-
Opening URLs from Jalview 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
+ 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
+ Default Link Settings
+ Adding additional links
+ Creating your own URL link URL links are specified as a
+ template containing special tokens that Jalview will replace with
+ the Sequence ID or Database Accession of the sequence when you
+ double click on its ID or open it's Link submenu.
+ Link URL templates must contain at least one token.
- eg.
+ Warning dialog about updating
+ your configured URL links
Regular Expression Substitution
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
+
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.
+ links are defined in the "Links" tab of the Jalview desktop
+ preferences, or specified as applet
+ parameters.
The "EMBL-EBI Search"
+ link is the default link shown in the "Link" submenu, and
+ opened when double-clicking on a sequence ID. When clicked, this
+ link will show a web page in your default browser with the selected
+ sequence ID as part of the URL.
+
You can configure your own
+ links via the Jalview Preferences
+ dialog. Jalview also provides 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.
+ UniRef100 =
+ http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
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
+ 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 2.4).
+ the sequence ID for the sequence (since Jalview 2.10.1).
+
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 $DB_ACCESSION$.
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
+ 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:
+
-
-
Many Thanks to Bernd Brandt of the Free University of
- Amsterdam for testing this new regular-expression expansion
- feature!
-
-