genetic drift sim

import java.util.ArrayList;
import java.util.Collections;
import java.util.Random;

public class GeneticDrift_RUN_SIM {

public static void main(String[] args){

GeneticDriftSim sim = new GeneticDriftSim();

for(int i=0; i<5; i++){  // Number of times you wish to run simulation
sim.go();
}

  }
}

///////////////////////////////////////////////////

class GeneticDriftSim {

public void go() {

int numOfAnimals = 1000; // total number of males (females will be the same)
                        // i.e number you input will be HALF the starting population

int numOfMatings = 10000; // i.e total number of generations

ArrayList<Animal> males = new ArrayList<Animal>();
ArrayList<Animal> females = new ArrayList<Animal>();
ArrayList<Animal> nextgenerationMales = new ArrayList<Animal>();
ArrayList<Animal> nextgenerationFemales = new ArrayList<Animal>();
ArrayList<Animal> lastGeneration = new ArrayList<Animal>();

for(int i=0; i<numOfAnimals; i++){
  males.add(new Animal('M'));
  females.add(new Animal('F'));
}

for(int j=0; j<numOfMatings; j++){

for(int i=0; i<males.size(); i++){   // male array same size as females anyway
  Animal offspring1 = males.get(i).mate(females.get(i));
  Animal offspring2 = males.get(i).mate(females.get(i));
  nextgenerationMales.add(offspring1);  //no need to check for M/F since first
  nextgenerationFemales.add(offspring2); //child always M, second always F
}
males.clear();
females.clear();
males.addAll(nextgenerationMales);
females.addAll(nextgenerationFemales);
nextgenerationMales.clear();
nextgenerationFemales.clear();

/*System.out.println(males);       // Uncomment this and next section if you
System.out.println(females); */    // wish to see each generation and the
Collections.shuffle(males);       // phenotypic distribution
Collections.shuffle(females);

/*System.out.println();
System.out.println("-----NEXT GEN-----");
System.out.println(); */

}

lastGeneration.addAll(males);
lastGeneration.addAll(females);

int totalA1Count = 0;
int totalA2Count = 0;
for(Animal a : lastGeneration){
  if(a.allele1 == "A1"){
    totalA1Count++;
  } else {
    totalA2Count++;
  }
  if(a.allele2 == "A1"){
    totalA1Count++;
  } else {
    totalA2Count++;
  }
} //closes for loop

System.out.println("totalA1Count: "+totalA1Count +" totalA2Count: " +totalA2Count);

}

}

///////////////////////////////////////////////

class Animal {

public String allele1;
public String allele2;
private char gender;
private int numOfChildren;

public Animal(char gender){
  this.gender = gender;       // Use no-arg constructor to make the
  this.allele1 = "A1";          // starting Animals so equal frequencies of A1 & A2
  this.allele2 = "A2";
  this.numOfChildren = 0;         // all A1/A2 heterozygotes
}

public Animal(char gender, String allele1, String allele2){
  this.gender = gender;
  this.allele1 = allele1;            // Use to create all future Animals once
  this.allele2 = allele2;            // program has started
  this.numOfChildren = 0;
}

public Animal mate(Animal parentTwo){
  char genderToPassOn;
  if(this.numOfChildren == 0){
    genderToPassOn = 'M';
  } else if(this.numOfChildren == 1){
    genderToPassOn = 'F';
  } else {
    genderToPassOn = 'N'; // N = neutral. But shouldn't be possible anyway
  }                       // since not allowed to have >2 children

  String parent1AlleleToPassOn;
  String parent2AlleleToPassOn;

  Random rand = new Random();
  int y = rand.nextInt(2);
  if(y ==0){
    parent1AlleleToPassOn = this.allele1;
  } else {
    parent1AlleleToPassOn = this.allele2;
  }
  int z = rand.nextInt(2);
  if(z ==0){
    parent2AlleleToPassOn = parentTwo.allele1;
  } else {
    parent2AlleleToPassOn = parentTwo.allele2;
  }

  this.numOfChildren++;

  return new Animal(genderToPassOn, parent1AlleleToPassOn, parent2AlleleToPassOn);
  }

@Override
public String toString(){
  return this.allele1 + this.allele2 +"("+this.gender+")";
}

}