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### =========================================================================
### RealizationSink objects
### -------------------------------------------------------------------------
###
### Virtual class with no slots. Intended to be extended by implementations
### of DelayedArray backends. Concrete subclasses must implement:
### 1) A constructor function that takes argument 'dim', 'dimnames', and
### 'type'.
### 2) A "dim", "dimnames", and "type" method.
### 3) A "write_block" method + optionally a "write_sparse_block" method.
### 4) A "close" method (optional).
### 5) Coercion to DelayedArray.
###
### Examples of RealizationSink concrete subclasses: arrayRealizationSink
### (see below), RleRealizationSink (see RleArray-class.R),
### HDF5RealizationSink and TENxRealizationSink (see HDF5Array package).
setClass("RealizationSink", representation("VIRTUAL"))
setGeneric("close")
### The default "close" method for RealizationSink objects is a no-op.
setMethod("close", "RealizationSink", function(con) invisible(NULL))
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### arrayRealizationSink objects
###
### The arrayRealizationSink class is a concrete RealizationSink subclass that
### implements an in-memory realization sink.
###
setClass("arrayRealizationSink",
contains="RealizationSink",
representation(
result_envir="environment"
)
)
.get_arrayRealizationSink_result <- function(sink)
{
get("result", envir=sink@result_envir)
}
.set_arrayRealizationSink_result <- function(sink, result)
{
assign("result", result, envir=sink@result_envir)
}
setMethod("dim", "arrayRealizationSink",
function(x) dim(.get_arrayRealizationSink_result(x))
)
arrayRealizationSink <- function(dim, dimnames=NULL, type="double")
{
result <- array(get(type)(0), dim=dim, dimnames=dimnames)
result_envir <- new.env(parent=emptyenv())
sink <- new("arrayRealizationSink", result_envir=result_envir)
.set_arrayRealizationSink_result(sink, result)
sink
}
setMethod("write_block", "arrayRealizationSink",
function(x, viewport, block)
{
result <- .get_arrayRealizationSink_result(x)
result <- write_block(result, viewport, block)
.set_arrayRealizationSink_result(x, result)
}
)
setAs("arrayRealizationSink", "DelayedArray",
function(from) DelayedArray(.get_arrayRealizationSink_result(from))
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Get/set the "realization backend" for the current session
###
.realization_backend_envir <- new.env(parent=emptyenv())
getRealizationBackend <- function()
{
BACKEND <- try(get("BACKEND", envir=.realization_backend_envir),
silent=TRUE)
if (is(BACKEND, "try-error"))
return(NULL)
BACKEND
}
.SUPPORTED_REALIZATION_BACKENDS <- data.frame(
BACKEND=c("RleArray", "HDF5Array", "TENxMatrix"),
package=c("DelayedArray", "HDF5Array", "HDF5Array"),
realization_sink_class=c("RleRealizationSink", "HDF5RealizationSink", "TENxRealizationSink"),
stringsAsFactors=FALSE
)
supportedRealizationBackends <- function()
{
ans <- .SUPPORTED_REALIZATION_BACKENDS[ , c("BACKEND", "package")]
backend <- getRealizationBackend()
Lcol <- ifelse(ans[ , "BACKEND"] %in% backend, "->", "")
Rcol <- ifelse(ans[ , "BACKEND"] %in% backend, "<-", "")
cbind(data.frame(` `=Lcol, check.names=FALSE),
ans,
data.frame(` `=Rcol, check.names=FALSE))
}
### NOT exported.
load_BACKEND_package <- function(BACKEND)
{
if (!isSingleString(BACKEND))
stop(wmsg("'BACKEND' must be a single string or NULL"))
backends <- .SUPPORTED_REALIZATION_BACKENDS
m <- match(BACKEND, backends[ , "BACKEND"])
if (is.na(m))
stop(wmsg("\"", BACKEND, "\" is not a supported backend. Please ",
"use supportedRealizationBackends() to get the list of ",
"supported \"realization backends\"."))
package <- backends[ , "package"][[m]]
class_package <- attr(BACKEND, "package")
if (is.null(class_package)) {
attr(BACKEND, "package") <- package
} else if (!identical(package, class_package)) {
stop(wmsg("\"package\" attribute on supplied 'BACKEND' is ",
"inconsistent with package normally associated with ",
"this backend"))
}
library(package, character.only=TRUE)
stopifnot(getClass(BACKEND)@package == package)
}
.get_REALIZATION_SINK_CONSTRUCTOR <- function(BACKEND)
{
backends <- .SUPPORTED_REALIZATION_BACKENDS
m <- match(BACKEND, backends[ , "BACKEND"])
realization_sink_class <- backends[ , "realization_sink_class"][[m]]
package <- backends[ , "package"][[m]]
REALIZATION_SINK_CONSTRUCTOR <- get(realization_sink_class,
envir=.getNamespace(package),
inherits=FALSE)
stopifnot(is.function(REALIZATION_SINK_CONSTRUCTOR))
stopifnot(identical(head(formalArgs(REALIZATION_SINK_CONSTRUCTOR), n=3L),
c("dim", "dimnames", "type")))
REALIZATION_SINK_CONSTRUCTOR
}
setRealizationBackend <- function(BACKEND=NULL)
{
if (is.null(BACKEND)) {
remove(list=ls(envir=.realization_backend_envir),
envir=.realization_backend_envir)
return(invisible(NULL))
}
load_BACKEND_package(BACKEND)
REALIZATION_SINK_CONSTRUCTOR <- .get_REALIZATION_SINK_CONSTRUCTOR(BACKEND)
assign("BACKEND", BACKEND,
envir=.realization_backend_envir)
assign("REALIZATION_SINK_CONSTRUCTOR", REALIZATION_SINK_CONSTRUCTOR,
envir=.realization_backend_envir)
return(invisible(NULL))
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Backend-agnostic RealizationSink constructor
###
.get_realization_sink_constructor <- function()
{
if (is.null(getRealizationBackend()))
return(arrayRealizationSink)
REALIZATION_SINK_CONSTRUCTOR <- try(get("REALIZATION_SINK_CONSTRUCTOR",
envir=.realization_backend_envir),
silent=TRUE)
if (is(REALIZATION_SINK_CONSTRUCTOR, "try-error"))
stop(wmsg("This operation requires a \"realization backend\". ",
"Please see '?setRealizationBackend' for how to set one."))
REALIZATION_SINK_CONSTRUCTOR
}
RealizationSink <- function(dim, dimnames=NULL, type="double")
{
.get_realization_sink_constructor()(dim, dimnames, type)
}
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