-## write.dna.R (2008-07-03)
+## write.dna.R (2012-05-03)
## Write DNA Sequences in a File
-## Copyright 2003-2008 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
{
format <- match.arg(format, c("interleaved", "sequential", "fasta"))
phylip <- if (format %in% c("interleaved", "sequential")) TRUE else FALSE
- if (class(x) == "DNAbin") x <- as.character(x)
+ if (inherits(x, "DNAbin")) x <- as.character(x)
aligned <- TRUE
if (is.matrix(x)) {
N <- dim(x)
}
## Prepare the names so that they all have the same nb of chars
max.nc <- max(nchar(names(x)))
- ## in case all names are 10 char long or less, sequences are
- ## always started on the 11th column of the file
- if (max.nc < 11) max.nc <- 9
+ ## always put a space between the sequences and the taxa names
fmt <- paste("%-", max.nc + 1, "s", sep = "")
names(x) <- sprintf(fmt, names(x))
}