X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=19de95e0d316598dc6232274d0f6e48183ade492;hb=76cfeb5e50dd69a3ba963096556f9677c9eea55a;hp=eaa5fa87123afea1a6b9792a60a724614aff072d;hpb=aada6c7d3345363bf8b889f960c6209e7bbe8c06;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index eaa5fa8..19de95e 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -65,6 +65,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -374,12 +375,17 @@ public class Jalview
         System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
 
-      if (!aparser.contains("nonews"))
+      if (!aparser.contains("nonews")
+              || Cache.getProperty("NONEWS") == null)
       {
         desktop.checkForNews();
       }
 
-      BioJsHTMLOutput.updateBioJS();
+      if (!aparser.contains("nohtmltemplates")
+              || Cache.getProperty("NOHTMLTEMPLATES") == null)
+      {
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
     // Move any new getdown-launcher-new.jar into place over old
@@ -690,12 +696,7 @@ public class Jalview
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = DataSourceType.FILE;
-
-      if (file.indexOf("http:") > -1)
-      {
-        protocol = DataSourceType.URL;
-      }
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       if (file.endsWith(".jar"))
       {