some updates for ape 3.0-6

[ape.git] / man / read.dna.Rd

diff --git a/man/read.dna.Rd b/man/read.dna.Rd
index 4c02232ba8d332708162c35d257fdac66066415b..2863ad85c32ec8c47efeca1fa852bf57a5a14315 100644 (file)
--- a/man/read.dna.Rd
+++ b/man/read.dna.Rd
@@ -3,8 +3,8 @@
 \title{Read DNA Sequences in a File}
 \usage{
 read.dna(file, format = "interleaved", skip = 0,
 \title{Read DNA Sequences in a File}
 \usage{
 read.dna(file, format = "interleaved", skip = 0,

-         nlines = 0, comment.char = "#", seq.names = NULL,
-         as.character = FALSE)
+         nlines = 0, comment.char = "#",
+         as.character = FALSE, as.matrix = NULL)

 }
 \arguments{
   \item{file}{a file name specified by either a variable of mode character,
 }
 \arguments{
   \item{file}{a file name specified by either a variable of mode character,


@@ -19,10 +19,14 @@ read.dna(file, format = "interleaved", skip = 0,
     read untill its end).}
   \item{comment.char}{a single character, the remaining of the line
     after this character is ignored.}
     read untill its end).}
   \item{comment.char}{a single character, the remaining of the line
     after this character is ignored.}

-  \item{seq.names}{the names to give to each sequence; by default the
-    names read in the file are used.}

   \item{as.character}{a logical controlling whether to return the
     sequences as an object of class \code{"DNAbin"} (the default).}
   \item{as.character}{a logical controlling whether to return the
     sequences as an object of class \code{"DNAbin"} (the default).}

+  \item{as.matrix}{(used if \code{format = "fasta"}) one of the three
+    followings: (i) \code{NULL}: returns the sequences in a matrix if
+    they are of the same length, otherwise in a list; (ii) \code{TRUE}:
+    returns the sequences in a matrix, or stops with an error if they
+    are of different lengths; (iii) \code{FALSE}: always returns the
+    sequences in a list.}

 }
 \description{
   This function reads DNA sequences in a file, and returns a matrix or a
 }
 \description{
   This function reads DNA sequences in a file, and returns a matrix or a


@@ -44,19 +48,15 @@ read.dna(file, format = "interleaved", skip = 0,
   way with blanks and line-breaks inside (with the restriction that the
   first ten nucleotides must be contiguous for the interleaved and
   sequential formats, see below). The names of the sequences are read in
   way with blanks and line-breaks inside (with the restriction that the
   first ten nucleotides must be contiguous for the interleaved and
   sequential formats, see below). The names of the sequences are read in

-  the file unless the `seq.names' option is used. Particularities for
-  each format are detailed below.
+  the file. Particularities for each format are detailed below.

 
 \itemize{
 
 \itemize{

-  \item{Interleaved:}{the function starts to read the sequences when it
-    finds 10 contiguous characters belonging to the ambiguity code of
-    the IUPAC (namely A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, and
-    N, upper- or lowercase, so you might run into trouble if you have a
-    taxa name with 10 contiguous letters among these!) All characters
-    before the sequences are taken as the taxa names after removing the
-    leading and trailing spaces (so spaces in a taxa name are
-    allowed). It is assumed that the taxa names are not repeated in the
-    subsequent blocks of nucleotides.}
+  \item{Interleaved:}{the function starts to read the sequences after it
+    finds one or more spaces (or tabulations). All characters before the
+    sequences are taken as the taxa names after removing the leading and
+    trailing spaces (so spaces in taxa names are allowed). It is assumed
+    that the taxa names are not repeated in the subsequent blocks of
+    nucleotides.}

 
   \item{Sequential:}{the same criterion than for the interleaved format
     is used to start reading the sequences and the taxa names; the
 
   \item{Sequential:}{the same criterion than for the interleaved format
     is used to start reading the sequences and the taxa names; the