some modifs for ape 3.0-8

[ape.git] / R / write.dna.R

diff --git a/R/write.dna.R b/R/write.dna.R
index 59712eafb182d1be4410d582fce08c4a99a5f160..3f53cb91d3e44ed82e7fda200add179bda13f1c3 100644 (file)
--- a/R/write.dna.R
+++ b/R/write.dna.R
@@ -1,8 +1,8 @@
-## write.dna.R (2008-07-03)
+## write.dna.R (2012-06-22)
 
 ##   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.
@@ -13,7 +13,7 @@ write.dna <- function(x, file, format = "interleaved", append = FALSE,
 {
     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)
@@ -62,13 +62,11 @@ write.dna <- function(x, file, format = "interleaved", append = FALSE,
         }
         ## 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))
     }
-    if (format == "interleaved") {
+    switch(format, "interleaved" = {
         ## Write the first block with the taxon names
         colsel <- if (nb.block == 1) 1:totalcol else 1:nbcol
         for (i in 1:N) {
@@ -89,8 +87,7 @@ write.dna <- function(x, file, format = "interleaved", append = FALSE,
             }
         }
 
-    }
-    if (format == "sequential") {
+    }, "sequential" = {
         if (nb.block == 1) {
             for (i in 1:N) {
                 cat(names(x)[i], file = zz)
@@ -110,10 +107,9 @@ write.dna <- function(x, file, format = "interleaved", append = FALSE,
                 }
             }
         }
-    }
-    if (format == "fasta") {
+    }, "fasta" = {
         for (i in 1:N) {
-            cat(">", names(x)[i], file = zz)
+            cat(">", names(x)[i], file = zz, sep = "")
             cat("\n", file = zz)
             X <- paste(x[[i]], collapse = "")
             S <- length(x[[i]])
@@ -131,5 +127,5 @@ write.dna <- function(x, file, format = "interleaved", append = FALSE,
                 cat("\n", file = zz)
             }
         }
-    }
+    })
 }