From 7585bdc21653bdb66d604ed5efa95497f28c7eb5 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 28 Nov 2016 14:16:39 +0000
Subject: [PATCH] JAL-2325 finalise release notes

---
 help/html/whatsNew.html |   25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e8b9c96..1c20885 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -40,13 +40,12 @@
     <li><strong>Select highlighted region</strong><br />Press 'B'
       or use the new menu option in the alignment window's Select menu
       to mark columns containing highlighted regions generated from
-      structure selections, mouse-overs, or resulting from a
-      Find operation.</li>
+      structure selections, mouse-overs, or resulting from a Find
+      operation.</li>
     <li><strong>New custom link mechanism for opening URLs
         for database cross references.</strong><br /> If you have customised URL
       links in your Jalview preferences, then you may already have seen
-      the <a href="webServices/urllinks.html">Update your links
-        warning dialog.</a></li>
+      the <a href="#warning"> warning dialog (see below).</a></li>
     <li><strong>New command line export option for BioJS
         MSAviewer</strong><br />A number of small bugs with the HTML export
       functions from the Jalview desktop were also fixed.</li>
@@ -55,7 +54,25 @@
       is no longer considered a non-hydrophobic residue in the protein
       conservation calculation, and minor bugs addressed in PID and
       consensus colouring.</li>
+    <li><strong>Correct display of disulphide bond
+        features</strong><br /> In linked structure views, Jalview would
+      highlight all residues between in addition to the two linked
+      cysteines. The 'select columns by feature' function in the feature
+      settings would also select all intermediate columns.
   </ul>
 
+  <p>
+    <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>
 </body>
 </html>
-- 
1.7.10.2