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

[s.neumann at wzw.tum.de]

Dear Jim,




thank you so much for the immediate answer. I have to apologize.
The error was indeed caused by my annotation file. The rights were
not set correctly. I must admit that this is a very stupid mistake.

But now it is working fine. :-) I can call jalview like below with
alignment, feature and annotation file.


Regards,
Sindy



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

> 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.
>
>
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>



-- 
Sindy Neumann (Dipl.-Bioinf. Univ.)
Department of Genome Oriented Bioinformatics
Group of Prof. Frishman
Wissenschaftszentrum Weihenstephan, TU Muenchen
Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
Tel: +49-8161-712154
E-mail: s.neumann at wzw.tum.de

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