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

[Chris Fields]

Makes sense to me.  I think, as long as they're documented, it  
shouldn't be a problem.

I think the main point is that the class methods for these don't show  
up using perldoc (something I ran into with Bio::DB::Fasta's  
inclusion of Bio::PrimarySeq::Fasta), but they do show up when using  
other documentation.  So 'perldoc Bio::DB::Fasta' works, but 'perldoc  
Bio::PrimarySeq::Fasta' doesn't.  So these can be problematic when  
looking for specific methods.

However, I think pod2html handles multiple package declarations in  
one module, and the PDOC online do as well.  Does the Deobfuscator?

Chris

On Oct 10, 2006, at 3:11 PM, Lincoln Stein wrote:

> 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
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu

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