[Jalview-discuss] opening jalviewLite with a pre defined alignment

Jim Procter jprocter at compbio.dundee.ac.uk
Thu Jan 19 16:11:35 GMT 2012

Hi there.

On 19/01/2012 14:33, T.G.P.Bolderink at lumc.nl wrote:
> i found the above code to start jalview with an alignment pre-loaded 
> in the discuss section
> <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>"
> i know this code is aged
:)  it's aged but still works (surprisingly ;) ). Although, that 
fragment seems to have &amp; entities instead of ampersands inside the 
'href' attribute string - which isn't going to work, because 
is going to be passed to the 'colour' parameter, rather than specifying 
the colour, open (alignment filename), features and annotations 
parameters to be passed to jalview.

> i am working on a website and i would like to have jalview open an 
> alignment (without having the user manualy input the file)
> is this possible with the above code?(eventually jalview will have to 
> run localy but i see no problems there)
> i have tried putting simpe fasta files in diffrent folders on the web 
> server but so far jalview has not been able to locate them
> (the link will open jalview but without the alignment).
The problem is usually that somehow Jalview is not getting proper paths 
in the JNLP file that is created to launch it. To see what it was given 
take a look at the JNLP generated by the launchApp servlet when given 
the parameters. To give you something to start with, try compare the 
URLs you see in the JNLP for your own links with the one created when 
you click on the link in this email:

In particular, pay attention to the escaping of any special symbols like 
'?' and '&' in the parameters that need to be passed to launchApp .. if 
you have some kind of web application generating alignments, you'll need 
to replace those symbols with %3F and %26  pass a fully escpaed URL


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