X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FQuickSort.java;h=94ec1aa2cd88c837475d2f7e950d7af0b16c2d07;hb=d25788049914c6da6c71d203822a9adfe548d3be;hp=36241447b4911a18ce629e1d69b7d03f5b0ec333;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 3624144..94ec1aa 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,110 +1,229 @@
-/*
-* 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.util;
+
+public class QuickSort
+{
+  public static void sort(int[] arr, Object[] s)
+  {
+    sort(arr, 0, arr.length - 1, s);
+  }
+
+  public static void sort(float[] arr, Object[] s)
+  {
+    sort(arr, 0, arr.length - 1, s);
+  }
+
+  public static void sort(double[] 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);
+    }
+  }
+
+  public 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);
+    }
+  }
+
+  public 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);
+    }
+  }
+
+  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 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;
+      }
+    }
+  }
+
+  private 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;
+      }
+    }
+  }
+
+  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;
+      }
+    }
+  }
+}