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### =========================================================================
### DelayedAperm objects
### -------------------------------------------------------------------------
###
### Representation of a delayed "extended aperm()" operation, that is, a
### delayed aperm() that can drop and/or add **ineffective** dimensions.
### Note that since only **ineffective** dimensions (i.e. dimensions with
### an extent of 1) can be dropped or added, the length of the output array
### is guaranteed to be the same as the length of the input array.
###
setClass("DelayedAperm",
contains="DelayedUnaryOp",
representation(
perm="integer" # Index into 'dim(seed)' describing the
# **rearrangement** of the dimensions i.e. which
# dimensions of the input to keep and in which order.
# Only ineffective dimensions can be dropped. Note
# that NAs are allowed and indicate the addition of
# an ineffective dimension. For example if 'dim(seed)'
# is c(20, 1, 15, 2, 1) then a DelayedAperm object
# where 'perm' is set to c(NA, NA, 3, 1, NA, 4, 5)
# represents an operation that returns an array with
# dimensions c(1, 1, 15, 20, 1, 2, 1).
),
prototype(
perm=1L
)
)
.validate_DelayedAperm <- function(x)
{
## 'perm' slot.
msg <- validate_perm(x@perm, dim(x@seed))
if (!isTRUE(msg))
return(msg)
TRUE
}
setValidity2("DelayedAperm", .validate_DelayedAperm)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
new_DelayedAperm <- function(seed=new("array"), perm=NULL)
{
perm <- normarg_perm(perm, dim(seed))
new2("DelayedAperm", seed=seed, perm=perm)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### is_noop() method
###
setMethod("is_noop", "DelayedAperm",
function(x) isSequence(x@perm, length(dim(x@seed)))
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Display
###
### S3/S4 combo for summary.DelayedAperm
.DelayedAperm_summary <- function(object)
{
perm <- as.character(object@perm)
if (length(perm) >= 2L)
perm <- sprintf("c(%s)", paste0(perm, collapse=","))
sprintf("Aperm (perm=%s)", perm)
}
summary.DelayedAperm <-
function(object, ...) .DelayedAperm_summary(object, ...)
setMethod("summary", "DelayedAperm", summary.DelayedAperm)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Seed contract
###
.get_DelayedAperm_dim <- function(x)
{
seed_dim <- dim(x@seed)
ans <- seed_dim[x@perm]
ans[is.na(x@perm)] <- 1L
ans
}
setMethod("dim", "DelayedAperm", .get_DelayedAperm_dim)
.get_DelayedAperm_dimnames <- function(x)
{
seed_dimnames <- dimnames(x@seed)
if (is.null(seed_dimnames))
return(NULL)
simplify_NULL_dimnames(seed_dimnames[x@perm])
}
setMethod("dimnames", "DelayedAperm", .get_DelayedAperm_dimnames)
project_index_on_seed <- function(index, x)
{
stopifnot(is(x, "DelayedAperm"),
is.list(index),
length(index) == length(x@perm))
nonNA_idx <- which(!is.na(x@perm))
perm0 <- x@perm[nonNA_idx]
index0 <- index[nonNA_idx]
seed_dim <- dim(x@seed)
seed_index <- vector("list", length=length(seed_dim))
seed_index[perm0] <- index0
seed_index
}
.extract_array_from_DelayedAperm <- function(x, index)
{
seed_index <- project_index_on_seed(index, x)
a <- extract_array(x@seed, seed_index)
a <- aperm2(a, x@perm)
index[!is.na(x@perm)] <- list(NULL)
subset_by_Nindex(a, index)
}
setMethod("extract_array", "DelayedAperm",
.extract_array_from_DelayedAperm
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Propagation of sparsity
###
setMethod("is_sparse", "DelayedAperm", function(x) is_sparse(x@seed))
### 'is_sparse(x)' is assumed to be TRUE and 'index' is assumed to
### not contain duplicates. See "extract_sparse_array() Terms of Use"
### in SparseArraySeed-class.R
setMethod("extract_sparse_array", "DelayedAperm",
function(x, index)
{
seed_index <- project_index_on_seed(index, x)
sas <- extract_sparse_array(x@seed, seed_index)
sas <- aperm(sas, x@perm)
index[!is.na(x@perm)] <- list(NULL)
extract_sparse_array(sas, index)
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Backward compatibility with DelayedArray < 0.5.24
###
### In DelayedArray 0.5.24 the SeedDimPicker class got renamed DelayedAperm.
### DelayedArray objects serialized with DelayedArray < 0.5.24 might contain
### SeedDimPicker instances nested in their "seed" slot so we need to keep
### the class around for now.
###
setClass("SeedDimPicker", contains="DelayedAperm")
setMethod("updateObject", "SeedDimPicker",
function(object, ..., verbose=FALSE)
{
object <- new2("DelayedAperm", seed=object@seed,
perm=object@dim_combination)
callNextMethod()
}
)
|
