JAL-2798 Aptx is now saved to the project

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7c10544..abb9fa7 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1112,7 +1112,15 @@ public class Jalview2XML
       for (TreeFrameI treeView : externalTreeViews)
       {
         TreeI tree = treeView.getTree();
-        // tree.writeToJalviewProject(outputFile);
+        try
+        {
+          tree.writeToXml(new File("word"));
+          copyFileToJar(jout, "word", tree.getTreeName());
+        } catch (IOException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
 
       }
 
@@ -1546,7 +1554,7 @@ public class Jalview2XML
 
                 String varnaStateFile = varna.getStateInfo(model.rna);
                 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
-                copyFileToJar(jout, varnaStateFile, jarEntryName);
+
                 rnaSessions.put(model, jarEntryName);
               }
               SecondaryStructure ss = new SecondaryStructure();