Jalview-discuss Digest, Vol 55, Issue 6

Dear Jim

many thanks for your prompt help.

I get a nice tree with a local installation of Jalview:

Jalview.exe -open /home/cgille/m2/strapOut/jalview/align.msf -tree
/home/cgille/m2/strapTmp/clustalw_2.1/0/named_input.dnd

But there is no tree with Webstart:

http://www.jalview.org/services/launchApp?open=C%3A\home\cgille\m2\strapOut\jalview\align.msf&features=C%3A\home\cgille\m2\strapOut\jalview\features.gff&tree=file%3A%2FC%3A%2Fhome%2Fcgille%2Fm2%2FstrapTmp%2Fclustalw_2.1%2F0%2Fnamed_input.dnd

Nevertheless, the gff sequence features are shown. That works very well!

Is the web variable tree=url_of_dnd correct?
Or should this parameter be encoded differently?

Many thanks

christoph

Hi Christophe, and everyone using the http://www.jalview.org/services/launchApp servlet!

http://www.jalview.org/services/launchApp?open=C%3A\home\cgille\m2\strapOut\jalview\align.msf&features=C%3A\home\cgille\m2\strapOut\jalview\features.gff&tree=file%3A%2FC%3A%2Fhome%2Fcgille%2Fm2%2FstrapTmp%2Fclustalw_2.1%2F0%2Fnamed_input.dnd

Nevertheless, the gff sequence features are shown. That works very well!

Is the web variable tree=url_of_dnd correct?
Or should this parameter be encoded differently?

Try the URL again. It should work now.

For everyone not in this conversation - I just revamped the launchApp service so it will write tree arguments, and also supports setting the maximum memory allocated to Jalview when launched via webstart. There's also now some documentation in the comments of the JNLP file that should help you in debugging. Here's a sample:

<!--

If you have downloaded this file after pressing "Launch Full Application" from Jalview on a web page and you don't know what to do with this file, you must install Java from http://www.java.sun.com then try opening this file again.

     JNLP generated by /jalviewServlet/launchApp
     JNLP generated from http://www.jalview.org/webstart/jalview.jnlp
Available servlet parameters (please URLEncode):
     open=<alignment file URL>
     jvm-max-heap=heap size in M or G
     features maps to '-features'
     treeFile maps to '-tree'
     tree maps to '-tree'
     annotations maps to '-annotations'
     colour maps to '-colour'

-->

The servlet also correctly translates parameters to UTF-8 encoded text, which should fix some of the character translation problems experienced by those of you opening complex URLs in Jalview.

Jim.

···

On 15/08/2012 13:24, Dr. med. Christoph Gille wrote: