[Bioc-devel] S4 overwrite inspector of virtual class

[Michael Lawrence]

In principle, there should be no need to override a validator, since
the constraints specified by the super class should not be violated.
Subclasses should only add constraints. But you can abstract the
constraints, e.g., make a generic for checking the chromosome ID
format, and have version-specific methods for that.

Moreover, it's not clear whether inheritance makes sense in this case,
i.e., you are using as a tool where there is no logical inheritance
relationship. You can always define separate methods for each format
version class and factor the common implementation into an underlying
function.

Michael


On Mon, Aug 15, 2016 at 9:56 AM, Zach Skidmore <zskidmor at wustl.edu> wrote:
> maybe validator is the proper term in R? i've highlighted what I refer to as the inspector below as an example:
>
> setClass("file",
>                 contains="file_virtual",
>                 validity=function(object){
>                 # Check that object is as expected
>
>                 }
> )
>
> On 8/15/16 11:46 AM, Gabe Becker wrote:
>
> Zach,
>
> Is an inspector a method you define on your classes? I'm not quite
> following what you mean by your question. AFAIK inspectors are not
> generally a thing in R (at least that go by that name).
>
> ~G
>
> On Mon, Aug 15, 2016 at 9:42 AM, Zach Skidmore <zskidmor at wustl.edu><mailto:zskidmor at wustl.edu> wrote:
>
>
>
> Hi All,
>
> I'm currently transforming the GenVisR package into an Object Oriented
> system. Currently I have a virtual class and several child-classes. I am
> wondering if there is a way to tell R to use the inspector of the virtual
> class only if the inspector of a child class in not defined.
>
> For example say I had a class to store versions of a file-type and I have
> a slot in the class to store the position. Between different versions of
> the file-type there may be small differences (for example Chromosome may be
> capitalized in version 2,3,4 but not version 1). Ideally the child classes
> for 2,3,4 would be able to inherit the inspector from the virtual class to
> check the chromosome name and I would define a separate inspector for
> version 1 which is different.
>
> Any thoughts? Currently both inspectors are called (virtual and the
> appropriate sub-class), meaning if i added more versions in the future I
> would have to re-write the virtual and child class. Whereas if I could say
> ignore the virtual (i.e. default) inspector if another is defined I would
> only have to write the child class inspector in the future.
>
> Hopefully this makes sense, let me know if it doesn't or if i'm violating
> a core OO principle, i'm relatively new to object oriented programming.
>
> Thanks, Zach!
>
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