/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
public class QuickSort
{
+ /**
+ * A comparator that compares two integers by comparing their respective
+ * indexed values in an array of floats
+ */
static class FloatComparator implements Comparator<Integer>
{
-
private final float[] values;
- FloatComparator(float[] v)
+ private boolean ascending;
+
+ FloatComparator(float[] v, boolean asc)
{
values = v;
+ ascending = asc;
}
@Override
public int compare(Integer o1, Integer o2)
{
- return Float.compare(values[o1], values[o2]);
+ return ascending ? Float.compare(values[o1], values[o2])
+ : Float.compare(values[o2], values[o1]);
+ }
+ }
+
+ /**
+ * A comparator that compares two integers by comparing their respective
+ * indexed values in an array of doubles
+ */
+ static class DoubleComparator implements Comparator<Integer>
+ {
+ private final double[] values;
+
+ private boolean ascending;
+
+ DoubleComparator(double[] v, boolean asc)
+ {
+ values = v;
+ ascending = asc;
}
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ if (ascending)
+ {
+ return Double.compare(values[o1], values[o2]);
+ }
+ else
+ {
+ return Double.compare(values[o2], values[o1]);
+ }
+ }
}
+ /**
+ * A comparator that compares two integers by comparing their respective
+ * indexed values in an array of ints
+ */
static class IntComparator implements Comparator<Integer>
{
-
private final int[] values;
- IntComparator(int[] v)
+ private boolean ascending;
+
+ IntComparator(int[] v, boolean asc)
{
values = v;
+ ascending = asc;
}
@Override
public int compare(Integer o1, Integer o2)
{
- return Integer.compare(values[o1], values[o2]);
+ return ascending ? Integer.compare(values[o1], values[o2])
+ : Integer.compare(values[o2], values[o1]);
+ }
+ }
+
+ /**
+ * A comparator that compares two integers by comparing their respective
+ * indexed values in an array of comparable objects.
+ */
+ static class ExternalComparator implements Comparator<Integer>
+ {
+ private final Comparable[] values;
+
+ private boolean ascending;
+
+ ExternalComparator(Comparable[] v, boolean asc)
+ {
+ values = v;
+ ascending = asc;
}
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return ascending ? values[o1].compareTo(values[o2])
+ : values[o2].compareTo(values[o1]);
+ }
}
/**
/**
* Sorts both arrays with respect to descending order of the items in the
- * first array.
+ * first array. The sorting is case-sensitive.
*
* @param arr
* @param s
}
/**
- * Sorts both arrays to give ascending order in the first array, by first
- * partitioning into zero and non-zero values before sorting the latter.
+ * Sorts both arrays to give ascending order by the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter. This
+ * is faster than a direct call to charSortByFloat in the case where most of
+ * the array to be sorted is zero.
*
* @param arr
* @param s
public static void sort(float[] arr, char[] s)
{
/*
- * Sort all zero values to the front
+ * Move all zero values to the front, non-zero to the back, while counting
+ * negative values
*/
float[] f1 = new float[arr.length];
char[] s1 = new char[s.length];
- int nextZeroValue = 0;
+ int negativeCount = 0;
+ int zerosCount = 0;
int nextNonZeroValue = arr.length - 1;
for (int i = 0; i < arr.length; i++)
{
float val = arr[i];
- if (val > 0f)
+ if (val != 0f)
{
f1[nextNonZeroValue] = val;
s1[nextNonZeroValue] = s[i];
nextNonZeroValue--;
+ if (val < 0f)
+ {
+ negativeCount++;
+ }
}
else
{
- f1[nextZeroValue] = val;
- s1[nextZeroValue] = s[i];
- nextZeroValue++;
+ f1[zerosCount] = val;
+ s1[zerosCount] = s[i];
+ zerosCount++;
}
}
+ int positiveCount = arr.length - zerosCount - negativeCount;
- /*
- * Copy zero values back to original arrays
- */
- System.arraycopy(f1, 0, arr, 0, nextZeroValue);
- System.arraycopy(s1, 0, s, 0, nextZeroValue);
-
- if (nextZeroValue == arr.length)
+ if (zerosCount == arr.length)
{
return; // all zero
}
+
+ /*
+ * sort the non-zero values
+ */
+ float[] nonZeroFloats = Arrays.copyOfRange(f1, zerosCount, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, zerosCount, s1.length);
+ charSortByFloat(nonZeroFloats, nonZeroChars, true);
+
/*
- * Sort the non-zero values
+ * Backfill zero values to original arrays, after the space reserved for
+ * negatives
*/
- float[] nonZeroFloats = Arrays
- .copyOfRange(f1, nextZeroValue, f1.length);
- char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
- externalSort(nonZeroFloats, nonZeroChars);
- // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+ System.arraycopy(f1, 0, arr, negativeCount, zerosCount);
+ System.arraycopy(s1, 0, s, negativeCount, zerosCount);
/*
- * Assemble sorted non-zero results
+ * Copy sorted negative values to the front of arr, s
*/
- System.arraycopy(nonZeroFloats, 0, arr, nextZeroValue,
- nonZeroFloats.length);
- System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ System.arraycopy(nonZeroFloats, 0, arr, 0, negativeCount);
+ System.arraycopy(nonZeroChars, 0, s, 0, negativeCount);
+
+ /*
+ * Copy sorted positive values after the negatives and zeros
+ */
+ System.arraycopy(nonZeroFloats, negativeCount, arr,
+ negativeCount + zerosCount, positiveCount);
+ System.arraycopy(nonZeroChars, negativeCount, s,
+ negativeCount + zerosCount, positiveCount);
}
/**
- * Sort by making an array of indices, and sorting it using a comparator that
- * refers to the float values.
+ * Sorts arrays of float and char by the float values, by making an array of
+ * indices, and sorting it using a comparator that refers to the float values.
*
* @see http
* ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
* after-sorting
* @param arr
* @param s
+ * @param ascending
*/
- protected static void externalSort(float[] arr, char[] s)
+ public static void charSortByFloat(float[] arr, char[] s,
+ boolean ascending)
{
final int length = arr.length;
Integer[] indices = makeIndexArray(length);
- Arrays.sort(indices, new FloatComparator(arr));
+ Arrays.sort(indices, new FloatComparator(arr, ascending));
/*
* Copy the array values as per the sorted indices
/**
* Sorts both arrays to give ascending order in the first array, by first
- * partitioning into zero and non-zero values before sorting the latter.
+ * partitioning into zero and non-zero values before sorting the latter. This
+ * is faster than a direct call to charSortByInt in the case where most of the
+ * array to be sorted is zero.
*
* @param arr
* @param s
*/
public static void sort(int[] arr, char[] s)
- {
- /*
- * Sort all zero values to the front
+ { /*
+ * Move all zero values to the front, non-zero to the back, while counting
+ * negative values
*/
int[] f1 = new int[arr.length];
char[] s1 = new char[s.length];
- int nextZeroValue = 0;
+ int negativeCount = 0;
+ int zerosCount = 0;
int nextNonZeroValue = arr.length - 1;
for (int i = 0; i < arr.length; i++)
{
int val = arr[i];
- if (val > 0f)
+ if (val != 0f)
{
f1[nextNonZeroValue] = val;
s1[nextNonZeroValue] = s[i];
nextNonZeroValue--;
+ if (val < 0)
+ {
+ negativeCount++;
+ }
}
else
{
- f1[nextZeroValue] = val;
- s1[nextZeroValue] = s[i];
- nextZeroValue++;
+ f1[zerosCount] = val;
+ s1[zerosCount] = s[i];
+ zerosCount++;
}
}
+ int positiveCount = arr.length - zerosCount - negativeCount;
- /*
- * Copy zero values back to original arrays
- */
- System.arraycopy(f1, 0, arr, 0, nextZeroValue);
- System.arraycopy(s1, 0, s, 0, nextZeroValue);
-
- if (nextZeroValue == arr.length)
+ if (zerosCount == arr.length)
{
return; // all zero
}
+
/*
- * Sort the non-zero values
+ * sort the non-zero values
*/
- int[] nonZeroInts = Arrays.copyOfRange(f1, nextZeroValue, f1.length);
- char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
- externalSort(nonZeroInts, nonZeroChars);
- // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+ int[] nonZeroInts = Arrays.copyOfRange(f1, zerosCount, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, zerosCount, s1.length);
+ charSortByInt(nonZeroInts, nonZeroChars, true);
/*
- * Assemble sorted non-zero results
+ * Backfill zero values to original arrays, after the space reserved for
+ * negatives
*/
- System.arraycopy(nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length);
- System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ System.arraycopy(f1, 0, arr, negativeCount, zerosCount);
+ System.arraycopy(s1, 0, s, negativeCount, zerosCount);
+
+ /*
+ * Copy sorted negative values to the front of arr, s
+ */
+ System.arraycopy(nonZeroInts, 0, arr, 0, negativeCount);
+ System.arraycopy(nonZeroChars, 0, s, 0, negativeCount);
+
+ /*
+ * Copy sorted positive values after the negatives and zeros
+ */
+ System.arraycopy(nonZeroInts, negativeCount, arr,
+ negativeCount + zerosCount, positiveCount);
+ System.arraycopy(nonZeroChars, negativeCount, s,
+ negativeCount + zerosCount, positiveCount);
}
/**
- * Sort by making an array of indices, and sorting it using a comparator that
- * refers to the float values.
+ * Sorts arrays of int and char, by making an array of indices, and sorting it
+ * using a comparator that refers to the int values.
*
* @see http
* ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
* after-sorting
* @param arr
* @param s
+ * @param ascending
*/
- protected static void externalSort(int[] arr, char[] s)
+ public static void charSortByInt(int[] arr, char[] s, boolean ascending)
{
final int length = arr.length;
Integer[] indices = makeIndexArray(length);
- Arrays.sort(indices, new IntComparator(arr));
+ Arrays.sort(indices, new IntComparator(arr, ascending));
/*
* Copy the array values as per the sorted indices
System.arraycopy(sortedInts, 0, arr, 0, length);
System.arraycopy(sortedChars, 0, s, 0, s.length);
}
+
+ /**
+ * Sorts arrays of int and Object, by making an array of indices, and sorting
+ * it using a comparator that refers to the int values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ * @param ascending
+ */
+ public static void sortByInt(int[] arr, Object[] s, boolean ascending)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new IntComparator(arr, ascending));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ int[] sortedInts = new int[length];
+ Object[] sortedObjects = new Object[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedInts[i] = arr[indices[i]];
+ sortedObjects[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedInts, 0, arr, 0, length);
+ System.arraycopy(sortedObjects, 0, s, 0, s.length);
+ }
+
+ /**
+ * Sorts arrays of String and Object, by making an array of indices, and
+ * sorting it using a comparator that refers to the String values. Both arrays
+ * are sorted by case-sensitive order of the string array values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ * @param ascending
+ */
+ public static void sortByString(String[] arr, Object[] s,
+ boolean ascending)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new ExternalComparator(arr, ascending));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ String[] sortedStrings = new String[length];
+ Object[] sortedObjects = new Object[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedStrings[i] = arr[indices[i]];
+ sortedObjects[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedStrings, 0, arr, 0, length);
+ System.arraycopy(sortedObjects, 0, s, 0, s.length);
+ }
+
+ /**
+ * Sorts arrays of double and Object, by making an array of indices, and
+ * sorting it using a comparator that refers to the double values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ * @param ascending
+ */
+ public static void sortByDouble(double[] arr, Object[] s,
+ boolean ascending)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new DoubleComparator(arr, ascending));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ double[] sortedDoubles = new double[length];
+ Object[] sortedObjects = new Object[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedDoubles[i] = arr[indices[i]];
+ sortedObjects[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedDoubles, 0, arr, 0, length);
+ System.arraycopy(sortedObjects, 0, s, 0, s.length);
+ }
}
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