[Bioc-devel] role of replaceSlots in BiocGenerics

[Michael Lawrence]

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.

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 ;)

> 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
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