## This code is part of the polenta package
## © C. Heibl 2017 (last update 2017-11-08)
#' @title Create Objects of Class "polentaDNA"
#' @description Create objects of class
#' \code{"\link[=polentaDNA-class]{polentaDNA}"} from objects of class
#' \code{"\link{DNAbin}"} and a matrix derived from \code{\link{guidance}} or
#' \code{\link{HoT}}.
#' @param msa An object of class \code{\link{DNAbin}}.
#' @param scores A matrix of quality scores.
#' @param method A characters string giving the method to derive the quality
#' scores.
#' @include polentaDNA-class.R
#' @seealso \code{\link{extractMSA}}
#' @importFrom methods new
#' @export
"polentaDNA" <- function(msa, scores, method){
new("polentaDNA",
msa = msa,
scores = scores,
method = method
)
}
## setMethod: indexing, extracting scores,
setMethod("show", signature = "polentaDNA",
function(object){
cat(nrow(object@msa), "DNA sequences with", object@method, "scores")
})
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