R/util-options.R

In michbur/tidysq: Tidy Processing and Analysis of Biological Sequences

#' Obtain current state of tidysq options
#'
#' @description Subsets all global options to display those related to
#' \pkg{tidysq} package.
#'
#' @return A \code{\link[=namedList-class]{named list}} with selected option
#' values.
#'
#' @details
#' The user can display value of selected option by calling
#' \code{getOptions(option_name)} and set its value with
#' \code{options(option_name = value)}, where \code{option_name} is an option
#' name and \code{value} is a value to assign to an option.
#'
#' Full list of options included in \pkg{tidysq} package is listed below:
#' \itemize{
#' \item tidysq_NA_letter [\code{character(1)}]\cr
#'  A letter to be used when printing, constructing or interpreting \code{NA}
#'  value. Defaults to \code{"!"}.
#' \item tidysq_on_warning [\code{"silent" || "message" || "warning" || "error"}]\cr
#'  Determines the method of handling warning message. Setting \code{"error"}
#'  makes any warning throw an exception and stop execution of the code. The
#'  difference between \code{"message"} and \code{"warning"} is that while both
#'  display warning text to the console, only the latter registers it so that
#'  it can be accessed with a call to \code{warnings()}. Lastly, \code{"silent"}
#'  setting causes any warnings to be completely ignored. Default value is
#'  \code{"warning"}.
#' \item tidysq_pillar_max_width [code{integer(1)}]\cr
#'  Determines max width of a column of \code{sq} class within a
#'  \code{\link[tibble]{tibble}}. Default value is 15.
#' \item tidysq_print_max_sequences [\code{integer(1)}]\cr
#'  Controls maximum number of sequences printed to console. If an \code{sq}
#'  object is longer than this value, then only first
#'  \code{tidysq_print_max_sequences} are printed, just like in any R vector.
#'  Default value is 10.
#' \item tidysq_print_use_color [\code{logical(1)}]\cr
#'  Determines whether coloring should be used to increase readability of text
#'  printed to console. While it is advised to keep this option turned on due
#'  to above concern, some environments may not support coloring and thus
#'  turning it off can be necessary. Defaults to \code{TRUE}.
#' \item tidysq_safe_mode [\code{logical(1)}]\cr
#'  Default value is \code{FALSE}. When turned on, safe mode guarantees that
#'  \code{NA} appears within a sequence if and only if input sequence contains
#'  value passed with \code{NA_letter}. This means that resulting type might be
#'  different to the one passed as argument, if there are letters in a sequence
#'  that does not appear in the original alphabet.
#' }
#'
#' @family display_functions
#' @aliases tidysq-options
#' @export
get_tidysq_options <- function() {
  options()[c("tidysq_NA_letter",
              "tidysq_on_warning",
              "tidysq_pillar_max_width",
              "tidysq_print_max_sequences",
              "tidysq_print_use_color",
              "tidysq_safe_mode")]
}

handle_warning_message <- function(msg,
                                   on_warning = getOption("tidysq_on_warning")) {
  if (!is.null(msg) && msg != "")
    switch(on_warning,
           error = stop(msg, call. = FALSE),
           warning = warning(msg, call. = FALSE),
           message = message(msg),
           silent = invisible())
}