X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FQuickSort.java;h=1e3e5c1ea0b41ecdc0f3bf404682f613716c8371;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=f32ff7c03f6e68e5c16970c572b4f43581fb6dc7;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index f32ff7c..1e3e5c1 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,130 +1,229 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 2.6)
+ * Copyright (C) 2010 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;
+      }
+    }
+  }
+}