[Bioperl-l] location of non-bioperl code in the Bio:: tree

[Reece Hart]

Cheers, bioperl community. Thanks for your contributions to bioperl.

I'm about to package a set of perl modules which facilitate execution,
manipulation, and visualization of Prospect protein threading
alignments. Is there consensus (or, lacking that, rational opinion)
about where bioperl developers and community would like to stash
non-bioperl code in the Bio:: tree? 

The package uses bioperl, but is not bioperl compliant (i.e., there're
no pure virtual interfaces, I use a home-grown exception class, hash
keys don't have hyphen prefixes, etc). For this reason, I'm strongly
inclined to keep these modules together in one tree rather than
scattering them among bioperl's Bio::Tools, Bio::Align, and perhaps
other Bio:: subtrees where the dissimilarity of the API would be
confusing to users.

I've tentatively chosen to name these Bio::Prospect::{ Thread,
ThreadSummary, SOAPClient, Options, ... }. This is akin to Bio::MAGE::
and is a tradeoff between isolation of related modules under one subtree
but not wanting to bury them under a lengthy name like
Bio::Interfaces::Prospect::Blah.pm. 

Before I release these modules, I'm open to comments about where these
should go. If there's no strong dissent, I'll go with Bio::Prospect::
and upload to CPAN in the very near future.

Comments?

Thanks,
Reece

-- 
Reece Hart, Ph.D.                       rkh at gene.com, http://www.gene.com/
Genentech, Inc.                         650/225-6133 (voice), -5389 (fax)
Bioinformatics and Protein Engineering
1 DNA Way, MS-93                        http://www.in-machina.com/~reece/
South San Francisco, CA  94080-4990     reece at in-machina.com, GPG: 0x25EC91A0