From 62eb39691722aae525b9aa5c65b38af87ffbcf24 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 16 Nov 2016 15:54:05 +0000
Subject: [PATCH] JAL-2282 Updated docs with information about when warning is
 shown

---
 help/html/webServices/urllinks.html |    6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 1a1f0d0..36c7c6b 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -66,6 +66,12 @@
     the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
   </p>
   <p>
+  If Jalview opens a project with links which include $SEQUENCE_ID$ tokens, it will present
+  the user with a warning message, as these links may need to be updated to use $DB_ACCESSION$, if
+  they were added before Jalview 2.10.1. The message lists the links which should be reviewed. 
+  The warning can be turned off completely via a checkbox in the message dialog.
+  </p>
+  <p>
     <strong>Regular Expression Substitution</strong><br> A url may
     contain a string of the form $SEQUENCE_ID=/<em>regular
     expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$. 
-- 
1.7.10.2