JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / MCview / Zsort.java

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index fd2c210..e7121d3 100755 (executable)
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,32 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.
- * 
+ * 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/>.
+ * 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.*;
+import java.util.Vector;
 
 public class Zsort
 {
-  public void Zsort(Vector bonds)
+  /**
+   * Sorts the Bond list in ascending order of the z-value of the bond start
+   * atom
+   * 
+   * @param bonds
+   */
+  public void sort(Vector<Bond> bonds)
   {
     sort(bonds, 0, bonds.size() - 1);
   }
 
-  public void sort(Vector bonds, int p, int r)
+  public void sort(Vector<Bond> bonds, int p, int r)
   {
     int q;
 
@@ -38,9 +47,9 @@ public class Zsort
     }
   }
 
-  private int partition(Vector bonds, int p, int r)
+  private int partition(Vector<Bond> bonds, int p, int r)
   {
-    float x = ((Bond) bonds.elementAt(p)).start[2];
+    float x = bonds.elementAt(p).start[2];
     int i = p - 1;
     int j = r + 1;
     Bond tmp;
@@ -49,17 +58,16 @@ public class Zsort
       do
       {
         j--;
-      } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
+      } while ((j >= 0) && (bonds.elementAt(j).start[2] > x));
 
       do
       {
         i++;
-      } while ((i < bonds.size())
-              && (((Bond) bonds.elementAt(i)).start[2] < x));
+      } while ((i < bonds.size()) && (bonds.elementAt(i).start[2] < x));
 
       if (i < j)
       {
-        tmp = (Bond) bonds.elementAt(i);
+        tmp = bonds.elementAt(i);
         bonds.setElementAt(bonds.elementAt(j), i);
         bonds.setElementAt(tmp, j);
       }