[Jalview-discuss] Starting Jalview with annotation file via Web Start

[s.neumann at wzw.tum.de]

Hi,



i want to run Jalview using Java Web Start with annotation and feature files.


Therefore, i used the following call to open Jalview from my website:

================================================================================================================
To view the alignment file using Jalview, please <a  
href="http://www.jalview.org/services/launchApp?colour=Taylor&amp;open=...alignment.aln&amp;features=...features.gff&amp;annotations=...annotations.txt" target="_blank">Click  
here</a>"

================================================================================================================

When i follow the link Jalview opens and loads the features. But it  
can't open the annotation file. I
get the following error message:

"Couldn't load file ...annotations.txt
Failed to read data from source:
CANNOT ACCESS DATA AT URL '...annotations.txt' (Server returned HTTP  
response code: 403 for URL: ...annotations.txt)
Formats currently supported are
BLC,CLUSTAL,FASTA,MSF,PileUp,PIR,PFAM,STH,PDB, and JnetFile"


The annotation file looks like this (Jalview format):

================================================================================================================
JALVIEW_ANNOTATION
# Created: Thu Apr 14 14:48:42 CEST 2011

NO_GRAPH        cores        
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|H,core1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2|H,core2||||||||||||||||||||||||||||||||||||||H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|H,core3|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 ||||||||
|||||||||||||||||||||||||||||||||

================================================================================================================


If i open Jalview without the annotation file and add it later via  
'File -> Load Features/Annotations' it is
working fine. So there seems to be no problem with the format.


Any suggestions why it is not working with the given link?



Regards,
Sindy Neumann


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