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]> 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]> > To: Peter Troshin <[email protected]> > Cc: JABAWS discussion list <[email protected]>, > [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), > 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]>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<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/<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<http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/develop> >>> >>> ______________________________**_________________ >>> Jalview-dev mailing list >>> [email protected] >>> http://www.compbio.dundee.ac.**uk/mailman/listinfo/jalview-**dev<http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev> >>> >> >> > > > -- > Plant and Computational Genomics Group > Joint Genome Institute - U.S. Dept. of Energy > http://www.phytozome.net > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev > > -- Plant and Computational Genomics Group Joint Genome Institute - U.S. Dept. of Energy http://www.phytozome.net
_______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
