How can I simulate pass by reference in Java?

I'm a complete Java noob. I know that Java treats all parameters as pass by value and there are several other threads where people explain this.

For example, in C++ I can do:

void makeAThree(int &n)
{
   n = 3;
}
int main()
{
   int myInt = 4;
   makeAThree(myInt);
   cout << myInt;
}

Which will output 3. I know that in Java, all parameters are passed by value and thus you can not manipulate the parameter passed in. Is there a standard way to simulate pass by reference in Java? Is there no way to call a function that manipulates a variable passed in? It's tough for me to wrap my head around the idea of there being no way to do this.

The primary way you can simulate passing a reference is to pass a container that holds the value.

static void makeAThree(Reference<Integer> ref)
{
   ref.set(3);
}

public static void main(String[] args)
{
  Reference<Integer> myInt = new Reference<>(4);
  makeAThree(myInt);
  System.out.println(myInt.get());
}

Since in Java, it is references to objects that are passed by value (the object itself is never passed at all), setting ref to 3 in makeAThree changes the same object referred to by myInt in main().

Disclaimer: Reference isn't a class you can just use with out-of-the-box Java. I'm using it here as a placeholder for any other object type. Here's a very simple implementation:

public class Reference<T> {
    private T referent;

    public Reference(T initialValue) {
       referent = initialValue;
    }

    public void set(T newVal) {
       referent = newVal;
    }

    public T get() {
       return referent;
    }
}

Edit

That's not to say it's great practice to modify the arguments to your method. Often this would be considered a side-effect. Usually it is best practice to limit the outputs of your method to the return value and this (if the method is an instance method). Modifying an argument is a very "C" way of designing a method and doesn't map well to object-oriented programming.