[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Fri Dec  7 15:32:29 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv2510/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Made MOBY data loading registry-aware
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2007/12/06 17:24:13	1.14
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2007/12/07 20:32:29	1.15
@@ -215,7 +215,14 @@
 		    contentGUI.getTransformer().transform(new StreamSource(url.openStream()),
 							  new StreamResult(stringWriter));
 		    htmlContents = stringWriter.toString();
-		    htmlContents = HTMLUtils.encapsulateBinaryData(url, htmlContents);
+		    // NOTE: If you switch the registry in the middle of using Seahawk,
+		    // the following might fail on documents in the history, as they were
+		    // encoded according to a different registry than the current value of 
+		    // SeahawkOptions.getRegistry().  If we really want to support multiple concurrent
+		    // registries, there has to be a way to note the source registry for the data in the 
+		    // document (preferred), or we must maintain a hash of the document:registry mappings
+		    // for the session.
+		    htmlContents = HTMLUtils.encapsulateBinaryData(url, htmlContents, SeahawkOptions.getRegistry());
 		}
 		catch(TransformerException te){
 		    status.setText("Sorry!  Could not transform the MOBY data into presentation form");
@@ -935,7 +942,7 @@
 	
 	// Create the Java MOBY API object based on the linked document DOM fragment
 	try{
-	    MobyDataInstance mdi = MobyDataObject.createInstanceFromDOM(mobyObject);
+	    MobyDataInstance mdi = MobyDataObject.createInstanceFromDOM(mobyObject, SeahawkOptions.getRegistry());
 	    if(mdi instanceof MobyDataObject){
 		mobyData = mdi;
 	    }