+
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:
+