JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 654eb80..20f034c 100755 (executable)
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -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 +58,17 @@ 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));
+              && (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);
       }