-## write.tree.R (2009-06-16)
+## write.tree.R (2010-09-27)
## Write Tree File in Parenthetic Format
-## Copyright 2002-2009 Emmanuel Paradis and Daniel Lawson
+## Copyright 2002-2010 Emmanuel Paradis, Daniel Lawson, and Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
phy$tip.label <- checkLabel(phy$tip.label)
if (nodelab) phy$node.label <- checkLabel(phy$node.label)
f.d <- paste("%.", digits, "g", sep = "")
- cp <- function(s) STRING <<- paste(STRING, s, sep = "")
+ cp <- function(x){
+ STRING[k] <<- x
+ k <<- k + 1
+ }
add.internal <- function(i) {
cp("(")
- br <- which(phy$edge[, 1] == i)
- for (j in br) {
- desc <- phy$edge[j, 2]
- if (desc > n) add.internal(desc)
- else add.terminal(j)
- if (j != br[length(br)]) cp(",")
+ desc <- kids[[i]]
+ for (j in desc) {
+ if (j > n) add.internal(j)
+ else add.terminal(ind[j])
+ if (j != desc[length(desc)]) cp(",")
}
cp(")")
- if (nodelab) cp(phy$node.label[i - n])
+ if (nodelab) cp(phy$node.label[ind[i] - n])
if (brl) {
cp(":")
- cp(sprintf(f.d, phy$edge.length[which(phy$edge[, 2] == i)]))
+ cp(sprintf(f.d, phy$edge.length[ind[i]]))
}
}
add.terminal <- function(i) {
cp(sprintf(f.d, phy$edge.length[i]))
}
}
+
n <- length(phy$tip.label)
- STRING <-
- if (output.tree.names) paste(tree.names, "(", sep = "") else "("
- br <- which(phy$edge[, 1] == n + 1)
- for (j in br) {
- desc <- phy$edge[j, 2]
- if (desc > n) add.internal(desc)
- else add.terminal(j)
- if (j != br[length(br)]) cp(",")
+
+ ## borrowed from phangorn:
+ parent <- phy$edge[, 1]
+ children <- phy$edge[, 2]
+ kids <- vector("list", n + phy$Nnode)
+ for (i in 1:length(parent))
+ kids[[parent[i]]] <- c(kids[[parent[i]]], children[i])
+
+ ind <- match(1:max(phy$edge), phy$edge[, 2])
+
+ LS <- 4*n + 5
+ if (brl) LS <- LS + 4*n
+ if (nodelab) LS <- LS + n
+ STRING <- character(LS)
+ k <- 1
+ if (output.tree.names) cp(tree.names)
+ cp("(")
+ k <- 2
+ getRoot <- function(phy)
+ phy$edge[, 1][!match(phy$edge[, 1], phy$edge[, 2], 0)][1]
+ root <- getRoot(phy) # replaced n+1 with root - root has not be n+1
+ desc <- kids[[root]]
+ for (j in desc) {
+ if (j > n) add.internal(j)
+ else add.terminal(ind[j])
+ if (j != desc[length(desc)]) cp(",")
}
+
if (is.null(phy$root.edge)) {
cp(")")
if (nodelab) cp(phy$node.label[1])
cp(sprintf(f.d, phy$root.edge))
cp(";")
}
- if (file == "") return(STRING)
- cat(STRING, file = file, append = append, sep = "\n")
+ STRING <- paste(STRING, collapse = "")
+ if (file == "")
+ return(STRING)
+ else cat(STRING, file = file, append = append, sep = "\n")
}
-