various fixes in C files

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

diff --git a/R/write.nexus.R b/R/write.nexus.R
index 14f77341c498bfcd4a2f3bfbadffd905bdc3de2d..ac383f73ec0415de4e7447acb46550fdcaf4a459 100644 (file)
--- a/R/write.nexus.R
+++ b/R/write.nexus.R
@@ -1,13 +1,13 @@
-## write.nexus.R (2009-10-27)
+## write.nexus.R (2012-03-30)
 
 ##   Write Tree File in Nexus Format
 
-## Copyright 2003-2009 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)
 {
     obj <- list(...)
     ## We insure that all trees are in a list, even if there is a single one:
@@ -21,71 +21,53 @@ 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
-    }
+
     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]]$tip.label, sep = ""),
+        sep = "\n", file = file, append = TRUE)
+    cat("\t;\n", file = file, append = TRUE)
+    cat("END;\n", file = file, append = TRUE)
+
     cat("BEGIN TREES;\n", file = file, append = TRUE)
     if (translate) {
-        ## We take arbitrarily the labels of the first tree, and
-        ## translate them as "1", "2", "3", ...
         cat("\tTRANSLATE\n", file = file, append = TRUE)
-        tmp <- checkLabel(obj[[1]]$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]
-            class(obj) <- NULL
-        }
-    } 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)
+        root.tag <- if (is.rooted(obj[[i]])) "= [&R] " else "= [&U] "
+        cat("\tTREE *", title[i], root.tag, file = file, append = TRUE)
         cat(write.tree(obj[[i]], file = ""),
             "\n", sep = "", file = file, append = TRUE)
     }
     cat("END;\n", file = file, append = TRUE)
-    if(original.data) cat(ORI, file = file, append = TRUE, sep = "\n")
 }