opening jalviewLite with a pre defined alignment

dear jalview crew,

i found the above code to start jalview with an alignment pre-loaded in the discuss section

Click here"

i know this code is aged but i have a few questions:

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).

are there any other ways to get jalview to open from a webpage with the alignment already defined?

Hi there.

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&open=...alignment.aln&features=...features.gff&annotations=...annotations.txt" target="_blank">Click here</a>"

i know this code is aged

:slight_smile: it's aged but still works (surprisingly :wink: ). Although, that fragment seems to have &amp; entities instead of ampersands inside the 'href' attribute string - which isn't going to work, because 'Taylor&amp;open=...alignment.aln&amp;features=...features.gff&amp;annotations=...annotations.txt' 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:
http://www.jalview.org/pipermail/jalview-discuss/2008-May/000062.html

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

Jim.

ยทยทยท

On 19/01/2012 14:33, T.G.P.Bolderink@lumc.nl wrote: