[Bioperl-l] new/unannounced methods

Jason Stajich jason at bioperl.org
Fri Mar 9 12:13:15 EST 2007


Difference objects so there is no conflict. The location trunc() is  
used when truncating a sequence which helps create the sequence  
object that you get back from the Seq trunc() so it makes sense to  
keep the names the same.

-jason
On Mar 9, 2007, at 8:03 AM, Phillip San Miguel wrote:

> 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.
>
> Phillip
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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org/

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