JAL-2798 added != null check for Aptx trees

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7c10544..c0246c3 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1112,13 +1112,24 @@ public class Jalview2XML
       for (TreeFrameI treeView : externalTreeViews)
       {
         TreeI tree = treeView.getTree();
-        // tree.writeToJalviewProject(outputFile);
+        try
+        {
+          tree.writeToXml(new File("word"));
+          copyFileToJar(jout, "word", "aptx-test");
+
+
+        } catch (IOException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
 
       }
 
     }
 
 
+
     // SAVE ANNOTATIONS
     /**
      * store forward refs from an annotationRow to any groups
@@ -1546,7 +1557,7 @@ 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();
@@ -3552,12 +3563,33 @@ 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)
+  {
+    String treeFile = copyJarEntry(jprovider, "aptx-test", "aptx", null);
+    if (treeFile != null)
+    {
+    try
+    {
+      AptxInit.createInstancesFromFile(treeFile, av);
+    } catch (IOException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+      }
+    }
+    
+  }
+
+
 
   /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna