R/findByCdf2.R

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

setMethodS3("findByCdf2", "default", function(chipType, tags=NULL, nbrOfUnits=NULL, validator=NULL, firstOnly=TRUE, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'chipType':
  chipType <- Arguments$getCharacter(chipType, length=c(1,1))

  # Argument 'tags':
  if (!is.null(tags)) {
    tags <- Arguments$getCharacters(tags)
    tags <- unlist(strsplit(tags, split=",", fixed=FALSE), use.names=FALSE)
    tags <- trim(tags)
    tags <- tags[nzchar(tags)]
    if (length(tags) == 0)
      tags <- NULL
  }

  # Argument 'validator':
  if (!is.null(validator)) {
    if (is.function(validator)) {
    } else {
      throw("Argument 'validator' is not a function: ", mode(validator))
    }
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  # Generate all possible fullname 'chipTypes' and search for the existance
  # of a CDF with the longest name.
  verbose && enter(verbose, "Searching for CDFs")
  verbose && cat(verbose, "Chip type: ", chipType)
  verbose && cat(verbose, "Tags: ", paste(tags, collapse=", "))

  pathnames <- NULL

  cdf <- NULL
  for (kk in rev(c(0,seq_along(tags)))) {
    cdfTags <- tags[seq_len(kk)]
    fullname <- paste(c(chipType, cdfTags), collapse=",")
    verbose && printf(verbose, "Trying '%s'...", fullname)
    tryCatch({
      cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags, nbrOfUnits=nbrOfUnits)

      # Validate?  If invalid, skip it.
      if (!is.null(validator)) {
        if (!validator(cdf)) {
          cdf <- NULL
        }
      }
    }, error = function(ex) {})

    # Found a CDF?
    if (!is.null(cdf)) {
      pathnames <- c(pathnames, getPathname(cdf))
      verbose && writeRaw(verbose, "found.\n")
      if (firstOnly)
        break
    } else {
      verbose && writeRaw(verbose, "no match.\n")
    }
  }
  verbose && exit(verbose)

  pathnames
}) # findByCdf2()