finally working correctly, however not optimized at all yet

src/backend/Cell.java

@@ -2,8 +2,11 @@ package backend;
 
 public class Cell {
 	int alive;
-	private Simulator mySimu;
+	//private Simulator mySimu;
 	
+	public Cell() {
+		
+	}
 	public Cell(int alive) {
 		this.alive = alive;
 	}

src/backend/Simulator.java

@@ -2,16 +2,19 @@ package backend;
 import java.util.ArrayList;
 
 import windowInterface.MyInterface;
+//import backend.Rules;
 
 public class Simulator extends Thread {
 
 	private MyInterface mjf;
 	
+	//private Rules rules;
+	
 	private final int COL_NUM = 100;
 	private final int LINE_NUM = 100;
 	private final int LIFE_TYPE_NUM = 4;
 	//Conway Radius : 1
-	private final int LIFE_AREA_RADIUS = 1;
+	public final int LIFE_AREA_RADIUS = 1;
 	//Animal Neighborhood Radius : 2
 	private final int ANIMAL_AREA_RADIUS = 2;
 	private ArrayList<Integer> fieldSurviveValues;
@@ -19,6 +22,8 @@ public class Simulator extends Thread {
 	
 	private ArrayList<Agent> agents;
 	private ArrayList<ArrayList<Cell>> cells;
+	private ArrayList<ArrayList<Integer>> newCells;
+
 	private boolean stopFlag;
 	private boolean pauseFlag;
 	private boolean loopingBorder;
@@ -34,6 +39,8 @@ public class Simulator extends Thread {
 		loopingBorder=false;
 		clickActionFlag=false;
 		cells = new ArrayList<ArrayList<Cell>>();
+		newCells = new ArrayList<ArrayList<Integer>>();
+
 		agents = new ArrayList<Agent>();
 		fieldBirthValues = new ArrayList<Integer>();
 		fieldSurviveValues = new ArrayList<Integer>();
@@ -42,7 +49,7 @@ public class Simulator extends Thread {
 		
 		//initialize grid with dead cells
 		for(int x=0; x <= getWidth();x++) {
-			ArrayList<Cell> arrayCell = new ArrayList<Cell>();	//initialise first dimension with ArrayLists
+			ArrayList<Cell> arrayCell = new ArrayList<Cell>();	//initialize first dimension with ArrayLists
 			cells.add(arrayCell);
 			for(int y=0; y <= getHeight(); y++) {
 				Cell cell = new Cell(0);	//create a dead cell
@@ -50,6 +57,14 @@ public class Simulator extends Thread {
 			}
 		}
 		
+		for(int x=0; x <= getWidth();x++) {
+			ArrayList<Integer> arrayNewCell = new ArrayList<Integer>();	//initialize first dimension with ArrayLists
+			newCells.add(arrayNewCell);
+			for(int y=0; y <= getHeight(); y++) {
+				newCells.get(x).add(0);		//assign dead cell to its position in second dimension array
+			}
+		}
+		
 		
 		//Default rule : Survive always, birth never
 		for(int i =0; i<9; i++) {
@@ -91,6 +106,45 @@ public class Simulator extends Thread {
 
 	}
 
+	
+	
+	//i put everything here for now
+	public void cellDies(int x, int y) {
+		int aliveNeighbors = getAliveNeighbors(x, y, LIFE_AREA_RADIUS);
+		
+		if(aliveNeighbors < 2 || aliveNeighbors > 3) {
+			//setNewCell(x, y, 0);
+			newCells.get(x).set(y, 0);
+			}
+		}
+	
+	public void cellBorns(int x, int y) {
+		int aliveNeighbors = getAliveNeighbors(x, y, LIFE_AREA_RADIUS);
+		
+		if(aliveNeighbors == 3) {
+			//setNewCell(x, y, 1);
+			newCells.get(x).set(y, 1);
+		}
+	}
+	
+	public int getAliveNeighbors(int x, int y, int radius) {
+		int aliveNeighbors = -1;
+		if(getCell(x,y) == 0) {
+			aliveNeighbors++;
+		}
+		
+		
+		//for each neighbor
+		for(int i = x-radius; i <= x+radius; i++) {
+			for(int j = y-radius; j <= y+radius; j++) {
+					if(getCell(i,j) == 1) {		//if alive, add 1 to counter
+						aliveNeighbors++;
+					}
+			}
+		}
+		
+		return aliveNeighbors;
+	}
 	/**
 	 * method called at each step of the simulation
 	 * makes all the actions to go from one step to the other
@@ -129,6 +183,40 @@ public class Simulator extends Thread {
 		 * 		then the cell becomes alive 	
 		 */
 		
+		//calculate and set newCells based on cells
+		//i started from 1 and ended < to ignore the borders
+		for(int x=1; x < getWidth();x++) {
+			for(int y=1; y < getHeight(); y++) {
+				int status = getCell(x,y);
+				
+				if(status == 1) {
+					//cellDies(x, y);
+					int aliveNeighbors = getAliveNeighbors(x, y, LIFE_AREA_RADIUS);
+					
+					if(aliveNeighbors < 2 || aliveNeighbors > 3) {
+						//setNewCell(x, y, 0);
+						newCells.get(x).set(y, 0);
+						}else{newCells.get(x).set(y, status);}
+				}else if(status == 0) {	
+					//cellBorns(x, y);
+					int aliveNeighbors = getAliveNeighbors(x, y, LIFE_AREA_RADIUS);
+					
+					if(aliveNeighbors == 3) {
+						//setNewCell(x, y, 1);
+						newCells.get(x).set(y, 1);
+					}else{newCells.get(x).set(y, status);}
+				}
+				
+			}
+		}
+		
+		//update cells
+		for(int x=1; x < getWidth();x++) {
+			for(int y=1; y < getHeight(); y++) {
+				int status = getNewCell(x,y);
+				setCell(x, y, status);
+			}
+		}
 		
 		
 		
@@ -162,6 +250,7 @@ public class Simulator extends Thread {
 		if(clickActionFlag) {
 			
 		}else {
+			//System.out.println(getAliveNeighbors(x, y, LIFE_AREA_RADIUS)); //print nb of neighbours
 			if(getCell(x, y)==0) {
 				setCell(x, y, 1);
 			}else {setCell(x, y, 0);}
@@ -180,6 +269,15 @@ public class Simulator extends Thread {
 		int status = cells.get(x).get(y).getAlive();
 		return status;
 	}
+	
+	public int getNewCell(int x, int y) {
+		//TODO : complete method with proper return
+		//int status = newCells.get(x).get(y).getAlive();
+		int status = newCells.get(x).get(y);
+		return status;
+	}
+
+
 	/**
 	 * 
 	 * @return list of Animals in simulated world
@@ -212,10 +310,11 @@ public class Simulator extends Thread {
 	 * @param val to set in cell
 	 */
 	public void setCell(int x, int y, int status) {
-		//TODO : complete method 
 		cells.get(x).get(y).setAlive(status);
-			
 	}
+	/*public void setNewCell(int x, int y, int status) {
+		newCells.get(x).get(y).setAlive(status);
+	}*/
 	
 	/**
 	 *