I have a 2D arraylist, named as adjLists, which contains arraylists, containing values like these. Each two values are a "pair" and each third is a "flag" for the pair.

[278, 106, 0, 397, 36, 0, 59, 208, 0, 366, 221, 0]
[366, 221, 0, 397, 36, 0, 132, 390, 0, 278, 106, 0, 295, 0, 0]

I use code above to search for specified value pairs in these lists. vertexnum is the number of "sub arraylists" in adjLists.

for (int l = 0; l < vertexnum; l++) {
    if (adjLists.get(l).get(0) == p.x && adjLists.get(l).get(1) == p.y) {
        for (int h = 0; h < adjLists.get(l).size(); h += 3) {
            for (int g = 0; g < vertexnum; g++) {
                if ((vertexSprite[g].getX() + vertexSprite[g].getWidth() / 2) == adjLists.get(l).get(h)
                    && (vertexSprite[g].getY() + vertexSprite[g].getHeight() / 2) == adjLists.get(l).get(h + 1)) {
                    vertexSprite[g].setTexture(img_d);

                    ArrayList sublist = new ArrayList();
                    sublist.add(0, adjLists.get(l).get(h));
                    sublist.add(1, adjLists.get(l).get(h + 1));

                    for (int lj = 0; lj < vertexnum; lj++) {
                        if (Collections.indexOfSubList(adjLists.get(lj), sublist) != -1) {
                            int found = Collections.indexOfSubList(adjLists.get(lj), sublist);
                            adjLists.get(lj).set(found + 2, 1);
                            score++;
                        }
                    }
                    scoreupdate();
                }
            }
        }
        break;
    }
}

This code is to search exact values and replace their flag in every occurences. It can not find all the occurences of the values/pair in the lists, it replaces flag value only a few time. Value of score should be incremented with plus 1 after each found occurence, but this code increments it more than the number of matches. For example one array is like this [pair1, pair1, flag1, pair2, pair2, flag2] and want to change flag1 to 1 if pair1 is equal to the searched.

Why do things that complex?
Far simpler to define a class to contain the data pairs and create a List of that class.
Create a proper equals and hashCode method in that class and it's easy to compare with what you're searching for.
And you can if needed work with Comparable as well.

Yes, you are right, but I have worked in that solution, so starting a new method from zero has much more time consumption than fix an existing one-

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