From 6603d33385e67db10a1d48f3ab7ec1910ce295ca Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 1 Feb 2011 03:15:05 +0000
Subject: [PATCH] bug fix in read.dna + change the default of tol in
 drop.fossil

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@144 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 ChangeLog           |  8 ++++++++
 DESCRIPTION         |  2 +-
 R/CDF.birth.death.R |  2 +-
 R/read.dna.R        | 14 ++++++++------
 man/rlineage.Rd     |  2 +-
 5 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index dd37289..a4985e5 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -14,6 +14,14 @@ BUG FIXES
     o as.hclust.phylo() failed with trees with node labels (thanks to
       Jinlong Zhang for pointing this bug out).
 
+    o read.dna(, "fasta") failed if sequences were not all of the same
+      length.
+
+
+OTHER CHANGES
+
+    o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
 
 
 		CHANGES IN APE VERSION 2.6-2
diff --git a/DESCRIPTION b/DESCRIPTION
index f5a28e0..c3f4954 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.6-3
-Date: 2010-12-24
+Date: 2011-02-01
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
diff --git a/R/CDF.birth.death.R b/R/CDF.birth.death.R
index 5fa088a..847c37d 100644
--- a/R/CDF.birth.death.R
+++ b/R/CDF.birth.death.R
@@ -287,7 +287,7 @@ rlineage <-
     .makePhylo(edge[1:j, ], edge.length[1:j], i)
 }
 
-drop.fossil <- function(phy, tol = 0)
+drop.fossil <- function(phy, tol = 1e-8)
 {
     n <- Ntip(phy)
     x <- dist.nodes(phy)[n + 1, ][1:n]
diff --git a/R/read.dna.R b/R/read.dna.R
index 98ebd65..88f3d61 100644
--- a/R/read.dna.R
+++ b/R/read.dna.R
@@ -1,8 +1,8 @@
-## read.dna.R (2010-05-17)
+## read.dna.R (2011-02-01)
 
 ##   Read DNA Sequences in a File
 
-## Copyright 2003-2010 Emmanuel Paradis
+## Copyright 2003-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -107,10 +107,12 @@ read.dna <- function(file, format = "interleaved", skip = 0,
         obj <- lapply(obj, tolower)
         LENGTHS <- unique(unlist(lapply(obj, length)))
         allSameLength <- length(LENGTHS) == 1
-        if (is.logical(as.matrix) && as.matrix && !allSameLength)
-            stop("sequences in FASTA file not of the same length")
-        if (is.null(as.matrix) && allSameLength)
-            as.matrix <- TRUE
+        if (is.logical(as.matrix)) {
+            if (as.matrix && !allSameLength)
+                stop("sequences in FASTA file not of the same length")
+        } else {
+            as.matrix <- allSameLength
+        }
         if (as.matrix) {
             obj <- matrix(unlist(obj), ncol = LENGTHS, byrow = TRUE)
             rownames(obj) <- seq.names
diff --git a/man/rlineage.Rd b/man/rlineage.Rd
index b2b1aed..5b20568 100644
--- a/man/rlineage.Rd
+++ b/man/rlineage.Rd
@@ -15,7 +15,7 @@ rlineage(birth, death, Tmax = 50, BIRTH = NULL,
          DEATH = NULL, eps = 1e-6)
 rbdtree(birth, death, Tmax = 50, BIRTH = NULL,
         DEATH = NULL, eps = 1e-6)
-drop.fossil(phy, tol = 0)
+drop.fossil(phy, tol = 1e-8)
 }
 \arguments{
   \item{birth, death}{a numeric value or a (vectorized) function
-- 
2.39.2