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[jalview.git] / src / jalview / util / QuickSort.java

diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 017921f..c28928d 100755 (executable)
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
@@ -20,11 +20,15 @@ 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);
@@ -58,6 +62,7 @@ public class QuickSort
       sort(arr, q + 1, r, s);
     }
   }
+
   public static void sort(double[] arr, int p, int r, Object[] s)
   {
     int q;
@@ -69,6 +74,17 @@ public class QuickSort
       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)
   {
@@ -81,14 +97,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j] > x);
+      } while (arr[j] > x);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i] < x);
+      } while (arr[i] < x);
 
       if (i < j)
       {
@@ -106,6 +120,41 @@ public class QuickSort
       }
     }
   }
+  
+  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)
   {
@@ -118,14 +167,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j] > x);
+      } while (arr[j] > x);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i] < x);
+      } while (arr[i] < x);
 
       if (i < j)
       {
@@ -155,14 +202,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j].compareTo(x) < 0);
+      } while (arr[j].compareTo(x) < 0);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i].compareTo(x) > 0);
+      } while (arr[i].compareTo(x) > 0);
 
       if (i < j)
       {