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

[Chris Fields]

There are a number of other bioperl-run examples (the  
Bio::Tools::Run::Analysis::soap issue I looked into revealed such).

I agree with both points, 1) that it depends on the size of the  
classes, and 2) from a maintainability standpoint, it can be very  
frustrating when looking for documentation.  Is there really any  
advantage to doing this?

Chris

On Oct 8, 2006, at 11:52 PM, Torsten Seemann wrote:

> 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
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign