final commit for ape 3.0

[ape.git] / R / write.nexus.R

diff --git a/R/write.nexus.R b/R/write.nexus.R
index 1db2252d74b0c4d8cd63531de1510a5280a7eed1..fd4407832b4c6ca2ddb12e78cc5a91b53466b7ab 100644 (file)
--- a/R/write.nexus.R
+++ b/R/write.nexus.R
@@ -1,13 +1,13 @@
-## write.nexus.R (2011-03-26)
+## write.nexus.R (2012-02-09)
 
 ##   Write Tree File in Nexus Format
 
-## Copyright 2003-2011 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-write.nexus <- function(..., file = "", translate = TRUE, original.data = TRUE)
+write.nexus <- function(..., file = "", translate = TRUE, original.data = NULL)
 {
     obj <- list(...)
     ## We insure that all trees are in a list, even if there is a single one:
@@ -21,40 +21,21 @@ write.nexus <- function(..., file = "", translate = TRUE, original.data = TRUE)
     cat("#NEXUS\n", file = file)
     cat(paste("[R-package APE, ", date(), "]\n\n", sep = ""),
         file = file, append = TRUE)
-    if (original.data) {
-        if (!is.null(attr(obj[[1]], "origin"))) {
-            if (!file.exists(attr(obj[[1]], "origin"))) {
-                warning(paste("the file", attr(obj[[1]], "origin"),
-                              "cannot be found,
-the original data won't be written with the tree."))
-                original.data <- FALSE
-            }
-            else {
-                ORI <- scan(file = attr(obj[[1]], "origin"), what = character(),
-                            sep = "\n", skip = 1)
-                start <- grep("BEGIN TAXA;", ORI)
-                ORI <- ORI[-(1:(start - 1))]
-                ORI <- gsub("ENDBLOCK;", "END;", ORI)
-                endblock <- grep("END;", ORI)
-                start <- grep("BEGIN TREES;", ORI)
-                end <- endblock[endblock > start][1]
-                cat(ORI[1:(start - 1)], file = file, append = TRUE, sep = "\n")
-                ORI <- ORI[-(1:end)]
-            }
-        }
-        else original.data <- FALSE
-    }
+
+    if (!is.null(original.data))
+        warning("the option 'original.data' is deprecated and will be removed soon. Please update your code.")
+
     N <- length(obj[[1]]$tip.label)
-    if (!original.data) {
-        cat("BEGIN TAXA;\n", file = file, append = TRUE)
-        cat(paste("\tDIMENSIONS NTAX = ", N, ";\n", sep = ""),
-            file = file, append = TRUE)
-        cat("\tTAXLABELS\n", file = file, append = TRUE)
-        cat(paste("\t\t", obj[[1]]$tip.label, sep = ""),
-            sep = "\n", file = file, append = TRUE)
-        cat("\t;\n", file = file, append = TRUE)
-        cat("END;\n", file = file, append = TRUE)
-    }
+
+    cat("BEGIN TAXA;\n", file = file, append = TRUE)
+    cat(paste("\tDIMENSIONS NTAX = ", N, ";\n", sep = ""),
+        file = file, append = TRUE)
+    cat("\tTAXLABELS\n", file = file, append = TRUE)
+    cat(paste("\t\t", obj[[1]]$tip.label, sep = ""),
+        sep = "\n", file = file, append = TRUE)
+    cat("\t;\n", file = file, append = TRUE)
+    cat("END;\n", file = file, append = TRUE)
+
     cat("BEGIN TREES;\n", file = file, append = TRUE)
     if (translate) {
         cat("\tTRANSLATE\n", file = file, append = TRUE)
@@ -93,5 +74,4 @@ the original data won't be written with the tree."))
             "\n", sep = "", file = file, append = TRUE)
     }
     cat("END;\n", file = file, append = TRUE)
-    if(original.data) cat(ORI, file = file, append = TRUE, sep = "\n")
 }