Error loading Jalview file

Jalview Discussion
1

Hi,

Quite suddenly as I was working on alignments today I became unable to load projects. When I try to load a project after I'm given this error message:
Error loading Jalview file
Error loading (file location)

I get this error with projects that were previously working fine, as well as new projects that I have created as tests. However, when I save the example files that open with the programme, under different names, they open just fine

I'm new to this and hoping there is a simple solution! I was going to increase the available memory, but I'm afraid I had difficulty with the instructions at http://www.jalview.org/jvmmemoryparams.html. Specifically I don't know how to 'make your own jnlp file and add the following parameter into the <resources> element.'

Thanks in advance,
Aoife

Attached is a jar file that was, but isn't now, opening

human and rat syngap alignment.aln (12.1 KB)

···

--
Aoife McMahon

PhD student
Kind Lab
School of Biomedical Science
Hugh Robson Building
George Sq
Edinburgh
EH8 9XD

0131 6503110

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

2

Dear Aoife - I’m sorry to hear you’re having problems.

Its quite possible that you have hit a bug with the annotation display preferences in the 2.5 release. This happens if you have disabled the automatic annotation but still have the annotation panel open (so you see the message ‘alignment has no annotations’ below the aligned sequences.

Could you try the following:

  1. Open the Tools->preferences dialog box from the Desktop’s dropdown menu, and make sure that at least one of the conservation/consensus/quality histogram annotations are enabled or that the annotations checkbox is disabled.
  2. try to load your alignments or project files again.

Please let me know if this solves your problem, otherwise, I need to have some more information. Could you open the Jalview Console window (see Tools->Java Console) and send me the contents in another email ?

Thanks very much
Jim.

··· 
-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
3

That did it!

Thank you SO much!

I had spent ages preparing alignments for thesis figures and was NOT very happy when they wouldn't open, so had just ignored it until now. You've made my day.

Thanks

Quoting Jim Procter <jprocter@compbio.dundee.ac.uk>:

···

Dear Aoife - I'm sorry to hear you're having problems.

Its quite possible that you have hit a bug with the annotation display
preferences in the 2.5 release. This happens if you have disabled the
automatic annotation but still have the annotation panel open (so you
see the message 'alignment has no annotations' below the aligned
sequences.

Could you try the following:

1. Open the Tools->preferences dialog box from the Desktop's dropdown
menu, and make sure that at least one of the
conservation/consensus/quality histogram annotations are enabled *or*
that the annotations checkbox is disabled.
2. try to load your alignments or project files again.

Please let me know if this solves your problem, otherwise, I need to
have some more information. Could you open the Jalview Console window
(see Tools->Java Console) and send me the contents in another email ?

Thanks very much
Jim.

On 27/05/2010 17:13, Aoife McMahon wrote:

Quite suddenly as I was working on alignments today I became unable to load projects. When I try to load a project after I'm given this error message:
Error loading Jalview file
Error loading (file location)

I get this error with projects that were previously working fine, as well as new projects that I have created as tests. However, when I save the example files that open with the programme, under different names, they open just fine

I'm new to this and hoping there is a simple solution! I was going to increase the available memory, but I'm afraid I had difficulty with the instructions at http://www.jalview.org/jvmmemoryparams.html. Specifically I don't know how to 'make your own jnlp file and add the following parameter into the <resources> element.'

Thanks in advance,
Aoife

Attached is a jar file that was, but isn't now, opening

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--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

--
Aoife McMahon

PhD student
Kind Lab
School of Biomedical Science
Hugh Robson Building
George Sq
Edinburgh
EH8 9XD

0131 6503110

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.