[Biojava-dev] RE: [Biojava-l] BLAST Parser in Anger!

[Schreiber, Mark]

Hi -

The only changes I know of are adding accessors to the interface (or a
subinterface if you really want to avoid breakage).

As for time, not sure. I'm not very familiar with the internals of the
blast parsing API. I suppose as long as the SAXAdapter can produce
everything in the BlastLikeDataSetCollection.dtd, It would be great to
have methods to access all the info that the dtd supports.

- Mark

> -----Original Message-----
> From: Thomas Down [mailto:td2 at sanger.ac.uk] 
> Sent: Tuesday, 28 January 2003 11:07 p.m.
> To: Schreiber, Mark
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-l] BLAST Parser in Anger!
> 
> 
> On Tue, Jan 28, 2003 at 09:24:05AM +1300, Schreiber, Mark wrote:
> > Hi -
> > 
> > There are some deficiencies in the blast parsing API. I know that 
> > there is some reluctance to add new methods to the 
> interface as things 
> > will break, however blast parsing is a core task and it would be v 
> > good if we could make this more functional. One way to get 
> around the 
> > interface thing is to simlply extend it and then make all 
> the classes 
> > we have now implement the extended interface.
> > 
> > Another way is to simply break the interface before bj1.3 
> is released 
> > and make it stable from there on.
> > 
> > Can we please, please sort this out before bj1.3 is 
> released? Perhaps 
> > the development team could get together over a beer at the 
> hackathon 
> > and nut this one out. It really can't be that hard can it?
> 
> Am I right in thinking that this is just going to be adding 
> accessors to the interfaces?  That's actually a relatively 
> low-risk change, especially since I don't think there are any 
> implementations of those interfaces outside the biojava-live 
> tree (someone please correct me if I'm wrong here).  If it 
> meant removing methods or changing their contracts, that's 
> quite a different thing.
> 
> How long do you think this would take to do?
> 
>      Thomas.
> 
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