X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FZsort.java;h=0e7a271c8862d2ea29d5cf2835458bb0aafc92b4;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=215f75321207b129c1ab495ba26cb9a821e5f700;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 215f753..0e7a271 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,69 +1,73 @@
-/*
-* 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 MCview;
-
-import java.util.*;
-
-public class Zsort {
-
-  public static void Zsort(Vector bonds) {
-
-    sort(bonds,0,bonds.size()-1);
-  }
-
-
-
-  public static void sort(Vector bonds,int p, int r) {
-    int q;
-
-    if (p < r) {
-      q = partition(bonds,p,r);
-      sort(bonds,p,q);
-      sort(bonds,q+1,r);
-    }
-  }
-
-  private static int partition(Vector bonds, int p, int r) {
-    float x = ((Bond)bonds.elementAt(p)).start[2];
-    int i = p-1;
-    int j = r+1;
-
-    while(true) {
-      do {
-        j = j-1;
-      }	while (j >= 0  && ((Bond)bonds.elementAt(j)).start[2] > x);
-
-      do {
-        i = i+1;
-      } while (i < bonds.size() && ((Bond)bonds.elementAt(i)).start[2] < x);
-
-      if ( i < j) {
-        Bond tmp = (Bond)bonds.elementAt(i);
-        bonds.setElementAt(bonds.elementAt(j),i);
-        bonds.setElementAt(tmp,j);
-      } else {
-        return j;
-      }
-    }
-  }
-}
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package MCview;
+
+import java.util.*;
+
+public class Zsort
+{
+  public void Zsort(Vector bonds)
+  {
+    sort(bonds, 0, bonds.size() - 1);
+  }
+
+  public void sort(Vector bonds, int p, int r)
+  {
+    int q;
+
+    if (p < r)
+    {
+      q = partition(bonds, p, r);
+      sort(bonds, p, q);
+      sort(bonds, q + 1, r);
+    }
+  }
+
+  private int partition(Vector bonds, int p, int r)
+  {
+    float x = ((Bond) bonds.elementAt(p)).start[2];
+    int i = p - 1;
+    int j = r + 1;
+    Bond tmp;
+    while (true)
+    {
+      do
+      {
+        j--;
+      } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
+
+      do
+      {
+        i++;
+      } while ((i < bonds.size())
+              && (((Bond) bonds.elementAt(i)).start[2] < x));
+
+      if (i < j)
+      {
+        tmp = (Bond) bonds.elementAt(i);
+        bonds.setElementAt(bonds.elementAt(j), i);
+        bonds.setElementAt(tmp, j);
+      }
+      else
+      {
+        return j;
+      }
+    }
+  }
+}