JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index e56fa3f..b5ada26 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -35,10 +35,10 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignViewport;
 import jalview.gui.TreePanel;
 import jalview.io.NewickFile;
 import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -510,7 +510,7 @@ public class Tree extends DatastoreItem
    */
   public Object[] recoverInputData(Provenance tp)
   {
-    AlignViewport javport = null;
+    AlignmentViewport javport = null;
     jalview.datamodel.AlignmentI jal = null;
     jalview.datamodel.CigarArray view = null;
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
@@ -604,7 +604,7 @@ public class Tree extends DatastoreItem
     return null;
   }
 
-  private AlignViewport getViewport(Vobject v_parent)
+  private AlignmentViewport getViewport(Vobject v_parent)
   {
     if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
     {