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
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