JAL-1678 - patch to make sure we only compare positions of the last / or ?

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e84c335..7afe1fa 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1281,7 +1281,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     StringBuffer url = new StringBuffer(jalviewServletURL);
 
     // allow servlet parameters to be passed in applet parameter
-    String firstSep = url.indexOf("?") > url.indexOf("/") ? "&" : "?";
+    String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
+            : "?";
     url.append(firstSep);
 
     url.append("open="