[Bioperl-l] use of no_* to mean 'number_of', negative booleans

[Scott Markel]

Chris,

I just checked our code for the Sequence Analysis Collection in
Pipeline Pilot.  We've got a few places we'd need to make code
changes, but we like your suggestion.  So, no objections from us.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Vice President, Board of Directors:
    International Society for Computational Biology
Co-chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Tuesday, 09 June 2009 9:09 AM
> To: BioPerl List
> Subject: [Bioperl-l] use of no_* to mean 'number_of', negative booleans
> 
> All,
> 
> I've noticed a few methods in bioperl with names like 'no_Foo' that
> mean 'number of Foo' (such as SimpleAlign's no_sequences).  The
> problem I foresee are possible ambiguities, particularly with negative
> boolean checks (eg 'no_Foo' could also mean 'this instance contains no
> Foo'), something that BioPerl also has with various settings.
> 
> I suggest we alias these as num_* to disambiguate that.  There's no
> easy way to change already in-place flag setting w/o going through a
> deprecation cycle, but we can promote using positive booleans where
> possible (eg 'is_foo' or 'has_foo' instead of 'no_foo').  We can leave
> the older 'no_*' methods as is for the time being and maybe deprecate
> them later.
> 
> If no one has objections I'll add these in as needed.
> 
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l