R/parse-kcf.R

In glyparse: Parsing Glycan Structure Text Representations

#' Parse KCF Structures
#'
#' This function parses KCF strings into a [glyrepr::glycan_structure()].
#' KCF is a graph-oriented format used by KEGG GLYCAN.
#'
#' @param x A character vector of KCF strings. NA values are allowed and will be returned as NA structures.
#' @param on_failure How to handle parsing failures. `"error"` aborts when a
#'   structure cannot be parsed. `"na"` returns `NA` at invalid positions.
#' @param progress Whether to show a progress bar while parsing.
#' @param validate Deprecated and ignored. Array records
#'   are always validated by [glyrepr::structure_from_arrays()].
#'
#' @return A [glyrepr::glycan_structure()] object.
#'
#' @examples
#' kcf <- paste0(
#'   "ENTRY       G00066                      Glycan\n",
#'   "NODE        6\n",
#'   "            1   Cer        18     0\n",
#'   "            2   Glc        12     0\n",
#'   "            3   Gal         6     0\n",
#'   "            4   GlcNAc     -2     0\n",
#'   "            5   Gal       -10     0\n",
#'   "            6   GlcNAc    -18     0\n",
#'   "EDGE        5\n",
#'   "            1     2:b1    1:1\n",
#'   "            2     3:b1    2:4\n",
#'   "            3     4:b1    3:3\n",
#'   "            4     5:b1    4:4\n",
#'   "            5     6:b1    5:3\n",
#'   "///"
#' )
#' parse_kcf(kcf)
#'
#' @export
parse_kcf <- function(
  x,
  on_failure = "error",
  progress = FALSE,
  validate = lifecycle::deprecated()
) {
  if (!missing(validate)) {
    warn_deprecated_validate("parse_kcf")
  }
  struc_parser_wrapper(
    x,
    "kcf",
    on_failure = on_failure,
    progress = progress
  )
}