+
+ 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:
+