The code doesn't run and it looks like you didn't post all of it (where's function  pythagoras?).

Thats the point it isnt complete as, the person helping me with it has gone away and hence I have no idea what to do with it, but it needs completing.

It is not completable. Without pythagoras() or cCell how is anyone supposed to know what it is supposed to do?

Just a little clean-up. But code isn't operative right now:

int[] ttt = {
  0, 1, 2, 3, 4
};

float a;
float scx, scy, sca;

cCell[] tst;

class cCell {
  float aa, bb, cc, dd, ee;
  PVector[] cP = new PVector[16];

  cCell(float a, float b, float c, float d, float e) {
    aa = aa;
    bb = bb;
    cc = cc;
    dd = dd;
    ee = ee;
  }
}

void arrow(float x, float y, float sx, float sy) {
  float pythagoras = 100;

  line(x, y, x+sy, y+sy);

  line(x+sx, y+sy, x+sx-sy / pythagoras(sx, sy, 0)*3 / pythagoras(sx, sy, 0)*3, 
  y+sy+sx/pythagoras(sx, sy, 0)*3 - sy/pythagoras);

  line(x+sx, y+sy, x+sx-sy / pythagoras(sx, sy, 0)*3 / pythagoras(sx, sy, 0)*3, 
  y+sy+sx/pythagoras(sx, sy, 0)*3 - sy/pythagoras);
}

float pythagoras(float a, float b, float c) {
  return a*b - c;
}

void setup() {
  size (800, 600);
  stroke (255);
  background (0, 0, 0);
  tst = new cCell[16];
  frameRate(20);
  smooth();

  textFont( createFont("Arial", 10) );

  a = pythagoras(4, 4, 0);

  tst[0]  = new cCell (400, 200, 20, 14000, 0);
  tst[1]  = new cCell (300, 200, 20, 28000, 0);
  tst[2]  = new cCell (150, 300, 20, 52000, 0);
  tst[3]  = new cCell (250, 340, 20, 18000, 0);
  tst[4]  = new cCell (450, 290, 20, 20000, 0);
  tst[5]  = new cCell (450, 350, 20, 16000, 0);
  tst[6]  = new cCell (510, 220, 20, 20000, 0);
  tst[7]  = new cCell (530, 300, 20, 25000, 0);
  tst[8]  = new cCell (420, 0, 20, 14000, 0);
  tst[9]  = new cCell (300, 0, 20, 28000, 0);
  tst[10] = new cCell (150, 100, 20, 32000, 0);
  tst[11] = new cCell (250, 140, 20, 18000, 0);
  tst[12] = new cCell (450, 90, 20, 20000, 0);
  tst[13] = new cCell (450, 160, 20, 20000, 0);
  tst[14] = new cCell (520, 20, 20, 20000, 0);
  tst[15] = new cCell (520, 100, 20, 25000, 0);
}

void draw() {
  lights();
  background(0);

  float cameraY = height>>1;
  float fov = mouseX / (width*HALF_PI);
  float cameraZ = cameraY / tan(fov/2.);
  float aspect = float(width)/float(height);

  if (mousePressed)    aspect /= 2.;

  //pushMatrix();
  translate(scx, scy);
  rotate(sca / 72*PI);

  noFill();

  line(0, 350, 400, 550);
  line(600, 450, 400, 550);
  line(600, 450, 1000, 650);

  fill(-1, 160);

  for (int i = 0; i < 16; i++) {
    beginShape();

    for (int ii = 0; ii < tst[i].cc; ii++)
      vertex(tst[i].cP[ii].x, tst[i].cP[ii].y);

    endShape(CLOSE);
  }
}

From what i understand from what I was told the arrow() method is not essential and all it does is provide and arrow to show the direction the cell is moving when a force acts upon it. 

Ok thank you very much for the help. 

I've just filled in some arbitrary garbage code as far enough to find out other obvious compiling bugs!
That function pythagoras() and class cCell are just gibberish code vessels I've made up!

Seems like the supposed original cCell class from your traveling friend
demands other instances of a mysterious class inside it! And Array cP[] was supposed to store those objects!
And that extra class would need to have field variables x & y there!

Dunno why his code needs to be so complicated though!? 

P.S.: Perhaps that extra mysterious class can be an Array of PVectors!

I see...

No idea! I'm not good at trigonometry at all.
And those line() monstrous parameters inside function arrow() gimme the chills! 

P.S.: Modified the "tidy-up" code to use PVector. And now at least it compiles!

Thanks a lot for the help GoToLoop, from what I understand the arrow() method is simply one that provides an arrow in the centre of each cell showing which direction the cell is being acted upon and hence moves, and is by no means essential to the simulation. 

For starters, a PVector instance grants 3 field float variables -> x, y & z.
And it seems like it's as far what your program does with it; that is, just uses variables x & y from it!
And I don't even believe it shoulda been an Array of PVectors. A simple instance of it would be enough!

Now, if you wanna know about what else a PVector can do besides those 3 variables, take a look at below:
http://processing.org/reference/PVector.html

I guess this is to do with missing parameters on cCell.

I don't think so. I see lotsa parameters passed when creating those 16 instances of cCell in variable tst[]

It's just what I've pre-warned you: my class cCell is just faux filling!
It doesn't do anything; but storing all of the parameters passed!

Of course, your traveling friend would probably make some methods to manipulate all those passed data!

Ok ive found out that the guy who was helping me based the code on this simulation:  http://www.youtube.com/watch?v=iRIGP45hebc

Please can someone help me with this, I understand the basics of this simulation but I cannot get any code to function. Like with the class cCell, what needs to be specified? I have no idea.

Now I see why you wanted to use this code, it is a portion of what is visible in some of the video. Unfortunately, the code that is there does not help much in figuring out how it works as the important parts are not shown.

Maybe this is a good place to start, let me know if you have questions:

Thank you very much asimes, this helps a lot. Once ive had a play around with the code I will get back to you if ive got any questions.

One quick question, with the example code you provided why does the mouse not interact with the outside of the circle, but instead with a smaller circle within?

I invented a rule that basically says, "Only allow mouse interaction if the mouse is inside the red circle". That is here:

Ok this maybe quite simple but i have this line in my code 

You can't call two at the same time, but you could call one then the other. Or make one method that has the code of both in whatever order it is supposed to be executed.

I i try an call on then the other such as,

Anyone?

I'm jumping on to the end of this thread without reading it, but I don't think you're using that switch like you think you are.

Ok thanks for the help tfguy44 but i've tried formatting it as you've suggested as follows:

2. public void drawMolecules()
3.   {
4.     switch(type) {
5.       case Molecule1: 
6.       fill(color(0,0,205)); 
7.       break;
8.       ellipse(position.x,position.y,max(4,R),max(4,R));
9.    
10.       case Molecule2: 
11.       fill(color(255,255,0)); 
12.       break;
13.       ellipse(position.x,position.y,max(4,R),max(4,R));
14.     }