Hi Jim, It turns out that the T-Coffee score file format has an extended syntax including the residue numbers at the begin and the end of each line.
This was not supported by my original parser. I've just submitted a patch to handle it correctly. I'm going to reply to the remaining part of your message in a separate email. Cheers, Paolo On Nov 15, 2012, at 4:49 PM, Jim Procter <[email protected]> wrote: > Hi Paolo. > > On 14/11/2012 20:21, Paolo Di Tommaso wrote: >> It's a think we could discuss. What would be the trickiest part to make >> Jalview able to run M-Coffee? Should it based on a web-service interaction? > Ideally, Jalview should be able to run M-Coffee from the Web > Service->Alignment submenu. This is nearly possible now, except that the > alignment webservices don't include support to send back any annotation, only > the alignment data. That means that a new type of service needs to be created > that returns annotation on the alignment. > One way might be to add a 'supplementary information' service to Jabaws that > Jalview could call to discover any additional information provided by a > service in addition to the standard data returned.. so for an M-COFFEE > alignment, jalview gets the alignment as normal, but then queries the jabaws > server for the score file. Such a service might also allow Jalview to recover > the guide trees and any other data generated that aren't currently returned > to the user. > > Apart from supporting this additional nuance, getting M-Coffee into JABAWS is > also a little tricky. The way that M-COFFEE downloads all the additional > tools is really amazing, but might alarm some sysadmins - who probably don't > expect a web service to start downloading and compiling code after they've > installed it. Ideally, the installation of the T-COFFEE suite shipped with > JABAWS should be preconfigured to run M-COFFEE using the four other alignment > methods available, and come with instructions for telling M-COFFEE about any > other alignment tools available on the system. Is there a standard way of > doing that when compiling the suite ? >> One more thing, I was trying to integrate the latest release in our web >> server to show the T-Coffee alignment score, but I'm unable to get it work. >> >> It shows the alignment as usual, but not the coloured scores. This is the >> applet code I'm using: >> >> <applet id="applet" code="jalview.bin.JalviewLite" width="800" height="600" >> archive="public/jalviewApplet.jar"> >> <param name="file" >> value="http://localhost:9000/data/7ce04b2b/result.fasta_aln";> >> <param name="scoreFile" >> value="http://localhost:9000/data/7ce04b2b/result.score_ascii"; > >> <param name="embedded" value="true"> >> <param name="showFeatureSettings" value="false"> >> <param name="widthScale" value="1.4"> >> <param name="heightScale" value="1.4"> >> <param name="nojmol" value="true" > > hmm. not sure - is there anything shown on the java console ? The code is > definitely in there still :) > > Add <param name="debug" value="true"> to the applet tag to make the applet > more verbose. There should be some kind of message explaining why it didn't > add the score file. > > Jim. > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
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