JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c32a40f..23fe057 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -122,6 +122,13 @@ public class Alignment implements AlignmentI
   {
     return sequences;
   }
+  @Override
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to work on this.
+    return sequences;
+  }
 
   public SequenceI[] getSequencesArray()
   {
@@ -1219,13 +1226,12 @@ public class Alignment implements AlignmentI
     {
       this.addCodonFrame(acod[a]);
     }
-    Vector sg = toappend.getGroups();
+    List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
-      Enumeration el = sg.elements();
-      while (el.hasMoreElements())
+      for (SequenceGroup _sg:sg)
       {
-        addGroup((SequenceGroup) el.nextElement());
+        addGroup(_sg);
       }
     }
     if (toappend.getHiddenSequences() != null)