Merge branch 'bug/addcustomlaunchdesktopparams' into develop

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1f32da0..7afe1fa 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1280,7 +1280,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     StringBuffer url = new StringBuffer(jalviewServletURL);
 
-    url.append("?open="
+    // allow servlet parameters to be passed in applet parameter
+    String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
+            : "?";
+    url.append(firstSep);
+
+    url.append("open="
             + appendProtocol(viewport.applet.getParameter("file")));
 
     if (viewport.applet.getParameter("features") != null)