a bunch of new stuff (see ChangeLog)

[ape.git] / R / read.nexus.R

diff --git a/R/read.nexus.R b/R/read.nexus.R
index 3edcd3f5903b610f42edce93884ad2665cb640a0..03aa34bc9bf53c43b55745fd2955dee4d79988e7 100644 (file)
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,20 +1,20 @@
-## read.nexus.R (2009-04-01)
+## read.nexus.R (2011-02-28)
 
 ##   Read Tree File in Nexus Format
 
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2011 Emmanuel Paradis and 2010 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, PACKAGE = "ape")
+    phy <- .Call("treeBuildWithTokens", x, PACKAGE = "apex")
     dim(phy[[1]]) <- c(length(phy[[1]])/2, 2)
-    nms <- c("edge", "edge.length", "Nnode", "node.label")
-    if (length(phy) == 5) nms <- c(nms, "root.edge")
+    nms <- c("edge", "edge.length", "Nnode", "node.label", "root.edge")
+    if (length(phy) == 4) nms <- nms[-5]
     names(phy) <- nms
-    if (!sum(phy[[4]])) phy[[4]] <- NULL
+    if (all(phy$node.label == "")) phy$node.label <- NULL
     class(phy) <- "phylo"
     phy
 }
@@ -25,18 +25,20 @@ clado.build <- function(tp)
         edge[j, 1] <<- current.node
         node <<- node + 1
         edge[j, 2] <<- current.node <<- node
+        index[node] <<- j # set index
         j <<- j + 1
     }
     add.terminal <- function() {
         edge[j, 1] <<- current.node
         edge[j, 2] <<- tip
+        index[tip] <<- j # set index
         tip.label[tip] <<- tpc[k]
         k <<- k + 1
         tip <<- tip + 1
         j <<- j + 1
     }
     go.down <- function() {
-        l <- which(edge[, 2] == current.node)
+        l <- index[current.node]
         node.label[current.node - nb.tip] <<- tpc[k]
         k <<- k + 1
         current.node <<- edge[l, 1]
@@ -45,7 +47,7 @@ clado.build <- function(tp)
         obj <- list(edge = matrix(c(2, 1), 1, 2), Nnode = 1)
         tp <- unlist(strsplit(tp, "[\\(\\);]"))
         obj$tip.label <- tp[2]
-        if (length(tp) == 3) obj$node.label <- tp[3]
+        if (tp[3] != "") obj$node.label <- tp[3]
         class(obj) <- "phylo"
         return(obj)
     }
@@ -69,11 +71,12 @@ clado.build <- function(tp)
     edge[nb.edge, 1] <- 0    # see comment above
     edge[nb.edge, 2] <- node #
 
+    index <- numeric(nb.edge + 1)
+    index[node] <- nb.edge
     ## j: index of the line number of edge
     ## k: index of the line number of tpc
     ## tip: tip number
     j <- k <- tip <- 1
-
     for (i in 2:nsk) {
         if (skeleton[i] == "(") add.internal()      # add an internal branch (on top)
         if (skeleton[i] == ",") {
@@ -87,7 +90,6 @@ clado.build <- function(tp)
             if (skeleton[i - 1] == ")") go.down()   # go down one level
         }
     }
-#    if(node.label[1] == "NA") node.label[1] <- ""
     edge <- edge[-nb.edge, ]
     obj <- list(edge = edge, tip.label = tip.label,
                 Nnode = nb.node, node.label = node.label)
@@ -224,7 +226,16 @@ read.nexus <- function(file, tree.names = NULL)
         }
     } else {
         if (!is.null(tree.names)) names(trees) <- tree.names
-        if (translation) attr(trees, "TipLabel") <- TRANS[, 2]
+        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 (length(grep("[\\/]", file)) == 1)