-## DNA.R (2012-02-14)
+## DNA.R (2012-06-19)
## Manipulations and Comparisons of DNA Sequences
nms <- names(x)
if (n == 1) {
cat("1 DNA sequence in binary format stored in a list.\n\n")
- cat("Sequence length:", length(x[[1]]), "\n\n")
+ nTot <- length(x[[1]])
+ cat("Sequence length:", nTot, "\n\n")
cat("Label:", nms, "\n\n")
} else {
cat(n, "DNA sequences in binary format stored in a list.\n\n")
tmp <- unlist(lapply(x, length))
- mini <- min(tmp)
- maxi <- max(tmp)
+ nTot <- sum(tmp)
+ mini <- range(tmp)
+ maxi <- mini[2]
+ mini <- mini[1]
if (mini == maxi)
cat("All sequences of same length:", maxi, "\n")
else {
}
cat("\nLabels:", paste(nms, collapse = " "), TAIL)
}
- } else if (is.matrix(x)) {
- nd <- dim(x)
- nms <- rownames(x)
- cat(nd[1], "DNA sequences in binary format stored in a matrix.\n\n")
- cat("All sequences of same length:", nd[2], "\n")
- TAIL <- "\n\n"
- if (printlen < nd[1]) {
- nms <- nms[1:printlen]
- TAIL <- "...\n\n"
- }
- cat("\nLabels:", paste(nms, collapse = " "), TAIL)
} else {
- cat("1 DNA sequence in binary format stored in a vector.\n\n")
- cat("Sequence length:", length(x), "\n\n")
+ nTot <- length(x)
+ if (is.matrix(x)) {
+ nd <- dim(x)
+ nms <- rownames(x)
+ cat(nd[1], "DNA sequences in binary format stored in a matrix.\n\n")
+ cat("All sequences of same length:", nd[2], "\n")
+ TAIL <- "\n\n"
+ if (printlen < nd[1]) {
+ nms <- nms[1:printlen]
+ TAIL <- "...\n\n"
+ }
+ cat("\nLabels:", paste(nms, collapse = " "), TAIL)
+ } else {
+ cat("1 DNA sequence in binary format stored in a vector.\n\n")
+ cat("Sequence length:", nTot, "\n\n")
+ }
}
- cat("Base composition:\n")
- print(round(base.freq(x), digits))
+ if (nTot <= 1e6) {
+ cat("Base composition:\n")
+ print(round(base.freq(x), digits))
+ } else cat("More than 1 million nucleotides: not printing base composition\n")
}
as.DNAbin <- function(x, ...) UseMethod("as.DNAbin")
if (!pairwise.deletion) {
keep <- .C("GlobalDeletionDNA", x, n, s,
rep(1L, s), PACKAGE = "ape")[[4]]
- x <- x[, as.logical(keep)]
+ x <- x[, as.logical(keep)]
s <- dim(x)[2]
}
Ndist <- if (imod == 11) n*n else n*(n - 1)/2