R/CopyNumberSegmentationModel.migrateTool.R

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

setMethodS3("migrateTool", "CopyNumberSegmentationModel", function(static, what=c("addMissingAsteriskTag"), ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'what':
  what <- match.arg(what)

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


  # In case the function was called using an instance.
  if (!inherits(static, "Class")) {
    static <- Class$forName(class(static)[1])
  }

  if (what == "addMissingAsteriskTag") {
    throw("Hohoho! Don't run this one. It is only here for future use.")

    # Find all non-abstract subclasses
    classes <- c(getKnownSubclasses(static), getName(static))
    for (cc in seq_along(classes)) {
      className <- classes[cc]
      clazz <- Class$forName(className)
      # Ignore abstract classes
      if (isAbstract(clazz))
        classes[cc] <- NA
    }
    classes <- na.omit(classes)


    # Scan the output directories for those classes
    for (cc in seq_along(classes)) {
      className <- classes[cc]
      clazz <- Class$forName(className)
      obj <- newInstance(clazz)
      aTag <- getAsteriskTags(obj)[1]
      pattern <- sprintf(",%s(,|$)", aTag)
      oldRootPath <- sprintf("%sData", tolower(aTag))

      verbose && enter(verbose, sprintf("Step #%d of %d - Scanning %s/ for datasets to be renamed", cc, length(classes), oldRootPath))

      dirs <- list.files(oldRootPath, full.names=TRUE)
      # Nothing to do?
      if (length(dirs) == 0) {
        verbose && exit(verbose)
        next
      }

      # Consider only directories
      dirs <- dirs[sapply(dirs, FUN=isDirectory)]
      # Nothing to do?
      if (length(dirs) == 0) {
        verbose && exit(verbose)
        next
      }

      # Identify data sets without the asterisk tag
      missingATag <- (regexpr(pattern, dirs) == -1)
      dirs <- dirs[missingATag]
      # Nothing to do?
      if (length(dirs) == 0) {
        verbose && exit(verbose)
        next
      }

      verbose && enter(verbose, "Adding asterisk tag (", aTag, ") to ", length(dirs), " data sets")
      newDirs <- paste(dirs, aTag, sep=",")
      for (jj in seq_along(dirs)) {
        file.rename(dirs[jj], newDirs[jj])
        verbose && printf(verbose, "Renamed '%s' to '%s' in '%s'.\n", basename(dirs[jj]), basename(newDirs[jj]), dirname(dirs[jj]))
      }
      verbose && exit(verbose)

      verbose && exit(verbose)
    } # for (cc ...)
  } # if (what == "addMissingAsteriskTag")
}, static=TRUE) # migrateTool()