Starting Jalview with annotation file via Web Start

Jalview Discussion
1

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&quot; 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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2

Hi Sindy. Sorry to hear you are having problems!

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&quot; 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.

···

On 14/04/2011 17:58, s.neumann@wzw.tum.de wrote:

3

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. :slight_smile: I can call jalview like below with
alignment, feature and annotation file.

Regards,
Sindy

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

···

Hi Sindy. Sorry to hear you are having problems!

On 14/04/2011 17:58, s.neumann@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&quot; 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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Jalview-discuss@jalview.org
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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@wzw.tum.de

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