javadoc and datastoreitem registry support for binding/rebinding methods

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 489f56f..738d14f 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -106,7 +106,7 @@ public abstract class DatastoreItem
 
   /**
    * note: this is taken verbatim from jalview.io.VamsasAppDatastore
-
+   * with added call to updateRegistryEntry
    * @param jvobj
    * @param vobj
    */
@@ -124,7 +124,6 @@ public abstract class DatastoreItem
                         : "unregisterable") + " object " + vobj);
       }
     }
-
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
@@ -152,11 +151,29 @@ public abstract class DatastoreItem
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
     jv2vobj.put(jvobj, vobj.getVorbaId());
+    if (jvobj==this.jvobj || vobj==this.vobj)
+    {
+        updateRegistryEntry(jvobj,vobj);
+    }
+  }
+  /**
+   * update the vobj and jvobj references and the registry entry for this datastore object
+   * called by bindjvvobj and replacejvobjmapping
+   */
+  private void updateRegistryEntry(Object jvobj,Vobject vobj)
+  {
+    if (this.jvobj!=null && this.vobj!=null) {
+      Cache.log.debug("updating dsobj registry. ("+this.getClass().getName()+")");
+    }
+    this.jvobj = jvobj;
+    this.vobj = vobj;
+    dsReg.registerDsObj(this);
   }
+
   /**
    * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
    * binding tables
-   * note: this is taken verbatim from jalview.io.VamsasAppDatastore
+   * note: originally taken verbatim from jalview.io.VamsasAppDatastore with added call to updateRegistryEntry
    * @param oldjvobject
    * @param newjvobject (may be null to forget the oldjvobject's document mapping)
    * 
@@ -174,6 +191,7 @@ public abstract class DatastoreItem
     {
       jv2vobj.put(newjvobject, vobject);
       vobj2jv.put(vobject, newjvobject);
+      updateRegistryEntry(newjvobject,(Vobject) vobject);
     }
   }