updates following PR #111

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ape
-Version: 5.7-1.8
-Date: 2024-01-28
+Version: 5.7-1.9
+Date: 2024-02-13
 Title: Analyses of Phylogenetics and Evolution
 Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr", comment = c(ORCID = "0000-0003-3092-2199")),
   person("Simon", "Blomberg", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1062-0839")),

NEWS

@@ -1,4 +1,4 @@
-		CHANGES IN APE VERSION 5.7-1.8
+		CHANGES IN APE VERSION 5.7-1.9
 
 
 NEW FEATURES
@@ -30,6 +30,10 @@ NEW FEATURES
       'keep.root.edge', to handle some complicated situations (see
       issue #103 on GitHub).
 
+    o read.GenBank() has a new argument 'type' to download AA
+      sequences. The default is type = "DNA", and the other choice is
+      type = "AA".
+
 
 BUG FIXES
 
@@ -70,6 +74,9 @@ OTHER CHANGES
 
     o ace() now uses node labels, if available, in the output.
 
+    o comparePhylo() now restores the graphical window in its previous
+      state (i.e., after calling layout() if plot = TRUE).
+
 
 
 		CHANGES IN APE VERSION 5.7-1

R/comparePhylo.R

@@ -1,8 +1,8 @@
-## comparePhylo.R (2024-01-13)
+## comparePhylo.R (2024-02-13)
 
 ##   Compare Two "phylo" Objects
 
-## Copyright 2018-2024 Emmanuel Paradis, 2021 Klaus Schliep
+## Copyright 2018-2024 Emmanuel Paradis, 2021-2024 Klaus Schliep
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.

R/read.GenBank.R

@@ -1,18 +1,18 @@
-## read.GenBank.R (2022-03-02)
+## read.GenBank.R (2024-02-13)
 
 ##   Read DNA Sequences and Annotations from GenBank
 
-## Copyright 2002-2022 Emmanuel Paradis
+## Copyright 2002-2022 Emmanuel Paradis and Klaus Schliep 2024
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
 read.GenBank <- function(access.nb, seq.names = access.nb, species.names = TRUE,
                          as.character = FALSE, chunk.size = 400, quiet = TRUE,
-                         type="DNA")
+                         type = "DNA")
 {
     type <- match.arg(type, c("DNA", "AA"))
-    db <- ifelse(type="DNA", "nucleotide", "protein")
+    db <- ifelse(type = "DNA", "nucleotide", "protein")
     chunk.size <- as.integer(chunk.size)
     N <- length(access.nb)
     ## if more than 400 sequences, we break down the requests
@@ -36,8 +36,7 @@ read.GenBank <- function(access.nb, seq.names = access.nb, species.names = TRUE,
         cat(" Done.\nNote: the downloaded sequences are in file:", fl)
         cat("\nReading sequences...")
     }
-    if(db=="nucleotide") res <- read.FASTA(fl, type = "DNA")
-    else res <- read.FASTA(fl, type = "AA")
+    res <- read.FASTA(fl, type = type)
     if (is.null(res)) return(NULL)
     attr(res, "description") <- names(res)
     if (length(access.nb) != length(res)) {

R/summary.phylo.R

@@ -1,8 +1,8 @@
-## summary.phylo.R (2023-04-03)
+## summary.phylo.R (2024-02-13)
 
 ##   Print Summary of a Phylogeny, "multiPhylo" operators, node degrees
 
-## Copyright 2003-2023 Emmanuel Paradis, 2006 Ben Bolker, and Klaus Schliep 2016
+## Copyright 2003-2023 Emmanuel Paradis, 2006 Ben Bolker, and Klaus Schliep 2016-2024
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.

man/read.GenBank.Rd

@@ -3,7 +3,8 @@
 \title{Read DNA Sequences from GenBank via Internet}
 \usage{
 read.GenBank(access.nb, seq.names = access.nb, species.names = TRUE,
-             as.character = FALSE, chunk.size = 400, quiet = TRUE)
+             as.character = FALSE, chunk.size = 400, quiet = TRUE,
+             type = "DNA")
 }
 \description{
   This function connects to the GenBank database, and reads nucleotide
@@ -22,8 +23,8 @@ read.GenBank(access.nb, seq.names = access.nb, species.names = TRUE,
   \item{quiet}{a logical value indicating whether to show the progress
     of the downloads. If \code{TRUE}, will also print the (full) name of
     the FASTA file containing the downloaded sequences.}
-  \item{type}{a character specifying to download "DNA" (nucleotide) or "AA"
-    (amino acid) sequences. }
+  \item{type}{a character specifying to download "DNA" (nucleotide) or
+    "AA" (amino acid) sequences.}
 }
 \details{
   The function uses the site \url{https://www.ncbi.nlm.nih.gov/} from
@@ -63,7 +64,7 @@ read.GenBank(access.nb, seq.names = access.nb, species.names = TRUE,
   \code{\link{read.dna}}, \code{\link{write.dna}},
   \code{\link{dist.dna}}, \code{\link{DNAbin}}
 }
-\author{Emmanuel Paradis}
+\author{Emmanuel Paradis and Klaus Schliep}
 \examples{
 ## This won't work if your computer is not connected
 ## to the Internet