X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FGrouping.java;h=32ea204b73d39b539c0ecdae9aa2e6d3bf125f85;hb=e498cc04385671872ab98220219aaeac2ec245f2;hp=2cb4753bc0368392fa2bb7b554bc650cc4856955;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 2cb4753..32ea204 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -17,13 +17,11 @@
  */
 package jalview.analysis;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
-import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -42,25 +40,24 @@ 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++)