- Right click a sequence id to see a popup menu with "Link" as one of
- the items. By default the item "SRS" 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>
- Jalview allows you to add your own custom links to other web pages. Click new
- to add a new link. You can name the link, this will be displayed on a new menu
- item under the "Link" menu when you right click on a sequence id.
- <br>
- You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen
- 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/$SEQUENCE_ID$
- <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>