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

[Robert Buels]

Why not just add deprecation warnings now?  Or you could add deprecation 
warnings now that only print if $Bio::Root::Version::VERSION >= 
something.  Best to do it while one is thinking about it, I always say. 
  Cause I always forget to do it later.  ;-)

Rob

Chris Fields wrote:
> We could probably alias nof_* with num_* just for consistency, but leave 
> nof_* as is and not deprecate it (I don't think anyone would confuse 
> nof* with no*).
> 
> chris
> 
> On Jun 9, 2009, at 1:41 PM, Florent Angly wrote:
> 
>> Agree! no_* is prone to misunderstandings.
>> Also, some BioPerl code uses nof_*, which I quite like.
>> Florent
>>
>> Hilmar Lapp wrote:
>>> Great suggestions, I'm all for it.
>>>
>>>    -hilmar
>>>
>>> On Jun 9, 2009, at 12:08 PM, Chris Fields wrote:
>>>
>>>> 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
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>>>
>>
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-- 
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu