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

[Matthew Pocock]

Hi Keith,

This sounds realy good. If you think that the listener API is generic, then
by all means add it to your flat package. The Fasta implementation can also
go in there if it is realy small (1-2 files). If it is in any way heavy (5+
classes), then I sudgest org.biojava.bio.programs.fasta package for the
Fasta-specific portion only. The filters sound like a realy sound idea.

Commit away!

Matthew

... now for writing the bridge to make/consume our SAX events with search
thingies ...

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.
>
> 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
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