[Biojava-dev] (no subject)

[Matthew Pocock]

Hi Keith,

I'm happy with this. I agree with Thomas that it's a
bit nasty to slip back into the land of the String,
but this seems like the most parsemoneous solution.

All in favor of using JNDI for this kind of mess in V2
say "eye"

All in favor of going to Keith's stringy ID interfaces
on the trunk say "eye"

Matthew

 --- Keith James <kdj@sanger.ac.uk> wrote: > >>>>>
"Matthew" == Matthew Pocock
> <matthew_pocock@yahoo.co.uk> writes:
> 
> [...]
> 
>     Matthew> Imho it's such a royal pain that it
> should be changed pre
>     Matthew> 1.3 release. Now, what should we change
> it to?
> 
> Well, SequenceDBInstallation uses database IDs to
> identify databases,
> so I'd go with the suggestion posted earlier in the
> thread i.e. use
> the ID instead.
> 
> Then SeqSimilaritySearchResult would go from
> 
> public interface SeqSimilaritySearchResult
> {
>     SymbolList getQuerySequence();
>     SequenceDB getSequenceDB();
>     Map getSearchParameters();
>     List getHits();
> }
> 
> to
> 
> public interface SeqSimilaritySearchResult
> {
>     SymbolList getQuerySequence();
>     String getDatabaseID();
>     Map getSearchParameters();
>     List getHits();
> }
> 
> There's a similar situation with the
> getQuerySequence() method. This
> forces the user to make a SequenceDB of query
> Sequences available to
> the builder when creating
> SeqSimilaritySearchResults. I think this
> could go the same way, giving a final interface
> 
> public interface SeqSimilaritySearchResult
> {
>     String getQuerySequenceID();
>     String getDatabaseID();
>     Map getSearchParameters();
>     List getHits();
> }
> 
> This doesn't define what the query sequence ID means
> as we don't know
> which database (if any) it came from. However, I
> think it's better
> than what we have now in that the programmer has the
> choice of whether
> to resolve the ID(s).
> 
> My 0.020601 Euro
> 
> Keith
> 
> -- 
> 
> - Keith James <kdj@sanger.ac.uk> bioinformatics
> programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust
> Sanger Institute, UK -
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev 

__________________________________________________
Do You Yahoo!?
Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
http://uk.my.yahoo.com