Bioperl: Parameter tag style
Steve A. Chervitz
Thu, 8 Jan 1998 15:40:39 -0800 (PST)
> I didn't modify _rearrange() at all. The statements below are equivalent:
> $aln = new Bio::Tools::UnivAln(SEQS =>\@seqs);
> $aln = new Bio::Tools::UnivAln(-seqs =>\@seqs);
This is not true. I did in fact change one line:
return @param unless (defined($param) && $param=~/^-/);
return @param unless (defined($param) && $param=~/^-|^[A-Z]$/);
So the two statements above are equivalent with my version only.
A potential problem with my version occurs when _rearrange() is
called with a set of arguments which are not to be treated as named
parameters, yet the first arg is all cap:
_rearrange('FOOVAL', 'barval') vs. _rearrange( FOO => 'fooval').
But in practice this has not been a problem (famous last words:).
Perhaps it would be best to require all named parameters to begin with
a hyphen, all caps or not.
Side Note (and new issue!):
All of my modules inherit rearrange() from my Obj::Object.pm
Note also that originally I removed the underscore from _rearrange()
since I considered this a protected method, not private. Traditionally in
perl, leading underscores are reserved for private methods. I haven't
discovered a perl convention for methods that are to be considered
protected. It may be best to also name these with leading underscores
since protected methods are not part of a class's public interface.
Consistent naming of private and protected methods would also facilitate
the operation of a module by itself or within an inheritance hierarchy,
as I am using PreSeq and UnivAln. Therefore, in the future I plan to use
leading underscores for protected as well as private methods (unless I
learn of a better perl convention or mechanism).
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