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 whichever URL is selected for 'popups' in the "Links" tab of the Jalview desktop
preferences.
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 list of available links in the preferences dialog box
contains the item "EMBL-EBI Search".
This link is initially configured so that it is the URL which opens on double-clicking on a sequence ID. It is also a
menu item in the "Link" menu. When clicked, this link will show a web page in your default
browser with the selected sequence id as part of the URL.
Also by default, the list of available links in the preferences dialog box contains persistent URLs for many common
bioinformatics databases. These links are downloaded by Jalview from
the identifiers.org website, and the names and URLs are not user editable.
The list of links can be sorted by clicking on the headers of the table. The list
can be filtered using the free text search box below the table, or the
"Custom Only" button, which displays only user-defined links.
In the preferences dialog box, the links which appear in the "Link" menu
can be configured by selecting or deselecting links in the "In Menu"
column. The names of selected links will be displayed
as menu items under the "Link" menu when you right
click on a sequence id.
You can configure which link is used when double-clicking on a sequence
by selecting or deselecting links in the "On Click" column. Exactly one
link must be configured for double-clicking. Since the link uses the sequence id
to construct the URL to open, the selected link must contain the
"$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$"
and other tokens).
Additionally you can click new to add a new link, and edit to modify an existing link, or delete to remove it. Only URLs entered by the user (or the default EMBL-EBI link) may be edited or deleted. When adding or editing a link, 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: