write.nexus.R
## write.nexus.R (2009-10-27)
## Write Tree File in Nexus Format
## Copyright 2003-2009 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)
{
obj <- list(...)
## We insure that all trees are in a list, even if there is a single one:
if (length(obj) == 1) {
if (class(obj[[1]]) == "phylo") ntree <- 1
else {
obj <- obj[[1]] # NOT use unlist()
ntree <- length(obj)
}
} else ntree <- length(obj)
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 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]]$tip.label)
X <- paste("\t\t", 1:N, "\t", tmp, ",", sep = "")
## We remove the last comma:
X[length(X)] <- gsub(",", "", X[length(X)])
cat(X, file = file, append = TRUE, sep = "\n")
cat("\t;\n", file = file, append = TRUE)
token <- as.character(1:N)
names(token) <- obj[[1]]$tip.label
obj[[1]]$tip.label <- token
if (ntree > 1) {
for (i in 2:ntree)
obj[[i]]$tip.label <- token[obj[[i]]$tip.label]
class(obj) <- NULL
}
} else {
for (i in 1:ntree)
obj[[i]]$tip.label <- checkLabel(obj[[i]]$tip.label)
}
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(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")
}