R/is_empty_sq.R

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

#' Test if sequence is empty
#' 
#' @description Test an \code{\link[=sq-class]{sq}} object for presence of
#' empty sequences.
#' 
#' @template x
#'  
#' @return A logical vector of the same length as input \code{sq}, indicating
#' whether elements are empty sequences (of length 0).
#' 
#' @details This function allows identification of empty sequences (that have
#' length 0) represented by the \code{NULL sq} values in the sq object. It
#' returns a logical value for every element of the \code{sq} object -
#' \code{TRUE} if its value is \code{NULL sq} and \code{FALSE} otherwise.
#' \code{NULL sq} values may be introduced as a result of
#' \code{\link{remove_ambiguous}} and \code{\link{remove_na}} functions. The
#' former replaces sequences containing ambiguous elements with \code{NULL sq}
#' values, whereas the latter replaces sequences with \code{NA} values with
#' \code{NULL sq}.
#'
#' @examples
#' # Creating an object to work on:
#' sq_dna_ext <- sq(c("ACGATTAGACG", "", "GACGANTCCAGNTAC"),
#'                  alphabet = "dna_ext")
#'
#' # Testing for presence of empty sequences:
#' is_empty_sq(sq_dna_ext)
#'
#' # Testing for presence of empty sequences after cleaning - sequence
#' # containing ambiguous elements is replaced by NULL sq:
#' sq_dna_bsc <- remove_ambiguous(sq_dna_ext)
#' is_empty_sq(sq_dna_bsc)
#'
#' # Testing for presence of empty sequences after using bite and removing NA.
#' # Extracting letters from first to fifteenth - NA introduced:
#' bitten_sq <- bite(sq_dna_ext, 1:15)
#' # Removing NA:
#' rm_bitten_sq <- remove_na(bitten_sq)
#' # Testing for presence of empty sequences:
#' is_empty_sq(rm_bitten_sq)
#'
#' @family cleaning_functions
#' @seealso \code{\link[=sq-class]{sq class}}
#' @export
is_empty_sq <- function(x) {
  UseMethod("is_empty_sq")
}

#' @export
is_empty_sq.default <- function(x)
  stop_no_method(is_empty_sq, x)

#' @rdname is_empty_sq
#' @export
is_empty_sq.sq <- function(x) {
  get_sq_lengths(x) == 0
}