[Bioc-devel] role of replaceSlots in BiocGenerics

[Hervé Pagès]

On 09/06/2017 03:51 PM, Michael Lawrence wrote:
> On Wed, Sep 6, 2017 at 2:23 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
>> Hi,
>>
>> Personally I like replaceSlots() better.
>>
>> Not only because it's more readable but also the fact that you can use
>> initialize() to update an existing object is an undocumented feature so
>> I prefer to not rely on it.
>>
>
> It seems documented to me:
>
>       In the default method, unnamed arguments in the ‘...’ are
>       interpreted as objects from a superclass, and named arguments are
>       interpreted as objects to be assigned into the correspondingly
>       named slots.

But before that paragraph:

      The generic function 'initialize' is not called directly. A call
      to 'new' begins by copying the prototype object from the class
      definition, and then calls 'intialize()' with this object as the
      first argument, followed by the ... arguments.

There are no examples showing the use of initialize() for updating an
existing object. So one has to kind of guess that it is OK to call
initialize() directly and in a context that is different from
initialization (i.e. on an "existing" object, not just on the prototype
object).

Might be obvious for S4 wizards but I like my code to be readable by
the average developer. First time I saw the use of initialize() for
updating purpose (a few years ago), I found it quite confusing.

>
> Granted, it could be made a lot more explicit, and it's just the
> behavior of the default method, not a general contract.
>
>> Also initialize() is a generic and there could be a method defined for
>> the object you're trying to update that won't behave the way you expect
>> (e.g. the names of its arguments won't necessarily match the names of
>> the slots).
>>
>
> This is a good point. Another best practice is not to override (or at
> least change the contract of) initialize(), but you're right, there's
> no protection against it. The documentation does make some
> recommendations along these lines.
>
>> Also validation can be expensive and there are many situations where
>> you know that you're replacing the object slots with thiings that
>> don't break the object so I like that I can call replaceSlots() with
>> check=FALSE.
>>
>> I actually wish the methods package had something like replaceSlots().
>>
>
> Patches welcome ;)

Fair enough...

H.

>
>> H.
>>
>> On 09/06/2017 01:11 PM, Michael Lawrence wrote:
>>>
>>> No, the best practice is to just use initialize(). It used to be that
>>> replaceSlots() saved some copying, but that's no longer really the
>>> case. The only potential benefit is that it can skip validity checks,
>>> but usually you want those.
>>>
>>> Michael
>>>
>>> On Wed, Sep 6, 2017 at 12:55 PM, Vincent Carey
>>> <stvjc at channing.harvard.edu> wrote:
>>>>
>>>> Is this the preferred way of adjusting content in a
>>>> live object?  It is not accessible except via ":::"
>>>>
>>>>           [[alternative HTML version deleted]]
>>>>
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>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319