms/1Mwwibp.
    It is quite similar with the one for tiling, you could edit it to fit your requirements.
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    Carl
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