X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=2c35547a69358651052cc9f4253172463d285c21;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=9d99084353cf94bb5a804b3166dbec7f03169926;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 9d99084..2c35547 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -43,7 +43,6 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
@@ -1433,7 +1432,7 @@ public class VamsasAppDatastore
         // to the align frames.
         boolean gathered = false;
         String newviewid = null;
-        Set<AlignedCodonFrame> mappings = av.getAlignment()
+        List<AlignedCodonFrame> mappings = av.getAlignment()
                 .getCodonFrames();
         for (int i = 0; i < views.length; i++)
         {
@@ -2732,7 +2731,7 @@ public class VamsasAppDatastore
 
       }
       // Store any sequence mappings.
-      Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+      List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
       if (cframes != null)
       {
         for (AlignedCodonFrame acf : cframes)