cleanName <- function(array_type) {

  gsub("[-_]", "", tolower(array_type))

}

#' Available Brainaaray versions

#'

#' Lists the available Brainaaray versions for \pkg{DLBCLdata}. The list is

#' currently hard coded. Newer versions may work.

#'

#' @return A character vector of the available versions.

#' @export

listVersions <- function() {

  c("19.0.0", "18.0.0", "17.1.0", "17.0.0", "16.0.0", "15.1.0", "15.0.0",

    "14.1.0", "14.0.0", "13.0.0")

}

getSubversion <- function(version, n = 1) {

  return(as.numeric(unlist(strsplit(version, "\\.")))[n])

}

arrayToBrainarrayName <- function(array_type) {

  ans <- switch(array_type,

                "HuGene-1_0-st-v1" = "hugene10st",

                cleanName(array_type))

  return(ans)

}

getCustomCDFName <- function(brain_dat, array_type) {

  custom_cdf_name <-

    with(brain_dat, CustomCDFName[match(arrayToBrainarrayName(array_type),

                                        tolower(Chip))])

  return(custom_cdf_name)

}

getBrainarrayPackages <- function(brain_dat, array_type) {

  custom_cdf_name <- getCustomCDFName(brain_dat, array_type)

  r_packages <- paste0(cleanName(custom_cdf_name), c("cdf", "probe"))

  return(r_packages)

}

#' @importFrom XML readHTMLTable

getBrainarrayTargets <- function(version) {

  base_url <- paste0("http://brainarray.mbni.med.umich.edu/Brainarray/",

                     "Database/CustomCDF/CDF_download.asp")

  brain_dat <- readHTMLTable(base_url, stringsAsFactors = FALSE)

  brain_dat <- brain_dat[sapply(brain_dat, is.data.frame)]

  brain_dat <- brain_dat[-(1:2)]

  if (missing(version)) {

    ans <- as.character(brain_dat[[length(brain_dat)]][["Custom CDF"]])

  } else {

    v <- getSubversion(version, n = 1)

    ans <- as.character(brain_dat[[v]][["Custom CDF"]])

  }

  return(ans)

}