[Bioperl-l] Multiple packages in the one .pm file

[Torsten Seemann]

Hi all,

The following modules have more than one "package xxxx;" declaration in 
them. For small, internal classes I guess this is fine, but for others,
they should be split up into the filesystem - otherwise they are 
troublesome to locate and the online documentation doesn't list them!

eg.
bioperl-run/Bio/Tools/Run/Analysis/Job.pm
is in
bioperl-run/Bio/Tools/Run/Analysis.pm

Here's the culprits:

% for NN in bioperl-live bioperl-run; do grep '^package ' -r $NN/Bio | 
sed 's/:.*$//' | sort | uniq -d ; done

bioperl-live/Bio/AnalysisI.pm
bioperl-live/Bio/DB/Fasta.pm
bioperl-live/Bio/DB/GFF.pm
bioperl-live/Bio/DB/GFF/Adaptor/berkeleydb.pm
bioperl-live/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
bioperl-live/Bio/DB/SeqFeature/Store/berkeleydb.pm
bioperl-live/Bio/DB/SeqFeature/Store/memory.pm
bioperl-live/Bio/SeqIO/interpro.pm

bioperl-run/Bio/Tools/Run/Analysis.pm
bioperl-run/Bio/Tools/Run/Analysis/soap.pm

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia