[Biojava-dev] Preliminary QBlast support in biojava-live

[Sylvain Foisy]

Hi all,

I just put some material into a new package (org.biojavax.bio.alignment) for
creating a remote service for alignment with its implementation for QBlast.

The philosophy for using these is this:

- Create an implementation of RemotePairwiseAlignmentService for a specific
remote service;

- Create an implementation of RemotePairwiseAlignementProperties to set
parameters for alignment;

- Use the sendAlignmentRequest() method with a sequence with the implemented
RemotePairwiseAlignementProperties to submit the sequence for alignmnent.

- Retrieve the results with an implementation of
RemotePairwiseAlignmentOutputProperties which specifies the format of the
output to get from the service.

This is done so that submission of sequence and retrieval of results can be
dissociated.

I think that I have addressed most of the points of a few weeks back. If
not, let me know ;-) I created a demo in the demos folder.

Best regards

Sylvain
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 Sylvain Foisy, Ph. D.
 Consultant Bio-informatique / Bioinformatics
 Diploide.net - TI pour la vie / IT for Life

 Courriel: sylvain.foisy at diploide.net
 Web: http://www.diploide.net
 Tel: (514) 893-4363
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