package beast.util;
import java.util.Comparator;
import java.util.List;
/**
* sorts numbers and comparable objects by treating contents of array as a binary beast.tree.
* KNOWN BUGS: There is a horrible amount of code duplication here!
*
* @author Alexei Drummond
* @author Korbinian Strimmer
* @version $Id: HeapSort.java,v 1.7 2006/02/20 17:36:23 rambaut Exp $
*/
public class HeapSort {
//
// Public stuff
//
/**
* Sorts an array of indices refering to a list of comparable objects
* into increasing order.
*
* @param list the list of comparable objects
* @param indices an array of indices describing an ascending order of the comparable object in the list
*/
public static void sort(@SuppressWarnings("rawtypes") List<? extends Comparable> list, int[] indices) {
// ensures we are starting with valid indices
for (int i = 0; i < indices.length; i++) {
indices[i] = i;
}
int temp;
int j, n = list.size();
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(list, indices, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = indices[0];
indices[0] = indices[j];
indices[j] = temp;
adjust(list, indices, 1, j);
}
}
/**
* Sorts an array of comparable objects into increasing order.
*
* @param array an array of Comparables to be sorted into ascending order
*/
public static void sort(Comparable<?>[] array) {
Comparable<?> temp;
int j, n = array.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(array, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = array[0];
array[0] = array[j];
array[j] = temp;
adjust(array, 1, j);
}
}
/**
* Sorts an array of objects into increasing order given a comparator.
*
* @param array and array of objects to be sorted
* @param comparator a comparator used to defined the ordering of the objects
*/
public static void sort(Object[] array, Comparator<?> comparator) {
Object temp;
int j, n = array.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(array, comparator, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = array[0];
array[0] = array[j];
array[j] = temp;
adjust(array, comparator, 1, j);
}
}
/**
* Sorts an array of doubles into increasing order.
*
* @param array an array of doubles to be sorted in ascending order.
*/
public static void sort(double[] array) {
double temp;
int j, n = array.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(array, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = array[0];
array[0] = array[j];
array[j] = temp;
adjust(array, 1, j);
}
}
/**
* Sorts an array of doubles into increasing order, ingoring sign.
*
* @param array and array of doubles to be sorted into increasing order, ignoring sign
*/
public static void sortAbs(double[] array) {
double temp;
int j, n = array.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjustAbs(array, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = array[0];
array[0] = array[j];
array[j] = temp;
adjustAbs(array, 1, j);
}
}
/**
* Sorts an array of indices into an array of doubles
* into increasing order.
*
* @param array an array of doubles
* @param indices an array of indices to be sorted so that they describe an ascending order of values in array
*/
public static void sort(double[] array, int[] indices) {
// ensures we are starting with valid indices
for (int i = 0; i < indices.length; i++) {
indices[i] = i;
}
int temp;
int j, n = indices.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(array, indices, j, n);
}
// remove largest elements and put them at the end
// of the unsorted region until you are finished
for (j = n - 1; j > 0; j--) {
temp = indices[0];
indices[0] = indices[j];
indices[j] = temp;
adjust(array, indices, 1, j);
}
}
// PRIVATE STUFF
/**
* helps sort an array of indices pointing into a list of comparable objects.
* Assumes that indices[lower+1] through to indices[upper] is
* already in heap form and then puts indices[lower] to
* indices[upper] in heap form.
*
* @param list a list of comparables
* @param indices an array of indices pointing into list
* @param lower starting index in array to heapify
* @param upper end index in array to heapify
*/
@SuppressWarnings("unchecked")
private static void adjust(@SuppressWarnings("rawtypes") List<? extends Comparable> list, int[] indices, int lower, int upper) {
int j, k;
int temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (list.get(indices[k - 1]).compareTo(list.get(indices[k])) < 0)) {
k += 1;
}
if (list.get(indices[j - 1]).compareTo(list.get(indices[k - 1])) < 0) {
temp = indices[j - 1];
indices[j - 1] = indices[k - 1];
indices[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* Assumes that array[lower+1] through to array[upper] is
* already in heap form and then puts array[lower] to
* array[upper] in heap form.
*
* @param array array to sort
* @param lower lower index of heapify
* @param upper upper index of heapify
*/
@SuppressWarnings("unchecked")
private static void adjust(@SuppressWarnings("rawtypes") Comparable[] array, int lower, int upper) {
int j, k;
Comparable<?> temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (array[k - 1].compareTo(array[k]) < 0)) {
k += 1;
}
if (array[j - 1].compareTo(array[k - 1]) < 0) {
temp = array[j - 1];
array[j - 1] = array[k - 1];
array[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* Assumes that array[lower+1] through to array[upper] is
* already in heap form and then puts array[lower] to
* array[upper] in heap form.
*
* @param array array of objects to sort
* @param comparator comparator to provide ordering
* @param lower lower index of heapify
* @param upper upper index of heapify
*/
@SuppressWarnings("unchecked")
private static void adjust(Object[] array, @SuppressWarnings("rawtypes") Comparator comparator, int lower, int upper) {
int j, k;
Object temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (comparator.compare(array[k - 1], array[k]) < 0)) {
k += 1;
}
if (comparator.compare(array[j - 1], array[k - 1]) < 0) {
temp = array[j - 1];
array[j - 1] = array[k - 1];
array[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* helps sort an array of doubles.
* Assumes that array[lower+1] through to array[upper] is
* already in heap form and then puts array[lower] to
* array[upper] in heap form.
*
* @param array array of doubles to sort
* @param lower lower index of heapify
* @param upper upper index of heapify
*/
private static void adjust(double[] array, int lower, int upper) {
int j, k;
double temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (array[k - 1] < array[k])) {
k += 1;
}
if (array[j - 1] < array[k - 1]) {
temp = array[j - 1];
array[j - 1] = array[k - 1];
array[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* helps sort an array of doubles.
* Assumes that array[lower+1] through to array[upper] is
* already in heap form and then puts array[lower] to
* array[upper] in heap form.
*
* @param array array of doubles to sort ignoring sign
* @param lower lower index of heapify
* @param upper upper index of heapify
*/
private static void adjustAbs(double[] array, int lower, int upper) {
int j, k;
double temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (Math.abs(array[k - 1]) < Math.abs(array[k]))) {
k += 1;
}
if (Math.abs(array[j - 1]) < Math.abs(array[k - 1])) {
temp = array[j - 1];
array[j - 1] = array[k - 1];
array[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* helps sort an array of indices into an array of doubles.
* Assumes that array[lower+1] through to array[upper] is
* already in heap form and then puts array[lower] to
* array[upper] in heap form.
*
* @param array array of doubles
* @param indices array of indices into double array to sort
* @param lower lower index of heapify
* @param upper upper index of heapify
*/
private static void adjust(double[] array, int[] indices, int lower, int upper) {
int j, k;
int temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (array[indices[k - 1]] < array[indices[k]])) {
k += 1;
}
if (array[indices[j - 1]] < array[indices[k - 1]]) {
temp = indices[j - 1];
indices[j - 1] = indices[k - 1];
indices[k - 1] = temp;
}
j = k;
k *= 2;
}
}
}