[Bioperl-l] new/unannounced methods

Phillip San Miguel pmiguel at purdue.edu
Fri Mar 9 11:03:15 EST 2007

Chris Fields wrote:
> On Mar 8, 2007, at 10:38 AM, Nathan Haigh wrote:
>> I've come across a couple of methods that are commented as being
>> new/unannounced e.g.:
>> Bio::Location::Atomic::trunc
> See:
> http://bugzilla.open-bio.org/show_bug.cgi?id=1572
>> As it's not been documented with POD it reduces the POD coverage  
>> metric.
>> I wondered if it makes sense to have these types of methods initially
>> made private with the use of a leading underscore until it's  
>> unveiling?
>> This way, programmers know not to touch the method from outside the
>> module and the POD coverage doesn't see it as being missed.
>> Any thoughts?
>> Nath
> That would be cheating, wouldn't it? ; >
> I think if a method is intended for public consumption it should be  
> vetted via Devel::Cover.  If it is obviously meant to be a private  
> method then it should get the underscore and be passed over.
> trunc(), judging from the bug report, doesn't seem to be a private  
> method (i.e. the idea was that one could obtain a truncated location  
> using this method).  If anything it needs tests and documentation,  
> but apparently it doesn't work as intended (or does it?).
> chris
Not sure if this constitutes a namespace collision but Bio::PrimarySeqI 
has a method trunc(). It is like subseq() but returns an object, rather 
than a string.


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