From 35ab8b00668b0993d0e8221094555adc997518c1 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Wed, 9 Jul 2008 07:36:08 +0000
Subject: [PATCH] bug fix in read.nexus()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@41 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 Changes        | 3 +++
 DESCRIPTION    | 2 +-
 R/read.nexus.R | 7 ++++---
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/Changes b/Changes
index 86d0131..2392e8a 100644
--- a/Changes
+++ b/Changes
@@ -30,6 +30,9 @@ BUG FIXES
     o read.nexus() failed to read a file with a single tree and no
       translation of tip labels.
 
+    o read.nexus() failed to place correctly tip labels when reading
+      a single tree with no edge lengths.
+
 
 OTHER CHANGES
 
diff --git a/DESCRIPTION b/DESCRIPTION
index c511656..6b1df81 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-1
-Date: 2008-07-03
+Date: 2008-07-09
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/read.nexus.R b/R/read.nexus.R
index 5438456..06acd2f 100644
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,4 +1,4 @@
-## read.nexus.R (2008-07-04)
+## read.nexus.R (2008-07-09)
 
 ##   Read Tree File in Nexus Format
 
@@ -110,7 +110,7 @@ read.nexus <- function(file, tree.names = NULL)
         if (any(w)) { # in case all comments use at least 2 lines
             s <- LEFT[w]
             X[s] <- gsub("\\[[^]]*\\]", "", X[s])
-            ## The previous regexp was quite tough to find: it makes
+            ## 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:
@@ -208,7 +208,8 @@ read.nexus <- function(file, tree.names = NULL)
     }
     if (Ntree == 1) {
         trees <- trees[[1]]
-        if (translation) trees$tip.label <- TRANS[, 2]
+        if (translation)
+            trees$tip.label <- TRANS[, 2][as.numeric(trees$tip.label)]
     } else {
         if (!is.null(tree.names)) names(trees) <- tree.names
         if (translation) attr(trees, "TipLabel") <- TRANS[, 2]
-- 
2.39.5