[Biojava-l] changed (improved) SequenceDB and stuff

[Gerald Loeffler]

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hi matthew!

I made the following slight changes to SequenceDB and related classes
and hope that you find them acceptable and hence check them into your
CVS repository:

o org.biojava.bio.seq.SequenceDB:
	o added getName() method which returns the (possibly null) name of a
sequence db

o org.biojava.bio.seq.HashSequenceDB:
	o HashSequenceDB() and HashSequenceDB(IDMaker idMaker) create a
SequenceDB with name null.
	o added public constructor HashSequenceDB(IDMaker idMaker, String name)
	o added protected constructor HashSequenceDB(String name)
	o implemented getName() method

o org.biojava.bio.seq.AbstractAnnotator:
	o changed (the now ambiguous) instantiation of a HashSequenceDB from
HashSequenceDB(null) to HashSequenceDB(null, null).

o org.acedb.seq.AceSequenceDB:
	o implemented getName() to return the name of the node
(AceSet.getName()).

o org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter:
	o implemented getName() to return the name of the primary corba
sequence db (PrimarySeqDB.database_name()).

The changed files are attached to this mail.

Though minor in nature, the addition of the getName() method to
interface SequenceDB will result in all implementations (outside the
BioJava distribution) of this interface to break in the sense that they
will all have to add an implementation of the getName() method...

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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