import java.awt.*;
import java.awt.event.*;
import java.lang.Math;
import java.lang.Object;
import java.util.Vector;

public class Genetics extends java.applet.Applet implements ActionListener
{

   int currentGen = 0;
 
   //Stuff for interface
   Graph currentGraph;
   Graph barGraph;
   Graph lineGraph;
   Panel topPanel, parameters;

   Button forwardButton;
   Button backButton;
   Button enterValuesButton;
   Button toggleGraphButton;
   Button showValuesButton;
   Button showGraphButton; 

   Label allele0Label, allele1Label;
   Label selfac0Label, selfac1Label, selfac2Label;

   FrameWindow InputWindow; 
   String alleleLabels[] = new String[2];

   //Stuff for Generation
   final int numGenerations = 100;
   Generation gen[] = new Generation[numGenerations]; 

   //Layout Stuff
   TextArea textOutput;
   int current_layout;
   static final int GRAPHLAYOUT = 1;
   static final int TEXT_LAYOUT = 2;
   static final int BASELENGTH = 12;
   static final int FIELDLENGTH = 14;
   static String spaces[] = new String[35];

   public void init()
   {
      InputWindow = new FrameWindow("Basic Information Input", this); 
      InputWindow.setSize(450,500);
      forwardButton = new Button("->");
      backButton = new Button("<-");
      enterValuesButton = new Button("Enter Values");
      toggleGraphButton = new Button("Toggle Graph Type");
      showValuesButton = new Button("Show Values");
      showGraphButton = new Button("Work with Graph");

      forwardButton.addActionListener(this);
      backButton.addActionListener(this);
      enterValuesButton.addActionListener(this);
      toggleGraphButton.addActionListener(this);
      showValuesButton.addActionListener(this);
      showGraphButton.addActionListener(this);

      spaces[0] = new String("");
      spaces[1] = new String(" ");
      spaces[2] = new String("  ");
      spaces[3] = new String("   ");
      spaces[4] = new String("    ");
      spaces[5] = new String("     ");
      spaces[6] = new String("      ");
      spaces[7] = new String("       ");
      spaces[8] = new String("        ");
      spaces[9] = new String("         ");
      spaces[10] = new String("          ");
      spaces[11] = new String("           ");
      spaces[12] = new String("            ");
      spaces[13] = new String("             ");
      spaces[14] = new String("              ");
      spaces[15] = new String("               ");
      spaces[16] = new String("                ");
      spaces[17] = new String("                 ");
      spaces[18] = new String("                  ");
      spaces[19] = new String("                   ");
      spaces[20] = new String("                    ");
      spaces[21] = new String("                     ");
      spaces[22] = new String("                      ");
      spaces[23] = new String("                       ");
      spaces[24] = new String("                        ");
      spaces[25] = new String("                         ");
      spaces[26] = new String("                          ");
      spaces[27] = new String("                           ");
      spaces[28] = new String("                            ");
      spaces[29] = new String("                             ");
      spaces[30] = new String("                              ");
      spaces[31] = new String("                               ");
      spaces[32] = new String("                                ");
      spaces[33] = new String("                                 ");
      spaces[34] = new String("                                  ");

      ChangeLayout(GRAPHLAYOUT);
   }

   public void ChangeLayout(int new_layout)
   {
      current_layout = new_layout;
      if (GRAPHLAYOUT == current_layout)
      {
System.out.println("Changing to Graph Layout");
         setGraphLayout();
      }
      else
      {
System.out.println("Changing to TEXT Layout");
         setTextLayout();
      }
   }

   public void setGraphLayout()
   {
      removeAll();
      setLayout(new BorderLayout()); 
      
      if (topPanel == null)
         {
         topPanel = new Panel();
         topPanel.setLayout(new GridLayout(1,5));
         topPanel.add(backButton);
         topPanel.add(enterValuesButton);
         topPanel.add(toggleGraphButton);
         topPanel.add(showValuesButton);
         showValuesButton.setEnabled(false);
                             // Do not let the use view the output values
                            //  until the input window has been filled in. 
         topPanel.add(forwardButton);
         topPanel.doLayout();
         }

      add ("North", topPanel);
      
      if (null == lineGraph)
      {
         lineGraph = new Graph(20, 450, 400, 400, 10, 1, 2, 1); 
         currentGraph = lineGraph;
      }
      if (null == barGraph)
      { 
         barGraph = new Graph(20, 450, 400, 400, 10, 1, 3, 0); 
         currentGraph = barGraph;
      }
      if (currentGraph == barGraph)
      {
         add("Center", barGraph);
      }
      else if (currentGraph == lineGraph)
      {
         add("Center", lineGraph);
      }
      
      if (parameters == null)
      {
         if (InputWindow != null)
         {
            parameters = new Panel();
            parameters.setLayout(new GridLayout(2, 5));
            parameters.add(new Label("Initial Allele Frequencies :")); 
            allele0Label = new Label("   50");
            parameters.add(allele0Label);
            allele1Label = new Label("   50");
            parameters.add(allele1Label);
            parameters.add(new Label(" "));
            parameters.add(new Label("Selection Factors"));
            selfac0Label = new Label("   50");
            parameters.add(selfac0Label);
            selfac1Label = new Label("   50");
            parameters.add(selfac1Label);
            selfac2Label = new Label("   50");
            parameters.add(selfac2Label);
            parameters.doLayout(); 
         }
      }
      add ("South", parameters);
      setBackground(Color.lightGray);
      doLayout();
      repaint();
   }

   public void setTextLayout()
   {
      StringBuffer outputBuf;
      String outputString = null;
      String nullString;

      removeAll();
      setLayout(new BorderLayout());
      if (null == textOutput)
      {
         textOutput = new TextArea(105, 80);
         textOutput.setEditable(false);
         textOutput.setFont(new Font("Courier", java.awt.Font.PLAIN, 12) );
      }
      add("Center", textOutput);
      //textOutput.setText("");
      //outputString = new String("Generation\tAllele Frequencies\tGenotype Frequencies\n");
      outputBuf = new StringBuffer("Generation");
      outputBuf.append(new String(spaces[BASELENGTH - outputBuf.length()]) );
      outputBuf.append("Allele Frequencies");
      outputBuf.append(new String(spaces[BASELENGTH + 2 * FIELDLENGTH - outputBuf.length()]) );
      outputBuf.append("Genotype Frequencies\n");

      //textOutput.appendText(new String(outputBuf) ); 
      textOutput.setText(new String(outputBuf) );
      //outputString = new String("\t\tA\tB\tAA\tAB\tBB\n");
      //outputBuf = new StringBuffer("");
      outputBuf = new StringBuffer(new String(spaces[BASELENGTH]));
      outputBuf.append(InputWindow.textfield2.getText() );
      outputBuf.append( new String(spaces[BASELENGTH + FIELDLENGTH - outputBuf.length() ]));
      outputBuf.append(InputWindow.textfield4.getText() );
      outputBuf.append( new String(spaces[BASELENGTH + 2 * FIELDLENGTH - outputBuf.length() ]));
      outputBuf.append(InputWindow.textfield7.getText() );
      outputBuf.append( new String(spaces[BASELENGTH + 3 * FIELDLENGTH - outputBuf.length() ]));
      outputBuf.append(InputWindow.textfield10.getText() );
      outputBuf.append( new String(spaces[BASELENGTH + 4 * FIELDLENGTH - outputBuf.length() ]));
      outputBuf.append(InputWindow.textfield13.getText() + "\n" );

      textOutput.append(new String(outputBuf) ); 
      for (int i=0; i<numGenerations; i++)
      {
if (false)
{
        outputString = new String((i+1) +
                "        " + gen[i].allele_freq[0] +
                "        " + gen[i].allele_freq[1] +
                "        " + gen[i].genotype_freq[0] +
                "        " + gen[i].genotype_freq[1] +  
                "        " + gen[i].genotype_freq[2] + "\n");
}

        outputBuf = new StringBuffer(Integer.toString(i+1));
        outputBuf.append( new String(spaces[BASELENGTH - outputBuf.length() ]));
        outputBuf.append(Float.toString(gen[i].allele_freq[0]));
        outputBuf.append(
                   new String(spaces[BASELENGTH + 1 * FIELDLENGTH - outputBuf.length() ]));
        outputBuf.append(Float.toString(gen[i].allele_freq[1]));                    
        outputBuf.append(
                   new String(spaces[BASELENGTH + 2 * FIELDLENGTH - outputBuf.length() ]));
        outputBuf.append(Float.toString(gen[i].genotype_freq[0]));                    
        outputBuf.append(
                   new String(spaces[BASELENGTH + 3 * FIELDLENGTH - outputBuf.length() ]));
        outputBuf.append(Float.toString(gen[i].genotype_freq[1]));                    
        outputBuf.append(
                   new String(spaces[BASELENGTH + 4 * FIELDLENGTH - outputBuf.length() ]));
        outputBuf.append(gen[i].genotype_freq[2] + "\n");                    
 
        textOutput.append(new String(outputBuf) ); 
      }
      add("North", showGraphButton);
      doLayout();
      repaint();
   }
 
   public void runSimulation()
   {
     float val[];           
     int currentVal;
     int allele_cnt = 2; 
     float initFreq[] = new float[2];
     float selFactor[] = new float[3];
     String alleleLabels[] = new String[2];
     String genotypeLabels[] = new String[3];

     float alleleGraphvals[] = new float[numGenerations * 2];
     float genotypeGraphvals[] = new float[numGenerations * 3];
   
     currentGraph.erase(); 
     showValuesButton.setEnabled(true); 
                    // Now allow the user to look at the output values

     InputWindow.getValues(initFreq, selFactor, genotypeLabels, alleleLabels); 
     gen[0] = new Generation(initFreq, selFactor, allele_cnt, genotypeLabels); 
     val = gen[0].get_allele_freq();
     for (int i=0; i < val.length; i++)
     {
        alleleGraphvals[i] = val[i];
     }
     val = gen[0].get_genotype_freq();
     for (int i=0; i < val.length; i++)
     {
        genotypeGraphvals[i] = val[i];
     }
     currentVal = 2; 
     for (int i=1; i<numGenerations; i++)
     {
        gen[i] = new Generation(gen[i-1]);
        val = gen[i].get_allele_freq();
        for (int j=0; j < val.length; j++)
        {
           alleleGraphvals[currentVal++] = val[j];
        }
     }
     currentVal = 3; 
     for (int i=1; i < numGenerations; i++)
     {
        val = gen[i].get_genotype_freq();
        for (int j=0; j < val.length; j++)
        {
           genotypeGraphvals[currentVal++] = val[j];
        }
     }
     lineGraph.getLabels(alleleLabels);
     lineGraph.setPoints(alleleGraphvals);
     barGraph.getLabels(genotypeLabels);
     barGraph.setPoints(genotypeGraphvals);
     repaint();
   } 

   public void paint(Graphics g)
   {
      if (TEXT_LAYOUT != current_layout)
      {
         currentGraph.update(currentGen);
      }
   }
  
   public void actionPerformed(ActionEvent e) 
           //  Invoked when a Button has been pressed on a component.
   {

      String command;
      int i, j;
      Object sourceObj;
      Button source;

      command = e.getActionCommand();
  System.out.println("Button " + command + " pressed");
      sourceObj = e.getSource();
      if (sourceObj instanceof Button)
      {
         source = (Button)sourceObj;
         if (source.equals(backButton))
         {
            if (currentGen != 0) 
            {
               currentGen--;
               currentGraph.update(currentGen); 
               return;
            }
         } 
         else if (source.equals(forwardButton))
         {
            currentGen++; 
            currentGraph.update(currentGen);
            return;
         }
         else if (source.equals(enterValuesButton))
         {
            if(!InputWindow.isShowing())
            {
              currentGraph.erase(); 
              InputWindow.show();  
            }
            return;
         }
         else if (source.equals(showValuesButton))
         {
            currentGraph.erase();
            ChangeLayout(TEXT_LAYOUT);
            return;
         }
         else if (source.equals(toggleGraphButton))
         {
            currentGraph.erase();
            if (currentGraph == lineGraph)
               currentGraph = barGraph;
            else 
               currentGraph = lineGraph;
            //currentGraph.update(currentGen); 
            ChangeLayout(GRAPHLAYOUT);
         }
         else if (source.equals(showGraphButton))
         {
            ChangeLayout(GRAPHLAYOUT);
            return;
         }
      } // end source was a button
   }  // end actionPerformed
}

   class Axis extends Object
   {
      int x_pos, y_pos, orientation, intervalCount, length;
      int intervalWidth;
      int tickWidth;  // Actually, half of an actual tick mark 
      Color color;
      Graph outerparent;
      Vector tickPos;
      static int prevHorzAxisOrigin = -1;

      Axis(int x, int y, int orient, int intervals, int len, Color col, Graph target)
      {
         Point currTick;

	 x_pos = x;
	 y_pos = y;
 	 orientation = orient;
	 intervalCount = intervals;
	 length = len;
         intervalWidth = length / intervalCount; 
	 color = col;
         tickWidth = 5;  
         outerparent = target;
         tickPos = new Vector();
 
         for (int i=1; i <= intervalCount; i++)
         {
             if (orientation == 0) 
             {
               currTick = new Point(i * intervalWidth + x_pos, y_pos);
             }
             else 
             {
               currTick = new Point(x_pos, y_pos - i * intervalWidth);
             } 
             tickPos.addElement(currTick);
         }   
      }

      public void draw()
      {
         this.draw(0);
      }
 
      public void draw(int axisOrigin)
      {
	 Color tempColor;
         Graphics g;
         Font f; 
         FontMetrics fm; 
         int xstart, ystart; //Location of string 
         String s;
       
         g = outerparent.getGraphics(); 
         tempColor = g.getColor();
         g.setColor(color);
         f = new Font("TimesRoman", Font.PLAIN, 12); //8);
         fm = g.getFontMetrics(f);
         g.setFont(f);
         if( orientation == 0) // 0 means orientation is horizontal
         {
           g.drawLine(x_pos, y_pos, x_pos + length, y_pos);
           for ( int i = 0; i <  intervalCount; i++ ) 
           {
              g.drawLine( ((Point)tickPos.elementAt(i)).x, y_pos - tickWidth, ((Point)tickPos.elementAt(i)).x, y_pos + tickWidth);

// new code -- erases old numbers
              if (-1 != prevHorzAxisOrigin)
              {
                 g.setColor(outerparent.getBackground());
                 s = String.valueOf(i + prevHorzAxisOrigin + 1);
                 xstart = ((Point)(tickPos.elementAt(i))).x - (fm.stringWidth(s) / 2);
                 ystart = y_pos + tickWidth + (fm.getHeight() * 3) / 2; //+ 10; 
                 //ystart = y_pos + tickWidth + 10; 
                 g.drawString(s, xstart, ystart);
              }
// end of new code -- erases old numbers
if (false)
{
              g.setColor(outerparent.getBackground());
              s = String.valueOf(i + axisOrigin);
              xstart = ((Point)(tickPos.elementAt(i))).x - (fm.stringWidth(s) / 2);
              ystart = y_pos + tickWidth + (fm.getHeight() * 3) / 2; //+ 10; 
              //ystart = y_pos + tickWidth + 10; 
              g.drawString(s, xstart, ystart);
              s = String.valueOf(i + axisOrigin + 2);
              xstart = ((Point)(tickPos.elementAt(i))).x - (fm.stringWidth(s) / 2);
              ystart = y_pos + tickWidth + (fm.getHeight() * 3) / 2; //+ 10; 
              // ystart = y_pos + tickWidth + 10; 
              g.drawString(s, xstart, ystart);
}              
              s = String.valueOf(i + axisOrigin + 1);
              xstart = ((Point)(tickPos.elementAt(i))).x - (fm.stringWidth(s) / 2);
              ystart = y_pos + tickWidth + (fm.getHeight() * 3) / 2; //+ 10; 
              g.setColor(color);
              g.drawString(s, xstart, ystart);
           }
     
           prevHorzAxisOrigin = axisOrigin;  // new code
         } 
	 else //axis orientation is vertical
         {
	   g.drawLine(x_pos, y_pos, x_pos, y_pos - length);
           for ( int i = 0; i < intervalCount; i++ )
           {
              g.drawLine( x_pos - tickWidth, ((Point)tickPos.elementAt(i)).y, x_pos + tickWidth, ((Point)tickPos.elementAt(i)).y);
              s = String.valueOf(i + axisOrigin);
              xstart = x_pos - tickWidth - 10;
              ystart = ((Point)tickPos.elementAt(i)).y + (fm.getHeight()/4) ;
              g.setColor(outerparent.getBackground());
              g.drawString(s, xstart, ystart);
              s = String.valueOf(i + axisOrigin + 1);
              xstart = x_pos - tickWidth - 10;
              ystart = ((Point)tickPos.elementAt(i)).y + (fm.getHeight()/4) ;
              g.setColor(color);
              g.drawString(s, xstart, ystart);
           } 
        }  
        g.setColor(tempColor);
      }
 
      public Vector getTicks() 
      {
        return tickPos;
      } 

   }


   class Graph extends Canvas 
   {
     int x_pos, y_pos;
     int width, height; 
     int pointsPerTick, lastVisibleTick, lastTick, currentLeftTick;
     int kindOfGraph; 
     int xIntervals, yIntervals; 
     String labels[] = null;

     Axis x_axis, y_axis;
     float values[] = null;  
     Color color[];

     Graph (int x, int y, int wid, int hgt, int xint, int yint, int ppt, int kog ) 
     {
        x_pos = x;
        y_pos = y;
        width = wid;
        height = hgt;
        xIntervals = xint;
        yIntervals = yint;
        pointsPerTick = ppt;
        kindOfGraph = kog;

        currentLeftTick = 0;
        lastVisibleTick = xIntervals;

        color = new Color[8];
        color[0] = Color.yellow;     color[1] = Color.green;
        color[2] = Color.blue;       color[3] = Color.red;
        color[4] = Color.magenta;    color[5] = Color.orange;
        color[6] = Color.cyan;       color[7] = Color.black;

        x_axis = new Axis(x_pos, y_pos, 0, xIntervals, width, Color.black, this);
        y_axis = new Axis(x_pos, y_pos, 1, yIntervals, height, Color.black, this);
     }
     
     public void update( int graphStart ) 
     {
        this.draw(0);
        currentLeftTick = graphStart;
        lastVisibleTick = graphStart + xIntervals;
        this.draw(1); 
     }
     
     public void draw()
     {
        this.draw(1);
     }
   
     public void erase()
     {
        this.draw(0);
     }
    
     private void draw(int drawFlag)
     {
        Graphics g;
        Vector loc;
        int gapMultiplier;
        float widMultiplier; 
        int barX, barY, barWidth, barHeight;  
        int lineX1, lineY1, lineX2, lineY2;
        int currentValue;
        Color barColor, lineColor;

        g = this.getGraphics();
        if (0 != drawFlag)
        {
           x_axis.draw(currentLeftTick);
           y_axis.draw(); 
        }

        loc = x_axis.getTicks();
        currentValue = currentLeftTick * pointsPerTick;
        if (values != null) 
        {
           if (kindOfGraph == 0) //This is a bar graph
           {
              if (pointsPerTick % 2 == 0)   //The pointsPerTick is even
              {
                 widMultiplier = ((float)-1.0 * (float)pointsPerTick * (float)0.5);
                 gapMultiplier = -1 * pointsPerTick / 2; 
              }
              else 
              { 
                 widMultiplier = gapMultiplier = -1 * pointsPerTick / 2;  
              }
              for (int i=0; i < xIntervals && currentValue < values.length; i++)
              {
                 for (int j=0; j < pointsPerTick; j++)
                 {
                 barX = ((Point)loc.elementAt(i)).x + (int)(widMultiplier * 5) + (gapMultiplier * 1);
                 barY = ((Point)loc.elementAt(i)).y;
                 barWidth = 5;
                 barHeight = (int)(values[currentValue] * height);
                 barColor = color[j];   
                 Bar b = new Bar( barX, barY, barWidth, barHeight, barColor, this);
                 if (drawFlag == 0)
                    b.erase();
                 else 
                    b.draw(); 
                 gapMultiplier++;
                 widMultiplier++;
                 currentValue++;
                 }
                 if (pointsPerTick % 2 == 0)   //The pointsPerTick is even
                 {
                    widMultiplier = ((float)-1.0 * (float)pointsPerTick * (float)0.5);     
                    gapMultiplier = -1 * pointsPerTick / 2;
                 }
                 else 
                 { 
                    widMultiplier = gapMultiplier = -1 * pointsPerTick / 2;  
                 }
              }
           }
           else //This is a line graph
           {
             for (int i=0; i < xIntervals - 1 && currentValue < values.length - pointsPerTick; i++) 
             {
                 for (int j=0; j < pointsPerTick; j++) 
                 {
                 Color tempColor = g.getColor(); 
                 if (drawFlag == 0)  
                    lineColor = this.getBackground();
                 else 
                    lineColor = color[j];   
                 g.setColor(lineColor);
                 lineX1 = ((Point)loc.elementAt(i)).x;
                 lineY1 = ((Point)loc.elementAt(i)).y - (int)(values[currentValue] * height);
                 lineX2 = ((Point)loc.elementAt(i+1)).x;
                 lineY2 = ((Point)loc.elementAt(i+1)).y - (int)(values[currentValue + pointsPerTick] * height); 
                 g.drawLine( lineX1, lineY1, lineX2, lineY2);
                 g.setColor(tempColor);
                 currentValue++;
                 }
             }
           }
           if (drawFlag == 0) 
              this.drawLegend(0); 
           else
              this.drawLegend(1);
         }
     }

     public void getLabels(String lab[])
     {
        labels = lab;
     } 

     private void drawLegend(int drawFlag)
     {
         Graphics g;
         Color tempColor;
         FontMetrics fm;
         Font f;
         int xstart, ystart;

         if (labels != null)
         {
            g = this.getGraphics();
            f = new Font("TimesRoman", Font.PLAIN, 10);
            fm = g.getFontMetrics(f);
            xstart = x_pos + 10;
            //ystart = y_pos + 25; 
            ystart = y_pos + fm.getHeight() * 3; 
            tempColor = g.getColor();
            for (int i=0; i < pointsPerTick; i++)
            {
               if (drawFlag == 0)
                  g.setColor(this.getBackground());
               else 
                  g.setColor(color[i]);
               g.fillRect(xstart, ystart, 20, 15);
               xstart = xstart + 25;
               if (drawFlag == 0)
                  g.setColor(this.getBackground());
               else 
                  g.setColor(Color.black);
               g.drawString(labels[i], xstart, ystart + 15);
               xstart = xstart + fm.stringWidth(labels[i]) + 30;
            }   
            g.setColor(tempColor);
         }
     }
     
     public void setPoints( float val[] )
     {
        values = val;
        lastTick = values.length / pointsPerTick;      
     }
  
     public void paint( Graphics g )
     {
        this.update(currentLeftTick);
     }
     
   }


   class Bar extends Object 
   {
     Color color;
     int x_pos, y_pos; 
     int width, height;
     Graph outerparent;

     Bar (int x, int y, int wid, int hgt, Color col, Graph target) 
     {
        color = col;
        x_pos = x;
        y_pos = y;
        width = wid;
        height = hgt;
        outerparent = target;
     }

     public void draw()
     {   
       Graphics g;
       Color tempColor;
  
       g = outerparent.getGraphics();
       tempColor = g.getColor(); 
       g.setColor(color);
       g.fillRect(x_pos-width/2, y_pos-height, width, height);
       g.setColor(tempColor);
     }
 
     public void erase()
     {
       Graphics g;
       Color tempColor;
     
       g = outerparent.getGraphics();
       tempColor = g.getColor();
       g.setColor(outerparent.getBackground());
       g.fillRect(x_pos-width/2, y_pos-height, width, height);
       g.setColor(tempColor);
     }
  }
     
class FrameWindow extends Frame implements ActionListener, AdjustmentListener
{
   GridBagLayout gridBag; // = new GridBagLayout();  // Layout manager for each of the containers
   Panel panel, buttonPanel;
   Button okay;
   TextField textfield1, textfield2, textfield4, textfield7, textfield10, textfield13;
   TextArea  textarea1, textarea2, textarea4, textarea7, textarea10, textarea13;

   Scrollbar Allele_freq_scroll;
   Label allele_freq_one_label;
   Label allele_freq_two_label;

   Scrollbar genotype_one_scroll;
   Label genotype_freq_one_label;
   Scrollbar genotype_two_scroll;
   Label genotype_freq_two_label;
   Scrollbar genotype_three_scroll;
   Label genotype_freq_three_label;

   Scrollbar genotype_scroll[];
   Label     genotype_sel_factor_label[];

   String allele_desc[] = new String[3];
   float init_freq[] = new float[3];
   float sel_factor[] = new float[3];

   Genetics myParent;

   FrameWindow(String title, Genetics parent)
   {
	super(title);				// Setting the title of the window
        myParent = parent;
        gridBag = new GridBagLayout();  // Layout manager for each of the containers
        
	okay = new Button("Okay");		// Creating 2 new buttons to run or cancel 
        okay.addActionListener(this);


        textfield1 = new TextField(50);
        textarea1  = new TextArea(6, 40);
        textfield2 = new TextField(10);
        textarea2  = new TextArea(6, 1);
        textfield4 = new TextField(10);
        textarea4  = new TextArea(6, 1);
        textfield7 = new TextField(10);
        textarea7  = new TextArea(6, 1);
        textfield10 = new TextField(10);
        textarea10  = new TextArea(6, 1);
        textfield13 = new TextField(10);
        textarea13  = new TextArea(6, 1);

        panel = new Panel();
        panel.setLayout(gridBag);

        genotype_scroll = new Scrollbar[4];
        genotype_sel_factor_label = new Label[4];
        for (int i = 1; i < 4; i++)
        {
           genotype_scroll[i] = new Scrollbar(Scrollbar.VERTICAL, 50, 1, 0, 100);
           genotype_scroll[i].addAdjustmentListener(this);
           genotype_sel_factor_label[i] = new Label(Integer.toString(50) );
        }
        allele_freq_one_label = new Label(Integer.toString(50) );
        allele_freq_two_label = new Label(Integer.toString(50) );

        Allele_freq_scroll = new Scrollbar(Scrollbar.VERTICAL, 50, 1, 0, 100);
        Allele_freq_scroll.addAdjustmentListener(this);

        //constrain(panel, new Label("Enter the description of gene in less than 60 characters"),  0,0,GridBagConstraints.REMAINDER,1);
	//constrain(panel, textfield1, 0,1,GridBagConstraints.REMAINDER,1);
        constrain(panel, new Label("Enter the required information for each ALLELE"), 0,2,GridBagConstraints.REMAINDER,1);
        constrain(panel, new Label("Description"), 1,3,1,1);
        constrain(panel, new Label("          "), 2,3,1,1);
        constrain(panel, new Label("Frequency"), 3,3,1,1);
        constrain(panel, new Label("Allele A "), 0,4,1,1);
        constrain(panel, textfield2, 1,4,1,1);
        constrain(panel, allele_freq_one_label, 3,4,1,1);

        constrain(panel, Allele_freq_scroll, 4, 4, 1, 2);


        constrain(panel, new Label("Allele B"), 0,5,1,1);
        constrain(panel, textfield4, 1,5,1,1);
        constrain(panel, allele_freq_two_label, 3,5,1,1);


        constrain(panel, new Label(""), 0,6,GridBagConstraints.REMAINDER,1);
        constrain(panel, new Label("Enter the required GENOTYPE information"), 0,7,GridBagConstraints.REMAINDER,1);
        constrain(panel, new Label("Description"), 1,8,1,1);
        constrain(panel, new Label("Selection Factor"), 3,8,1,1);

        constrain(panel, new Label("Genotype AA"), 0,9,1,1);
        constrain(panel, textfield7, 1,9,1,1);


        constrain(panel, genotype_sel_factor_label[1], 3, 9, 1, 1);
        constrain(panel, genotype_scroll[1], 4, 9, 1, 1);


        constrain(panel, new Label("Genotype AB"), 0, 10, 1, 1);
        constrain(panel, textfield10, 1,10,1,1);
        constrain(panel, genotype_sel_factor_label[2], 3, 10, 1, 1);
        constrain(panel, genotype_scroll[2], 4, 10, 1, 1);

        constrain(panel, new Label("Genotype BB"), 0,11,1,1);
        constrain(panel, textfield13, 1,11,1,1);
        constrain(panel, genotype_sel_factor_label[3], 3, 11, 1, 1);
        constrain(panel, genotype_scroll[3], 4, 11, 1, 1);


	// Creating a Panel for the bottons to show up at the bottom of the screen
        buttonPanel = new Panel();
        buttonPanel.setLayout(new FlowLayout());
        buttonPanel.setLayout(gridBag);
		
	constrain(buttonPanel, okay, 0, 0, 1, 1, GridBagConstraints.NONE, GridBagConstraints.CENTER, 0.3, 0.0, 0, 0, 0, 0);

        this.setLayout(gridBag);

	// Adding Panels to Top Level Window
        constrain(this, panel, 0,0,1,1,GridBagConstraints.VERTICAL,GridBagConstraints.NORTHWEST,0.0,1.0,10,10,5,5);
	constrain(this, buttonPanel, 0, 1, 2, 1, GridBagConstraints.HORIZONTAL, GridBagConstraints.CENTER, 1.0, 0.0, 5, 0, 0, 0);
   }

   public void constrain(Container container, Component component, int  grid_x, int grid_y,
			 int grid_width, int grid_height, int top, int left, int bottom, int right)
   {
	constrain(container, component, grid_x, grid_y, grid_width, grid_height, GridBagConstraints.NONE,
	          GridBagConstraints.NORTHWEST, 0.0, 0.0, top, left, bottom, right);
   }

   public void constrain(Container container, Component component, int  grid_x, int grid_y,
			 int grid_width, int grid_height)
   {
	constrain(container, component, grid_x, grid_y, grid_width, grid_height, GridBagConstraints.NONE,
	          GridBagConstraints.NORTHWEST, 0.0, 0.0, 0, 0, 0, 0);
   }

   public void constrain(Container container, Component component, int  grid_x, int grid_y,
			 int grid_width, int grid_height, int fill, int anchor, double weight_x,
			 double weight_y, int top, int left, int bottom, int right)
   {
	GridBagConstraints c = new GridBagConstraints();

	c.gridx = grid_x;
	c.gridy = grid_y;
	c.gridwidth = grid_width;
	c.gridheight = grid_height;
	c.fill = fill;
	c.anchor = anchor;
	c.weightx = weight_x;
	c.weighty = weight_y;

	if(top+bottom+left+right > 0)
	   c.insets = new Insets(top, left, bottom, right);

	((GridBagLayout)container.getLayout()).setConstraints(component, c);
        container.add(component);
   }

   public void adjustmentValueChanged(AdjustmentEvent e)
   {
      int i;

      Object sourceObj = e.getSource();
      if (sourceObj instanceof Scrollbar)
      {
         if (((Scrollbar)sourceObj).equals(Allele_freq_scroll)) 
         {
            repaint();
            return;
         } /* endif -- Allele frequency scrollbar was adjusted */
         for (i = 1; i < 4; i++)
         {
            if (((Scrollbar)sourceObj).equals(genotype_scroll[i]))
            {
               repaint();
               return;
            }
         }  /* endfor -- i */
         return;
      } /* endif -- A scrollbar was adjusted */
   }  // end processEvent()

   public void actionPerformed(ActionEvent e) 
   {
      if (e.getSource() instanceof Button)
      {
         if ( ((Button)e.getSource()).equals(okay))
         {
                  this.hide();
                  myParent.allele0Label.setText(
                          textfield2.getText() + " " +
                          allele_freq_one_label.getText());
                  myParent.allele1Label.setText(
                          textfield4.getText() + " " +
                          allele_freq_two_label.getText());
                  myParent.selfac0Label.setText(
                          textfield7.getText() + " " +
                          genotype_sel_factor_label[1].getText());  
                  myParent.selfac1Label.setText(
                          textfield10.getText() + " " +
                          genotype_sel_factor_label[2].getText());  
                  myParent.selfac2Label.setText(
                          textfield13.getText() + " " +
                          genotype_sel_factor_label[3].getText());  
                  myParent.runSimulation();
                  return;
           }  // endif -- the okay button was pushed
        } // the event was a button press
   } // end actionPerformed

   public void getValues(float init_frequency[], float selection_factor[],
                         String genotype_description[], String allele_description[])
   {
      int i;

      for(i=0; i<2; i++)
         init_frequency[i] = init_freq[i];

      for(i=0; i<3; i++)
         selection_factor[i] = sel_factor[i];

      genotype_description[0] = textfield7.getText();
      genotype_description[1] = textfield10.getText();
      genotype_description[2] = textfield13.getText();

      allele_description[0] = textfield2.getText();
      allele_description[1] = textfield4.getText();
   }

   public void paint(Graphics g)
   {
      int i;

      for (i = 1; i < 4; i++)
      {
         genotype_sel_factor_label[i].setText(Integer.toString(100 - genotype_scroll[i].getValue() ) );
	 sel_factor[i-1] = (float) (100 -  genotype_scroll[i].getValue());
      }
      allele_freq_one_label.setText(Integer.toString( 100 - Allele_freq_scroll.getValue() ) );
      init_freq[0] = (float)(( 100 - Allele_freq_scroll.getValue()) / 100.0 );
      allele_freq_two_label.setText(Integer.toString( Allele_freq_scroll.getValue() ) );
      init_freq[1] = (float)((Allele_freq_scroll.getValue() ) / 100.0);

      super.paint(g);
   }


}