X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2FVorbaXmlBinder.java;h=0f4feb18f5dd6e1960a4dfd12673f8cb0e885683;hb=705044b23ff07576f5827f68a4677eef007635fd;hp=c172de3c9b90bf3cd8f0f75544f55be553143675;hpb=2b329d524c11576c358e631d2005640fd51b1c55;p=vamsas.git

diff --git a/src/org/vamsas/client/VorbaXmlBinder.java b/src/org/vamsas/client/VorbaXmlBinder.java
index c172de3..0f4feb1 100644
--- a/src/org/vamsas/client/VorbaXmlBinder.java
+++ b/src/org/vamsas/client/VorbaXmlBinder.java
@@ -24,8 +24,8 @@ import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
 import org.vamsas.objects.core.VamsasDocument;
 /**
- * Implements the Vamsas object ID machinery for translating 
- * between non-volatile XML IDs and object references. Use the
+ * Implements the Vamsas Vobject ID machinery for translating 
+ * between non-volatile XML IDs and Vobject references. Use the
  * marshalling and unmarshalling methods in this class in order
  * to avoid validation exceptions when marshalling new objects
  * into the vamsas document.
@@ -58,6 +58,12 @@ public class VorbaXmlBinder implements UnmarshalListener {
    *      java.lang.Object, java.lang.Object)
    */
   public void fieldAdded(String fieldName, Object parent, Object child) {
+    if (parent instanceof Vobject && child instanceof Vobject) {
+      if (((Vobject) child).V_parent==null) {
+        // System.err.println("Setting parent of "+fieldName);
+        ((Vobject) child).setV_parent((Vobject) parent);
+      }
+    }
   }
 
   /*
@@ -70,20 +76,20 @@ public class VorbaXmlBinder implements UnmarshalListener {
   
   /*
    * Check if the object has an 'id' field - if it does, copy the value into
-   * the VorbaId field of object, and add the object to the VorbaId hash.
+   * the VorbaId field of Vobject, and add the Vobject to the VorbaId hash.
    * 
    * @see org.exolab.castor.xml.UnmarshalListener#unmarshalled(java.lang.Object)
    */
   public void unmarshalled(Object newobj) {
-    if (newobj instanceof object) {
-      object nobj = (object) newobj;
+    if (newobj instanceof Vobject) {
+      Vobject nobj = (Vobject) newobj;
       nobj.set__stored_in_document(true);
       Field fd = null;
       try {
         if (nobj.isRegisterable()) {
           // look for the id field (should be an NCName string)
           nobj.__vorba = vorbafactory;
-          fd = nobj.getClass().getField("id");
+          fd = nobj.getClass().getDeclaredField("_id");
           String idstring;
           if (fd.get(nobj) != null) {
             idstring = (String) fd.get(nobj);
@@ -140,7 +146,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
       sync=false; // document is out of sync - ids have been created.
       java.util.Iterator newobj = unrefed.listIterator();
       while (newobj.hasNext()) {
-        object o = (object) newobj.next();
+        Vobject o = (Vobject) newobj.next();
         // forces registration and id field update.
         VorbaId id = o.getVorbaId();
         if (!objrefs.containsKey(id)) {
@@ -153,9 +159,9 @@ public class VorbaXmlBinder implements UnmarshalListener {
     return sync;
   }
   /**
-     * Unmarshals a vamsasDocument object from a stream, registers
+     * Unmarshals a vamsasDocument Vobject from a stream, registers
      * unregistered objects, records existing VorbaIds, and completes 
-     * the org.vamsas.client.object housekeeping fields.
+     * the org.vamsas.client.Vobject housekeeping fields.
      * For a valid unmarshalling, the array of returned objects also includes
      * a <return>sync</return> parameter which is true if new VorbaIds
      * were created. If sync is false, then the caller should ensure that the
@@ -163,11 +169,11 @@ public class VorbaXmlBinder implements UnmarshalListener {
      *  TODO: ensure that provenance is correct for newly registered objects
      * @param instream - the XML input stream 
    * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
-   * @param root the root element's org.vamsas.objects.core object.
-     * @return null or {(Object) VamsasDocument object, (Object) Hashtable of object references, (Object) Boolean(sync) }
+   * @param root the root element's org.vamsas.objects.core Vobject.
+     * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync) }
      */
   public static Object[] getVamsasObjects(Reader instream,
-        IVorbaIdFactory factory, object root) {
+        IVorbaIdFactory factory, Vobject root) {
       Unmarshaller unmarshaller = new Unmarshaller(root);
       unmarshaller.setIDResolver(new IDResolver() {
         public Object resolve(String id) {
@@ -187,7 +193,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
         while (instream.ready()) {
           Object obj = unmarshaller.unmarshal(instream);
           boolean sync=ensure_references(unrefed, objrefs);
-          if (!(obj instanceof object))
+          if (!(obj instanceof Vobject))
             return null;
           return new Object[] { obj, objrefs, new Boolean(sync)};
           }