R/Package.XTRA.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("getDefaultSettings", "Package", function(this, ...) {
  NULL
})


setMethodS3("getSettings", "Package", function(this, ...) {
  # Use default settings
  settings <- getDefaultSettings(this)

  # Add package settings in options()
  optionName <- sprintf("%s.settings", getName(this))
  options <- getOption(optionName)

  if (length(options) > 0) {
    keys <- names(unlist(options))
    keys <- strsplit(keys, split=".", fixed=TRUE)

    for (key in keys) {
      settings[[key]] <- options[[key]]
    }
  }

  attr(settings, "option") <- optionName

  settings
})


setMethodS3("setSettings", "Package", function(this, value=list(), ...) {
  key <- sprintf("%s.settings", getName(this))
  args <- list(value)
  names(args) <- key
  do.call(options, args)
})

setMethodS3("updateSettings", "Package", function(this, ...) {
  # Get all settings; if any is missing, the default value will be used
  settings <- getSettings(this)
  # Update the options list
  setSettings(this, settings)

  # aromaSettings? /HB 2009-05-17  ('settings' does not work)
  # The solution here is still ad hoc. /HB 2010-02-22
  flat <- getLeaves(Options(settings))
  for (key in names(flat)) {
    # Update only settings not already set.
    if (!hasOption(aromaSettings, key)) {
      setOption(aromaSettings, key, flat[[key]])
    }
  }
})