1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
### =========================================================================
### realize()
### -------------------------------------------------------------------------
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Internal helper to support block by block realization
###
### Used by coercion to RleArray, HDF5Array::writeHDF5Array(), and
### HDF5Array::writeTENxMatrix().
###
BLOCK_write_to_sink <- function(sink, x, verbose=NA)
{
stopifnot(identical(dim(x), dim(sink)))
verbose <- normarg_verbose(verbose)
## 'x' and 'sink' might both have their physical chunks but we must
## choose a grid that is compatible with the physical chunks of 'sink'.
## Calling 'defaultSinkAutoGrid()' on 'sink' will produce such grid.
## TODO: Note that it might be beneficial to use a grid that is **also**
## compatible with the physical chunks of 'x' so we might want to add
## that kind of capability to 'defaultSinkAutoGrid()'.
grid <- defaultSinkAutoGrid(sink)
FUN <- function(sink, viewport, x, verbose, verbose_read_block)
{
effective_grid <- effectiveGrid()
current_block_id <- currentBlockId()
if (verbose) {
x_is_sparse <- is_sparse(x)
nblock <- length(effective_grid)
block <- verbose_read_block(x, viewport, x_is_sparse,
as.sparse=NA, current_block_id, nblock)
} else {
block <- read_block(x, viewport, as.sparse=NA)
}
if (verbose)
message("\\ Writing it ... ", appendLF=FALSE)
sink <- write_block(sink, viewport, block)
if (verbose)
message("OK")
sink
}
sinkApply(sink, FUN, x, verbose, verbose_read_block,
grid=grid, verbose=FALSE)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### realize()
###
setGeneric("realize", function(x, ...) standardGeneric("realize"))
setMethod("realize", "ANY",
function(x, BACKEND=getAutoRealizationBackend())
{
x <- DelayedArray(x)
if (is.null(BACKEND))
return(DelayedArray(as.array(x)))
load_BACKEND_package(BACKEND)
ans <- as(x, BACKEND)
## Temporarily needed because coercion to HDF5Array currently drops
## the dimnames. See R/writeHDF5Array.R in the HDF5Array package for
## more information about this.
## TODO: Remove line below when this is addressed.
set_dimnames(ans, dimnames(x))
}
)
|
