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|
### =========================================================================
### Simplify a tree of delayed operations
### -------------------------------------------------------------------------
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### simplify()
###
.normarg_incremental <- function(incremental)
{
if (!isTRUEorFALSE(incremental))
stop("'incremental' must be TRUE or FALSE")
incremental
}
setGeneric("simplify", signature="x",
function(x, incremental=FALSE) standardGeneric("simplify")
)
setMethod("simplify", "ANY",
function(x, incremental=FALSE)
{
.normarg_incremental(incremental)
x
}
)
setMethod("simplify", "DelayedSubset",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seed <- simplify(x@seed)
x1 <- x@seed
if (is_noop(x))
return(x1)
if (is(x1, "DelayedSubset")) {
## ACTION: merge ops + remove if no-op.
x1 <- subset_DelayedSubset(x1, x@index)
if (is_noop(x1))
return(x1@seed)
return(x1)
}
if (is(x1, "DelayedAperm")) {
## ACTION: swap ops.
index2 <- project_index_on_seed(x@index, x1)
x2 <- new_DelayedSubset(x1@seed, index2)
x2 <- simplify(x2, incremental=TRUE)
x1 <- BiocGenerics:::replaceSlots(x1, seed=x2, check=FALSE)
return(x1)
}
if (is(x1, "DelayedUnaryIsoOpStack")) {
## ACTION: swap ops.
x2 <- x
x2@seed <- x1@seed
x2 <- simplify(x2, incremental=TRUE)
x1 <- BiocGenerics:::replaceSlots(x1, seed=x2, check=FALSE)
return(x1)
}
if (is(x1, "DelayedUnaryIsoOpWithArgs")) {
## ACTION: swap ops.
x2 <- x
x2@seed <- x1@seed
x2 <- simplify(x2, incremental=TRUE)
Largs <- subset_args(x1@Largs, x1@Lalong, x@index)
Rargs <- subset_args(x1@Rargs, x1@Ralong, x@index)
x1 <- BiocGenerics:::replaceSlots(x1, seed=x2,
Largs=Largs,
Rargs=Rargs,
check=FALSE)
return(x1)
}
if (is(x1, "DelayedSubassign")) {
## ACTION: swap ops.
x1 <- subset_DelayedSubassign(x1, x@index)
x1@seed <- simplify(x1@seed, incremental=TRUE)
x1@Rvalue <- simplify(x1@Rvalue, incremental=TRUE)
return(x1)
}
if (is(x1, "DelayedSetDimnames")) {
## ACTION: swap ops.
x2 <- x
x2@seed <- x1@seed
x2 <- simplify(x2, incremental=TRUE)
x1 <- new_DelayedSetDimnames(x2, dimnames(x))
return(x1)
}
x
}
)
setMethod("simplify", "DelayedAperm",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seed <- simplify(x@seed)
x1 <- x@seed
if (is_noop(x))
return(x1)
if (is(x1, "DelayedAperm")) {
## ACTION: merge ops + remove if no-op.
x1@perm <- x1@perm[x@perm]
if (is_noop(x1))
return(x1@seed)
return(simplify(x1, incremental=TRUE))
}
if (is(x1, "DelayedUnaryIsoOpStack")) {
## ACTION: swap ops.
x@seed <- x1@seed
x1@seed <- simplify(x, incremental=TRUE)
return(x1)
}
if (is(x1, "DelayedUnaryIsoOpWithArgs")) {
perm0 <- x@perm[!is.na(x@perm)]
set_Lalong_to_NA <- !(x1@Lalong %in% perm0)
set_Ralong_to_NA <- !(x1@Ralong %in% perm0)
if (all(set_Lalong_to_NA) && all(set_Ralong_to_NA)) {
## ACTION: swap ops.
x1@Lalong[set_Lalong_to_NA] <- NA_integer_
x1@Ralong[set_Ralong_to_NA] <- NA_integer_
x@seed <- x1@seed
x1@seed <- simplify(x, incremental=TRUE)
return(x1)
}
}
if (is(x1, "DelayedSetDimnames")) {
## ACTION: swap ops.
x2 <- x
x2@seed <- x1@seed
x2 <- simplify(x2, incremental=TRUE)
x1 <- new_DelayedSetDimnames(x2, dimnames(x))
return(x1)
}
x
}
)
setMethod("simplify", "DelayedUnaryIsoOpStack",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seed <- simplify(x@seed)
x1 <- x@seed
if (is(x1, "DelayedUnaryIsoOpStack")) {
## ACTION: merge ops.
x1@OPS <- c(x1@OPS, x@OPS)
return(x1)
}
if (is(x1, "DelayedSetDimnames")) {
## ACTION: swap ops.
x@seed <- x1@seed
x1@seed <- simplify(x, incremental=TRUE)
return(x1)
}
x
}
)
setMethod("simplify", "DelayedUnaryIsoOpWithArgs",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seed <- simplify(x@seed)
x1 <- x@seed
if (is(x1, "DelayedSetDimnames")) {
## ACTION: swap ops.
x@seed <- x1@seed
x1@seed <- simplify(x, incremental=TRUE)
return(x1)
}
x
}
)
setMethod("simplify", "DelayedSubassign",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental)) {
x@seed <- simplify(x@seed)
x@Rvalue <- simplify(x@Rvalue)
}
x1 <- x@seed
if (is_noop(x))
return(x1)
if (all(x@.nogap) && !is.null(dim(x@Rvalue))) {
## "Full replacement" case with an array-like object on the right.
## 'x' represents a subassignment that replaces all the array
## elements in the left value. This is a degenerate case of
## subassignment where we never need to extract any array element
## from 'x@seed'.
if (all(S4Vectors:::sapply_isNULL(x@Lindex))) {
## "Filling" case (a special case of "Full replacement") with
## an array-like object on the right.
## ACTION: replace DelayedSubassign op with right value.
x1 <- x@Rvalue
} else {
## ACTION: replace DelayedSubassign op with a subset of
## right value.
index <- vector("list", length=length(x@Lindex))
Mindex <- make_Mindex(index, x)
x1 <- new_DelayedSubset(x@Rvalue, Mindex)
x1 <- simplify(x1, incremental=TRUE)
}
## Propagate dimnames of left value.
x <- new_DelayedSetDimnames(x1, dimnames(x@seed))
x <- simplify(x, incremental=TRUE)
return(x)
}
Rvalue <- x@Rvalue
if (is(Rvalue, "DelayedSetDimnames")) {
## ACTION: remove DelayedSetDimnames op from right value.
x@Rvalue <- Rvalue@seed
}
if (is(x1, "DelayedSetDimnames")) {
## ACTION: swap ops.
x@seed <- x1@seed
x1@seed <- x
return(x1)
}
x
}
)
setMethod("simplify", "DelayedSetDimnames",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seed <- simplify(x@seed)
x1 <- x@seed
if (is_noop(x))
return(x1)
if (is(x1, "DelayedSetDimnames")) {
## ACTION: merge ops + remove if no-op.
x <- new_DelayedSetDimnames(x1@seed, dimnames(x))
if (is_noop(x))
return(x@seed)
return(x)
}
x
}
)
setMethod("simplify", "DelayedNaryIsoOp",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seeds <- lapply(x@seeds, simplify)
x
}
)
setMethod("simplify", "DelayedAbind",
function(x, incremental=FALSE)
{
if (!.normarg_incremental(incremental))
x@seeds <- lapply(x@seeds, simplify)
if (is_noop(x))
return(x@seeds[[1L]])
x
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### isPristine()
###
### A pristine DelayedArray object is an object that carries no delayed
### operation. Note that an object that carries delayed operations that
### do nothing (e.g. A + 0) is not considered pristine.
###
isPristine <- function(x, ignore.dimnames=FALSE)
{
if (!is(x, "DelayedArray"))
stop(wmsg("'x' must be a DelayedArray object"))
if (!isTRUEorFALSE(ignore.dimnames))
stop(wmsg("'ignore.dimnames' should be TRUE or FALSE"))
if (ignore.dimnames && is(x@seed, "DelayedSetDimnames"))
x@seed <- x@seed@seed # drop DelayedSetDimnames op
!is(x@seed, "DelayedOp")
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### contentIsPristine()
###
### Return FALSE if the tree contains delayed operations that modify
### the "original array values" (i.e. the values contained in the seeds).
### The value-modifying nodes are:
### - DelayedUnaryIsoOpStack, DelayedUnaryIsoOpWithArgs, and
### DelayedNaryIsoOp nodes;
### - DelayedSubassign nodes that are not no-ops.
contentIsPristine <- function(x)
{
if (!is.list(x) || is.array(x)) {
if (!is(x, "DelayedOp"))
return(TRUE)
if (is(x, "DelayedUnaryIsoOpStack") ||
is(x, "DelayedUnaryIsoOpWithArgs") ||
is(x, "DelayedNaryIsoOp"))
return(FALSE)
if (is(x, "DelayedUnaryOp")) {
if (is(x, "DelayedSubassign") && !is_noop(x))
return(FALSE)
x <- list(x@seed)
} else {
x <- x@seeds
}
}
nchildren <- length(x)
for (i in seq_len(nchildren)) {
if (!contentIsPristine(x[[i]]))
return(FALSE)
}
TRUE
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### netSubsetAndAperm()
###
### Only supported if nseed() == 1
###
### Remove DelayedUnaryIsoOp nodes from a linear tree.
### Raise an error if the tree is not linear.
.remove_unary_iso_ops <- function(x)
{
if (!is(x, "DelayedOp"))
return(x)
if (is(x, "DelayedNaryOp")) {
## Tree is not linear.
stop(wmsg("netSubsetAndAperm() ",
IS_NOT_SUPOORTED_IF_MULTIPLE_SEEDS))
}
x1 <- .remove_unary_iso_ops(x@seed)
if (is(x, "DelayedUnaryIsoOp")) {
x <- x1
} else {
x@seed <- x1
}
x
}
setGeneric("netSubsetAndAperm", signature="x",
function(x, as.DelayedOp=FALSE) standardGeneric("netSubsetAndAperm")
)
setMethod("netSubsetAndAperm", "ANY",
function(x, as.DelayedOp=FALSE)
{
if (!isTRUEorFALSE(as.DelayedOp))
stop("'as.DelayedOp' must be TRUE or FALSE")
reduced <- simplify(.remove_unary_iso_ops(x))
if (!is(reduced, "DelayedAperm"))
reduced <- new_DelayedAperm(reduced)
x1 <- reduced@seed
if (!is(x1, "DelayedSubset"))
reduced@seed <- new_DelayedSubset(x1)
if (as.DelayedOp)
return(reduced)
ans <- reduced@seed@index
if (!is_noop(reduced))
attr(ans, "dimmap") <- reduced@perm
ans
}
)
|
