From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Fri, 11 Jul 2008 15:12:16 +0000 (+0000)
Subject: final fix in read.nexus() for ape 2.2-1
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e45ffadf622e6b0569cec89d391a6f0866f6b603;p=ape.git

final fix in read.nexus() for ape 2.2-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@42 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/R/read.nexus.R b/R/read.nexus.R
index 06acd2f..d252096 100644
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,4 +1,4 @@
-## read.nexus.R (2008-07-09)
+## read.nexus.R (2008-07-11)
 
 ##   Read Tree File in Nexus Format
 
@@ -208,8 +208,11 @@ read.nexus <- function(file, tree.names = NULL)
     }
     if (Ntree == 1) {
         trees <- trees[[1]]
-        if (translation)
-            trees$tip.label <- TRANS[, 2][as.numeric(trees$tip.label)]
+        if (translation) {
+            trees$tip.label <-
+                if (length(colon)) TRANS[, 2] else
+                TRANS[, 2][as.numeric(trees$tip.label)]
+        }
     } else {
         if (!is.null(tree.names)) names(trees) <- tree.names
         if (translation) attr(trees, "TipLabel") <- TRANS[, 2]