From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 23 Nov 2016 15:22:44 +0000 (+0000)
Subject: JAL-2282 revised docs about warning message.
X-Git-Tag: Release_2_10_1~8^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c1c13eb37eb978969f43fb6574587d18416f55cd;p=jalview.git

JAL-2282 revised docs about warning message.
---

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 36c7c6b..088a539 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -66,10 +66,19 @@
     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.
+    <strong><a name="warning">Warning dialog about updating
+        your configured URL links</a></strong><br /> In the desktop
+    prior to Jalview 2.10.1, the only way to configure custom links for
+    a particular database cross-reference for a sequence was to give it
+    a name that
+    <em>exactly</em> matched the database source, and a regular
+    expression for filtering out any spurious matches generated when the
+    custom linked was tested against the Sequence's ID string. Since the
+    introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$
+    will not be used for database cross-reference accession strings, and
+    if you have custom links configured, Jalview will raise a warning
+    message so let you know that you may need to update your links to
+    use $DB_ACCESSION$.
   </p>
   <p>
     <strong>Regular Expression Substitution</strong><br> A url may