Thank you Peter! Can you please send me the link to where I download the
version of JABAWS2 that I should use?
I want to make sure I'm working with the correct builds of both Jalview and
Jabaws. I'm having trouble today with the two tools not working together.
For example, the development version of Jalview includes the following code
from jalview.ws.jws2.JabaWsServerQuery:
.
.
.
compbio.data.msa.RegistryWS registry = null;
Set svccategories = null;
boolean noservices = true;
// look for services
boolean jabasws2 = false;
// If we are dealing with a JABAWS2 service, then just go and ask
the
// JABAWS 2 service registry
Set<Services> srv_set = new HashSet<Services>();
Set<Category> categories = Category.getCategories();
String svc_cat;
try
{
// JBPNote: why is RegistryWS in compbio.data.msa ?
registry = Jws2Client.connectToRegistry(jwsservers);
if (registry != null)
{
// System.err.println("Test Services Output\n"
// + registry.testAllServices());
// TODO: enumerate services and test those that haven't been
tested
// in the last n-days/hours/etc.
jabasws2 = true;
srv_set = registry.getSupportedServices();
svccategories = registry.getServiceCategories();
.
.
.
The version of compbio.data.msa.RegistryWS in my jaba2 source does not have
the method getServiceCategories. I'm not sure if my Jalview is out of
date, or my Jabaws2...
Any help would be much appreciated. I really need to get myself working
with the right versions of your codes. I am supposed to have something
"working" by the end of the month.
Thanks,
Joni
On Fri, Nov 18, 2011 at 10:52 AM, Peter Troshin <[email protected]>wrote:
> 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]> 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). 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
>>>>
>>>> _______________________________________________
>>>> 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
>>
>>
>
>
> --
> Plant and Computational Genomics Group
> Joint Genome Institute - U.S. Dept. of Energy
> http://www.phytozome.net
>
>
>
--
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
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