R/build_tree.R

In esnapd/DegeneratePrimerTools: Tools for Designing Degenerate Primers

#' build tree
#' 
#' Create a Tree from An MSA
#'
#' @param dgprimer Required. A \code{\link{degeprimer}} object.
#' @param force  Optional. Default is \code{FALSE}. If an msa already 
#' exists, you must set FORCE to TRUE to overwrite it.
#'
#' @export
build_tree <- function(dgprimer, force=FALSE,...) {
  
  if (is.null(dgprimer@msa)) {
    stop("Your degeprime object does not have a MultipleSequenceAlignment. Try using run-alignment")
  }
  if (force==FALSE  & !is.null(dgprimer@phy_tree)) {
    stop("Your degeprime object already has a phylogenetic tree. To overwrite use force=TRUE")
  }
  
  seqs <- dgprimer@msa
  seqs <- as(seqs, "DNAStringSet")
  tree <- run_fasttree(seqs)
  dgprimer@phy_tree <- tree
  
  return(dgprimer)
}