Q:

User input java array

I need to create a program that will query the user for the size of a 2-dimentional array, and then fill the array with sequential integer data, starting with a user defined initial vale. I have some part of the program but I am stuck at the end. 

A:

What you want is this:
int value = scanner.nextInt(); 
for (int i = 0; i < rows; i++){
    for (int j = 0; j < columns; j++){
        array[i][j] = value + i * columns + j;
    }
}

Try that out and it should work as expected.
Input: 
2
2
5

Output:
[5, 6]
[7, 8]

Be sure to use Arrays.deepToString(array) to print out the array properly.
This will print out the row and column it is going to request for, then prompt you to fill it in.
Also:
array[rows][columns] = scanner.nextInt();

Will not work as you expect. That will fill in a single cell in the array, not to even mention it will throw an IndexOutOfBounds exception.

