JAL-3210 JAL-3330 use SequenceOntologyLite in JalviewJS

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 521b674..7701229 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -401,26 +401,18 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model if preferences say to, else use the default (SO
-     * Lite)
+     * configure 'full' SO model if preferences say to, else use the default (full SO)
+     * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
      */
-    if (Cache.getDefault("USE_FULL_SO", true))
+    boolean soDefault = !Platform.isJS();
+    if (Cache.getDefault("USE_FULL_SO", soDefault))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
 
     if (!headless)
     {
-      desktop = new Desktop() 
-//      {
-// // BH testing
-//       @Override
-//       protected void processEvent(AWTEvent e) {
-//               System.out.println("Jalview.java " + e);
-//               super.processEvent(e);
-//       }
-//       }
-      ;
+      desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
       try