-
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:
-