#' @describeIn get_design 
 #'   If 
 #'   \code{method} is a character, it will return the design
 #'   matrix corresponding to the normalization scheme specified
 #'   by the character string. The string must be one of the
 #'   \code{row.names} of the slot \code{scone_params}.
 #'   

 #' @export

 #' 
 #' 

 setMethod(
   f = "get_design",
   signature = signature(x = "SconeExperiment", method = "character"),
   definition =  function(x, method) {
 
     params <- unlist(x@scone_params[method,])
 
     ruv_factors <- qc_factors <- NULL
     if(params[3] != "no_uv") {
 
       k <- as.numeric(strsplit(params[3], "=")[[1]][2])
 
       if(grepl("ruv", params[3])) {

 
         if(length(x@impute_args) > 0) {
           impute_args <- unlist(x@impute_args)
         } else {
           impute_args <- NULL
         }
 
         imputed <- x@imputation_fn[[params[1]]](assay(x), impute_args)
         scaled <- x@scaling_fn[[params[2]]](imputed)
 
         if(x@rezero) {
           toz = assay(x) <= 0
           scaled <- scaled - scaled*toz
         }
 

         r <- RUVg(log1p(scaled), get_negconruv(x), k, isLog=TRUE)$W
         ruv_factors <- list(r)
         names(ruv_factors) <- paste(params[1:2], collapse="_")
       }
 
       if(grepl("qc", params[3])) {
         qc_factors <- prcomp(get_qc(x), center=TRUE, scale=TRUE)$x
       }
 
     }
 

     parsed <- .parse_row(params, get_bio(x), get_batch(x), 
                          ruv_factors, qc_factors)

     design_mat <- make_design(parsed$bio, parsed$batch, parsed$W,

                               nested=(x@nested &
                                         !is.null(parsed$bio) &
                                         !is.null(parsed$batch)))

 
     return(design_mat)
   }
 )
 

 #' @describeIn get_design
 #'   If
 #'   \code{method} is a numeric, it will return the design matrix
 #'   according to the scone ranking.
 #'   
 #' @details The numeric method will always return the design matrix 
 #'   corresponding to row \code{method} of the \code{scone_params} 
 #'   slot. This means that if \code{\link{scone}} was run with 
 #'   \code{eval=TRUE}, \code{get_design(x, 1)} will return the top
 #'   ranked method. If \code{\link{scone}} was run with 
 #'   \code{eval=FALSE}, \code{get_design(x, 1)} will return the first
 #'   normalization in the order saved by scone.
 #'   

 #' @export

 #' 

 setMethod(
   f = "get_design",
   signature = signature(x = "SconeExperiment", method = "numeric"),
   definition =  function(x, method) {
     norm_method <- rownames(x@scone_params)[method]
 
     return(get_design(x, norm_method))
   }
 )