R/get_alignment.R

In richelbilderbeek/wiritttes: WIRITTE simulation

#' Extract an alignment from an index from a file
#' @param file A loaded parameter file
#' @param i the index of the alignment
#' @return the alignment
#' @export
#' @author Richel Bilderbeek
get_alignment_by_index <- function(
  file,
  i
) {
  if (i < 1) {
    stop("index must be at least 1")
  }
  if (i > length(file$alignments)) {
    stop("index must be less than number of alignments")
  }

  alignment <- file$alignments[[i]][[1]]
  if (!ribir::is_alignment(alignment)) {
    # The alignment may not be added yet
    stop(
      "alignment absent at index ",
      i
    )
  }
  alignment
}

#' Extract an alignment from an index from a file
#' @param file A loaded parameter file
#' @param sti the species tree index, a value from 1 to and including 2
#' @param ai the alignment index,
#'   the ai-th alignment of that species tree,
#'   a value from 1 to and including
#'   the number of alignments per species tree
#' @return the alignment
#' @export
#' @author Richel Bilderbeek
get_alignment <- function(
  file, sti, ai
) {
  if (sti < 1) {
    stop("sti must be at least 1")
  }
  if (sti > 2) {
    stop("sti must at most be 2")
  }
  if (ai < 1) {
    stop("ai must be at least 1")
  }
  napst <- wiritttes::extract_napst(file = file)
  if (ai > napst) {
    stop("ai must at most be napst")
  }
  i <- wiritttes::a2i(sti = sti, ai = ai, nstpist = 2, napst = napst)
  alignment <- NA
  tryCatch(
    alignment <- get_alignment_by_index(
      file = file,
      i = i
    ),
    error = function(msg) {
      stop(msg$message)
    }
  )
  alignment
}