First thing you need to understand here is that all the three reference matrix, are referring to the same object you have passed as the input (disruption_matrix object). This is the reason why also the original and weighted_matrix are being changed.
In the first line,
int[][] original=disruption_matrix;
refers to the same object in disruption_matrix.
Then on the next line,
int[][] weighted_matrix=disruption_matrix;
refers to the same old object as well. So, you do not need to reach the line,
weighted_matrix = s1.buildMatrix(disruption_matrix);
to see that both original and weighted matrix have been changed. Actually the they have been changed when you have done the calculation to the disruption_matrix itself.
This situation is quite similar to a something like, where,
int a=10;
int b=a;
int c=a;
So, not only 'a' but also 'b' and 'c' will have their value assigned to 10.
In a OOP manner, where such same object is being assigned to different references, once a change has been made to the object through a single reference no matter that you're accessing the object through a different reference, the object has been changed.
For an example let's take this simple class,
Class A{
int val=10;
}
now, in some method we create an object and assign it to references,
A a=new A();
a.val=20;
A b=a;
b.val=30;
A c=a;
c.val=40;
As for the above code, an object is created under the reference called 'a'. In the next line, the value 'val' is accessed through that reference and has been changed from 10 to 20.
Then, the reference 'b' has been declared and it is initialized and pointed to the same object which 'a' is holding. Then in the next line, the value of that object (val) is changed again 20 to 30, but this time through 'b' instead of the reference 'a'.
Same goes to the next three lines where the value of the object is being changed from 30 to 40 through the reference 'c'.
So finally what will be the output?
System.out.println(a.val);
System.out.println(b.val);
System.out.println(c.val);
It is obviously going to give you the output,
40
40
40
This is the concept you are missing here (Pass by value and pass by reference).