[Biojava-l] SequenceDBInstallation

[Gerald Loeffler]

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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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 filename="SequenceDBInstallation.java"

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