[Biojava-dev] Annotation conversions

[Matthew Pocock]

Hi Len,

Have a root around in web cvs. Look in the obf-common project, 
obda-specs/naming - this is a spec for URNs for entities (things or 
ideas) that all the obf projects share. This would be an ideal place to 
put stable cross-project identifiers for things like comments. The exact 
form of the registry for the URNs is not nailed down right now, so if 
you get keen then take a look at that as well. Relationships between 
URNs (such as sub-typing, composition etc.) is explicitly defined as 
being off topic.

Matthew

Len Trigg wrote:

>Matthew Pocock wrote:
>  
>
>>Enum away. Use the type-safe enum design pattern?
>>    
>>
>
>Yep. I started having a crack at it, and the stuff in the seq/io
>package seemed pretty straightforward. I introduced a translation
>table to the *Processors and simplified the *FileFormats to only look
>for the canonical keys.
>
>My current point of difficulty is with biosql. First, what to do with
>sequences that have been previously stored. Basically it needs a
>translation table that handles either embl or genbank formats and
>converts to the canonical key.
>
>The second problem is what to do when storing sequences. I was
>initially just going to use the name associated with the canonical key
>(and map from this string to the required object when
>reading). However, that's bad juju for compatibility with BioPerl etc,
>who won't know how to interpret them correctly. Maybe have an idea of
>the preferred format for the sequence and use that? It's getting back
>to the reason for introducing the canonical keys in the first
>place. Ewww. Suggestions?
>
>
>Cheers,
>Len.
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>  
>