JAL-1925 update source version in license

[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..cd382f3 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,6 @@
  */
 package jalview.io.vamsas;
 
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.NJTree;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -35,10 +29,17 @@ 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 java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -421,8 +422,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -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++)
@@ -595,8 +595,7 @@ public class Tree extends DatastoreItem
           // off by
           // one for to
         }
-        return new Object[]
-        { new AlignmentView(view), jal };
+        return new Object[] { new AlignmentView(view), jal };
       }
     }
     Cache.log
@@ -604,7 +603,7 @@ 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)
     {