R/DATA-objects.R

In jmstrat/NMR.Utils: Importing and processing Bruker NMR data

# NOTE These functions are created in the .onLoad function and added to the namespace,
# we need to export and document them here, and add overrides to the default behaviour
# if necessary.

##' @title NMR data objects
##' @param x The object
##' @rdname data_objects_null_exports

##' @name nmr.data.object
##' @usage nmr.data.object(...)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name nmr2d.data.object
##' @usage nmr2d.data.object(...)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name nmr2dinsitu.data.object
##' @usage nmr2dinsitu.data.object(...)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name as.nmr.data.object
##' @usage as.nmr.data.object(x)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name as.nmr2d.data.object
##' @usage as.nmr2d.data.object(x)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
as.nmr2d.data.object <- function(...) {
  df <- as.nmr2d.data.object.super(...)
  ycols <- 1:ncol(df)
  ycols <- ycols[!ycols %in% attr(df, "x_column")]
  attr(df, "y_column") <- ycols
  df
}

##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
as.nmr2dinsitu.data.object <- function(x) {
  if (!requireNamespace("Echem.Data", quietly=TRUE)) {
    stop("Insitu data processing requires the Echem.Data package")
  }
  if (is.nmr2d.data.object(x)) {
    xl <- jms.classes::xlab(x)
    x <- as.nmr2dinsitu.data.object.super(x)
    jms.classes::xlab(x) <- xl
    attr(x, "echem") <- Echem.Data::echem.data.object()
  } else {
    stop("as.nmr2dinsitu.data.object can only be called with an nmr2d.data.object")
  }
  return(x)
}

##' @name is.nmr.data.object
##' @usage is.nmr.data.object(x)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name is.nmr2d.data.object
##' @usage is.nmr2d.data.object(x)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

##' @name is.nmr2dinsitu.data.object
##' @usage is.nmr2dinsitu.data.object(x)
##' @export
##' @rdname data_objects_null_exports
##' @keywords internal
NULL

#' @export
`[.nmr2d.data.object` <- function(x, ...) {
  r <- `[.nmr2d.data.object.super`(x, ...)
  if (length(attributes(r)[["y_column"]]) < 2) {
    # Result now a 1D scan -- change class
    classR <- class(r)
    class(r) <- classR[!(classR == "nmr2dinsitu.data.object" | classR == "nmr2d.data.object")]
  }
  r
}

#' @export
`[.nmr2dinsitu.data.object` <- `[.nmr2d.data.object`