[Biojava-dev] registered alphabets

[Matthew Pocock]

 --- "Schreiber, Mark"
<mark.schreiber at agresearch.co.nz> wrote: > Hi -
>  
> I have added a registered(String alphaName) method
> to the AlphabetManager to allow you to test if an
> Alphabet had been registered with that name so you
> can avoid using a try catch block which can be ugly.

cool

>  
> I noticed while doing this that it is perfectly
> possible to register and Alphabet that already
> exists. Eg I can register my own Alphabet as DNA.
> There is really no problem with that except that I
> will get odd results. There could be a problem if
> anyone ever tries to use biojava for distributed
> programming or webservices as there is no way to
> guarentee that the Alphabet requested from a remote
> server by name is really the Alphabet you wanted.

that's bad

>  
> Am I being paranoid or do we need UIDs or LSIDs or
> some such thing to keep track of things?

We need UIDs. If you look in the obf-common cvs
module, there's a recently added URN spec. It
specifies some URNs for alphabets (among other
things). Basicaly, they look something like:

urn:open-bio.org:alphabet:dna

I guess we should fold them in as soon as the spec is
stable.

Matthew

>  
> - Mark
> 
>
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