[Bioc-devel] s4 guidance

[Joern Toedling]

Hello,

there are a several good introductions to S4 classes out there, for example 
check out "A (not so) short introduction to S4" by Christophe Genolini which 
is available from this page:
http://cran.r-project.org/other-docs.html

And to avoid the use of "@" at user-level, one should provide accessor 
methods to users to retrieve and set the values for all slots.
However, as far as I am aware, there is no way to prevent users from making 
use of "@" altogether.

Regarding your example, I think it would be best if populating test at doubleX 
happens either in the initialization function and/or the replace method for 
test at x.

Cheers,
Joern


On Mon, 21 Feb 2011 13:53:39 +0000, Stefano Berri wrote
> Hi.
> 
> could somebody give me some guidance and direction?
> 
> I started to make a S4 module for bioconductor.
> I am stuck to adding values to a slot using a method.
> 
> here a proof of concept
> 
> The code, class and methods:
> ############################
> 
> setClass (
>     Class = 'test',
>     representation = representation (
>         x = "numeric",
>         doubleX = "numeric"
>     )   
> )
> 
> setGeneric(name = "myDouble", function(object)
> {standardGeneric("myDouble")}) setMethod("myDouble", "test", 
> function(object){        object at doubleX <- 2*object at x    })
> 
> ###########################
> 
> # then I type
> 
> myT <- new(Class = "test", x = c(1,2,3))
> # hoping to populate "myDouble" slot
> myDouble(myT)
> # but if I look into
> myT at doubleX
> # I get "numeric(0)"
> 
> to make it work I have to return the object
> {object at doubleX <- 2*object at x; return (object)}
> but then it returns the object (with associated "show" method) which 
> I do not want.
> 
> I also struggle to find documentation online on S4. I have "R programming
> for bioinformatics" which cover the basics and then a few bits here and
> there, but I could not find a nice tutorial and a reference guide...
> 
> I have some other questions:
> Comparing to other object-oriented programming languages, I expect 
> to find similar concepts.  - Is there a way to hide/encapsulate 
> slots and methods? If I type "myT" and then press Tab twice it shows 
> all slots that can be read and even written to! I makes the whole 
> hassle to object oriented programming useless if the user can 
> overwrite variables, does it not?
> 
> Sorry if my questions are naive...
> 
> Thanks for your help
> 
> Stefano Berri
> 
> _______________________________________________
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---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927