jabaws question about tree web service

Jalview Discussion
1

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

2

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,
JobSubmissionException;

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.

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

customBuildTree(
@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:
http://www.compbio.dundee.ac.uk/jabaws/jaba-project.zip

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!
Regards,
Peter

···

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
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3

Hello Joni.

···

On 09/09/2011 11:57, Peter Troshin wrote:

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.

I'd also like to second what Peter said. It is high time that Jalview included services for phylogeny, and I would be very happy to help out if you are willing to contribute your work to Jalview's codebase.

Hope to hear from you soon...
Jim.