add some more comments

src/cancergrowth/CellPanel.java

@@ -46,7 +46,7 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
     //cells.add(t1);
     Cell t2 = new Cell(475, 475); // Create the initial cell (would be inserted into blood stream)
     //choice1.addItem(t2);
-    cells.add(t2); // add our cell to the ArrayList of cells
+    cells.add(t2); //                add our cell to the ArrayList of cells
     //choice2.addItem(t2);
     
     //choice1.setRenderer(new ComboBoxRenderer());
@@ -121,8 +121,8 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
       }
       else g.drawImage(t.getImage(), t.getX(), t.getY(), this); // otherwise, draw the cell
         
-      if(t.currentStage == 0) {
-        g1 ++;
+      if(t.currentStage == 0) { // record which phase the cell is in to calculate cyclin levels
+        g1 ++; 
       }
       if(t.currentStage == 1) {
         s ++;
@@ -136,7 +136,7 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
         //swingTimer.stop();
       //}
     }
-    if(kill && !dontkill) { // draw pacman if he needs to be drawn
+    if(kill && !dontkill) { // draw pacman if he needs to eat
       g.setColor(Color.YELLOW);
       g.fillArc(pacmanx, pacmany, 100, 100, 220 - cycle * 2, 280 + cycle * 4); 
       if (pacmanx > -100) {
@@ -156,10 +156,14 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
       }
       kill = false; // turn off pacman
     }
+    g1 *= 99;
+    s *= 99;
+    g2 *= 99;
+    m *= 99;
     jLabel1.setText("Delay: " + delay + "ms. Hours since start: " + count + ". Cell Count: " + cells.size());
-    jLabel2.setText("Cyclin G1: " + g1 * 99 + ". Cyclin S: " + s * 99 + ". Cyclin G2: " + g2 * 99 + ". Cyclin M: " + m * 99);
+    // Calculate and print cyclin levels:
+    jLabel2.setText("Cyclin G1: " + g1 + ". Cyclin S: " + s + ". Cyclin G2: " + g2 + ". Cyclin M: " + m + ".");
     System.out.println("Cell Count: " + cells.size());
-    //growing = false;
   }
 
 
@@ -167,7 +171,7 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
   /** This method is called from within the constructor to initialize the form.
     * 
     * WARNING: Do NOT modify this code by hand. The content of this method is
-    * always regenerated by the Form Editor. Ignore this part! this just creates the buttons and slider
+    * always regenerated by the Form Editor. Ignore this part! this just creates the buttons and slider, keep scrolling
     */
   @SuppressWarnings("unchecked")
   // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
@@ -286,7 +290,7 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
 
   private void jButton2ActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_jButton2ActionPerformed
   {//GEN-HEADEREND:event_jButton2ActionPerformed
-    if(dontkill) {
+    if(dontkill) {   //           if we are currently in "stable" mode, then kill them
       dontkill = false;
       kill = true;
       swingTimer.setDelay(10);
@@ -300,7 +304,7 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
         e.printStackTrace();
       }	
     }
-    else if(kill) { // if we press the kill button, then begin the killing
+    else if(kill) { //            if we press the kill button while growing normally, then begin the killing
       kill = false;
       swingTimer.setDelay(delay);
     }
@@ -321,9 +325,9 @@ public class CellPanel extends javax.swing.JPanel implements ActionListener, Cha
 
   private void jButton3ActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_jButton3ActionPerformed
   {//GEN-HEADEREND:event_jButton3ActionPerformed
-    // TODO add your handling code here:
-    kill = true;
-    dontkill = true;
+    // enter stable mode
+    kill = true; // bad variable names, we're not actually killing them
+    dontkill = true; // remind the program NOT to kill them even though kill == true
     swingTimer.setDelay(100);
   }//GEN-LAST:event_jButton3ActionPerformed