JAL-2798 comments

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index abb9fa7..b4ded67 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1116,6 +1116,8 @@ public class Jalview2XML
         {
           tree.writeToXml(new File("word"));
           copyFileToJar(jout, "word", tree.getTreeName());
+          jms.addExtTreeViewer(treeView);
+
         } catch (IOException e)
         {
           // TODO Auto-generated catch block
@@ -1127,6 +1129,7 @@ public class Jalview2XML
     }
 
 
+
     // SAVE ANNOTATIONS
     /**
      * store forward refs from an annotationRow to any groups
@@ -3560,12 +3563,26 @@ public class Jalview2XML
     if (loadTreesAndStructures)
     {
       loadTrees(jms, view, af, av, ap);
+      loadExternalTrees(jprovider, jms, av);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
     }
     // and finally return.
     return af;
   }
+    
+  private void loadExternalTrees(jarInputStreamProvider jprovider,
+          JalviewModelSequence jms, AlignViewport av)
+  {
+   for (TreeFrameI externalTreeViewer: jms.getExtTreeViewer()) {
+      // String treeFile = copyJarEntry(jprovider, errorMessage, "aptx", null);
+      TreeViewerUtils.addTreeViewFrameToJalview(externalTreeViewer);
+
+    }
+    
+  }
+
+
 
   /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna