[Biojava-l] The org.biojava.bio.program.* hierarchy

[Keith James]

>>>>> "Thomas" == Thomas Down <td2@sanger.ac.uk> writes:

    Thomas> I'm starting to get a little worried about the growth of
    Thomas> the bio.program hierarchy.  The original contract of this
    Thomas> package (and all it's sub-packages) was for wrappers for
    Thomas> interacting with external tools.  This seems to be
    Thomas> stretching thinner and thinner, though...

    Thomas> What definitely belongs there:

    Thomas>   - All the search-related stuff.  That's fine, and
    Thomas> shouldn't move an inch.

[...]

Related to this, I'm working on Blast/Fasta SAX2 -> Biojava objects
(org.biojava.bio.search.* objects so far, rather than
org.biojava.bio.seq.homol) and was puzzling over where this should
go. Any preferences?

As an aside, this means that I'm making necessary changes to
org.biojava.bio.search.* as the hit objects were missing key methods
such as getting the position/strand of the hit on the query and
subject sequences. For some reason they were missing from the original
interfaces.

-- 

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