bug fix in root()

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

diff --git a/R/write.nexus.R b/R/write.nexus.R
index 1a816f0573ff35d5b30d64e3e18c9619e775b073..1db2252d74b0c4d8cd63531de1510a5280a7eed1 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 (2011-03-26)
 
 ##   Write Tree File in Nexus Format
 
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -57,30 +57,38 @@ the original data won't be written with the tree."))
     }
     cat("BEGIN TREES;\n", file = file, append = TRUE)
     if (translate) {
-        ## We take arbitrarily the labels of the first tree, and
-        ## translate them as "1", "2", "3", ...
         cat("\tTRANSLATE\n", file = file, append = TRUE)
-        tmp <- checkLabel(obj[[1]]$tip.label)
-        X <- paste("\t\t", 1:N, "\t", tmp, ",", sep = "")
+        obj <- .compressTipLabel(obj)
+        X <- paste("\t\t", 1:N, "\t", attr(obj, "TipLabel"), ",", sep = "")
         ## We remove the last comma:
         X[length(X)] <- gsub(",", "", X[length(X)])
         cat(X, file = file, append = TRUE, sep = "\n")
         cat("\t;\n", file = file, append = TRUE)
-        token <- as.character(1:N)
-        names(token) <- obj[[1]]$tip.label
-        obj[[1]]$tip.label <- token
-        if (ntree > 1)
-          for (i in 2:ntree)
-            obj[[i]]$tip.label <- token[obj[[i]]$tip.label]
-    } else {
+        class(obj) <- NULL
         for (i in 1:ntree)
-          obj[[i]]$tip.label <- checkLabel(obj[[i]]$tip.label)
+            obj[[i]]$tip.label <- as.character(1:N)
+    } else {
+        if (is.null(attr(obj, "TipLabel"))) {
+            for (i in 1:ntree)
+                obj[[i]]$tip.label <- checkLabel(obj[[i]]$tip.label)
+        } else {
+            attr(obj, "TipLabel") <- checkLabel(attr(obj, "TipLabel"))
+            obj <- .uncompressTipLabel(obj)
+        }
     }
+
+    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)
     }