#' @title Final Preprocessing

#' @description This function generates the final filtered normalized dataset.

#' @param object \code{DISCBIO} class object.

#' @param GeneFlitering GeneFlitering has to be one of the followings:

#'   ["NoiseF","ExpF"]. Default is "NoiseF"

#' @param export A logical vector that allows writing the final gene list in

#'   excel file. Default is TRUE.

#' @param quiet if `TRUE`, intermediary output is suppressed

#' @param fileName File name for exporting (if `export = TRUE`)

#' @return The DISCBIO-class object input with the FinalGeneList slot filled.

#' @examples

#' #sc <- DISCBIO(valuesG1msTest)

#' #sc <- NoiseFiltering(sc, percentile = 0.9, CV = 0.2, export = FALSE)

#' #sc <- FinalPreprocessing(sc, GeneFlitering = "NoiseF", export = FALSE)

#'

setGeneric(

  "FinalPreprocessing",

  function(object,

           GeneFlitering = "NoiseF",

           export = FALSE,

           quiet = FALSE,

           fileName = "filteredDataset") {

    standardGeneric("FinalPreprocessing")

  }

)

#' @export

#' @rdname FinalPreprocessing

setMethod(

  "FinalPreprocessing",

  signature = "DISCBIO",

  definition = function(object, GeneFlitering, export, quiet, fileName) {

    if (GeneFlitering == "NoiseF") {

      if (length(object@noiseF) < 1) {

        stop("run NoiseFiltering before running FinalPreprocessing")

      }

      if (nrow(object@fdata) < 1) {

        stop("run Normalizedata before running FinalPreprocessing")

      }

      gene_list <- object@noiseF

      gene_names <- rownames(object@fdata)

      idx_genes <- is.element(gene_names, gene_list)

      gene_names2 <- gene_names[idx_genes]

      filteredDataset <- object@fdata[gene_names2, ]

      object@fdata <- filteredDataset

      object@FinalGeneList <- rownames(filteredDataset)

    }

    if (GeneFlitering == "ExpF") {

      if (nrow(object@fdata) < 1) {

        stop("run Normalizedata before running FinalPreprocessing")

      }

      filteredDataset <- object@fdata

      object@FinalGeneList <- rownames(filteredDataset)

    }

    if (!quiet) {

      message(

        "The gene filtering method = Noise filtering\n\n",

        "The Filtered Normalized dataset contains:\n",

        "Genes: ", length(filteredDataset[, 1]), "\n",

        "cells: ", length(filteredDataset[1, ]), "\n\n"

      )

    }

    if (export) {

      fileNameExt <- paste0(fileName, ".Rdata")

      if (!quiet) {

        message(

          "The Filtered Normalized dataset was saved as: ",

          fileNameExt

        )

      }

      save(filteredDataset, file = fileNameExt)

    }

    return(object)

  }

)