/*
* HeapSort.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.util;
import java.util.AbstractList;
import java.util.Comparator;
import java.util.Random;
import java.util.Vector;
/**
* sorts numbers and comparable objects by treating contents of array as a binary 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 to vector of comparable objects
* into increasing order.
*/
public static void sort(AbstractList 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 = array.size();
// 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);
}
}
/**
* Sorts a vector of comparable objects into increasing order.
*/
public static void sort(AbstractList array) {
Object temp;
int j, n = array.size();
// 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.get(0);
array.set(0, array.get(j));
array.set(j, temp);
adjust(array, 1, j);
}
}
/**
* Sorts an array of comparable objects into increasing 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.
*/
public static void sort(Object[] array, Comparator c) {
Object temp;
int j, n = array.length;
// turn input array into a heap
for (j = n / 2; j > 0; j--) {
adjust(array, c, 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, c, 1, j);
}
}
/**
* Sorts an array of doubles into increasing 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.
*/
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.
*/
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);
}
}
/**
* test harness for heapsort algorithm
*/
public static void main(String[] args) {
int testSize = 100;
// test array of Comparable objects
ComparableDouble[] test = new ComparableDouble[testSize];
Random random = new Random();
for (int i = 0; i < test.length; i++) {
test[i] = new ComparableDouble(random.nextInt(testSize * 10));
}
sort(test);
for(ComparableDouble aTest : test) {
System.out.print(aTest + " ");
}
System.out.println();
// test index to Vector of Comparable objects
Vector testv = new Vector();
int[] indices = new int[testSize];
for (int i = 0; i < testSize; i++) {
testv.addElement(new ComparableDouble(random.nextInt(testSize * 10)));
}
sort(testv, indices);
for (int i = 0; i < test.length; i++) {
System.out.print(testv.elementAt(indices[i]) + " ");
}
System.out.println();
// test index to array of doubles
double[] testd = new double[testSize];
//int[] indices = new int[testSize];
for (int i = 0; i < testSize; i++) {
testd[i] = random.nextInt(testSize * 10);
}
sort(testd, indices);
for (int i = 0; i < test.length; i++) {
System.out.print(testd[indices[i]] + " ");
}
System.out.println();
}
// PRIVATE STUFF
/**
* helps sort an array of indices into a vector of comparable objects.
* 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.
*/
private static void adjust(AbstractList<Comparable> array, int[] indices, int lower, int upper) {
int j, k;
int temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (array.get(indices[k - 1]).compareTo(array.get(indices[k])) < 0)) {
k += 1;
}
if (array.get(indices[j - 1]).compareTo(array.get(indices[k - 1])) < 0) {
temp = indices[j - 1];
indices[j - 1] = indices[k - 1];
indices[k - 1] = temp;
}
j = k;
k *= 2;
}
}
/**
* helps sort an vector of comparable objects.
* 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.
*/
private static void adjust(AbstractList array, int lower, int upper) {
int j, k;
Object temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (((Comparable) array.get(k - 1)).compareTo(array.get(k)) < 0)) {
k += 1;
}
if (((Comparable) array.get(j - 1)).compareTo(array.get(k - 1)) < 0) {
temp = array.get(j - 1);
array.set(j - 1, array.get(k - 1));
array.set(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.
*/
private static void adjust(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.
*/
private static void adjust(Object[] array, Comparator c, int lower, int upper) {
int j, k;
Object temp;
j = lower;
k = lower * 2;
while (k <= upper) {
if ((k < upper) && (c.compare(array[k - 1], array[k]) < 0)) {
k += 1;
}
if (c.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.
*/
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.
*/
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.
*/
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;
}
}
}