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

[Brian Osborne]

Torsten,

Fixed interpro.pm, it could have been written more simply (or more like
other SeqIO modules). Can't really address the others.

Brian O.


On 10/9/06 12:52 AM, "Torsten Seemann"
<torsten.seemann at infotech.monash.edu.au> 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