Nothing
"as.fasta" <- function(x, id=NULL, ...) {
cl <- match.call()
if(is.list(x)) {
if(is.null(id))
id <- x$id
x <- x$ali
}
if(is.vector(x)) {
if(any(nchar(x)>1))
stop("provide a matrix/vector of one letter amino acid codes")
##x <- seqbind(lapply(lapply(x, strsplit, ""), unlist))
x <- as.matrix(t(x))
}
if(is.matrix(x)) {
if(is.null(id))
id <- rownames(x)
if(is.null(id))
id <- paste("seq",1:nrow(x), sep="")
if(any(id=="") | any(is.na(id))) {
id[id==""] <- NA
inds <- which(is.na(id))
id[inds] <- paste("seq", inds, sep="")
}
if(nrow(x) != length(id))
stop("length of 'id' does not match number of rows in alignment")
rownames(x) <- id
}
else {
stop("provide a sequence character matrix/vector")
}
out <- list(id=id, ali=x, call=cl)
class(out) <- "fasta"
return(out)
}
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