[Biojava-l] SequenceDBInstallation

[Matthew Pocock]

Gerald,

Thanks for this code. Can I add it to org.biojava.bio.seq? I think that this is a short-tearm
solution to a difficult problem, with things like URNs and JNDI being the more scalable &
maintainable solution. But - KISS & all that - if SequenceDBInstallation works for you then I
sudgest that we use it. To develop a URN scheim or implement JNDI will take more than 2 weeks - so
it wouldn't make it into 1.0 anyhow.

Matthew

Gerald Loeffler wrote:

> Hi!
>
> We need factories for SequenceDB objects and we need managers for
> SequenceDB objects such that e.g. there is only exactly one SequenceDB
> object that accesses the SwissProt flat file /data/sprot/sprot.dat.
>
> I attach 2 files: SequenceDBInstallation is an interface that defines
> such a factory/manager for SequenceDB objects. It is very short and
> documented rigorously, so please have a look at it for a more detailed
> explanation why we need it. File StupidSequenceDBInstallation.java
> contains an implementation of this interface for testing purposes.
>
> Once interface SequenceDBInstallation is in place and implemented
> widely, we should be able to do things like this:
>
> SequenceDBInstallation inst = new SRSSequenceDBInstallation();
> // or inst = new CorbaSequenceDBInstallation("bsa_naming_context");
> // or inst = new FASTAFileSequenceDBInstallation("/data/sequences/");
> SequenceDB sprot     = inst.getSequenceDB("swissprot");
> Sequence   important = sprot.getSequence("FOO_DROME");
>
>         what do you think?,
>         cheers,
>         gerald
> --
>    Gerald.Loeffler@vienna.at _________________ Software Architect
>    http://www.imp.univie.ac.at ____ http://www.daemonstration.com
>    OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
>
>   ------------------------------------------------------------------------

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