X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FGrouping.java;h=91fef84ae2cf23f71992e9f5edd7906010a380f1;hb=9c9bc24a6be8af1a97914b246b8ce2d0eaabf5fd;hp=4a641ccb8fc1d4da8dad979666731dae3ddd7b4f;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 4a641cc..91fef84 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -24,6 +24,7 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -42,25 +43,24 @@ public class Grouping
    * 
    * @param sequences
    * @param selectedChars
-   * @param exgroups
+   * @param list
    * @return
    */
   public static SequenceGroup[] makeGroupsFrom(SequenceI[] sequences,
-          String[] selectedChars, Vector exgroups)
+          String[] selectedChars, List<SequenceGroup> list)
   {
     // TODO: determine how to get/recover input data for group generation
     Hashtable gps = new Hashtable();
     int width = 0, i;
     Hashtable pgroup = new Hashtable();
-    if (exgroups != null)
+    if (list != null)
     {
-      SequenceGroup sg;
-      for (Enumeration g = exgroups.elements(); g.hasMoreElements();)
+      for (SequenceGroup sg:list)
       {
-        sg = (SequenceGroup) g.nextElement();
-        for (Enumeration sq = sg.getSequences(null).elements(); sq
-                .hasMoreElements();)
-          pgroup.put(sq.nextElement().toString(), sg);
+        for (SequenceI sq :sg.getSequences(null))
+        {
+          pgroup.put(sq.toString(), sg);
+        }
       }
     }
     for (i = 0; i < sequences.length; i++)