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

[Jim Procter]

Hi Sindy. Sorry to hear you are having problems!

On 14/04/2011 17:58, s.neumann at wzw.tum.de wrote:
> 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"
>
>
> Any suggestions why it is not working with the given link?
I think there must be a typo with the annotation file's URL, since the 
HTTP error code 403 indicates that the annotation file's URL didn't 
return a document. You need to verify that you've provided an absolute 
URL for the annotations.txt file in the href attribute, and it is 
actually retrievable if you paste it in to a web browser.

let me know if this doesn't work and I'll take a closer look ...
Jim.

ps. You can check what arguments are actually being passed to jalview by 
downloading the JNLP file returned from the launchApp url and looking 
for the command line argument tags at the end of the XML document.