X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=1cab8ca897b315b96af5ef62922f0f01d60a1cfe;hb=c1f777a6a4a74ee1573e5f3f883e0de902818ae7;hp=a093ebed54466995b914d531e1bf8f56414d8a46;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index a093ebe..1cab8ca 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -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++)
         {
@@ -1943,7 +1942,7 @@ public class VamsasAppDatastore
                 TreePanel tp = null;
                 if (vstree.isValidTree())
                 {
-                  tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
+                  tp = alignFrame.showNewickTree(vstree.getNewickTree(),
                           vstree.getTitle(), vstree.getInputData(), 600,
                           500, t * 20 + 50, t * 20 + 50);
 
@@ -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)