X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=75504be93f3bfb872dc08327bfbf01dc9b70c5f4;hp=70aaa421b0ae1cb988f39246ba590cdd3c395295;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hpb=54f6fe32b978af0932428981a56c9960b0df44a7

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 70aaa42..75504be 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -186,8 +186,8 @@ public class Jalview implements ApplicationSingletonI
   class FeatureFetcher
   {
     /*
-     * TODO: generalise to track all jalview events to orchestrate batch processing
-     * events.
+     * TODO: generalise to track all jalview events to orchestrate batch
+     * processing events.
      */
 
     private int queued = 0;
@@ -461,7 +461,12 @@ public class Jalview implements ApplicationSingletonI
         System.out.println("Error setting Taskbar: " + t.getMessage());
       }
       desktop.setVisible(true);
-
+      if (Platform.isJS())
+        Cache.setProperty("SHOW_JWS2_SERVICES", "false");
+      if (allowServices)
+      {
+        desktop.startServiceDiscovery();
+      }
       if (!isJS)
       /**
        * Java only
@@ -469,8 +474,6 @@ public class Jalview implements ApplicationSingletonI
        * @j2sIgnore
        */
       {
-        if (allowServices)
-          desktop.startServiceDiscovery();
         if (!aparser.contains("nousagestats"))
         {
           startUsageStats(desktop);
@@ -763,6 +766,10 @@ public class Jalview implements ApplicationSingletonI
           createOutputFiles(aparser, format);
         }
       }
+      if (headless)
+      {
+        af.getViewport().getCalcManager().shutdown();
+      }
     }
     // extract groovy arguments before anything else.
     // Once all other stuff is done, execute any groovy scripts (in order)