X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FQuickSort.java;h=e99ddb0cd1c849f336d7c539307ec5843b217085;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=80734f791b5d7e7d2af287c6b481ad02da83186e;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 80734f7..e99ddb0 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,130 +1,554 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.util;
-
-public class QuickSort
-{
- public static void sort(float[] arr, Object[] s)
- {
- sort(arr, 0, arr.length - 1, s);
- }
-
- public static void sort(String[] arr, Object[] s)
- {
- stringSort(arr, 0, arr.length - 1, s);
- }
-
- public static void stringSort(String[] arr, int p, int r, Object[] s)
- {
- int q;
-
- if (p < r)
- {
- q = stringPartition(arr, p, r, s);
- stringSort(arr, p, q, s);
- stringSort(arr, q + 1, r, s);
- }
- }
-
- public static void sort(float[] arr, int p, int r, Object[] s)
- {
- int q;
-
- if (p < r)
- {
- q = partition(arr, p, r, s);
- sort(arr, p, q, s);
- sort(arr, q + 1, r, s);
- }
- }
-
- private static int partition(float[] arr, int p, int r, Object[] s)
- {
- float x = arr[p];
- int i = p - 1;
- int j = r + 1;
-
- while (true)
- {
- do
- {
- j = j - 1;
- }
- while (arr[j] > x);
-
- do
- {
- i = i + 1;
- }
- while (arr[i] < x);
-
- if (i < j)
- {
- float tmp = arr[i];
- arr[i] = arr[j];
- arr[j] = tmp;
-
- Object tmp2 = s[i];
- s[i] = s[j];
- s[j] = tmp2;
- }
- else
- {
- return j;
- }
- }
- }
-
- private static int stringPartition(String[] arr, int p, int r, Object[] s)
- {
- String x = arr[p];
- int i = p - 1;
- int j = r + 1;
-
- while (true)
- {
- do
- {
- j = j - 1;
- }
- while (arr[j].compareTo(x) < 0);
-
- do
- {
- i = i + 1;
- }
- while (arr[i].compareTo(x) > 0);
-
- if (i < j)
- {
- String tmp = arr[i];
- arr[i] = arr[j];
- arr[j] = tmp;
-
- Object tmp2 = s[i];
- s[i] = s[j];
- s[j] = tmp2;
- }
- else
- {
- return j;
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.util.Arrays;
+import java.util.Comparator;
+
+/**
+ * A class to perform efficient sorting of arrays of objects based on arrays of
+ * scores or other attributes. For example, residues by percentage frequency.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class QuickSort
+{
+ static class FloatComparator implements Comparator
+ {
+
+ private final float[] values;
+
+ FloatComparator(float[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Float.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ static class IntComparator implements Comparator
+ {
+
+ private final int[] values;
+
+ IntComparator(int[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Integer.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(int[] arr, Object[] s)
+ {
+ sort(arr, 0, arr.length - 1, s);
+ }
+
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(float[] arr, Object[] s)
+ {
+ sort(arr, 0, arr.length - 1, s);
+ }
+
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(double[] arr, Object[] s)
+ {
+ sort(arr, 0, arr.length - 1, s);
+ }
+
+ /**
+ * Sorts both arrays with respect to descending order of the items in the
+ * first array.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(String[] arr, Object[] s)
+ {
+ stringSort(arr, 0, arr.length - 1, s);
+ }
+
+ static void stringSort(String[] arr, int p, int r, Object[] s)
+ {
+ int q;
+
+ if (p < r)
+ {
+ q = stringPartition(arr, p, r, s);
+ stringSort(arr, p, q, s);
+ stringSort(arr, q + 1, r, s);
+ }
+ }
+
+ static void sort(float[] arr, int p, int r, Object[] s)
+ {
+ int q;
+
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, s);
+ }
+ }
+
+ static void sort(double[] arr, int p, int r, Object[] s)
+ {
+ int q;
+
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, s);
+ }
+ }
+
+ static void sort(int[] arr, int p, int r, Object[] s)
+ {
+ int q;
+
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, s);
+ }
+ }
+
+ static int partition(float[] arr, int p, int r, Object[] s)
+ {
+ float x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ float tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ Object tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int partition(float[] arr, int p, int r, char[] s)
+ {
+ float x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ float tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ char tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int partition(int[] arr, int p, int r, Object[] s)
+ {
+ int x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ int tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ Object tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int partition(double[] arr, int p, int r, Object[] s)
+ {
+ double x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ double tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ Object tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int stringPartition(String[] arr, int p, int r, Object[] s)
+ {
+ String x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j].compareTo(x) < 0);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i].compareTo(x) > 0);
+
+ if (i < j)
+ {
+ String tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ Object tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ /**
+ * Sorts both arrays to give ascending order in the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(float[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ float[] f1 = new float[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ float val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * 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)
+ {
+ return; // all zero
+ }
+ /*
+ * Sort the non-zero values
+ */
+ 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);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroFloats, 0, arr, nextZeroValue,
+ nonZeroFloats.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort 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
+ */
+ protected static void externalSort(float[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new FloatComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ float[] sortedFloats = new float[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedFloats[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedFloats, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
+
+ /**
+ * Make an array whose values are 0...length.
+ *
+ * @param length
+ * @return
+ */
+ protected static Integer[] makeIndexArray(final int length)
+ {
+ Integer[] indices = new Integer[length];
+ for (int i = 0; i < length; i++)
+ {
+ indices[i] = i;
+ }
+ return indices;
+ }
+
+ static void sort(float[] arr, int p, int r, char[] s)
+ {
+ int q;
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, 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.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(int[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ int[] f1 = new int[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ int val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * 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)
+ {
+ return; // all zero
+ }
+ /*
+ * 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);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort 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
+ */
+ protected static void externalSort(int[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new IntComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ int[] sortedInts = new int[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedInts[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedInts, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
+}