JAL-3274 resource path correction, code tidying (constants etc)

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 521b674..9ba7a7f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -401,39 +401,26 @@ 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
       {
         JalviewTaskbar.setTaskbar(this);
-      } catch (Exception e)
-      {
-        System.out.println("Cannot set Taskbar");
-        // e.printStackTrace();
       } catch (Throwable t)
       {
-        System.out.println("Cannot set Taskbar");
-        // t.printStackTrace();
+        System.out.println("Error setting Taskbar: " + t.getMessage());
       }
 
       desktop.setVisible(true);