X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FZsort.java;h=6bdbafa14a3d8d7e32ae01f29ff28bd6f10c1f11;hb=4815037f13748676b04b91dc761b73cf6f2d6ecd;hp=16731efdcb7e97dacedadcd474ced75d70270c1c;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 16731ef..6bdbafa 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,16 +20,22 @@
  */
 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;
 
@@ -41,9 +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;
@@ -52,17 +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);
       }