+
+ 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 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 "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:
+