[Biojava-l] Packed DNA Symbol List

[Matthew Pocock]

Cool David! Have you got any stats about the relative performance of 
the raw and packed implementations? The issue with AlphabetIndex and 
ambiguities is my fault. I wrote the imlementations not to index 
ambiguities. What do you use an indexer for? I'm happy for you to commit 
away. Thomas? Others?

David Huen wrote:
> I've written a packed version of a DNA symbol list (4 bits per symbol, 8 
> times cheaper than the current). Surprisingly, the performance seems OK -
> I expected it to be abysmal.  Its constructor can take and return data in
> a byte array so data can be serialised from/to a database.
> 
> The drawback is that it uses its own AlphabetIndex because I could not 
> make the ones in the package take ambiguity tokens for whatever reason.
> Most likely I am missing some thing here.  My main concern is that if I
> were to use this class in a persistent implementation and the Alphabet
> Index for this class needed to be  changed later, it would scramble
> these objects so the necessity to get it right now.
> 
> Any suggestions as to solutions before I consider committing it to
> development trunk?
> 
> Regards,
> David Huen
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
>