Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / datamodel / AlignmentOrder.java

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 7012c76..6d09145 100755 (executable)
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -20,7 +20,9 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 public class AlignmentOrder
 {
@@ -51,7 +53,7 @@ public class AlignmentOrder
 
   private String Name;
 
-  private Vector Order = null;
+  private List<SequenceI> Order = null;
 
   /**
    * Creates a new AlignmentOrder object.
@@ -64,9 +66,8 @@ public class AlignmentOrder
    * AlignmentOrder
    * 
    * @param anOrder
-   *          Vector
    */
-  public AlignmentOrder(Vector anOrder)
+  public AlignmentOrder(List<SequenceI> anOrder)
   {
     Order = anOrder;
   }
@@ -79,11 +80,11 @@ public class AlignmentOrder
    */
   public AlignmentOrder(AlignmentI orderFrom)
   {
-    Order = new Vector();
+    Order = new ArrayList<SequenceI>();
 
-    for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+    for (SequenceI seq : orderFrom.getSequences())
     {
-      Order.addElement(orderFrom.getSequenceAt(i));
+      Order.add(seq);
     }
   }
 
@@ -95,12 +96,7 @@ public class AlignmentOrder
    */
   public AlignmentOrder(SequenceI[] orderFrom)
   {
-    Order = new Vector();
-
-    for (int i = 0, ns = orderFrom.length; i < ns; i++)
-    {
-      Order.addElement(orderFrom[i]);
-    }
+    Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
   }
 
   /**
@@ -151,7 +147,7 @@ public class AlignmentOrder
    * @param Order
    *          DOCUMENT ME!
    */
-  public void setOrder(Vector Order)
+  public void setOrder(List<SequenceI> Order)
   {
     this.Order = Order;
   }
@@ -161,7 +157,7 @@ public class AlignmentOrder
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getOrder()
+  public List<SequenceI> getOrder()
   {
     return Order;
   }
@@ -178,7 +174,7 @@ public class AlignmentOrder
     int found = Order.indexOf(oldref);
     if (found > -1)
     {
-      Order.setElementAt(newref, found);
+      Order.set(found, newref);
     }
     return found > -1;
   }
@@ -189,9 +185,14 @@ public class AlignmentOrder
    * @param o
    * @return true if o orders the same sequenceI objects in the same way
    */
-  public boolean equals(AlignmentOrder o)
+  @Override
+  public boolean equals(Object o)
   {
-    return equals(o, true);
+    if (o == null || !(o instanceof AlignmentOrder))
+    {
+      return false;
+    }
+    return equals((AlignmentOrder) o, true);
   }
 
   /**
@@ -217,13 +218,14 @@ public class AlignmentOrder
       {
         if (!identity)
         {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
+          throw new Error(
+                  "Weak sequenceI equivalence not yet implemented.");
         }
         else
         {
           for (int i = 0, j = o.Order.size(); i < j; i++)
           {
-            if (Order.elementAt(i) != o.Order.elementAt(i))
+            if (Order.get(i) != o.Order.get(i))
             {
               return false;
             }
@@ -271,7 +273,7 @@ public class AlignmentOrder
       }
       if (Order != null && o.Order != null)
       {
-        Vector c, s;
+        List<SequenceI> c, s;
         if (o.Order.size() > Order.size())
         {
           c = o.Order;
@@ -284,7 +286,8 @@ public class AlignmentOrder
         }
         if (!identity)
         {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
+          throw new Error(
+                  "Weak sequenceI equivalence not yet implemented.");
         }
         else
         {
@@ -292,7 +295,7 @@ public class AlignmentOrder
           int last = -1;
           for (int i = 0, j = s.size(); i < j; i++)
           {
-            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
+            int pos = c.indexOf(s.get(i)); // JBPNote - optimize by
             // incremental position search
             if (pos > last)
             {