[Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Rather than a class union, how about an internal function that is called 
by the methods for both matrix and DelayedArray:


setGeneric("myNewRowMeans", function(x,...) { 
standardGeneric("myNewRowMeans")})

#' @importFrom DelayedArray rowMeans
.myNewRowMeans <- function(x,...){
 ??? # a lot of code independent of x
 ??? print("This is a lot of code shared regardless of class of x\n")
 ??? # a lot of code that depends on x, but is dispatched by the 
functions called
 ??? out<-rowMeans(x)
 ??? #a lot of code based on output of out
 ??? out<-out+1
 ??? return(out)
}

setMethod("myNewRowMeans",
 ????????? signature = "matrix",
 ????????? definition = function(x,...){
 ????????????? .myNewRowMeans(x,...)
 ????????? }
)

setMethod("myNewRowMeans",
 ????????? signature = "DelayedArray",
 ????????? definition = function(x,...){
 ????????????? .myNewRowMeans(x,...)
 ????????? }
)


On 4/30/18 9:10 AM, Tim Triche, Jr. wrote:

But if you merge methods like that, the error method can be that much 
more
difficult to identify. It took a couple of weeks to chase that bug down
properly, and it ended up down to rowMeans2 vs rowMeans.

I suppose the merged/abstracted method allows to centralize any such
dispatch into one place and swap out ill-behaved methods once identified,
so as long as DelayedArray/DelayedMatrixStats quirks are
documented/understood, maybe it is better to create this union class?

The Matrix/matrixStats/DelayedMatrix/DelayedMatrixStats situation has 
been
"interesting" in practical terms, as seemingly simple abstractions appear
to require more thought. That was my only point.


--t

On Mon, Apr 30, 2018 at 11:28 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

But that issue will be fixed, so Tim's advice is inappropriate.


On 04/30/2018 10:42 AM, Tim Triche, Jr. wrote:

Don't do that.? Seriously, just don't.

https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_DelayedArray_issues_16&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Rhy4i6H9xaY8HzWv9v_jhOnp5OyEpJcG52RP3nHorU8&s=olbErqY3_l7i45-WeTkaUNGalrQQr-7i59rhJVF6OGQ&e= 


--t

On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom <
epurdom at stat.berkeley.edu> wrote:

Hello,

I am trying to extend my package to handle `HDF5Matrix` class ( or 
more
generally `DelayedArray`). I currently have S4 functions for `matrix`
class. Usually I have a method for `SummarizedExperiment`, which will
call
call the method on `assay(x)` and I want the method to be able to deal
with
if `assay(x)` is a `DelayedArray`.

Most of my functions, however, do not require separate code 
depending on
whether `x` is a `matrix` or `DelayedArray`. They are making use of
existing functions that will make that choice for me, e.g. rowMeans or
subsetting. My goal right now is compatibility, not cleverness, and 
I'm
not
creating HDF5 methods to handle other cases. (If something doesn't
currently exist, then I just enclose `x` with `data.matrix` or
`as.matrix`
and call the matrix into memory ? for cleanliness and ease in updating
with
appropriate methods in future, I could make separate S4 functions for
these
specific tasks to dispatch, but that's outside of the scope of my
question). So for simplicity assume I don't really need to dispatch 
*my
code* -- that the methods I'm going to use do that.

The natural solution for me seem to use `setClassUnion` and I was
wondering if such a virtual class already exists? Or is there a better
way
to handle this?

Here's a simple example, using `rowMeans` as my example:

```
setGeneric("myNewRowMeans", function(x,...) { standardGeneric("
myNewRowMeans")})
setClassUnion("matrixOrDelayed",members=c("matrix", "DelayedArray"))

#' @importFrom DelayedArray rowMeans
setMethod("myNewRowMeans",
??????????? signature = "matrixOrDelayed",
??????????? definition = function(x,...){
????????????????????????? # a lot of code independent of x
????????????????????????? print("This is a lot of code shared 
regardless
of
class of x\n")
????????????????????????? # a lot of code that depends on x, but is
dispatched by the functions called
????????????????????????? out<-rowMeans(x)
????????????????????????? #a lot of code based on output of out
????????????????????????? out<-out+1
????????????????????????? return(out)
????????????????? }
)
```

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