new image.DNAbin()

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

diff --git a/R/write.nexus.R b/R/write.nexus.R
index 1a816f0573ff35d5b30d64e3e18c9619e775b073..2a3c32ada3ce1a5102abf6d0c1492a25bcb6fc90 100644 (file)
--- a/R/write.nexus.R
+++ b/R/write.nexus.R
@@ -1,8 +1,8 @@
-## write.nexus.R (2009-07-27)
+## write.nexus.R (2011-02-26)
 
 ##   Write Tree File in Nexus Format
 
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2011x Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -69,18 +69,28 @@ the original data won't be written with the tree."))
         token <- as.character(1:N)
         names(token) <- obj[[1]]$tip.label
         obj[[1]]$tip.label <- token
-        if (ntree > 1)
-          for (i in 2:ntree)
-            obj[[i]]$tip.label <- token[obj[[i]]$tip.label]
+        if (ntree > 1) {
+            for (i in 2:ntree)
+                obj[[i]]$tip.label <- token[obj[[i]]$tip.label]
+            class(obj) <- NULL
+        }
     } else {
         for (i in 1:ntree)
-          obj[[i]]$tip.label <- checkLabel(obj[[i]]$tip.label)
+            obj[[i]]$tip.label <- checkLabel(obj[[i]]$tip.label)
+    }
+
+    title <- names(obj)
+    if (is.null(title))
+        title <- rep("UNTITLED", ntree)
+    else {
+        if (any(s <- title == "")) title[s] <- "UNTITLED"
     }
+
     for (i in 1:ntree) {
         if (class(obj[[i]]) != "phylo") next
         if (is.rooted(obj[[i]]))
-          cat("\tTREE * UNTITLED = [&R] ", file = file, append = TRUE)
-        else cat("\tTREE * UNTITLED = [&U] ", file = file, append = TRUE)
+          cat("\tTREE *,", title[i], "= [&R] ", file = file, append = TRUE)
+        else cat("\tTREE *", title[i], "= [&U] ", file = file, append = TRUE)
         cat(write.tree(obj[[i]], file = ""),
             "\n", sep = "", file = file, append = TRUE)
     }