sequence id when you click on it. </p>
<p>eg.<br>
UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&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
git://source.jalview.org / jalview.git / blobdiff