[Biojava-l] package: org.biojava.bio.program.?

[Thomas Down]

On Mon, Jan 22, 2001 at 04:48:05PM +0000, Keith James wrote:
> 
> Before I commit my classes for parsing Fasta search output, I'd like
> to get some feedback on what people feel is a good package for them to
> go in.
> 
> So I have (guided by seq io and gff design):
> 
>  SearchContentHandler (listener interface)
>   SearchBuilder (subinterface of SearchContentHandler)
> 
>  SearchParser (interface)
> 
> 
>  FastaSearchBuilder (implementation of SearchBuilder)  
>  FastaSearchParser (implementation of SearchParser)
> 
>  SearchReader (implementation of Iterator)

Sounds good....

> At the moment I've got all the files in org.biojava.bio.program.flat
> (arbitrary flat file) as the current packages seem to be named after
> the data source (xml, gff, das etc) rather than the content (search,
> structural).

The contract for the org.biojava.bio.program.* hierarchy has
never been 100% clear, at least to me.  However, I guess that's
a fair enough place to put the functionality.  The other possibility
would be a sub-package of bio.search (I must admit this seems
a bit more logical than bio.program, but I don't have particularly
strong feelings).

Calling the package `flat' is kind-of limited though -- I think
I'd prefer `fasta' (which everyone else has heard of) than
`flat', which is kind-of value.  You can always make it clear in
the first sentance of package.html that the parsers work with
EMBOSS tools as well.

Anyway, it'll be good to see the code whichever package you decide
on.

   Thomas.