[Biojava-l] Packed DNA Symbol List

Schreiber, Mark mark.schreiber@agresearch.co.nz
Tue, 12 Feb 2002 09:09:23 +1300

Hi -

I am looking into Serialization issues at the moment and for many
distributions the AlphabetIndex must be marked as transient since it
cannot be guarenteed to be rebuilt in an identicle fashion on all JVMs.
I'm not sure how it would affect your class but it may be an idea to
include writeObject() and readObject() methods to prevent nasty


-----Original Message-----
From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
Sent: Tuesday, 12 February 2002 1:32 a.m.
To: David Huen
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] Packed DNA Symbol List

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
> 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
> Most likely I am missing some thing here.  My main concern is that if
> 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
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