[Biojava-l] reading nib sequence files

[Richard HOLLAND]

I would have thought anything that makes life easier when you need it
but doesn't make life harder when you don't would be a good thing, as
long as it doesn't take too much programming effort. Seeing as you are
intending to rewrite BioJava from scratch anyway, I think this would be
a good thing to work into the mechanism.

Richard Holland
Bioinformatics Specialist
GIS extension 8199   
 
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Thomas Down
> Sent: Monday, January 24, 2005 5:22 PM
> To: mark.schreiber at group.novartis.com
> Cc: biojava-list List
> Subject: Re: [Biojava-l] reading nib sequence files
> 
> 
> 
> On 24 Jan 2005, at 09:17, mark.schreiber at group.novartis.com wrote:
> 
> > BioJava uses (or at least can use) the PackedSymbolList for large
> > sequences. It uses an array of longs to represent the packed bits.
> >
> > There may be some advantage to using a ByteBuffer, hard to know.
> 
> The main reason I was thinking for using MappedByteBuffer is that if 
> you're accessing a large amount of sequence it won't necessarily all 
> get loaded into memory at once.  This could, for example, make random 
> access to a multi-gigabase sequence database bearable on a basic 
> desktop computer.  Just a thought, not sure how much demand there is 
> for this.
> 
>             Thomas.
> 
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