[Jalview-discuss] New version Stuck on Loading Data

Rob Wieck rwieck at nd.edu
Mon Jan 11 14:53:54 GMT 2016


Thanks Mungo,

Adding in that JmolApplet allowed it to run without errors.  Just so you
know, we haven't needed that applet before and haven't changed anything
else with the output of that feature.

Thanks for your help!

-Rob W

On Wed, Jan 6, 2016 at 9:08 AM, Mungo Carstairs (Staff) <
g.m.carstairs at dundee.ac.uk> wrote:

> Thanks Rob.
>
> Running with Java console shows up the error as
>
> ClassNotFoundException: org.jmol.api.JmolSelectionListener
>
>
> Can you ensure your applet has been updated to include the updated
> Jmol library, available at http://www.jalview.org/examples/ at the link to
>
> http://www.jalview.org/examples/JmolApplet-14.2.14_2015.06.11.jar
>
> and let me know if that resolves the problem.
>
>
> Our documentation for updating applet deployments could maybe be clearer.
> What steps did you follow to update after the certificate expired?
>
>
> Thanks and regards,
>
>
> Mungo
>
>
> Mungo Carstairs
> Jalview Computational Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK.
> www.jalview.org
> www.compbio.dundee.ac.uk
>
>
> ------------------------------
> *From:* Rob Wieck <rwieck at nd.edu>
> *Sent:* 06 January 2016 13:37
> *To:* Mungo Carstairs (Staff)
> *Cc:* jalview-discuss at jalview.org
> *Subject:* Re: [Jalview-discuss] New version Stuck on Loading Data
>
> Hi Mungo,
>
> Thanks for the prompt reply.  I only sent the file in rtf, so I can attach
> it to an email.  We point the applet to a unique ur for the input and is
> just plain text,
> https://www.vectorbase.org/sites/all/modules/custom/clustalw/clustalwPrintResults.php?id=111045&type=align
> for example.
>
> https://www.vectorbase.org/clustalw is the site where jalview is
> implemented.  In order to see the applet, sequences must be ran through
> clustalw first, then under the results, the applet loads in the data.
>
> Best,
>
> Rob W
>
>
> On Wed, Jan 6, 2016 at 4:00 AM, Mungo Carstairs (Staff) <
> g.m.carstairs at dundee.ac.uk> wrote:
>
>> Hi Rob,
>>
>>
>> Just to eliminate one possible problem - I notice the data file is in RTF
>> format and includes control characters. Jalview expects only plain text
>> files.
>>
>> Are you able to generate the file as plain text, and does that make a
>> difference?
>>
>>
>> Though having said that, I can load your RTF file into Jalview (Desktop
>> or applet), albeit with the control characters rendered as extra 'nonsense'
>> sequences - so this may not be the root of your problem. Is there a public
>> link to your site / applet?
>>
>>
>> Thanks,
>>
>>
>> Mungo
>>
>>
>> Mungo Carstairs
>> Jalview Computational Scientist
>> The Barton Group
>> Division of Computational Biology
>> School of Life Sciences
>> University of Dundee, Dundee, Scotland, UK.
>> www.jalview.org
>> www.compbio.dundee.ac.uk
>>
>>
>> ------------------------------
>> *From:* jalview-discuss-bounces at jalview.org <
>> jalview-discuss-bounces at jalview.org> on behalf of Rob Wieck <
>> rwieck at nd.edu>
>> *Sent:* 05 January 2016 20:47
>> *To:* jalview-discuss at jalview.org
>> *Subject:* [Jalview-discuss] New version Stuck on Loading Data
>>
>> To whom it may concern,
>>
>> We have a site that has the jalviewApplet.jar applet installed that pulls
>> a file from a page within the same domain.
>>
>> The previous versions worked, but after we upgraded to the most recent
>> version after the certificate expired last November, it was no longer able
>> to load data, it just hangs on 'Loading Data' (screenshot attached).
>>
>> I have attached the file that gets passed to the applet.
>>
>> Thanks!
>> -Rob
>>
>> --
>> Rob Wieck
>> Research Programmer
>> Center for Research Computing
>> University of Notre Dame
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
>
> --
> Rob Wieck
> Research Programmer
> Center for Research Computing
> University of Notre Dame
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
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