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/* |
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Copyright @ 1999-2003, The Institute for Genomic Research (TIGR). |
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All rights reserved. |
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*/ |
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/* |
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* $RCSfile: QSort.java,v $ |
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* $Revision: 1.5 $ |
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* $Date: 2004/01/21 20:10:08 $ |
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* $Author: nbhagaba $ |
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* $State: Exp $ |
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*/ |
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package org.tigr.util; |
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import java.util.Vector; |
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|
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//import java.io.*; |
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|
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//SORTS IN ASCENDING ORDER |
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|
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public class QSort { |
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|
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private int[] origIndx; |
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private float[] sorted; |
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private double[] sortedDouble; |
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private int[] NaNIndices; |
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private int[] negInfinityIndices; |
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public static final int ASCENDING = 1; |
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public static final int DESCENDING = 2; |
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private boolean ascending; |
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|
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public QSort(float[] origA){ |
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float[] copyA = new float[origA.length]; |
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this.ascending = true; |
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Vector NaNIndicesVector = new Vector(); |
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Vector negInfinityIndicesVector = new Vector(); |
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|
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for (int i = 0; i < copyA.length; i++) { |
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copyA[i] = origA[i]; |
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if (Float.isNaN(origA[i])) { |
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NaNIndicesVector.add(new Integer(i)); |
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copyA[i] = Float.NEGATIVE_INFINITY; // so that NaN's are always first when the array is sorted in ascending order |
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} |
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if (Float.isInfinite(origA[i]) && (origA[i] < 0)) { // in case there are actual negative infinity values in origA |
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negInfinityIndicesVector.add(new Integer(i)); |
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} |
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} |
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|
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|
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NaNIndices = new int[NaNIndicesVector.size()]; |
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|
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for (int i = 0; i < NaNIndices.length; i++) { |
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NaNIndices[i] = ((Integer)(NaNIndicesVector.get(i))).intValue(); |
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} |
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|
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negInfinityIndices = new int[negInfinityIndicesVector.size()]; |
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|
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for (int i = 0; i < negInfinityIndices.length; i++) { |
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negInfinityIndices[i] = ((Integer)(negInfinityIndicesVector.get(i))).intValue(); |
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} |
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|
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sort(copyA); |
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} |
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|
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public QSort(double[] origA){ |
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double[] copyA = new double[origA.length]; |
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this.ascending = true; |
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Vector NaNIndicesVector = new Vector(); |
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Vector negInfinityIndicesVector = new Vector(); |
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|
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for (int i = 0; i < copyA.length; i++) { |
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copyA[i] = origA[i]; |
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if (Double.isNaN(origA[i])) { |
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NaNIndicesVector.add(new Integer(i)); |
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copyA[i] = Double.NEGATIVE_INFINITY; // so that NaN's are always first when the array is sorted in ascending order |
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} |
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if (Double.isInfinite(origA[i]) && (origA[i] < 0)) { // in case there are actual negative infinity values in origA |
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negInfinityIndicesVector.add(new Integer(i)); |
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} |
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} |
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|
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NaNIndices = new int[NaNIndicesVector.size()]; |
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|
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for (int i = 0; i < NaNIndices.length; i++) { |
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NaNIndices[i] = ((Integer)(NaNIndicesVector.get(i))).intValue(); |
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} |
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|
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negInfinityIndices = new int[negInfinityIndicesVector.size()]; |
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|
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for (int i = 0; i < negInfinityIndices.length; i++) { |
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negInfinityIndices[i] = ((Integer)(negInfinityIndicesVector.get(i))).intValue(); |
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} |
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|
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sort(copyA); |
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} |
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|
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public QSort(float[] origA, int ascOrDesc) { |
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this(origA); |
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if (ascOrDesc == QSort.ASCENDING) { |
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this.ascending = true; |
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} else if (ascOrDesc == QSort.DESCENDING) { |
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this.ascending = false; |
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} |
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} |
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|
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public QSort(double[] origA, int ascOrDesc) { |
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this(origA); |
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if (ascOrDesc == QSort.ASCENDING) { |
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this.ascending = true; |
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} else if (ascOrDesc == QSort.DESCENDING) { |
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this.ascending = false; |
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} |
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} |
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|
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public void sort(float a[]) { |
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|
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origIndx = new int[a.length]; |
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for (int i = 0; i <= origIndx.length - 1; i++){ |
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origIndx[i] = i; |
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} |
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quickSort(a, 0, a.length - 1); |
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} |
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|
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public void sort(double a[]) { |
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|
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origIndx = new int[a.length]; |
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for (int i = 0; i <= origIndx.length - 1; i++){ |
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origIndx[i] = i; |
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} |
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quickSort(a, 0, a.length - 1); |
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} |
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|
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void quickSort(float a[], int lo0, int hi0) { |
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int lo = lo0; |
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int hi = hi0; |
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float mid; |
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|
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if ( hi0 > lo0) { |
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|
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/* Arbitrarily establishing partition element as the midpoint of |
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* the array. |
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*/ |
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mid = a[ ( lo0 + hi0 ) / 2 ]; |
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|
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// loop through the array until indices cross |
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while( lo <= hi ) { |
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/* find the first element that is greater than or equal to |
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* the partition element starting from the left Index. |
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*/ |
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while( ( lo < hi0 ) && ( a[lo] < mid )) |
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++lo; |
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|
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/* find an element that is smaller than or equal to |
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* the partition element starting from the right Index. |
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*/ |
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while( ( hi > lo0 ) && ( a[hi] > mid )) |
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--hi; |
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|
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// if the indexes have not crossed, swap |
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if( lo <= hi ) { |
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swap(a, lo, hi); |
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++lo; |
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--hi; |
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} |
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} |
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|
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/* If the right index has not reached the left side of array |
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* must now sort the left partition. |
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*/ |
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if( lo0 < hi ) |
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quickSort( a, lo0, hi ); |
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|
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/* If the left index has not reached the right side of array |
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* must now sort the right partition. |
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*/ |
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if( lo < hi0 ) |
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quickSort( a, lo, hi0 ); |
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|
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} |
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sorted = a; |
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} |
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|
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void quickSort(double a[], int lo0, int hi0) { |
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int lo = lo0; |
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int hi = hi0; |
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double mid; |
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|
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if ( hi0 > lo0) { |
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|
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/* Arbitrarily establishing partition element as the midpoint of |
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* the array. |
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*/ |
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mid = a[ ( lo0 + hi0 ) / 2 ]; |
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|
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// loop through the array until indices cross |
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while( lo <= hi ) { |
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/* find the first element that is greater than or equal to |
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* the partition element starting from the left Index. |
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*/ |
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while( ( lo < hi0 ) && ( a[lo] < mid )) |
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++lo; |
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|
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/* find an element that is smaller than or equal to |
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* the partition element starting from the right Index. |
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*/ |
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while( ( hi > lo0 ) && ( a[hi] > mid )) |
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--hi; |
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|
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// if the indexes have not crossed, swap |
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if( lo <= hi ) { |
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swap(a, lo, hi); |
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++lo; |
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--hi; |
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} |
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} |
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|
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/* If the right index has not reached the left side of array |
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* must now sort the left partition. |
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*/ |
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if( lo0 < hi ) |
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quickSort( a, lo0, hi ); |
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|
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/* If the left index has not reached the right side of array |
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* must now sort the right partition. |
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*/ |
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if( lo < hi0 ) |
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quickSort( a, lo, hi0 ); |
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|
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} |
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sortedDouble = a; |
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} |
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|
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private void swap(float a[], int i, int j) { |
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|
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float T; |
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T = a[i]; |
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a[i] = a[j]; |
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a[j] = T; |
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|
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int TT = origIndx[i]; |
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origIndx[i] = origIndx[j]; |
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origIndx[j] = TT; |
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} |
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|
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private void swap(double a[], int i, int j) { |
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|
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double T; |
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T = a[i]; |
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a[i] = a[j]; |
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a[j] = T; |
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|
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int TT = origIndx[i]; |
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origIndx[i] = origIndx[j]; |
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origIndx[j] = TT; |
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} |
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|
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public float[] getSorted(){ |
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/* |
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Vector sortedVector = new Vector(); |
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Vector NaNSortedIndices = new Vector(); |
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|
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for (int i = 0; i < sorted.length; i++) { |
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if (Float.isNaN(sorted[i])) { |
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NaNSortedIndices.add(new Integer(i)); |
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} else { |
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sortedVector.add(new Float(sorted[i])); |
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} |
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} |
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|
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for (int i = 0; i < NaNSortedIndices.size(); i++) { |
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sortedVector.add(0, new Float(Float.NaN)); |
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} |
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for (int i = 0; i < sortedVector.size(); i++) { |
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sorted[i] = ((Float)(sortedVector.get(i))).floatValue(); |
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273 |
} |
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*/ |
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for (int i = 0; i < NaNIndices.length; i++) { |
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sorted[i] = Float.NaN; |
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} |
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if (!ascending) { |
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float[] revSorted = reverse(sorted); |
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return revSorted; |
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} else { |
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return sorted; |
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} |
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//return sorted; |
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} |
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|
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public double[] getSortedDouble(){ |
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/* |
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26 Feb 07 |
jari |
Vector sortedVector = new Vector(); |
2 |
26 Feb 07 |
jari |
Vector NaNSortedIndices = new Vector(); |
2 |
26 Feb 07 |
jari |
291 |
|
2 |
26 Feb 07 |
jari |
for (int i = 0; i < sortedDouble.length; i++) { |
2 |
26 Feb 07 |
jari |
if (Double.isNaN(sortedDouble[i])) { |
2 |
26 Feb 07 |
jari |
NaNSortedIndices.add(new Integer(i)); |
2 |
26 Feb 07 |
jari |
} else { |
2 |
26 Feb 07 |
jari |
sortedVector.add(new Double(sortedDouble[i])); |
2 |
26 Feb 07 |
jari |
297 |
} |
2 |
26 Feb 07 |
jari |
298 |
} |
2 |
26 Feb 07 |
jari |
299 |
|
2 |
26 Feb 07 |
jari |
for (int i = 0; i < NaNSortedIndices.size(); i++) { |
2 |
26 Feb 07 |
jari |
sortedVector.add(0, new Double(Double.NaN)); |
2 |
26 Feb 07 |
jari |
302 |
} |
2 |
26 Feb 07 |
jari |
for (int i = 0; i < sortedVector.size(); i++) { |
2 |
26 Feb 07 |
jari |
sortedDouble[i] = ((Double)(sortedVector.get(i))).doubleValue(); |
2 |
26 Feb 07 |
jari |
305 |
} |
2 |
26 Feb 07 |
jari |
306 |
*/ |
2 |
26 Feb 07 |
jari |
307 |
for (int i = 0; i < NaNIndices.length; i++) { |
2 |
26 Feb 07 |
jari |
308 |
sortedDouble[i] = Double.NaN; |
2 |
26 Feb 07 |
jari |
309 |
} |
2 |
26 Feb 07 |
jari |
310 |
|
2 |
26 Feb 07 |
jari |
311 |
if (!ascending) { |
2 |
26 Feb 07 |
jari |
312 |
double[] revSortedDouble = reverse(sortedDouble); |
2 |
26 Feb 07 |
jari |
313 |
return revSortedDouble; |
2 |
26 Feb 07 |
jari |
314 |
} else { |
2 |
26 Feb 07 |
jari |
315 |
return sortedDouble; |
2 |
26 Feb 07 |
jari |
316 |
} |
2 |
26 Feb 07 |
jari |
317 |
} |
2 |
26 Feb 07 |
jari |
318 |
|
2 |
26 Feb 07 |
jari |
319 |
public int[] getOrigIndx(){ |
2 |
26 Feb 07 |
jari |
320 |
/* |
2 |
26 Feb 07 |
jari |
Vector origIndxVector = new Vector(); |
2 |
26 Feb 07 |
jari |
for (int i = 0; i < origIndx.length; i++) { |
2 |
26 Feb 07 |
jari |
if (!isNaNIndex(origIndx[i])) { |
2 |
26 Feb 07 |
jari |
origIndxVector.add(new Integer(origIndx[i])); |
2 |
26 Feb 07 |
jari |
325 |
} |
2 |
26 Feb 07 |
jari |
326 |
} |
2 |
26 Feb 07 |
jari |
327 |
|
2 |
26 Feb 07 |
jari |
for (int i = 0; i < NaNIndices.length; i++) { |
2 |
26 Feb 07 |
jari |
origIndxVector.add(0, new Integer(NaNIndices[i])); |
2 |
26 Feb 07 |
jari |
330 |
} |
2 |
26 Feb 07 |
jari |
331 |
|
2 |
26 Feb 07 |
jari |
for (int i = 0; i < origIndxVector.size(); i++) { |
2 |
26 Feb 07 |
jari |
origIndx[i] = ((Integer)(origIndxVector.get(i))).intValue(); |
2 |
26 Feb 07 |
jari |
334 |
} |
2 |
26 Feb 07 |
jari |
335 |
*/ |
2 |
26 Feb 07 |
jari |
336 |
|
2 |
26 Feb 07 |
jari |
337 |
for (int i = 0; i < NaNIndices.length; i++) { |
2 |
26 Feb 07 |
jari |
338 |
origIndx[i] = NaNIndices[i]; |
2 |
26 Feb 07 |
jari |
339 |
} |
2 |
26 Feb 07 |
jari |
340 |
|
2 |
26 Feb 07 |
jari |
341 |
for (int i = NaNIndices.length; i < NaNIndices.length + negInfinityIndices.length; i++) { |
2 |
26 Feb 07 |
jari |
342 |
origIndx[i] = negInfinityIndices[i - NaNIndices.length]; |
2 |
26 Feb 07 |
jari |
343 |
} |
2 |
26 Feb 07 |
jari |
344 |
|
2 |
26 Feb 07 |
jari |
345 |
if (!ascending) { |
2 |
26 Feb 07 |
jari |
346 |
return reverse(origIndx); |
2 |
26 Feb 07 |
jari |
347 |
} else { |
2 |
26 Feb 07 |
jari |
348 |
return origIndx; |
2 |
26 Feb 07 |
jari |
349 |
} |
2 |
26 Feb 07 |
jari |
350 |
} |
2 |
26 Feb 07 |
jari |
351 |
|
2 |
26 Feb 07 |
jari |
352 |
private boolean isNaNIndex(int index) { |
2 |
26 Feb 07 |
jari |
353 |
for (int i = 0; i < NaNIndices.length; i++) { |
2 |
26 Feb 07 |
jari |
354 |
if (index == NaNIndices[i]) { |
2 |
26 Feb 07 |
jari |
355 |
return true; |
2 |
26 Feb 07 |
jari |
356 |
} |
2 |
26 Feb 07 |
jari |
357 |
} |
2 |
26 Feb 07 |
jari |
358 |
|
2 |
26 Feb 07 |
jari |
359 |
return false; |
2 |
26 Feb 07 |
jari |
360 |
} |
2 |
26 Feb 07 |
jari |
361 |
|
2 |
26 Feb 07 |
jari |
362 |
private int[] reverse(int[] arr) { |
2 |
26 Feb 07 |
jari |
363 |
int[] revArr = new int[arr.length]; |
2 |
26 Feb 07 |
jari |
364 |
int revCount = 0; |
2 |
26 Feb 07 |
jari |
365 |
int count = arr.length - 1; |
2 |
26 Feb 07 |
jari |
366 |
for (int i=0; i < arr.length; i++) { |
2 |
26 Feb 07 |
jari |
367 |
revArr[revCount] = arr[count]; |
2 |
26 Feb 07 |
jari |
368 |
revCount++; |
2 |
26 Feb 07 |
jari |
369 |
count--; |
2 |
26 Feb 07 |
jari |
370 |
} |
2 |
26 Feb 07 |
jari |
371 |
return revArr; |
2 |
26 Feb 07 |
jari |
372 |
} |
2 |
26 Feb 07 |
jari |
373 |
|
2 |
26 Feb 07 |
jari |
374 |
private float[] reverse(float[] arr) { |
2 |
26 Feb 07 |
jari |
375 |
float[] revArr = new float[arr.length]; |
2 |
26 Feb 07 |
jari |
376 |
int revCount = 0; |
2 |
26 Feb 07 |
jari |
377 |
int count = arr.length - 1; |
2 |
26 Feb 07 |
jari |
378 |
for (int i=0; i < arr.length; i++) { |
2 |
26 Feb 07 |
jari |
379 |
revArr[revCount] = arr[count]; |
2 |
26 Feb 07 |
jari |
380 |
revCount++; |
2 |
26 Feb 07 |
jari |
381 |
count--; |
2 |
26 Feb 07 |
jari |
382 |
} |
2 |
26 Feb 07 |
jari |
383 |
return revArr; |
2 |
26 Feb 07 |
jari |
384 |
} |
2 |
26 Feb 07 |
jari |
385 |
|
2 |
26 Feb 07 |
jari |
386 |
private double[] reverse(double[] arr) { |
2 |
26 Feb 07 |
jari |
387 |
double[] revArr = new double[arr.length]; |
2 |
26 Feb 07 |
jari |
388 |
int revCount = 0; |
2 |
26 Feb 07 |
jari |
389 |
int count = arr.length - 1; |
2 |
26 Feb 07 |
jari |
390 |
for (int i=0; i < arr.length; i++) { |
2 |
26 Feb 07 |
jari |
391 |
revArr[revCount] = arr[count]; |
2 |
26 Feb 07 |
jari |
392 |
revCount++; |
2 |
26 Feb 07 |
jari |
393 |
count--; |
2 |
26 Feb 07 |
jari |
394 |
} |
2 |
26 Feb 07 |
jari |
395 |
return revArr; |
2 |
26 Feb 07 |
jari |
396 |
} |
2 |
26 Feb 07 |
jari |
397 |
|
2 |
26 Feb 07 |
jari |
398 |
public static void main(String[] args) { |
2 |
26 Feb 07 |
jari |
399 |
|
2 |
26 Feb 07 |
jari |
400 |
double[] arr = {120d, 0.01d, -4.5d, Double.NaN, 7.6d, -65d, Double.NEGATIVE_INFINITY, 3.5d, -0.95d, Double.POSITIVE_INFINITY, 600d, Double.NaN, 65d, Double.NEGATIVE_INFINITY, Double.MAX_VALUE}; |
2 |
26 Feb 07 |
jari |
401 |
|
2 |
26 Feb 07 |
jari |
402 |
QSort sortArr = new QSort(arr, QSort.ASCENDING); |
2 |
26 Feb 07 |
jari |
403 |
double[] sortedArr = sortArr.getSortedDouble(); |
2 |
26 Feb 07 |
jari |
404 |
int[] sortedArrIndices = sortArr.getOrigIndx(); |
2 |
26 Feb 07 |
jari |
405 |
for (int i = 0; i < sortedArr.length; i++) { |
2 |
26 Feb 07 |
jari |
406 |
System.out.println("arr[" + i + "] = " + arr[i] + ", sortedArr[" + i + "] = " + sortedArr[i] + ", sortedArrIndices[" + i + "] = " + sortedArrIndices[i]); |
2 |
26 Feb 07 |
jari |
407 |
} |
2 |
26 Feb 07 |
jari |
408 |
|
2 |
26 Feb 07 |
jari |
409 |
} |
2 |
26 Feb 07 |
jari |
410 |
|
2 |
26 Feb 07 |
jari |
411 |
} |
2 |
26 Feb 07 |
jari |
412 |
|