[Jalview-discuss] jabaws question about tree web service

Peter Troshin p.v.troshin at dundee.ac.uk
Fri Sep 9 11:57:25 BST 2011

Dear Joni,

Currently there is no interface in JABAWS for tree like data but you 
should be able to add a new interface for the data like this.

I'd recommend you to extend the following interfaces - JABAService, 
JManagement, Metadata<T>.
There are implementations for all the methods for these interfaces and 
you should be able to use them without any modifications. Also, they are 
pretty well documented so just read the Javadoc, but if something is not 
clear feel free to ask.

If you do that then you only need to add new methods to deal with your 
specific data types.

MsaWS interface should give you a good example. To be simplify the 
integration with Jalview and keep the service consistent with the other 
JABAWS services it is best to implements these methods

String buildTree(
@WebParam(name = "fastaSequences") List<FastaSequence> sequences)
throws UnsupportedRuntimeException, LimitExceededException,

I assume here that the input for the tree-puzzle is the list of the 
sequences, please modify it accordingly if that is not the case.

@WebParam(name = "fastaSequences") List<FastaSequence> sequences,
@WebParam(name = "preset") Preset<T> preset)
throws UnsupportedRuntimeException, LimitExceededException,
JobSubmissionException, WrongParameterException;

@WebParam(name = "fastaSequences") List<FastaSequence> sequences,
@WebParam(name = "options") List<Option<T>> options)
throws UnsupportedRuntimeException, LimitExceededException,
JobSubmissionException, WrongParameterException;

Tree getResult(@WebParam(name = "jobId") String jobId)
throws ResultNotAvailableException;

Once you’ve done with the coding you then, need to update wsbuild.xml 
“build server” Ant task to include a new web service and execute it to 
generate webservices artefacts.

For further steps please refer to the "how to add a new web service" guide.

All the above is true for the current JABAWS version which you can 
download from here:

Last but not least - we are very much interested in having a Tree-Puzzle 
service in JABAWS. I wonder if you would consider sharing your work with 
us. In that case I may be able to help you with the implementation.

Have fun!

On 08/09/2011 23:43, Joni Fazo wrote:
> Hello,
> I would like to provide a web service in jabaws that wraps
> tree-puzzle.  It looks like all of the current web services implement
> the interface MsaWS.  Is there a similar interface (eg TreeWS) that is
> appropriate for tree construction?  Any tips?
> Thanks,
> Joni Fazo
> Plant and Computational Genomics Group
> Joint Genome Institute - U.S. Dept. of Energy
> http://www.phytozome.net
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss at jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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