[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Thu Dec  6 18:42:55 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv31194/src/main/org/biomoby/shared/data

Modified Files:
	MobyDataObjectSet.java MobyDataObjectSetSAI.java 
Log Message:
Added registry support in c-tors
moby-live/Java/src/main/org/biomoby/shared/data MobyDataObjectSet.java,1.11,1.12 MobyDataObjectSetSAI.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSet.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSet.java	2007/12/06 20:12:26	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSet.java	2007/12/06 23:42:55	1.12
@@ -21,6 +21,7 @@
 public class MobyDataObjectSet extends MobyPrimaryDataSet implements MobyDataInstance, Collection<MobyDataObject>{
 
     Vector<MobyDataObject> bag;
+    Registry registry;
     private int xmlMode = MobyDataInstance.CENTRAL_XML_MODE;
 
     public MobyDataObjectSet(org.w3c.dom.Element e) throws MobyException{
@@ -55,30 +56,40 @@
      * Creates an empty collection bag with a name.
      */
     public MobyDataObjectSet(String name){
+	this(name, (Registry) null);
+    }
+
+    public MobyDataObjectSet(String name, Registry reg){
 	super(name);
+	registry = reg;
 	bag = new Vector<MobyDataObject>();
     }
 
     /**
-     * Creates a collection with a name, initializing the members with the given array
+     * Creates a collection with a name, initializing the members with the given array.  
+     * The registry is inferred from the input values.  If the values array is blank, the default
+     * registry is used. This can be avoided by using the (name, registry) c-tor instead,
+     * which created a blank array for you automatically.
+     *
+     * @param values a set of MobyDataObjects, all from the same registry
      *
      * @throws NullPointerException if the input array is null, or contains null elements
      */
     public MobyDataObjectSet(String name, MobyDataObject[] values) throws NullPointerException{
-	this(name);
+	this(name, (Registry) (values.length == 0 ? null : values[0].getDataType().getRegistry()));
 	setElements(values);
     }
 
     /**
      * Creates a collection with a name, initializing the members with the members of the given collection.
      *
-     * @param c usually another MobyDataObjectSet, or a Vector of MobyDataObjects
+     * @param c usually another MobyDataObjectSet, or a Vector of MobyDataObjects, all in the same namespace
      *
      * @throws ClassCastException if a member of the input collection is not a MobyDataObject
      * @throws NullPointerException if the collection or one of its members is a null object
      */
     public MobyDataObjectSet(String name, Collection<? extends MobyDataObject> c) throws ClassCastException, NullPointerException{
-	this(name);
+	this(name, (Registry) (c.isEmpty() ? null : c.iterator().next().getDataType().getRegistry()));
 	addAll(c);
     }
 
@@ -129,13 +140,13 @@
 		    }
 		}
 		if(lineage != null && lineage.length == 0){
-		    return MobyDataType.getDataType("Object");
+		    return MobyDataType.getDataType(MobyTags.MOBYOBJECT, registry);
 		}
 		return lineage == null ? null : lineage[lineage.length-1];
 	    }
 	    else{
 		// We know that any we could hold would at least be an Object...
-		return MobyDataType.getDataType("Object");
+		return MobyDataType.getDataType(MobyTags.MOBYOBJECT, registry);
 	    }
 	}
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSetSAI.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSetSAI.java	2007/12/06 16:45:19	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObjectSetSAI.java	2007/12/06 23:42:55	1.4
@@ -3,6 +3,7 @@
 import java.util.Collection;
 import java.util.Iterator;
 
+import org.biomoby.registry.meta.Registry;
 import org.biomoby.shared.*;
 
 /**
@@ -24,9 +25,13 @@
      * Constructor for base Objects.
      */
     public MobyDataObjectSetSAI(String name, MobyService[] services){
-	super("");  // Not using c-tor(namespace, id), then assigning "this" to
-	            // dataInstance, because that would cause recursion in the shadowed calls
-	dataInstance = new MobyDataObjectSet(name);
+	this(name, services, null);
+    }
+
+    public MobyDataObjectSetSAI(String name, MobyService[] services, Registry registry){
+	super("", registry);  // Not using c-tor(namespace, id), then assigning "this" to
+	                      // dataInstance, because that would cause recursion in the shadowed calls
+	dataInstance = new MobyDataObjectSet(name, registry);
 	mobyServices = services;
     }
 
@@ -34,7 +39,7 @@
      * Constructor that takes an existing object and associates services with it.
      */
     public MobyDataObjectSetSAI(MobyDataObjectSet collection, MobyService[] services){
-	super(collection.getName());
+	super(collection.getName(), collection.getDataType().getRegistry());
 	dataInstance = collection;
 	mobyServices = services;
     }