##' sequence alignment
##'
##'
##' @title bs_aln
##' @param x XStringSet object
##' @param method alignment method
##' @param ... additional parameter
##' @return aligned sequences, XStringSet object
##' @importFrom Biostrings DNAStringSet
##' @importFrom Biostrings RNAStringSet
##' @importFrom Biostrings AAStringSet
##' @export
##' @author Guangchuang Yu
##' @examples
##' \dontrun{
##' fa_file <- system.file("extdata/HA.fas", package="seqmagick")
##' x <- fa_read(fa_file)
##' bs_aln(x)
##' }
bs_aln <- function(x, method = 'muscle', ...) {
method <- match.arg(method, c('muscle'))
if (method == 'muscle') {
res <- muscle::muscle(x, ...)
}
switch(class(res),
DNAMultipleAlignment = DNAStringSet(res),
RNAMultipleAlignment = RNAStringSet(res),
AAMultipleAlignment = AAStringSet(res)
)
}
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