Hi Joni,
It is great to see that you are using the JABAWS framework to make a new
service! I'm sure Jim and Peter will be able to help you out with the
gap problem.
Once it is all working, would you be willing to add your implementation
to the main Jabaws distribution so that others can access Gblocks in
this way?
All the best,
Geoff.
On 15/11/2011 19:48, Joni Fazo wrote:
Hello,
I'm working to create a new jabaws web service for the tool gblocks
(http://molevol.cmima.csic.es/castresana/Gblocks.html). I am using
the MsaWS interface. I have the web service working - sort of :)
My problem is that gblocks expects aligned sequence as input. My
gblocks web service works fine when given input sequence that is all
the same length, with no gaps. But otherwise it fails, reporting that
the sequences are of different lengths. All gaps seem to be stripped
off the sequence prior to the web service being called.
I see that the Jalview class MsaWSClient has an attribute "submitGaps"
with a default value of false. Is there anyway to set this to true
when calling a specific web service?
This class also has a method canSubmitGaps with a TODO that makes me
think this capability is not yet available. (see below). Any tips on
a work-around?
private boolean canSubmitGaps()
{
// TODO: query service or extract service handle props to check if
we can
// realign
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
Thanks,
Joni
--
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net <http://www.phytozome.net/>
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--
Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, [email protected]
Tel:+44 1382 385860/388731 (Fax:385764)www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096
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