[Biojava-dev] List vs LinkedHashMap

[Andy Yates]

Can't see any reason why not after all to get a collection back it's  
just a case of calling values() on the Map. The only other things I  
would say is I would prefer returning a Map rather than a  
LinkedHashMap but if there's a good reason why you want to return the  
solid class then that's fine :). I've done some work as well to  
cleanup the generics situation in these which I hope are okay. If you  
commit your changes in then I'll commit mine in & you can see what you  
think.

Andy

On 19 Feb 2010, at 19:30, Scooter Willis wrote:

>
> I am starting to use the new FastaReader in a project and the  
> default implementation I setup returns a List<ProteinSequence>. The  
> very next thing I needed to do was convert to a  
> LinkedHashMap<String,ProteinSequence> so I could query the sequence  
> of interest. It would seem that this is probably a fairly standard  
> use case. If I returned a LinkedHashMap<String,ProteinSequence> as  
> the default container then we have a slight memory hit on keeping a  
> hash of the accession ID and a linked list for preserving order.
>
> Does anyone have objections to returning the sequences read from a  
> Fasta file as a LinkedHashMap?
>
> Thanks
>
> Scooter
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/