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## write.nexus.R (2017-09-08)
## Write Tree File in Nexus Format
## Copyright 2003-2017 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
write.nexus <- function(..., file = "", translate = TRUE)
{
obj <- .getTreesFromDotdotdot(...)
ntree <- length(obj)
cat("#NEXUS\n", file = file)
cat(paste("[R-package APE, ", date(), "]\n\n", sep = ""),
file = file, append = TRUE)
N <- length(obj[[1]]$tip.label)
cat("BEGIN TAXA;\n", file = file, append = TRUE)
cat(paste("\tDIMENSIONS NTAX = ", N, ";\n", sep = ""),
file = file, append = TRUE)
cat("\tTAXLABELS\n", file = file, append = TRUE)
cat(paste("\t\t", obj[[1]]$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)
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)
class(obj) <- NULL
for (i in 1:ntree)
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 (!inherits(obj[[i]], "phylo")) next
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)
}
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