[Jalview-discuss] EMBL-EBI SRS server retirement and sequence identifier links

Hamish McWilliam hpm at ebi.ac.uk
Thu Jan 9 16:13:06 GMT 2014


Hi folks,

By default the JalView provides a link to the the the EMBL-EBI SRS
server in the menu accessed by right-clicking on a sequence identifier.
Since the EMBL-EBI SRS server has been retired (see
http://srs.ebi.ac.uk/srs-retirement.html) users will want to change the
link configuration.

In Desktop JalView this can be done by modifying the "Connections" in
the "Preferences" (see
http://www.jalview.org/help/html/features/preferences.html#connections).

For the JalView applet this can be done by providing a link
configuration using the 'linkLabel' and 'linkUrl' applet parameters (see
http://www.jalview.org/examples/appletParameters.html).

For example to use the "EBI Search" service
(http://www.ebi.ac.uk/ebisearch/) for a link:

A. In Desktop JalView:
- Select "Tools" -> "Preferences..." from the desktop window
- Select the "Connections" tab
- Select the link definition for "SRS" in the "URL link from Sequence ID"
- Click the "Edit" button
- Set the "Link Name" to "Find in EBI Search"
- Set the URL to:
http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
- Click "OK"
- Click "OK"

B. For the JalView applet add the following applet parameters to the
'applet' tag:

<param name="linkLabel_1"    value="Find in EBI Search" />
<param name="linkUrl_1"
value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
/>

All the best,

Hamish
-- 
============================================================
Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/
============================================================



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