JAL-2316 tweaking docs and links in help

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index db47351..52eaf85 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -135,7 +135,7 @@
                </tocitem>
                <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
                <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
-                   <tocitem text="Configuring URL Links" target="linkspref" />
+                   <tocitem text="Configuring URL Links" target="linksprefs" />
                </tocitem>
                <tocitem text="VAMSAS Data Exchange" target="vamsas">
                        <!-- what can Jalview share with other apps -->

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index da5d7dd..56469e5 100644 (file)
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -57,12 +57,12 @@
     <em>Adding additional links</em><br /> You can configure your own
     links via the Jalview <a href="../features/preferences.html#links"><strong>Preferences</strong></a>
     dialog. Jalview also provides persistent URLs for many common
-    bioinformatics databases. These links are downloaded by Jalview from
+    bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
     the <em>identifiers.org</em> website, and the names and URLs are not
     user editable.
   </p>
   <p>
-    <em>Creating your own URL link</em> URL links are specified as a
+    <em>Creating your own URL link</em> <br/>URL links are specified as a
     template containing special tokens that Jalview will replace with
     the Sequence ID or Database Accession of the sequence when you
     double click on its ID or open it's <strong>Link</strong> submenu.
@@ -73,10 +73,18 @@
     Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> </pre>
   <p>
     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 $DB_ACCESSION$ string will be replaced with
+    with the sequence for any link templates whose name begins with the database 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 2.10.1</em>).
+    <br /> <em>For example: to create a link for viewing MACiE records
+      from PDB Entries, create a new custom link entry with the name
+      "PDB in MACiE", and link URL template:
+      <pre>https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/index.pl?query_pdb=1&amp;pdb=$DBACCESSION$</pre>
+      <br />The sequence ID popup menu for seuqences with a PDB entry
+      will now show 'PDB in MACiE|1xyz..' links in the <strong>links</strong>
+      submenu.
+    </em>
   </p>
   <p>
     <strong><a name="warning">Warning dialog about updating

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index c5859ea..0734271 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -30,6 +30,8 @@
     Full details about Jalview 2.10.2 are in the <a href="releases.html#Jalview.2.10.2">
       Release Notes</a>, but the highlights are below.</p>
   <ul>
+  <li>
+  <li>New preferences for <a href="webServices/urllinks.html">opening web pages for database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM database and identifiers.org services.</li>
   </ul>
 
 </body>