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.
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