R/get_pir_params_filenames.R

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

#' Extract the filenames from a \code{pir_params}
#' @inheritParams default_params_doc
#' @return a character vector of filenames
#' @author Richèl J.C. Bilderbeek
#' @examples
#' if (beautier::is_on_ci()) {
#'   pir_params <- create_pir_params(
#'     alignment_params = create_test_alignment_params(),
#'     experiments = list(create_test_experiment())
#'   )
#'   get_pir_params_filenames(
#'     pir_params = pir_params
#'   )
#' }
#' @export
get_pir_params_filenames <- function(
  pir_params
) {
  pirouette::check_pir_params(pir_params)

  # Initialize so the tracelog and treelog filenames are filled in
  pir_params <- pirouette::init_pir_params(pir_params)

  filenames <- NA
  flat_pir_params <- unlist(pir_params)
  filename_indices <- stringr::str_detect(
    string = names(flat_pir_params),
    pattern = "filename"
  )
  # List has a nice legend
  filenames_as_list <- flat_pir_params[filename_indices]
  filenames <- as.character(unlist(filenames_as_list))

  # screenlog may be two quotes
  filenames <- stats::na.omit(filenames)
  filenames <- filenames[filenames != ""]
  testthat::expect_true(all(filenames != ""))
  if (pirouette::has_twinning(pir_params)) {
    twin_filenames <- pirouette::get_experiments_filenames(
      pir_params$experiments
    )
    twin_filenames <- stats::na.omit(twin_filenames)
    twin_filenames <- twin_filenames[twin_filenames != ""]
    twin_filenames <- pirouette::to_twin_filenames(twin_filenames)
    filenames <- c(filenames, twin_filenames)
  }

  unique(sort(filenames))
}