Dear Dr Procter,
Thank you so much for your help. I did what you indicated and it did not work once again… Here is the text from the console:
Jalview Desktop 2.8.1
Build Date: 04 June 2014
Java version: 1.7.0_65
x86 Windows 7 6.1
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
INFO - Completed construction of reader.
INFO - Saved last read date as 02-Sep-2014 09:27:08
INFO - Saved last read date as 02-Sep-2014 09:27:08
INFO - Saved last read date as 02-Sep-2014 09:27:08
INFO - Loading mapping descriptors from jar:http://www.jalview.org/webstart/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Content is not allowed in prolog.{File: [not available]; line: 1; column: 1}
Error getUniprotEntries() Content is not allowed in prolog.{File: [not available]; line: 1; column: 1}
Many thanks and kind regards,
Ipek
From: James Procter
Sent: 08 September 2014 12:34
To: Ipek Birced
Subject: Re: Jalview bug reportHello Ipek - I’m very sorry to hear you are having problems !
I am writing to you to report a bug on Jalview. I tried emailing the jalview-discuss mailing list but although I subscribed my emails were not going through
that’s worrying in itself. I’ll check that you’re properly subscribed and confirm in a separate email.
I am sorry to bother you with such a small thing, but I am quite pressed since I need Jalview for my project.
no problem… it’s part of my role here in Dundee!
The issue is that when I try to fetch sequences from Uniprot, a message pops up saying that it was not possible to fetch the sequence (for instance p00519). I have been working with JalView and doing the same routine for about a month, so I am not sure what is happening now. I have tried restarting the computer and uninstalling the desktop application, but nothing seems to work. My memory is also free (above 66%).
OK. If you start Jalview again, then enable the Jalview Java Console (from the Tools menu). That will open a window showing some text output from the program. Then - try retrieving the Uniprot sequence again - if it doesn’t work, cut and paste the text from the console window into an email and send it to me!
Hear from you soon…
Jim
The University of Dundee is a registered Scottish Charity, No: SC015096
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Hello Ipek.
I found I had the same problem as you - and then, strangely, I stopped getting the error.
Could you close Jalview then open it again and try retrieving sequences once more ?
Jim.
On 08/09/2014 12:48, Ipek Birced wrote:
