Opening URLs from Jalview
Opening URLs from Jalview
Both the applet and the desktop application are able to open URLs as
'popups' in your web browser.
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 Configuring URL Links
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or
specified as applet
parameters.
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.
In the preferences dialog box, click new to add a new
link, and edit to modify an existing link, or delete
to remove it.
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.
The URL string must contain a token that can be replaced with a sequence
ID. The simplest token is "$SEQUENCE_ID$", which will be
replaced by the chosen sequence id when you click on it.
eg.
UniRef100 =
http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
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 (since Jalview 2.4).
Regular Expression Substitution
A url may contain a string of the form $SEQUENCE_ID=/regular
expression/=$. 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 parentheses can be used to specify which regions
of the regular expression will be used to generate the URL: