[Bioc-devel] S4 initialize methods (was Re: "patches" for Gviz: utr plotting support and direct BamFile plotting)

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Aug 22 22:47:50 CEST 2012


And since we're already getting pretty deep into the woods, I guess it
can't hurt to keep going:

On Wed, Aug 22, 2012 at 4:11 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Martin has a great technical explanation.
> A briefer explanation is the following.
> 'We' used to use an initialize method to construct new objects, like
>   new("ExpressionSet", exprs = MATRIX)
> This paradigm is used in a number of packages, including Biobase.
> 'We' later realized - for reasons Martin explains below - that this is prone
> to failure and should not be used.  However, you can still find tons of code
> using it - for legacy reasons.
> In general, you should not define the initialize method, you should set a
> prototype when you define the class and you should write an explicit
> constructor, like
>   ExpressionSet <- function() {}

With the exception when your class has slots that are environments.

If it's true that some things will still call new("YourClass", ...)
that aren't your constructor, then you will be surprised:

setClass("A", representation=representation(cache="environment"),
ctr <- function(cache=new.env()) new("A", cache=cache)

## This is the behavior you probably expect:
a = ctr()
b = ctr()
a at cache[['a']] = 1
b at cache[['a']]

## This isn't
y = new("A")
z = new("A")
y at cache[['a']] = 1
z at cache[['a']]
[1] 1    ## Woops!

But if you set an appropriate initialize method:

setMethod(initialize, "A", function(.Object, ..., cache=new.env()) {
  .Object at cache <- cache
  callNextMethod(.Object, ...)

All is well:
y = new("A")
z = new("A")
y at cache[['a']] = 1
z at cache[['a']]

I think ReferenceClasses replaces (most(?)) of the use cases that I
use the `cache` idiom for, although I'm not sure about the gotchas
with them because I haven't tried to grok RefClasses yet.

Still ... thought I'd point this out (I think it was actually one of
you two, who must have alerted me to this years ago (perhaps on


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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