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## read.nexus.R (2024-07-22)
## Read Tree File in Nexus Format
## Copyright 2003-2024 Emmanuel Paradis and 2010-2017 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
.treeBuildWithTokens <- function(x)
{
phy <- .Call(treeBuildWithTokens, x)
dim(phy[[1]]) <- c(length(phy[[1]])/2, 2)
nms <- c("edge", "edge.length", "Nnode", "node.label", "root.edge")
if (length(phy) == 4) nms <- nms[-5]
names(phy) <- nms
if (all(phy$node.label == "")) phy$node.label <- NULL
class(phy) <- "phylo"
attr(phy, "order") <- "cladewise"
phy
}
## for read.nexus clado with TRANSLATION
.cladoBuildWithTokens <- function(x)
{
phy <- .Call(cladoBuildWithTokens, x)
dim(phy[[1]]) <- c(length(phy[[1]])/2, 2)
nms <- c("edge", "Nnode", "node.label", "root.edge")
if (length(phy) == 3) nms <- nms[-4]
names(phy) <- nms
if (all(phy$node.label == "")) phy$node.label <- NULL
class(phy) <- "phylo"
attr(phy, "order") <- "cladewise"
phy
}
.treeBuild <- function(x)
{
if (!length(grep(",", x))) {
## only one tip but can be several nodes (GH's issues #104 and #124)
Nnode <- length(gregexpr("\\)", x)[[1]])
edge <- if (Nnode == 1L) 2:1 else c(2L, rep(3:(Nnode + 1L), each = 2), 1L)
edge <- matrix(edge, Nnode, 2L, TRUE)
phy <- list(edge = edge, Nnode = Nnode)
labs <- unlist(strsplit(x, "[\\(\\):;]"))
nt <- Nnode + 1L
phy$tip.label <- labs[nt]
labs <- labs[-(1:nt)]
s <- c(TRUE, FALSE)
tmp <- as.numeric(labs[s])
if (length(tmp) == Nnode) {
phy$edge.length <- tmp
} else { # length(tmp) == Nnode + 1L (not checked)
phy$edge.length <- tmp[-length(tmp)]
phy$root.edge <- tmp[length(tmp)]
}
phy$node.label <- labs[!s]
} else {
phy <- .Call(treeBuild, x)
dim(phy[[1]]) <- c(length(phy[[1]])/2, 2)
nms <- c("edge", "edge.length", "Nnode", "node.label", "tip.label", "root.edge")
if (length(phy) == 5) nms <- nms[-6]
names(phy) <- nms
}
if (all(phy$node.label == "")) phy$node.label <- NULL
class(phy) <- "phylo"
attr(phy, "order") <- "cladewise"
phy
}
.cladoBuild <- function(x)
{
if (!length(grep(",", x))) {
## only one tip but can be several nodes (GH's issue #104)
Nnode <- length(gregexpr("\\)", x)[[1]])
edge <- if (Nnode == 1L) 2:1 else c(2L, rep(3:(Nnode + 1L), each = 2), 1L)
dim(edge) <- c(Nnode, 2L)
phy <- list(edge = edge, Nnode = Nnode)
labs <- unlist(strsplit(x, "[\\(\\);]"))
phy$tip.label <- labs[Nnode + 1L]
phy$node.label <- labs[(Nnode + 2L):length(labs)]
} else {
phy <- .Call(cladoBuild, x)
dim(phy[[1]]) <- c(length(phy[[1]])/2, 2)
nms <- c("edge", "Nnode", "node.label", "tip.label", "root.edge")
if (length(phy) == 4) nms <- nms[-5]
names(phy) <- nms
}
if (all(phy$node.label == "")) phy$node.label <- NULL
class(phy) <- "phylo"
attr(phy, "order") <- "cladewise"
phy
}
read.nexus <- function(file, tree.names = NULL, force.multi = FALSE)
{
X <- scan(file = file, what = "", sep = "\n", quiet = TRUE)
## remove all comments
## (this might not work if there are square brackets within the comments)
LEFT <- grep("\\[", X)
RIGHT <- grep("\\]", X)
if (length(LEFT)) { # in case there are no comments at all
w <- LEFT == RIGHT
if (any(w)) { # in case all comments use at least 2 lines
s <- LEFT[w]
X[s] <- gsub("\\[[^]]*\\]", "", X[s])
## The above regexp was quite tough to find: it makes
## possible to delete series of comments on the same line:
## ...[...]xxx[...]...
## without deleting the "xxx". This regexp is in three parts:
## \\[ [^]]* \\]
## where [^]]* means "any character, except "]", repeated zero
## or more times" (note that the ']' is not escaped here).
## The previous version was:
## X[s] <- gsub("\\[.*\\]", "", X[s])
## which deleted the "xxx". (EP 2008-06-24)
}
w <- !w
if (any(w)) {
s <- LEFT[w]
X[s] <- gsub("\\[.*", "", X[s])
sb <- RIGHT[w]
X[sb] <- gsub(".*\\]", "", X[sb])
if (any(s < sb - 1))
X <- X[-unlist(mapply(":", (s + 1), (sb - 1)))]
}
}
endblock <- grep("END;|ENDBLOCK;", X, ignore.case = TRUE)
semico <- grep(";", X)
i1 <- grep("BEGIN TREES;", X, ignore.case = TRUE)
i2 <- grep("TRANSLATE", X, ignore.case = TRUE)
translation <- if (length(i2) == 1 && i2 > i1) TRUE else FALSE
if (translation) {
end <- semico[semico > i2][1]
x <- X[(i2 + 1):end] # assumes there's a 'new line' after "TRANSLATE"
#x <- unlist(strsplit(x, "[,; \t]"))
################################################
# when the label of translation contains space #
# 1 "tip 1 a", #
# 2 "tip 2" #
################################################
# remove the space and tab before the string
x <- gsub("^\\s+", "", x)
# remove the , ; symbol
x <- gsub("[,;]", "", x)
# split with the first space
x <- unlist(regmatches(x, regexpr("\\s+", x), invert=TRUE))
###############################################
x <- x[nzchar(x)]
TRANS <- matrix(x, ncol = 2, byrow = TRUE)
TRANS[, 2] <- gsub("['\"]", "", TRANS[, 2])
n <- dim(TRANS)[1]
}
start <-
if (translation) semico[semico > i2][1] + 1
else i1 + 1 # semico[semico > i1][1] ## fix done on 2014-08-25
end <- endblock[endblock > i1][1] - 1
tree <- X[start:end]
rm(X)
## check whether there are empty lines from the above manips:
tree <- tree[tree != ""]
semico <- grep(";", tree)
Ntree <- length(semico) # provisional -- some ";" may actually mark end of commands
## are some trees on several lines?
## -- this actually 'packs' all characters ending with a ";" in a single string --
if (Ntree == 1 && length(tree) > 1) STRING <- paste(tree, collapse = "") else {
if (any(diff(semico) != 1)) {
STRING <- character(Ntree)
s <- c(1, semico[-Ntree] + 1)
j <- mapply(":", s, semico)
if (is.list(j)) {
for (i in 1:Ntree)
STRING[i] <- paste(tree[j[[i]]], collapse = "")
} else {
for (i in 1:Ntree)
STRING[i] <- paste(tree[j[, i]], collapse = "")
}
} else STRING <- tree
}
rm(tree)
## exclude the possible command lines ending with ";":
STRING <- STRING[grep("^[[:blank:]]*tree.*= *", STRING, ignore.case = TRUE)]
Ntree <- length(STRING) # update Ntree
## get the tree names:
nms.trees <- sub(" *= *.*", "", STRING) # only the first occurence of "="
nms.trees <- sub("^[[:blank:]]*tree[[:blank:]\\*]*", "", nms.trees, ignore.case = TRUE) # fix by Graham Gower (2014-10-20)
STRING <- sub("^.*= *", "", STRING) # delete title and 'TREE' command with 'sub'
STRING <- gsub(" ", "", STRING) # delete all white spaces
colon <- grep(":", STRING)
if (!length(colon)) {
trees <- lapply(STRING, .cladoBuild)
} else if (length(colon) == Ntree) {
trees <-
if (translation) lapply(STRING, .treeBuildWithTokens)
else lapply(STRING, .treeBuild)
} else {
trees <- vector("list", Ntree)
trees[colon] <- lapply(STRING[colon], .treeBuild)
nocolon <- (1:Ntree)[!1:Ntree %in% colon]
trees[nocolon] <- lapply(STRING[nocolon], .cladoBuild)
if (translation) {
for (i in 1:Ntree) {
tr <- trees[[i]]
for (j in 1:n) {
ind <- which(tr$tip.label[j] == TRANS[, 1])
tr$tip.label[j] <- TRANS[ind, 2]
}
if (!is.null(tr$node.label)) {
for (j in 1:length(tr$node.label)) {
ind <- which(tr$node.label[j] == TRANS[, 1])
tr$node.label[j] <- TRANS[ind, 2]
}
}
trees[[i]] <- tr
}
translation <- FALSE
}
}
for (i in 1:Ntree) {
tr <- trees[[i]]
if (!translation) n <- length(tr$tip.label)
}
if (Ntree == 1 && !force.multi) {
trees <- trees[[1]]
if (translation) {
trees$tip.label <-
if (length(colon)) TRANS[, 2] else
TRANS[, 2][as.numeric(trees$tip.label)]
}
} else {
if (!is.null(tree.names)) names(trees) <- tree.names
if (translation) {
if (length(colon) == Ntree) # .treeBuildWithTokens() was used
attr(trees, "TipLabel") <- TRANS[, 2]
else { # reassign the tip labels then compress
for (i in 1:Ntree)
trees[[i]]$tip.label <-
TRANS[, 2][as.numeric(trees[[i]]$tip.label)]
trees <- .compressTipLabel(trees)
}
}
class(trees) <- "multiPhylo"
if (!all(nms.trees == "")) names(trees) <- nms.trees
}
trees
}
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