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

[Keith James]

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.

Although I've only made an implementation for Fasta, I tried to make
the interfaces applicable to any search output which is an arbitrary
flat file containing a "start", a header (1+ lines) , hits (1 + lines)
with optional subhits and an "end". This would hope to cover stuff
like some of the EMBOSS programs.

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)

The SearchReader constructor takes a SearchParser, SearchBuilder and
BufferedReader and at the moment produces (SeqSimilaritySearchResult)
Objects from next().

I'm intending to add filtering by having a decorator for
SearchContentHandler which also takes a filter object (something like
scoreFilter, EvalueFilter, PvalueFilter, topNhitsFilter).

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).

Any preferences?

cheers,

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA