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

Lincoln Stein lincoln.stein at gmail.com
Tue Oct 10 16:11:00 EDT 2006


Hi,

These ones are all mine:

> 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

In each case, the second modules are teeny tiny ones that implement
iterators which are at most two methods long (typically a new() and a
next()). I prefer not to split them out because they will just clutter up
the file tree with stuff that is already well documented in the "parent
ship" modules.

Lincoln


On 10/10/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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