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#' Transform a vector to save in a HDF5 file
#'
#' This handles type casting and missing placeholder value selection/substitution.
#' It is primarily intended for developers of \pkg{alabaster.*} extensions.
#'
#' @param x An atomic vector to be saved to HDF5.
#' @param .version Internal use only.
#'
#' @return
#' A list containing:
#' \itemize{
#' \item \code{transformed}, the transformed vector.
#' This may be the same as \code{x} if no \code{NA} values were detected.
#' Note that logical vectors are cast to integers.
#' \item \code{placeholder}, the placeholder value used to represent \code{NA} values.
#' This is \code{NULL} if no \code{NA} values were detected in \code{x},
#' otherwise it is the same as the output of \code{\link{chooseMissingPlaceholderForHdf5}}.
#' }
#'
#' @author Aaron Lun
#' @examples
#' transformVectorForHdf5(c(TRUE, NA, FALSE))
#' transformVectorForHdf5(c(1L, NA, 2L))
#' transformVectorForHdf5(c(1L, NaN, 2L))
#' transformVectorForHdf5(c("FOO", NA, "BAR"))
#' transformVectorForHdf5(c("FOO", NA, "NA"))
#'
#' @export
transformVectorForHdf5 <- function(x, .version=3) {
placeholder <- NULL
if (is.logical(x)) {
storage.mode(x) <- "integer"
if (anyNA(x)) {
placeholder <- -1L
x[is.na(x)] <- placeholder
}
} else if (is.character(x)) {
x <- enc2utf8(x) # avoid mis-encoding multi-byte characters from Latin-1.
if (anyNA(x)) {
placeholder <- chooseMissingPlaceholderForHdf5(x)
x[is.na(x)] <- placeholder
}
} else if (is.double(x)) {
if (any_actually_numeric_na(x)) {
placeholder <- chooseMissingPlaceholderForHdf5(x, .version=.version)
if (!any_actually_numeric_na(placeholder)) {
x[is_actually_numeric_na(x)] <- placeholder
}
}
} else {
if (anyNA(x)) {
placeholder <- as(NA, storage.mode(x))
}
}
list(transformed = x, placeholder = placeholder)
}
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