Java object array element setting to null

I have problem with order crossover in genetic algorithm. It should copy part of first parent between pointers to offspring, delete from second parent numbers(city number in my tsp problem) that exists in offspring, add one-by-one numbers, that left from second parent. For example:

parent1 . . . . . . . . . . . . . 3 4 1 5 2

parent2 . . . . . . . . . . . . . 4 2 1 5 3

firstPointer = 1, secondPointer = 3

offspring after first step: null 4 1 5 null

final offspring . . . . . . . . 2 4 1 5 3

Sorry for this point, they are just for alignment

Here the code, it should work for 2 offspring, algorithm the same like for first offspring

I think, problem could be in this line: parent2Copy[j] = null;

But not pretty sure, is it a copy or just reference

City.java

// just main part to understand structure not all `standard` methods

public class City {

    private String name;
    private int x, y;

    public City(String name, int x, int y) {
        this.name = name;
        this.x = x;
        this.y = y;
    }
}





Main.java

public class Main {

    public static void main(String[] args) {

        City[] cities1 = {new City("3", 4, 6), new City("4", 4, 6), new City("1", 4, 6),
                new City("5", 4, 6), new City("2", 4, 6)};

        City[] cities2 = {new City("4", 4, 6), new City("2", 4, 6), new City("1", 4, 6),
                new City("5", 4, 6), new City("3", 4, 6)};

        Chromosome one = new Chromosome(cities1);
        Chromosome two = new Chromosome(cities2);


        System.out.println(one.toString());
        System.out.println(two.toString());

        Chromosome[] offspring = Crossover.orderedCrossover(one, two);

        System.out.println(offspring[0].toString());
        System.out.println(offspring[1].toString());

    }

}




Crossover.java

public static Chromosome[] orderedCrossover(Chromosome parentOne, Chromosome parentTwo) {

        Chromosome[] offspring = new Chromosome[2];

        City[] parent1 = parentOne.getArray();
        City[] parent2 = parentTwo.getArray();

        City[] parent1Copy = new City[parent1.length];
        City[] parent2Copy = new City[parent2.length];

        City[] offspring1 = new City[parent1.length];
        City[] offspring2 = new City[parent2.length];

        int firstPointer = new Random().nextInt(parent1.length);
        int secondPointer = new Random().nextInt(parent1.length - firstPointer) + firstPointer;

        while (firstPointer >= secondPointer)
            secondPointer = new Random().nextInt(parent1.length - firstPointer) + firstPointer;

        for (int i = firstPointer; i < secondPointer; i++)
            offspring1[i] = parent1[i];

        for (int i = 0; i < parent1.length; i++) {
            parent1Copy[i] = parent1[i];
            parent2Copy[i] = parent2[i];
        }

        // remove cities from parent2Copy that exists in offspring1 and parent2Copy
        for (int i = 0; i < offspring1.length; i++) {
            for (int j = 0; j < parent2.length; j++) {
                if (offspring1[i] == parent2[j])
                    parent2Copy[j] = null;
            }
        }

        // adds last cities from parent2 to offspring1 empty slots
        for (int i = 0; i < parent2.length; i++) {
            for (int j = 0; j < parent2.length; j++) {
                if (offspring1[i] == null)
                    if (parent2Copy[j] != null) {
                        offspring1[i] = parent2[j];
                        parent2Copy[j] = null;
                        break;
                    }
            }
        }

        // put back cities to copy
        for (int i = 0; i < parent1.length; i++)
            parent2Copy[i] = parent2[i];


        for (int i = firstPointer; i < secondPointer; i++)
            offspring2[i] = parent2[i];

        // remove cities from parent2 that exists in offspring and parent2
        for (int i = 0; i < offspring2.length; i++) {
            for (int j = 0; j < parent1.length; j++) {
                if (offspring2[i] == parent1[j])
                    parent1Copy[j] = null;
            }
        }

        // adds last cities from parent2 to offspring1 empty slots
        for (int i = 0; i < parent1.length; i++) {
            for (int j = 0; j < parent1.length; j++) {
                if (offspring1[i] == null)
                    if (parent1Copy[j] != null) {
                        offspring2[i] = parent1[j];
                        parent1Copy[j] = null;
                        break;
                    }
            }
        }

        offspring[0] = new Chromosome(offspring1);
        offspring[1] = new Chromosome(offspring2);

        return offspring;
    }

When you create an array of an object type (like City), array holds the reference of assigned object, not the object. So, parent2Copy[j] = null does not affect on arrays that earlier copied from the parent2Copy.

Also you should create Object and then assign them to both cities1 and cities2. also it's better to check the equality of cities by overriding equals method of City or by comparing their name!

Maybe simplifying the code can solve the problem by decreasing the code complexity. Here is a sample code for generation offesprings:

import java.util.Random;

public final class Crossover {
  private Crossover() {
    throw new IllegalStateException("Crossover");
  }

  public static Chromosome[] orderedCrossover(Chromosome parentOne, Chromosome parentTwo) {
    Chromosome[] offspring = new Chromosome[2];

    City[] parent1 = parentOne.getArray();
    City[] parent2 = parentTwo.getArray();
    int citiesCount = parent1.length;

    City[] offspring1 = new City[citiesCount];
    City[] offspring2 = new City[citiesCount];

    int firstPointer = new Random().nextInt(citiesCount - 2);
    int secondPointer = new Random().nextInt(citiesCount - firstPointer) + firstPointer;

    while (firstPointer >= secondPointer) {
      secondPointer = new Random().nextInt(citiesCount - firstPointer) + firstPointer;
    }

    System.arraycopy(parent1, firstPointer, offspring1, firstPointer, secondPointer - firstPointer);
    System.arraycopy(parent2, firstPointer, offspring2, firstPointer, secondPointer - firstPointer);

    for (int i = 0; i < citiesCount; i++) {
      for (int j = 0; j < citiesCount; j++) {
        if (offspring1[i] == null) {
          boolean parent2IsInOffspring1 = isCityInTheOffspring(parent2[j], offspring1);
          if (!parent2IsInOffspring1) {
            offspring1[i] = parent2[j];
          }
        } else {
          break;
        }
      }
    }

    for (int i = 0; i < citiesCount; i++) {
      for (int j = 0; j < citiesCount; j++) {
        if (offspring2[i] == null) {
          boolean parent1IsInOffspring2 = isCityInTheOffspring(parent1[j], offspring2);
          if (!parent1IsInOffspring2) {
            offspring2[i] = parent1[j];
          }
        } else {
          break;
        }
      }
    }

    offspring[0] = new Chromosome(offspring1);
    offspring[1] = new Chromosome(offspring2);

    return offspring;
  }

  private static boolean isCityInTheOffspring(City city, City[] offspring) {
    for (int i = 0; i < offspring.length; i++) {
      if (offspring[i] != null && offspring[i].getName().equals(city.getName())) {
        return true;
      }
    }
    return false;
  }
}