X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2FVorbaXmlBinder.java;h=94624943cf42597a0d8d697bc1d84e5507d3d08d;hb=0e95b1e51ee83557e26b520c7b10ea172fbd0a43;hp=dadd3faf23bb198d4524c1b3113e57122bd3677d;hpb=11dfd6edca6d81c20e7ae0f6098b5a0251611473;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/VorbaXmlBinder.java b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
index dadd3fa..9462494 100644
--- a/src/uk/ac/vamsas/client/VorbaXmlBinder.java
+++ b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
@@ -167,7 +167,8 @@ public class VorbaXmlBinder implements UnmarshalListener {
     if (doc.__vorba==null)
       doc.__vorba = vorba;
     doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ? 
-    doc.marshal(outstream);
+    Marshaller mshl = new Marshaller(outstream);
+    mshl.marshal(doc);
 
   }
   /**
@@ -216,8 +217,9 @@ public class VorbaXmlBinder implements UnmarshalListener {
     Unmarshaller unmarshaller = new Unmarshaller(root);
     unmarshaller.setIDResolver(new IDResolver() {
       public Object resolve(String id) {
+        // TODO: allow for external ID resolution
         VorbaXmlBinder.log.warn("Warning - id " + id
-            + " is not found in the Vamsas XML!");
+            + " is not found in the Vamsas XML! (TODO: Ignore if this is a forward reference!)");
         return null;
       }
     });