[Biojava-l] "packed" SymbolLists?

[Matthew Pocock]

Yes. There are two classes - PackedDNASymbolList was
the original try, and PackedSymbolList was mark 2.
PackedSymbolList lets you choose how to map symbols to
bit patterns, and to use the compact representation
(no ambiguities) or the complete one (with
ambiguities). If you don't care about the details of
the packing, use methods on PackingFactory to
configure the symbol list for you.

I've just added a quick example code-fragment to
PackedSymbolList - hope it helps.

Matthew

 --- "Schreiber, Mark"
<mark.schreiber@agresearch.co.nz> wrote: > Hi -
> 
> There is a PackedSymbolList and a
> PackedDNASymbolList in
> org.biojava.bio.symbol. Can't say I've used them but
> I think they
> operate pretty much the same as normal SymbolLists.
> 
> - Mark
> 
> 
> > -----Original Message-----
> > From: Dave Barkan
> [mailto:dbarkan@snowball.pcbi.upenn.edu] 
> > Sent: Thursday, 24 October 2002 11:24 a.m.
> > To: biojava-l@biojava.org
> > Subject: [Biojava-l] "packed" SymbolLists?
> > 
> > 
> > Hey all,
> > 
> > I saw in the tutorial on the Biojava home page
> that it is 
> > possible to implement a "packed" symbolList that
> only uses 
> > 2-4 bits per nucleotide. Is there a class
> available that 
> > implements this yet?  (If not, what is the
> reasoning behind 
> > this and would it be something I could easily set
> up and give 
> > back to the community?)
> > 
> > Thanks,
> > dave
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
>
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