[Jalview-discuss] user generated file does not get displayed correctly(?)

[Jim Procter]

Dear Andrea.

Thanks for reposting the email about your problems with the annotations 
format -
I've verified what you observed using the image attached to your 
original mail - and have some fixes for you.

On 22/03/2010 16:39, Andrea Rossi wrote:
>
> I am trying to use Jalview with an user generated feature/annotation 
> file.  However, I get the following errors:
>
> 1) For the BAR_GRAPH command, only the histogram bars get displayed 
> (not the labels below the histogram).
This is a problem with the annotationFile parser. If you try out the 
jalview development version (http://www.jalview.org/versions.html),  
you'll find that your annotation rows now get displayed with the labels.
> 2) For the SEQUENCE_GROUP/PROPERTIES commands, it seems that nothing 
> gets loaded into Jalview.
This was actually a problem with your annotation file. The 
SEQUENCE_GROUP lines should be:

SEQUENCE_GROUP	JGroup:0	4	4	*
SEQUENCE_GROUP	JGroupA	6	6	1-3


In both cases, you had a '-1' in the 5th column - which indicates to 
Jalview that it should expect the 6th column to contain a series of 
comma separated sequence ID strings (ie SEQ1,SEQ2,SEQ3).

> As an additional test, to make sure I am using thre proper format, I 
> have tried to export the features and reload them - when the 
> BAR_GRAPHs get reloaded the histogram labels do not get displayed 
> correctly.

Regarding the importing of exported annotation - there has been an 
inconsistency in the jalview annotations file parser and generator for a 
number of jalview releases and I am trying to resolve this for the next 
major jalview release. Your files were very helpful - since they 
exhibited a couple of subtle bugs in both the parser and the file 
emitter!  If you can, I suggest you try using the jalview development 
version until the next release.

Cheers
Jim.

-- 
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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
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