My project to create a simulation of cellular life.

Question

I little while ago I began to create a program to simulate cellular life, complete with reproduction, evoltuion, and mutation.
So far, all I have is the process for creating a cell, and creating a sperm cell from that cell.
Please look over the code, and tell me if I should change something, or give me some tips.
My next step would be to create a 'mate' class, to get the sperm and the egg (same as sperm, just another name) to combine and create a full cell.
Some background about the classes:
The genes will be stored in 2 bases (1, and 0) instead of 4, to simplify the process of creating fenotype.
Genes.java's goal
- randomly generate dominant and rececive DNA for a cell which is stored in two different boolean arrays.
DivideGenes.java's goal
-Convert the boolean arrays to int arrays
-Randomly replace a value of the rececive OR the dominant array with a 3
I'm kinda tired, I don't remember if they do anything else.
Here is the source code:
Genes.java
public class Genes {
public boolean[] domgenes = new boolean[501];
public boolean[] recgenes = new boolean[501];
    public void randgenes()
        for(int i=0; i<500; i++) {
            double tempgene = (Math.round((Math.random())));
            int tempdomgene = (int)(tempgene);
              if(tempdomgene == 1) {
              domgenes[i] = true;
              else {
              domgenes[i] = false;
            System.out.println("Dominant Gene is " + domgenes);
for (int x = 0; x<500; x++) {
double tempgene = (Math.round((Math.random())));
int temprecgene = (int)(tempgene);
if(temprecgene == 1) {
recgenes[x] = true;
else {
recgenes[x] = false;
System.out.println("Rececive Gene is " + recgenes[x]);
public boolean[] getdomGenes()
return domgenes;
public boolean[] getrecGenes()
return recgenes;
DivideGenes.java
public class DivideGenes
    int badcopy =0;
    boolean[] domgenes;
    boolean[] recgenes;
    int[] tempdomgenes = new int[501];
    int[] temprecgenes = new int[501];
    int tempgene;
    int geneholder;
    public DivideGenes(boolean[] domgenes, boolean[] recgenes)
        this.domgenes = domgenes;
        this.recgenes = recgenes;
   public int randommath() { //finds a random number
            double tempgene2 = Math.random();
            tempgene2 = tempgene2*500;
            tempgene = (int)tempgene2;
      return tempgene;
    public void randdivide() //main process
for (int i = 0; i < 500; i++) {
if (domgenes[i] == true) {
tempdomgenes[i] = 1;
else {
tempdomgenes[i] = 0;
if (recgenes[i] == true) {
temprecgenes[i] = 1;
else {
temprecgenes[i] = 0;
        for (int i = 0; i < 500; i++) { //creates the sperm cell
if (binmath() == 1) {
tempdomgenes[i] = 3;
else {
temprecgenes[i] = 3;
System.out.println("tempdomgenes is " + tempdomgenes);
System.out.println("temprecgenes is " + temprecgenes[i]);
public boolean[] getNewDomGenes()
return tempdomgenes;
public boolean[] getNewRecGenes()
return temprecgenes;
public int binmath() {
double tempbingene = (Math.round((Math.random())));
int bingene = (int)(tempbingene);
return bingene;
TestMain (the launching class)
public class TestMain
    public static void main(String[] args)
System.out.println(" ");
System.out.println(" ");
System.out.println(" ");
        Genes cell = new Genes();
        cell.randgenes();
        boolean[] theDominantGenes = cell.getdomGenes();
        boolean[] theRececiveGenes = cell.getrecGenes();
System.out.println(" ");
System.out.println(" ");
System.out.println(" ");
        DivideGenes cell2 = new DivideGenes(theDominantGenes, theRececiveGenes);
        cell2.randdivide();

Answer 1

I have a question.
Say I want to combine my sperm cell with my egg cell.
I am blanking out, how would I do that.The process goes this way in real life:
Sperm and egg cells are generated by process called mithosis from ordinary cell that multiplyes twice to create 4 cells with half the cromosome number. Say there are 23 cromosome pairs. I won't discuss the actual process here, but to final result there are chosen randomly 23 cromosomes from in either one of the pairs. Put it isn't so simple. During process, every other cromosome pair breaks in random location and concats with it's opposing pieces and vise versa. This is called crossing over. You propably need pictures to get it.
To simulate offspring process, you take two individuals. You make random egg and sperm cells of them (there's really no difference in them, so you probably won't need any subclasses). Then you simple take the cromosomes from both cells to come up with cromosome pairs again.
somehing like this exluding xover.
class HalfGenome
  Cromosome cromosomes[];
class Genome
  HalfGenome mother, father;
  public Genome(Mother,father) {...}
  public Genome createOffspring(Genome parent)
    HalfGenome sperm=getHalf();
    HalfGenome egg=parent.getHalf();
    return new Genome(sperm, egg);
  private HalfGenome getHalf()
    // randomly select cromosomes from mother or father
    HalfGenome half=new HalfGenome();
    for (int i=0;i<mother.cromosomes.length;i++)
       switch (random)
        case 0:half.cromosomes=mother.cromosomes[i];
case 1:half.cromosomes[i]=father.cromosomes[i];
return half;
..anyway the idea is that it's encapsulated nicely (except for halfgenome in this case) providing easy and compact interface. I think that the genome and halfgenome aren't probably engilish words, but they'll do for me.