Question

What is the best (or anyway, really) of going through a bi-dimensional ArrayList<ArrayList<Integer>> and for every Int that is equal to 1 you leave it, otherwise you subtract 1 from it.
i.e. if arrayList.get(i).get(j) == 3 it will now be 2 and so forth, but if it is 1 it stays 1) Only in specific columns of the ARRAYLIST<ARRAYLIST<INTEGER>>.

Answer 1

Get a shovel – there’s just one way to do it. Iterate over all the columns in all the rows:

// example declaration only - initially all zeros until you set them.
// assumes nrows and ncols are initialized and declared elsewhere
int [][] matrix = new int[nrows][ncols];
for (int i = 0; i < matrix.length; ++i) {
    for (int j = 0; j < matrix[i].length; ++j) {
        // operate on the values here.
        if (matrix[i][j] != 1) {
            matrix[i][j] -= 1;
        }
    }
}

If you’ve got an List of List it looks like this:

List<List<Integer>> matrix = new ArrayList<List<Integer>>();
List<Integer> columnIdsToTransform = Arrays.asList({0, 4, 6 });
// You have to initialize the references; all are null right now.
for (List<Integer> row : matrix) {
    for (int j = 0; j < row.size(); ++j) {            
        // operate on the values here.
        value = row.get(j);
        if (columnsIdsToTransform.contains(j) && (value != 1)) {
            row.set(value-1, j);
        }
    }
}

UPDATE:

Based on your edit, you should add an array or List of columns you want to perform this transformation on. I’ve added an example to the second snippet.