R/auto-parse.R

In glyparse: Parsing Glycan Structure Text Representations

#' Automatic Structure Parsing
#'
#' @description
#' Detect the structure string type and use the appropriate parser
#' to parse automatically.
#' Mixed types are supported.
#'
#' Supported types:
#' 1. GlycoCT
#' 2. IUPAC-condensed
#' 3. IUPAC-extended
#' 4. IUPAC-short
#' 5. GlyCAM IUPAC
#' 6. IUPAC-compact
#' 7. WURCS
#' 8. Linear Code
#' 9. pGlyco
#' 10. StrucGP
#' 11. KCF
#' 12. LINUCS
#' 13. GlycoWorkbench
#'
#' @param x A character vector of structure 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.
#'
#' @return A [glyrepr::glycan_structure()] object.
#'
#' @examples
#' # Single structure
#' x <- "Gal(b1-3)GlcNAc(b1-4)Glc(a1-"  # IUPAC-condensed
#' auto_parse(x)
#'
#' # Mixed types
#' x <- c(
#'   "Gal(b1-3)GlcNAc(b1-4)Glc(a1-",  # IUPAC-condensed
#'   "Neu5Aca3Gala3(Fuca6)GlcNAcb-"  # IUPAC-short
#' )
#' auto_parse(x)
#'
#' @export
auto_parse <- function(
  x,
  on_failure = "error",
  progress = FALSE
) {
  on_failure <- validate_struc_parser_wrapper_args(
    x,
    on_failure,
    progress,
    call = rlang::current_env()
  )
  input <- prepare_struc_parser_input(x)
  if (input$all_na) {
    return(make_na_glycan_structure(input$size, input$names))
  }

  formats <- native_convert(input$unique_x, "detect")
  groups <- split(seq_along(input$unique_x), formats)
  parsed <- lapply(names(groups), function(format) {
    parser <- get(format, envir = environment(auto_parse))
    parser(
      input$unique_x[groups[[format]]],
      on_failure = "na",
      progress = progress
    )
  })
  # Merge the already validated graph stores once. Repeated vctrs prototype
  # merges otherwise recheck an increasingly large store for each format.
  keys <- rep(NA_character_, length(input$unique_x))
  for (i in seq_along(groups)) {
    keys[groups[[i]]] <- as.character(parsed[[i]])
  }
  graphs <- unlist(lapply(parsed, attr, "graphs"), recursive = FALSE)
  graphs <- graphs[!duplicated(names(graphs))]
  used <- unique(keys[!is.na(keys)])
  graphs <- if (length(used)) graphs[used] else list()
  unique_result <- glyrepr::new_glycan_structure(keys, graphs)
  abort_on_invalid_parse(
    input$unique_x[is.na(unique_result)],
    on_failure,
    call = rlang::current_env()
  )
  result <- unique_result[build_normalized_structure_indices(input)]
  if (!is.null(input$names)) {
    attr(result, "names") <- input$names
  }
  result
}