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Implementing Wikipedia in-place quicksort pseudocode in Java

I'm using the pseudocode called Lomuto partition scheme on https://en.wikipedia.org/wiki/Quicksort. But I just don't understand what it is that I am doing wrong here. The array never gets organized (regardless of the input size). This is preparation for my final exam. My professor wants us to use this algorithm, but I can't just learn it unless I have an understanding of how it works by testing it.
private static void quickSort(Integer A[], int l, int r) {
if (l < r) {
int k = partition(A, l, r);
quickSort(A, l, k - 1);
quickSort(A, k + 1, r);
}
}
private static int partition(Integer A[], int l, int r) {
int pivot = A[r];
int i = l;
for (int j = l; j <= r - 1; j++) {
if (A[j] <= pivot) {
i++;
int temp = A[j];
A[j] = pivot;
pivot = temp;
}
}
int temp = A[i + 1];
A[i + 1] = A[r];
A[r] = temp;
return i + 1;
}

I don't know what else to say other than that you just didn't transcribe the pseudocode correctly. At the beginning of partition, i should equal l - 1, but you set it to l.
Also, you're not swapping A[i] with A[j] within the nested loop. Here's the correct implementation:
private static int partition(Integer A[], int l, int r) {
int pivot = A[r];
int i = l - 1;
for (int j = l; j <= r - 1; j++) {
if (A[j] < pivot) {
i++;
int temp = A[i];
A[i] = A[j];
A[j] = temp;
}
}
int temp = A[i + 1];
A[i + 1] = A[r];
A[r] = temp;
return i + 1;
}

Why is this test for my quick sort failing?

I'm trying to implement quicksort using the median of three algo and it fails a unit test I wrote related to a small partition. I changed my earlier partition and now it passes one of the tests it used to fail, but still fails the one at the bottom:
My code is:
public class QuickSort {
static void swap(int[] A, int i, int j) {
int tmp = A[i];
A[i] = A[j];
A[j] = tmp;
}
static final int LIMIT = 15;
static int partition(int[] a, int left, int right){
int center = (left + right) / 2;
if(a[center] < (a[left]))
swap(a,left,center);
if(a[right-1] < a[left])
swap(a,left,right);
if(a[right-1] < a[center])
swap(a,center,right);
swap(a,center,right - 1);
return a[right - 1];
}
static void quicksort(int[] a, int left, int right){
if(left + LIMIT <= right){
int pivot = partition(a,left,right);
int i = left;
int j = right - 1;
for(;;){
while(a[++i] < pivot){}
while(a[--j] > pivot){}
if(i < j)
swap(a,i,j);
else
break;
}
swap(a,i,right - 1);
quicksort(a,left,i-1);
quicksort(a,i+1,right);
}
else{
insertionSort(a);
}
}
public static void insertionSort(int[] a){
int j;
for(int p = 1; p < a.length; p++){
int tmp = a[p];
for(j = p; j > 0 && tmp < a[j-1]; j--)
a[j] = a[j-1];
a[j] = tmp;
}
}
}
This test fails:
public void smalltest() throws Exception {
int[] Arr_orig = {3,9,8,2,4,6,7,5};
int[] Arr = Arr_orig.clone();
int pivot = QuickSort.partition(Arr, 0, Arr.length);
for (int i = 0; i != pivot; ++i)
assertTrue(Arr[i] <= Arr[pivot]); //fails!
for (int i = pivot + 1; i != Arr.length; ++i)
assertTrue(Arr[pivot] < Arr[i]);
}

There is a conflict between using right-1 and right in this sequence:
if(a[right-1] < a[left])
swap(a,left,right);
You need to decide if right is going to be the index to the last element, or 1 + index to the last element (an "ending" index).
There may be other problems, but this is the first one I noticed.

QuickSort Java implementation issue

I'm trying to implement a QuickSort algorithm as a homework at the university, but I just fail to understand where there is a mistake in my code. I suppose it's a logical mistake, I think I swap my pivot wrongly. I could really use some help, thank you in advance. There is the code:
public class QuickSort {
private int [] array;
public QuickSort(int [] array){
this.array = array;
}
public void sort(){
partition(0, array.length - 1);
}
public void partition(int start, int end){
if (end - start < 2){
return;
}
int pivot_index = end;
int i = start;
int j = end - 1;
while (i < j){
//both elements are not in the right place
if(array[i] > array[pivot_index] && array[j] <= array[pivot_index]){
swap(array, i, j);
i++;
j--;
}
//the element on the left is not in place
else if (array[i] > array[pivot_index] && array[j] > array[pivot_index]){
j--;
}
//the element on the right is not in place
else if (array[i] < array[pivot_index] && array[j] < array[pivot_index]){
i++;
}
//both elements are in place
else {
i++;
j--;
}
}
if (array[i] > array[pivot_index]){
swap(array, pivot_index, i);
pivot_index = i;
}
partition(start, pivot_index - 1);
partition(pivot_index + 1, end);
}
private static void swap(int [] tab, int index1, int index2){
int temp = tab[index1];
tab[index1] = tab[index2];
tab[index2] = temp;
}
}

Solution one
The idea is iterating through the array to check whether the current element is smaller than the last one (the pivot), if yes swap with the first one that is not (index is lastSmaller + 1).
private void partition(int start, int end) {
if (start >= end) {
return;
}
int lastSmallest = start - 1;
for (int i = start; i < end; i++) {
if (array[i] < array[end])
swap(++lastSmallest, i);
}
swap(++lastSmallest, end);
partition(start, lastSmallest - 1);
partition(lastSmallest + 1, end);
}
Solution two
I think this is what you want to implement. Iterate through the array, skip all the elements in good place on the left and right. Swap the two in wrong place.
private void partition(int start, int end) {
if (end <= start) {
return;
}
int k = end;
int i = start;
int j = end - 1;
while (i < j) {
// left is in place
while (i < j && array[i] < array[k]) {
i++;
}
// right is in place
while (i < j && array[j] >= array[k]) {
j--;
}
// both are not good
if (i < j) {
// swap
int temp = array[i];
array[i] = array[j];
array[j] = temp;
i++;
j--;
}
}
// swap left and pivot
if (array[i] >= array[k]) {
int temp = array[i];
array[i] = array[k];
array[k] = temp;
}
partition(start, i - 1);
partition(i + 1, end);
}
The reason why your solution does not work is that when you find both are not in place, you swap them and continue to partition the rest of the array. However, you can not guarantee what you have swapped does not violate the rule. Therefore, you need to skip all the elements in place on both side first then swap.

Counting Loops and Comparisons

I need to count the number of loops and comparisons which occur over four different sorting methods. I am using the Selection, Bubble, Insertion, and Quick sort methods. Ideally, I would just place a int such as loopCounter and ++ it every time it loops/compares. Although, being quite new to all of this, I am having trouble distinguishing when I need to include such counters. As you will be able to see in the following code, I attempted to create multiple counters. Although, I think only the selection counters are correct so far.
Additionally, I am required to count the number of times that a value is shifted. In other words, how many times integers are swapped.
Any help with this would be extremely appreciated!
Thanks
ArrayList<Integer> list = new ArrayList<Integer>();
//Counters for Selection Sort
int loopCounter = 0;
int compCounter = 0;
//Counters for Bubble Sort
int loopCounter2 = 0;
int compCounter2 = 0;
//Counters for Insertion Sort
int loopCounter3 = 0;
int compCounter3 = 0;
//Counters for Quick Sort
int loopCounter4 = 0;
int compCounter4 = 0;
public void selectionSort(Integer[] a) {
for(int i = 0; i < a.length; i++) {
int smallestValue = a[i];
int smallestIndex = i;
if(ascButton.isSelected()){
for(int j = i+1; j < a.length; j++) {
if (smallestValue > a[j]) {
smallestValue = a[j];
smallestIndex = j;
loopCounter++;
compCounter++;
}
}
a[smallestIndex] = a[i];
a[i] = smallestValue;
} else if(desButton.isSelected()){
for(int j = i+1; j < a.length; j++) {
if (smallestValue < a[j]) {
smallestValue = a[j];
smallestIndex = j;
loopCounter++;
compCounter++;
}
}
a[smallestIndex] = a[i];
a[i] = smallestValue;
}
}
}
public void bubbleSort(Integer[] a) {
int temp;
for (int i = a.length - 1; i > 0; i--) {
if(ascButton.isSelected()) {
for(int j = 0; j < i; j++) {
loopCounter2++;
compCounter2++;
if(a[j] > a[j + 1]) {
temp = a[j];
a[j] = a[j + 1];
a[j + 1] = temp;
}
}
} else if(desButton.isSelected()) {
for(int j = 0; j < i; j++) {
loopCounter2++;
compCounter2++;
if(a[j] < a[j + 1]) {
temp = a[j];
a[j] = a[j + 1];
a[j + 1] = temp;
}
}
}
}
}
public void insertionSort(Integer[] a) {
for(int i = 1; i < a.length; i++) {
loopCounter3++;
compCounter3++;
int temp = a[i];
int j = i - 1;
if(ascButton.isSelected()) {
while(j >= 0 && a[j] > temp) {
a[j + 1] = a[j];
j--;
}
a[j + 1] = temp;
} else if(desButton.isSelected()) {
while(j >= 0 && a[j] < temp) {
a[j + 1] = a[j];
j--;
}
a[j + 1] = temp;
}
}
}
public void quickSort(Integer[] a, int left, int right) {
int i = left;
int j = right;
int temp;
int pivot = a[(left + right)/2];
while(i <= j) {
if(ascButton.isSelected()) {
while(a[i] < pivot)
i++;
while(a[j] > pivot)
j--;
} else if(desButton.isSelected()) {
while(a[i] > pivot)
i++;
while(a[j] < pivot)
j--;
}
if(i <= j) {
temp = a[i];
a[i] = a[j];
a[j] = temp;
i++;
j--;
}
}
if(left < j) {
quickSort(a,left,j);
}
if(i < right) {
quickSort(a, i, right);
}
}

With counters, you simply want to "count" when you want to program to count something. So if you don't understand your own code, then it will be difficult to know when you want to "count" something. I suggest you figure out when a swap is happening, when that is happening in your code, that is when you want to do some sort of:
swapCount++;//Each time a swap happens increment by 1
iterationCount++//A full pass has happened increment by 1
Note: above just because a full pass has happened in many sort, which you probably know, does not mean it is sorted, it is just saying it has done 1 pass.
I'm not sure if this theory will help you any. Give me some feedback on what your still having trouble with and I'll see if I can change my answer to better reflect what your looking for.

As #Andreas suggested, your loop and comparison counters are in place correctly.
As far as the swap counter is concerned, think of it this way - you cannot swap without a temp variable. As a result, whenever a temp variable is involved you want to increase your swap counter.
As an example, for your quicksort, it would look like this:
public void quickSort(Integer[] a, int left, int right) {
int i = left;
int j = right;
int temp;
int pivot = a[(left + right)/2];
while(i <= j) {
if(ascButton.isSelected()) {
while(a[i] < pivot)
i++;
while(a[j] > pivot)
j--;
} else if(desButton.isSelected()) {
while(a[i] > pivot)
i++;
while(a[j] < pivot)
j--;
}
if(i <= j) {
temp = a[i];
a[i] = a[j];
a[j] = temp;
i++;
j--;
swapCounterForQuickSort++;
}
}
if(left < j) {
quickSort(a,left,j);
}
if(i < right) {
quickSort(a, i, right);
}
}
Follow the same logic for your other sorts.
Also, some general suggestions:
Always name variables so that they tell you what they are used for. Rather than loopCounter1 try using loopCounterForSelectionSort and so on. Don't be afraid of long variable names. Information is power!
Make your functions as short and reusable as possible. For example, you swap integers a lot in your code. Maybe you can just copy the swap code and paste it into a swapIntegers() function. Then everytime you just call this function when you want to swap! Also, notice how this makes your swap counter question easier to answer since you can put a counter in the swap method to do the counting for you. (Although be aware since multiple methods will call the swap counter so you may want to pass it as an argument etc.)

Quick Sort. Handling Duplicates

Can someone show me how to handle duplicates in QuickSort with my function here?
private static int[] quickSort(int[] input, int left, int right) {
int mid = (left + right) / 2;
int i = left;
int j = right;
if((right - left) < 1) {
return new int[]{};
}
while(i <= j) {
while((input[i] < input[mid])) {
i++;
}
while((input[j] > input[mid])) {
j--;
}
if(i <= j) {
int temp = input[i];
input[i] = input[j];
input[j] = temp;
i++;
j--;
}
}
if(j > left) {
input = quickSort(input, left, j);
}
if(i < right) {
input = quickSort(input, i, right);
}
return input;
}

The code has several problems.
"return new int[]{};" This will generate new arrays and consumes memory unnecessarily. You may return "input".
For the first inner loops, you may want to have "input[i] <= input[mid] && i < mid". This will handle duplicates.
There are some well-tested code here: Quick Sort