[Biojava-l] org.biojava.bio.search interfaces

[Thomas Down]

On Mon, Jan 08, 2001 at 01:45:35PM +0000, Keith James wrote:
> 
> I've made some progress on Fasta search output parsing to the extent
> that I'm happy with the initial design and implementation and I'm
> about to write a demo application to debug it.

Cool...

> In doing this I've had some difficulties with the interfaces, most of
> which were caused by my inexperience with Java, but some which appear
> to be issues with the interface design. Specifically, the
> SeqSimilaritySearchResult, Hit and SubHit implementations are required
> to contain circular references (Result->List->Hit and Hit->Result,
> Hit->List->SubHit and SubHit->Hit).

Oookay, this does look like a problem, at least with the
Simple* implementations.  I must admit that I'd tend towards
removing the SeqSimilaritySearchSubHit.getHit() method.  Gerald,
are you still around?  Are there any objections to this?

It certainly seems worth a try to get a working implementation.

> By the way, thanks to the authors of the tutorials.

Fancy writing a tutorial for the bio.search package, once you've
got things working? ;)

Thomas.
-- 
``If I was going to carry a large axe on my back to a diplomatic
function I think I'd want it glittery too.''
           -- Terry Pratchett