From 6e7fa24a178048d007dd6f96a9467be846b8066c Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Sat, 12 Oct 2024 14:47:21 +0200
Subject: [PATCH] improved output of write.pml, allow serialization.

---
 R/pml_generics.R | 27 ++++++++++++++++++++++++---
 man/write.pml.Rd |  5 ++++-
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/R/pml_generics.R b/R/pml_generics.R
index 9aab4a05..07d3c159 100644
--- a/R/pml_generics.R
+++ b/R/pml_generics.R
@@ -132,6 +132,8 @@ print.pml <- function(x, ...) {
 #'
 #' @param x an object of class ancestral.
 #' @param file a file name. File endings are added.
+#' @param save_rds logical, if TRUE saves the pml object as a rds file,
+#' otherwise the alignment is saved as a fasta file.
 #' @param ... Further arguments passed to or from other methods.
 #' @returns \code{write.pml}  returns the input x invisibly.
 #' @seealso \code{\link{ancestral.pml}}, \code{\link{plotAnc}}
@@ -141,15 +143,34 @@ print.pml <- function(x, ...) {
 #' write.pml(fit, "woodmouse")
 #' unlink(c("woodmouse_pml.txt", "woodmouse_tree.nwk"))
 #' @export
-write.pml <- function(x, file=tempfile(), ...){
+write.pml <- function(x, file="pml", save_rds=TRUE, ...){
   digits <- -1
   if (hasArg("digits")) digits <- list(...)$digits
   write.tree(x$tree, file=paste0(file, "_tree.nwk"))
-  saveRDS(x, file=paste0(file, ".rds"))
+  if(save_rds) saveRDS(x, file=paste0(file, ".rds"))
+  else write.phyDat(x$data, file=paste0(file, "_align.fasta"), format="fasta")
   if(!is.null(x$bs)) write.nexus(x$bs, file=paste0(file, "_bs.nex"),
                                  digits=digits)
   sink(paste0(file, "_pml.txt"))
-  print.pml(x)
+  cat("phangorn", packageDescription("phangorn", fields = "Version"), "\n\n")
+  print(x)
+  cat("\n\n")
+  cat("You can (re-)create the pml object using:\n\n")
+  if(save_rds){
+    cat("fit <- readRDS(\"", file,".rds\")", sep="")
+  }
+  else {
+    call <- x$call
+    call$data <- "align"
+    cat("tree <- read.tree(\"", file, "_tree.nwk\")\n", sep="")
+    cat("align <- read.fasta(\"", file, "_align.fasta\", format=\"fasta\")",
+        sep="")
+    cat( "\nfit <- ")
+    print(call)
+  }
+  cat("\n\nREFERENCES\n\n")
+  cat("To cite phangorn please use:\n\n")
+  print(citation("phangorn") [[1]], style="text")
   sink()
   invisible(x)
 }
diff --git a/man/write.pml.Rd b/man/write.pml.Rd
index a7c1a285..7c81886d 100644
--- a/man/write.pml.Rd
+++ b/man/write.pml.Rd
@@ -4,13 +4,16 @@
 \alias{write.pml}
 \title{Export pml objects}
 \usage{
-write.pml(x, file = tempfile(), ...)
+write.pml(x, file = "pml", save_rds = TRUE, ...)
 }
 \arguments{
 \item{x}{an object of class ancestral.}
 
 \item{file}{a file name. File endings are added.}
 
+\item{save_rds}{logical, if TRUE saves the pml object as a rds file,
+otherwise the alignment is saved as a fasta file.}
+
 \item{...}{Further arguments passed to or from other methods.}
 }
 \value{