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 by default the EMBL-EBI site, but you can easily configure your own sequence URL links.
Other links for a sequence either derived from any other configured URL links, or imported from the sequence's annotation, are accessed by right clicking to open the sequence pop-up menu, and selecting from the Links submenu.
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 "EMBL-EBI Search" 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 or DB accession 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 $DB_ACCESSION$ string will be replaced with
the accession string for the database cross-reference, rather than
the sequence ID for the sequence (since Jalview 2.10.1).
Warning dialog about updating
your configured URL links
In the desktop
prior to Jalview 2.10.1, the only way to configure custom links for
a particular database cross-reference for a sequence was to give it
a name that
exactly matched the database source, and a regular
expression for filtering out any spurious matches generated when the
custom linked was tested against the Sequence's ID string. Since the
introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$
will not be used for database cross-reference accession strings, and
if you have custom links configured, Jalview will raise a warning
message so let you know that you may need to update your links to
use $DB_ACCESSION$.
Regular Expression Substitution
A url may
contain a string of the form $SEQUENCE_ID=/regular
expression/=$ or $DB_ACCESSION=/regular expression/=$.
In this case, the regular expression will be
applied to the full sequence ID or DB accession 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: