[Biojava-l] ABI file parser

[David Huen]

On Wed, 5 Sep 2001, David H Klatte wrote:

> Hello all,
> 
> A fellow named Tim Dilks came across my website and suggested 
> to me that some code I have there for opening ABI trace files might 
> be a useful addition to the biojava project.
> 
> I thought about that for a while and I looked at the code. I said, 
> "yuk." I re-wrote the code. It is far from perfect, but the (initial) 
> result is here:
> 
> http://people.ne.mediaone.net/dhk42/newabi/ABITrace.html
> 
> I do not know whether you all would consider this useful, nor do I 
> know whether the equivalent already exists in the project. 
> 
I've had an opportunity to take a quick look thru' the javadocs and the
source itself- I think it'll be a very useful addition to BioJava.  Thank
you for considering this possibility.

BioJava has some conventions that emphasise typing very strongly and 
the rationale can be looked at at:-
http://www.biojava.org/tutorials/chap1.html

The changes which I think needed to maintain a uniform look-and-feel
are:-
1) getSequence should return a SymbolList
2) getTrace should take a Symbol as its parameter.

I wondered about whether the returned int[] from getTrace ought to be a
typed object but perhaps that's a bit too retentive.

The licensing for BioJava is LGPL (as opposed to GPL) so inclusion will
require you to consent to permitting that.

I don't know whether you want to make the changes yourself? Otherwise I'd
be happy to adapt and send you back the source for your inspection and
approval.  WOuld you be happy with either of the possibilities?

Best wishes,
David Huen