I'd need to brush up on my nio, and my c !
Thomas Down <[EMAIL PROTECTED]>
01/24/2005 04:34 PM
To: "Richard HOLLAND" <[EMAIL PROTECTED]>
cc: "<[EMAIL PROTECTED]>", biojava-list List
<biojava-l@biojava.org>, Mark
Schreiber/GP/[EMAIL PROTECTED]
Subject: Re: [Biojava-l] reading nib sequence files
On 24 Jan 2005, at 02:48, Richard HOLLAND wrote:
> It's a compressed binary format. I doubt BioJava would be able to read
> it without a lot of effort as the current parser framework is set up
> for
> text input only.
Nib support probably wouldn't fit into the text-oriented parsing
framework, but I'm sure it could be supported somehow if there was
demand. A quick google doesn't turn up any format documentation, but
Jim Kent's IO code is at:
http://www.soe.ucsc.edu/~kent/src/unzipped/lib/nib.c
One interesting way to handle this might be to open the nib file as a
MappedByteBuffer, and back a SymbolList directly using that --
potentially giving us an efficient way of working with huge sequences..
Any interest in that?
Thomas.
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