URL help update

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 08e210e..c173212 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -71,7 +71,26 @@ vbersion of the font to sequence labels.</p>
   sequence id when you click on it. </p>
 <p>eg.<br>
   UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&amp;library=uniref100<br>
-  Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$</p>
+  Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
+  <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 
+  the accession string for the database cross-reference, rather than the 
+  sequence ID for the sequence (<em>since Jalview 2.4</em>).
+  <br>
+  <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 be inserted into the URL.
+  Groups of parentheseses can be used to specify which regions of the regular expression will be used to generate the URL:
+  <ul>
+  <li>Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
+  </li>
+  <li>Regions matching sub-parentheseses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.</li>
+  <em>Please Note: the regular expressions supported by Jalview are those provided by the <a href="www.javaregex.com">Stevesoft javaregex package</a>. 
+  <br>Many Thanks to Bernd Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature!
+  </em>
+  </ul>
+  </p>
 <p><em>Default Browser (Unix)</em><br>
   Its difficult in Java to detect the default web browser for Unix users. If Jalview 
   can't find your default web browser, enter the name or full path to your web 

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9393570..a836c9f 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -86,7 +86,10 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         sequence will be propagated to the hidden sequences. </em></li>
       <li><strong>Link</strong><br>
         <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> 
-        Connections tab.</em><strong><br>
+        Connections tab.<br>
+        Since Jalview 2.4, links will also be made for database cross 
+        references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
+        </em><strong><br>
         </strong></li>
     </ul>
   </li>

diff --git a/help/html/releases.html b/help/html/releases.html
index c9265f0..2f340ff 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -45,6 +45,8 @@
                        <li>Fetch sequences from DAS sources supporting the sequence command</li>
                        <li>Fetch either seed alignment or full alignment from PFAM</li>
                        <li>Sequence Fetcher GUI provides example accession numbers and 'clear' button</li>
+                       <li>URL Links created for matching database cross references as well as sequence ID</li> 
+                       <li>URL Links can be created using regular-expressions</li>
                        <li>Application command line
                        <ul>
                                <li>-tree parameter to open trees (introduced for passing from

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 7bad5c0..98f01dc 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -10,7 +10,9 @@
   DAS Sequence Fetching<br>
   PFAM full alignment retrieval<br>
   DNA/Protein Product traversal (Experimental)</br>
-  .. (more to come) 
+  .. (more to come)<br> 
+  URL links can be generated using regular 
+  expressions and created for sequence database cross references<br>
 </ul>
 <p><strong>Issues Resolved</strong></p>
 <ul>