From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 2 Nov 2016 14:18:52 +0000 (+0000)
Subject: JAL-2282 Updated help documentation
X-Git-Tag: Release_2_10_1^2~18^2~2^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=582e1d6c851e8acd26f188bdc9949f3ac557f32b;p=jalview.git

JAL-2282 Updated help documentation
---

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 0a4c650..1a1f0d0 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -28,7 +28,7 @@
     and the desktop application are able to open URLs as 'popups' in
     your web browser. <br> Double-clicking on the ID of a sequence
     will open the first URL that can be generated from its sequence ID.
-    This is often the SRS site, but you can easily configure your own <a
+    This is by default the EMBL-EBI site, but you can easily configure your own <a
       href="#urllinks">sequence URL links</a>.
   </p>
   <p>
@@ -40,10 +40,10 @@
   <p>
     <strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
     links are defined in the &quot;Connections&quot; tab of the <a
-      href="../features/preferences.html">Jalview desktop
-      preferences</a>, or specified as <a
-      href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
-      parameters</a>. <br> By default the item &quot;SRS&quot; is added
+    href="../features/preferences.html">Jalview desktop
+    preferences</a>, or specified as <a
+    href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
+    parameters</a>. <br> By default the item &quot;EMBL-EBI Search&quot; is added
     to this link menu. This link will show a web page in your default
     browser with the selected sequence id as part of the URL.<br>
     In the preferences dialog box, click <strong>new</strong> to add a
@@ -51,9 +51,9 @@
     to remove it.<br> You can name the link, this will be displayed
     on a new menu item under the &quot;Link&quot; menu when you right
     click on a sequence id. <br> The URL string must contain a
-    token that can be replaced with a sequence ID. The simplest token is
+    token that can be replaced with a sequence ID or DB accession ID. The simplest token is
     &quot;$SEQUENCE_ID$&quot;, which will be replaced by the chosen
-    sequence id when you click on it.
+    sequence id when you click on it. 
   </p>
   <p>
     eg.<br> UniRef100 =
@@ -61,15 +61,16 @@
     Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> <br>
     Links will also be made for any database cross references associated
     with the sequence where the database name exactly matches a URL link
-    name. In this case, the $SEQUENCE_ID$ string will be replaced with
+    name. In this case, the $DB_ACCESSION$ string will be replaced with
     the accession string for the database cross-reference, rather than
-    the sequence ID for the sequence (<em>since Jalview 2.4</em>).
+    the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
   </p>
   <p>
     <strong>Regular Expression Substitution</strong><br> A url may
     contain a string of the form $SEQUENCE_ID=/<em>regular
-      expression</em>/=$. In this case, the regular expression will be
-    applied to the full sequence ID string and the resulting match will
+    expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$. 
+    In this case, the regular expression will be
+    applied to the full sequence ID or DB accession ID string and the resulting match will
     be inserted into the URL. Groups of parentheses can be used to
     specify which regions of the regular expression will be used to
     generate the URL: