some changes for ape 3.0-6

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

diff --git a/R/write.tree.R b/R/write.tree.R
index e4614d8e0a97973637c53b280238046c1ba24166..08de505eaf78f90db4a2000a94d7dd733b3eaa9e 100644 (file)
--- a/R/write.tree.R
+++ b/R/write.tree.R
@@ -1,8 +1,8 @@
-## write.tree.R (2007-12-22)
+## write.tree.R (2010-12-07)
 
 ##   Write Tree File in Parenthetic Format
 
-## Copyright 2002-2007 Emmanuel Paradis
+## 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.
@@ -27,53 +27,56 @@ checkLabel <- function(x, ...)
     x
 }
 
-write.tree <- function(phy, file = "", append = FALSE,
-                       digits = 10)
+write.tree <-
+    function(phy, file = "", append = FALSE, digits = 10, tree.names = FALSE)
 {
-    if (class(phy) == "multiPhylo") {
-        write.tree(phy[[1]], file = file,
-                   append = append, digits = digits)
-        if (length(phy) > 1)
-            for (i in 2:length(phy))
-                write.tree(phy[[i]], file = file,
-                           append = TRUE, digits = digits)
-        return(invisible(NULL))
-    }
+    if (!(inherits(phy, c("phylo", "multiPhylo"))))
+        stop("object \"phy\" has no trees")
 
-    if (class(phy) != "phylo")
-      stop('object "phy" is not of class "phylo"')
+    if (inherits(phy, "phylo")) phy <- c(phy)
+    N <- length(phy)
+    res <- character(N)
 
-    brl <- !is.null(phy$edge.length)
+    if (is.logical(tree.names)) {
+        if (tree.names) {
+            tree.names <-
+                if (is.null(names(phy))) character(N)
+                else names(phy)
+        } else tree.names <- character(N)
+    }
 
-### Ne serait-il pas plus efficace de créer des node labels vides
-### "" et d'éviter l'évaluation if (nodelab) ????
-### Autre possibilité : créer plusieurs variants de ces fonctions
-### (au moins deux avec/sans edge.length)
+    for (i in 1:N)
+        res[i] <- .write.tree2(phy[[i]], digits = digits,
+                               tree.prefix = tree.names[i])
 
-### Encore autre chose: les appels à which ne peuvent-ils pas
-### être évités ??? surtout si l'arbre est en cladewise order...
+    if (file == "") return(res)
+    else cat(res, file = file, append = append, sep = "\n")
+}
 
+.write.tree2 <- function(phy, digits = 10, tree.prefix = "")
+{
+    brl <- !is.null(phy$edge.length)
     nodelab <- !is.null(phy$node.label)
     phy$tip.label <- checkLabel(phy$tip.label)
-    if (nodelab)
-      phy$node.label <- checkLabel(phy$node.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$node.label[i - n])
+        if (nodelab && i > n) cp(phy$node.label[i - n]) # fixed by Naim Matasci (2010-12-07)
         if (brl) {
             cp(":")
-            cp(sprintf(f.d, phy$edge.length[which(phy$edge[, 2] == i)]))
+            cp(sprintf(f.d, phy$edge.length[ind[i]]))
         }
     }
     add.terminal <- function(i) {
@@ -83,25 +86,46 @@ write.tree <- function(phy, file = "", append = FALSE,
             cp(sprintf(f.d, phy$edge.length[i]))
         }
     }
+
     n <- length(phy$tip.label)
-    STRING <- "("
-    br <- which(phy$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
+    cp(tree.prefix)
+    cp("(")
+    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$node.label[1])
         cp(";")
-    } else {
+    }
+    else {
         cp(")")
         if (nodelab) cp(phy$node.label[1])
         cp(":")
         cp(sprintf(f.d, phy$root.edge))
         cp(";")
     }
-    if (file == "") return(STRING)
-    else cat(STRING, file = file, append = append, sep = "\n")
+    paste(STRING, collapse = "")
 }