JAL-1953 2.11.2 with Archeopteryx!

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index d4b2c04..1a48a16 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -104,6 +104,10 @@ import jalview.datamodel.features.FeatureMatcher;
 import jalview.datamodel.features.FeatureMatcherI;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
@@ -1276,9 +1280,35 @@ public class Jalview2XML
               object.getTree().add(tree);
             }
           }
+
         }
       }
     }
+    if (!storeDS && av.getCurrentExtTree() != null)
+    {
+      Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+              .getActiveTreeViews()
+              .keySet();
+      for (TreeFrameI treeView : externalTreeViews)
+      {
+        TreeI tree = treeView.getTree();
+        try
+        {
+          tree.outputAsFile(new File("word"));
+          copyFileToJar(jout, "word", "aptx-test","Archeopteryx Tree Session");
+
+
+        } catch (IOException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
+
+      }
+
+    }
+
+
 
     /*
      * save PCA viewers
@@ -4055,6 +4085,7 @@ public class Jalview2XML
     if (loadTreesAndStructures)
     {
       loadTrees(jalviewModel, view, af, av, ap);
+      loadExternalTrees(jprovider, jalviewModel, av);
       loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
@@ -4062,6 +4093,27 @@ public class Jalview2XML
     // and finally return.
     return af;
   }
+    
+  private void loadExternalTrees(jarInputStreamProvider jprovider,
+          JalviewModel jms, AlignViewport av)
+  {
+    // TODO: allow more than one archeopteryx session per project
+    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
@@ -4179,6 +4231,10 @@ public class Jalview2XML
 
         Tree tree = jm.getTree().get(t);
 
+        TreeFrameI externalViewer = AptxInit.createInstanceFromNhx(
+                tree.getTitle(), tree.getNewick(),
+                av);
+
         TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
         if (tp == null)
         {