applet application_url value

Hi and happy new year to all JalView users and to the JalView team.

For a while it looks that the applet application_url parameter cannot reach the default URL that is http://www.jalview.org/services/launchApp according to the documentation at http://www.jalview.org/examples/appletParameters.html

Did this URL change at some point?
Or is this service disabled?

Regards

···

--
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/

Hi and happy new year to all JalView users and to the JalView team.

Thanks Sébastian !

For a while it looks that the applet application_url parameter cannot
reach the default URL that is http://www.jalview.org/services/launchApp
according to the documentation at
http://www.jalview.org/examples/appletParameters.html

Oops - the servlet at that URL didn't seem to make it through to the new year. It's now working again !

Sorry about that :slight_smile:
Jim.

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On 06/01/2014 11:43, Sébastien Moretti wrote:

Thanks Jim

as usual you are fast and efficient.

···

Hi and happy new year to all JalView users and to the JalView team.

Thanks Sébastian !

For a while it looks that the applet application_url parameter cannot
reach the default URL that is http://www.jalview.org/services/launchApp
according to the documentation at
http://www.jalview.org/examples/appletParameters.html

Oops - the servlet at that URL didn't seem to make it through to the new
year. It's now working again !

Sorry about that :slight_smile:
Jim.

--
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/

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

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--

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/