Hi,
I have one protein alignment that I am editing manually since weeks and which jalview 2.5 does not seems to be able to open anymore... I used to have 2.4 on my windows machine which I updated recently.
The file was .jar file which I choose to be able to keep features to the MSA.
I have 2.4 on Linux which seems to be able to open it (so no file corruption).
What shall I do? I do not want to lose my annotations and hope the jar format from Jalview should be compatible. Any ideas? I can provide the .jar file.
Thanks in advance
Cheers,
Jean
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Jean Muller, MCU-PH
Laboratoire Diagnostic Génétique (NHC)
Laboratoire de Biologie et Génomique Intégratives (IGBMC)
Phone: +33 3 88 65 32 80, Fax: +33 3 88 65 32 76
email: jean.muller@igbmc.fr
http://www-bio3d-igbmc.u-strasbg.fr/~jmuller/
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Hello Jean.
This sounds very much like a bug. Could you send me the jar file ? If possible, could you also send me the contents of the Jalview console window - this should contain any exceptions raised when parsing the file on your machine.
Jim.
···
On 25/05/2010 08:26, Jean Muller wrote:
Hi,
I have one protein alignment that I am editing manually since weeks and
which jalview 2.5 does not seems to be able to open anymore... I used to
have 2.4 on my windows machine which I updated recently.
The file was .jar file which I choose to be able to keep features to the
MSA.
I have 2.4 on Linux which seems to be able to open it (so no file
corruption).
What shall I do? I do not want to lose my annotations and hope the jar
format from Jalview should be compatible. Any ideas? I can provide the
.jar file.
Thanks in advance
Cheers,
Jean
--
-------------------------------------------------------------------
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.
Hi Jean.
I've not worked out what the problem is with your file, but I do have a workaround.
The symptom I see is that whilst I can load the file into jalview 2.5 without any exceptions, but the alignment panel isn't updated when I move the horizontal scroll bar to the left or the right.
The workaround is to press 'Ctrl-T' - which will open up a new view - this one should work as normal. Once the new view is created you can close the other view (select it's tab, then press Ctrl-W).
I hope this helps! Hopefully I'll find the bug before I make the next release...
Jim.
···
On 25/05/2010 10:24, Jean Muller wrote:
Hi,
I have one protein alignment that I am editing manually since weeks and
which jalview 2.5 does not seems to be able to open anymore... I used to
have 2.4 on my windows machine which I updated recently.
The file was .jar file which I choose to be able to keep features to the
MSA.
I have 2.4 on Linux which seems to be able to open it (so no file
corruption).
What shall I do? I do not want to lose my annotations and hope the jar
format from Jalview should be compatible. Any ideas? I can provide the
.jar file.
Thanks in advance
Cheers,
Jean
--
-------------------------------------------------------------------
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.