some changes done before the HD failure of my laptop... I presume

[ape.git] / R / reorder.phylo.R

diff --git a/R/reorder.phylo.R b/R/reorder.phylo.R
index e06b26bb44e6a7e9439819d03544c52f4c4971a7..e717eb26c2583c6d3cf0e371f289538c851d6ac2 100644 (file)
--- a/R/reorder.phylo.R
+++ b/R/reorder.phylo.R
@@ -1,34 +1,44 @@
-## reorder.phylo.R (2010-04-02)
+## reorder.phylo.R (2012-10-12)
 
 ##   Internal Reordering of Trees
 
-## Copyright 2006-2010 Emmanuel Paradis
+## Copyright 2006-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-reorder.phylo <- function(x, order = "cladewise", ...)
+reorder.phylo <- function(x, order = "cladewise", index.only = FALSE, ...)
 {
-    order <- match.arg(order, c("cladewise", "pruningwise"))
+    ORDER <- c("cladewise", "postorder", "pruningwise")
+    io <- pmatch(order, ORDER)
+    if (is.na(io)) stop("ambiguous order")
+    order <- ORDER[io]
+    nb.edge <- dim(x$edge)[1]
     if (!is.null(attr(x, "order")))
-        if (attr(x, "order") == order) return(x)
+        if (attr(x, "order") == order)
+            if (index.only) return(1:nb.edge) else return(x)
     nb.node <- x$Nnode
     if (nb.node == 1) return(x)
     nb.tip <- length(x$tip.label)
-    nb.edge <- dim(x$edge)[1]
-    neworder <- if (order == "cladewise")
-      .C("neworder_cladewise", as.integer(nb.tip),
-         as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-         as.integer(nb.edge), integer(nb.edge),
-         PACKAGE = "ape")[[5]]
-    else
-      .C("neworder_pruningwise", as.integer(nb.tip),
-         as.integer(nb.node), as.integer(x$edge[, 1]),
-         as.integer(x$edge[, 2]), as.integer(nb.edge),
-         integer(nb.edge), PACKAGE = "ape")[[6]]
+    if (io == 3) {
+        x <- reorder(x)
+        neworder <-
+            .C("neworder_pruningwise", as.integer(nb.tip),
+               as.integer(nb.node), as.integer(x$edge[, 1]),
+               as.integer(x$edge[, 2]), as.integer(nb.edge),
+               integer(nb.edge), PACKAGE = "ape")[[6]]
+    } else {
+        neworder <-
+            .C("neworder_phylo", as.integer(nb.tip),
+               as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+               as.integer(nb.edge), integer(nb.edge), io,
+               DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[5]]
+    }
+    if (index.only) return(neworder)
     x$edge <- x$edge[neworder, ]
     if (!is.null(x$edge.length))
-      x$edge.length <- x$edge.length[neworder]
+        x$edge.length <- x$edge.length[neworder]
     attr(x, "order") <- order
     x
 }
+