R/processXYXY.R

In readJDX: Import Data in the JCAMP-DX Format

#'
#' Extract the values in JCAMP-DX file with a (XY..XY) variable list.
#'
#' This function is NOT EXPORTED.
#' Users would not normally call this function.  See \code{\link{readJDX}}.
#' Documentation is provided for developers wishing to contribute to the package.
#'
#' @template VL-arg
#' @template params-arg
#' @template SOFC-arg
#' @template debug-arg
#' @template mode-arg
#'
#' @return A data frame with elements \code{x} and \code{y}.
#'
#' @noRd
#'

processXYXY <- function(VL, params, mode, SOFC, debug = 0) {
  fmt <- VL[1]
  VL <- VL[-1] # Remove the pre-pended format string
  if (debug >= 1) cat("\nProcessing variable list...\n")

  # This format is typical of a single mass spectrum

  # Verify expected numerical format
  comp <- getComp(VL)
  if (length(comp) != 1L) {
    cat("\nCompression found:", comp, "\n")
    stop("For (XY..XY) data is expected to be in AFFN format")
  }
  if (comp != "AFFN") {
    cat("\nCompression found:", comp, "\n")
    stop("For (XY..XY) data is expected to be in AFFN format")
  }

  ### Step 1. Convert to numeric values
  xValues <- charXYnumXY(VL)$x
  yValues <- charXYnumXY(VL)$y

  ### Step 2. Check the integrity of the results
  # Check that we got the right number of data points

  npoints <- as.integer(params[1])
  if (debug == 2) cat("\nNPOINTS =", npoints, "\n")
  if (debug == 2) cat("Actual no. data points found  =", length(xValues), "\n")
  if (!npoints == length(xValues)) stop("NPOINTS and length of parsed data don't match")

  ### And we're done...

  xydata <- data.frame(x = xValues, y = yValues)
  return(xydata)
}