X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=a23aad5e837e04ad8d4e19a8feacadb76b2aba0b;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=4bd1acec0397dbe0f2e563478aefd97fe796f929;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 4bd1ace..a23aad5 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@ import jalview.util.ShiftList;
 
 import java.io.PrintStream;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -105,7 +106,7 @@ public class AlignmentView
     SequenceI[] selseqs;
     if (selection != null)
     {
-      Vector sel = selection.getSequences(null);
+      List<SequenceI> sel = selection.getSequences(null);
       this.selected = new Vector();
       selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
     }
@@ -116,12 +117,8 @@ public class AlignmentView
 
     // get the alignment's group list and make a copy
     Vector grps = new Vector();
-    Vector gg = alignment.getGroups();
-    Enumeration gge = gg.elements();
-    while (gge.hasMoreElements())
-    {
-      grps.addElement(gge.nextElement());
-    }
+    List<SequenceGroup> gg = alignment.getGroups();
+    grps.addAll(gg);
     ScGroup[] sgrps = null;
     boolean addedgps[] = null;
     if (grps != null)
@@ -1047,12 +1044,10 @@ public class AlignmentView
                 + " wide and has " + visal.getHeight() + " seqs.");
         if (visal.getGroups() != null && visal.getGroups().size() > 0)
         {
-          SequenceGroup sg;
-          Enumeration en = visal.getGroups().elements();
+          
           int i = 1;
-          while (en.hasMoreElements())
+          for (SequenceGroup sg:visal.getGroups())
           {
-            sg = (SequenceGroup) en.nextElement();
             os.println("Group " + (i++) + " begins at column "
                     + sg.getStartRes() + " and ends at " + sg.getEndRes());
           }