Hi Joni,
Sorry about that perhaps Jim meant this URL
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/
Peter
On 18/11/2011 18:03, Joni Fazo wrote:
Hi Jim,
I get a "404 Not Found" when I try to go to the link in your previous
email:
http://www.compbio.dundee.ac.uk/users/ws-dev1/jalview/develop/
Is that the link you are referring to?
Thanks,
Joni
On Fri, Nov 18, 2011 at 12:24 AM, <[email protected]
<mailto:[email protected]>> wrote:
Hi joni.
The development branch build of Jalview that you are looking for
is in my last email. The link on the website points to a different
build at the moment.
Please be aware that the Jalview client for jaba2 is still in
development! User interface integration is by no means complete.
Jim.
J. B. Procter Jalview/enfin Barton group
-----Original Message-----
From: Joni Fazo <[email protected] <mailto:[email protected]>>
To: Peter Troshin <[email protected]
<mailto:[email protected]>>
Cc: JABAWS discussion list <[email protected]
<mailto:[email protected]>>,
[email protected] <mailto:[email protected]>
Sent: Fri, 18 Nov 2011 0:30
Subject: Re: [Jalview-dev] jabaws question - creating new web service
Hi Peter,
I just downloaded the development version of JABAWS today. I had
been working with JABAWS1.
I was able to get my JABAWS2 server working, but can't seem to
access all the web services via Jalview. I've tried with both
Jalview 2.7 and my downloaded latest dev version of Jalview.
Do I need to include a new client jar for JABAWS2 when I build
Jalview? I tried building Jalview after replacing
lib/min_jaba_client.jar with lib/min_jaba_client2.jar build get
the following error from ant:
[javac] C:\Documents and Settings\jfazo\My
Documents\compgen_workspace\JalviewDev\src\jalview\ws\jws2\JabaWsServerQuery.java:85:
incompatible types
[javac] found : compbio.data.msa.JABAService
[javac] required: compbio.data.msa.MsaWS
[javac] service = Jws2Client.connect(jwsservers, srv);
[javac]
Also - I when I run the development version of Jalview from your
website
(http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jnlp
<http://www.compbio.dundee.ac.uk/%7Ews-dev1/jalview/latest/webstart/jalview.jnlp>),
I don't see the new web services. This Jalview seems to be
connecting to http://www.compbio.dundee.ac.uk/jabaws/ which is
JABAWS1. Is there a version of Jalview available that works with
JABAWS2? It would be nice for me to see what the new services do
and how the UI works.
Thanks in advance for you help!
Joni
I am able to get Jalview to connect to my JABAWS2 server, but only
On Wed, Nov 16, 2011 at 9:50 AM, Peter Troshin
<[email protected] <mailto:[email protected]>> wrote:
Hi Joni,
I am pleased to know that you have succeeded in creating a web
service in JABAWS framework!
I think that what Jim said makes a lot of sense. I just like
to point out that refactoring from MsaWS to SequenceAnnotation
interface should not be too painful, as both web service
interfaces share the same methods with the only exception of
"result returning" methods which returns ScoreManager object
instead of Alignment.
Have a look at the other services that implements
SequenceAnnotation interface to have a better idea what might
be involved.
We assume that you work with the development version of
JABAWS, as JABAWS 1 does not have SequenceAnnotation interface.
Let us know how it goes.
Regards,
Peter
On 16/11/2011 15:50, Jim Procter wrote:
Hi Joni.
I'm seconding Geoff's email - it's really good to hear you're
progressing with adding services to JABAWS ! I've been
working on
adding JABAWS2 services to Jalview for the v2.8 release -
and I think we
might be able to help each other out here...
On 15/11/2011 19:48, Joni Fazo wrote:
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!
}
There's no straightforward workaround for version 2.7 of
Jalview, I'm
afraid. If you take a close look at the execution steps
leading to a job
being submitted by Jalview, you'll see that the
'canSubmitGaps' method
is not actually used to decide if gaps are removed, but
instead used to
decide if a 'Realign with ..' menu entry is generated in
addition to the
standard 'align with ..' menu entries for alignment web
services.
However, hopefully, you've developed your service with the
JABAWS 2
development code that Peter Troshin sent you, in which
case there's a
definite way forward...
The real problem here is that GBlocks isn't a multiple
alignment
service, and trying to use code that expects to be talking
to one kind
of program but instead does something else is simply not
going to work.
The GBlocks service is a specific variant of an alignment
analysis
service where you submit an alignment and get back
annotation of some
kind; which, in this case, is annotation indicating which
columns should
be hidden in the view. Implementing a service for GBlocks
following this
pattern will ensure that it is robust and ultimately more
usable, since
it does what it says on the tin.
Fortuitously, JABAWS 2 already includes a canonical
alignment annotation
service model that would suit GBlocks, and I have already
coded a client
in the Jalview development branch[1] that could be easily
adapted to
mark the regions on the alignment annotated by the service
as hidden
regions.
All that would be needed is for you to refactor your new
service code to
implement the compbio.data.msa.SequenceAnnotation
interface, and then
add some semantic sugar in order to inform Jalview that
the annotation
should be used to mark the given regions as hidden. The
semantic sugar
comes in two forms:
1. Label the service with an appropriate service category
in the JABAWS2
discovery service. GBlocks performs a specific form of
conservation
analysis to identify conserved regions in the alignment,
so it could be
put in the 'Conservation' category - but this contains
methods that
produce alignment quality and conservation histograms.
Instead, I'd
suggest creating another category, such as 'Conserved
Region Detection'.
This will mean it gets placed in its own submenu on the
web services menu.
2. Label the results in a way that makes it clear what
Jalview should do
with them. The result from an annotation service is a
series of named
sets associated with each sequence or the alignment as a
whole, and each
set consists of either a series of scores for each column
of the
reference (sequence or alignment) and a series of
intervals which may
optionally have scores associated with them. In the case
of a single
Gblocks run, you'd return the conserved regions as
intervals in a single
score set associated with the whole alignment. I'd
recommend calling
that score set something obvious like 'CONSERVED_REGION'
.. that way
it's quite clear what the interval refers to, and isn't
specific to
GBlocks - in case other conserved region detection
programs get added to
JABAWS.
The point of the sugar is to allow Jalview to do something
sensible with
the results. Typically, phylogenetically informative
columns get marked
with a '*' - so Jalview could add an annotation row where
a '*' is
present within each column of the conserved region. It
could also
automatically hide the columns outside the regions in the
alignment view
that GBlocks identified.
I'm happy to code the client that would do this, if you'd
be happy to
refactor the Gblocks service !
Jim.
[1] The jalview development branch build is at
http://www.compbio.dundee.ac.uk/users/ws-dev1/jalview/develop/,
and you
can see the branch history at
http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/develop
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Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net <http://www.phytozome.net/>
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--
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Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net <http://www.phytozome.net/>
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