[Biojava-l] Re: [Bioperl-l] RE: [Open-bio-l] seq namespace method

[Michael L. Heuer]

Said omnigene code is at

> http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/omnigene/omnigene/edu/mit/wi/omnigene/webservice/LSID.java
> http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/omnigene/omnigene/edu/mit/wi/omnigene/webservice/MalformedLSIDException.java

   michael


On Mon, 22 Jul 2002, Michael L. Heuer wrote:

>
> Hello Matthew,
>
> It's probably best to wait a bit before importing this into biojava
> proper.  Things are still a little bit up in the air here on the list(s),
> and I believe there is a LSID implementation in the omnigene codebase
> that we should take a look at before committing to any one design.
>
> I like the idea of removing the accessors from the Identifiable interface,
> but would advocate leaving them in the abstract and support implementations.
>
>    michael
>
>
> On Fri, 19 Jul 2002, Matthew Pocock wrote:
>
> > Great Michael,
> >
> > LifeScienceIdentifier looks good. I'd prefer Identifiable to drop all
> > methods except getPreferredIdentifier() and getIdentifiers(). I think
> > the other methods duplicate already available information (e.g.
> > getAuthority etc can be found by calling
> > getPreferredIdentifier().getAuthority() ). Putting functionality/api in
> > exactly one place is generaly a good idea. What are your thoughts?
> >
> > What package would you like to put these classes/interfaces into? An
> > existing package, or org.biojava.bio.lsid or org.biojava.bio.program.lsid?
> >
> > Matthew
> >
> > Michael L. Heuer wrote:
> > > Having spent too much time in meetings lately, I felt the need to
> > > actually code something, and whipped up a java implementation of LSIDs
> > > based on the discussion here.  Being that this has been a moving target, I
> > > may not have nailed it exactly right -- I went with containment and the
> > > idea of a "preferred identifier", eg.
> > >
> > > interface LifeScienceIdentifier extends Immutable {
> > >   public String getAuthority();
> > >   public String getNamespace();
> > >   public Object getObjectId();
> > >   public Object getVersion();
> > >
> > >   public String asIdentifier();  // authority:namespace:object_id
> > >   public String asCommonName();  //  namespace:object_id.version
> > > }
> > >
> > > interface Identifiable {
> > >   // delegate to preferred
> > >   public String getAuthority();
> > >   public String getNamespace();
> > >   public Object getObjectId();
> > >   public Object getVersion();
> > >
> > >   public LifeScienceIdentifier getPreferredIdentifier();
> > >   public boolean hasMultipleIdentifiers();
> > >   public List getIdentifiers();
> > > }
> > >
> > > A tarball with implementations, factories, junit tests, etc. is available
> > >
> > >
> > >>http://shore.net/~heuermh/lsid-PROPOSAL.tar.gz
> > >
> > >
> > >    michael
> > >
> > >
> >
> > _______________________________________________
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> > Open-Bio-l@open-bio.org
> > http://open-bio.org/mailman/listinfo/open-bio-l
> >
>
>