Really nice work Thomas!!
Regarding the rest method in the iterator. The original BSA spec says: method sets the iterator to the start of the set. I think the 'least suprise option' is the best interpretation. BTW The spec says also that CORBA::NO_IMPLEMENT is thrown if the iterator cannot be reseted e.g. the iterator provides access to streaming data Cheers, Juha Thomas Down wrote: > Hi... > > I've just checked in some code which provides both server > and client-side bridges between the BioJava sequence model > and BioCorba 0.3 (a.k.a. BSANE). At the moment, the best > way to get hold of it is from CVS: check out the `biojava-bsane' > module. > > The CORBA idl files were taken from the BioPython CVS > repository. Are these the right ones to be using, or have > they been superceded by something else? > > This is a new implementation which is significantly different > from the old (BioCorba 0.1) support code -- After looking at > the old code and the new interfaces, I decided it was probably > easier to start again. I've taken the opportunity to write > thee serverbridge in the new style (Servant/POA). This means > that it won't work with the builtin ORB in J2SE 1.2 or 1.3. > It does, however, work nicely in J2SE 1.4, and should also > work with most of the commercial ORBs. So far, I've been testing > with J2SE 1.4, and I'd be interested to hear about experiences > with other ORBs. The client-side code should work fine on > 1.3. > > It should build in the normal BioJava-ish way: > > - Copy over the dependancy .jar files. With J2SE1.4, all you > need it biojava.jar. With other ORBs, you'll probably also > need to copy a jar containing the org.omg.PortableServer package, > and edit build.xml > > - Type `ant' to build biojava-bsane.jar > > - `ant javadocs' builds the API documentation. > > - If you've got a recent version of JUnit installed, try > `ant runtests' to start the test suite. > > There are the following known limitations: > > - BSANE iterators returned by some of the methods don't > implement the reset() method. I wasn't clear about the > correct semantics for this. All methods which return > an iterator also return the first `block' of results as > an array. So the question is: does the reset method take > you back to the iterator's original state (`least surprise' > option), or right back to the start of the data set (seems > potentially more useful). I can't really see a sensible use > case for this method -- can someone who's actually going to > use it give an opinion on this? > > - NucleotideSequence isn't implemented. Everything just gets > returned as a BioSequence at the moment. > > - On the client side, custom alphabets aren't yet supported > (but I plan to add these soon). The serverbridge already > exposes BioJava alphabets correctly as BSANE objects (where > possible). > > Other than these, it seems to work quite nicely. There are > some (very) simple clients and servers in the demos/ directory. > You can do something like serving up an Ensembl database as > CORBA, then using one of the clients to dump features from a > region as GFF. > > I'd be interested in doing some interoperability testing at > some point. If anyone is curious, I can probably put some > test servers up to experiment (but I'll have to run them on > my home machine, so I don't want to put IORs out publically). > > Hope people find this useful, > > Thomas. > _______________________________________________ > Biocorba-l mailing list > [EMAIL PROTECTED] > http://www.biocorba.org/mailman/listinfo/biocorba-l > -- +--------------------------------------------------------------------+ |Juha Muilu, Ph.D., EMBL Outstation| Email: [EMAIL PROTECTED] | |European Bioinformatics Institute | Phone: +44 (0)1223 494 624 | |Wellcome Trust Genome Campus | Fax: +44 (0)1223 494 468 | |Hinxton, Cambridge CB10 1SD, UK | http://industry.ebi.ac.uk/~muilu| +--------------------------------------------------------------------+ _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
