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

[Matthew Pocock]

Hi Brian.

Great to hear that you're interested. The bottom line from my point of 
view is that any LSID object should natively fit into the java naming & 
directory system so that it's a resolvable name just like all the other 
name implementations. That way we are not tied to LSID unnecisarialy, 
but we are able to make sensible name objects for embl entries et al. 
Everything else is up to you guys.

Perhaps if there was a Nameable interface with getName() that returns a 
jndi name object, and we mixin this interface as needed? Oh, I don't 
know. Come up with something. Suprise us.

I look forward to seeing (or not noticing ;-) ) what you come up with.

Matthew

ps Will either of you be at BOSC or ISMB? There will be beer there :-)

Brian Gilman wrote:
> Hello Guys, 
> 
> 	I'd like to work with Michael to see where we differ in out LSID
> implementations and where we agree. Then we can both submit an
> implementation to biojava. 
> 
> 	I'd like to note that this is still a work in progress!! We are in
> the midst of gathering feedback on the spec and will produce another draft
> after our next I3C meeting which is next week. 
> 
> 	Michael, we should get together and discuss this over a
> beer...You're only down the road!
> 
> 					Best, 
> 
> 						-B
> 
> -----------------------
> Brian Gilman <gilmanb@genome.wi.mit.edu>
> Group Leader Medical & Population Genetics Dept.
> MIT/Whitehead Inst. Center for Genome Research
> One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> phone +1 617  252 1069 / fax +1 617 252 1902
> 
> 
> 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
>>>>
>>>>
>>>
>>>_______________________________________________
>>>Open-Bio-l mailing list
>>>Open-Bio-l@open-bio.org
>>>http://open-bio.org/mailman/listinfo/open-bio-l
>>>
>>
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> 
>