R/DChipCdfBinFile.mapToUnitNamesFile.R

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

# DChipCdfBinFile.mapToUnitNamesFile.R
setMethodS3("mapToUnitNamesFile", "DChipCdfBinFile", function(this, unf=NULL, ..., force=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'unf':
  if (!is.null(unf)) {
    unf <- Arguments$getInstanceOf(unf, "UnitNamesFile")
  }

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

  verbose && enter(verbose, "Generating index map of unit names from CDF.bin to UnitNamesFile (typically a CDF)")
  chipType <- getChipType(this)
  verbose && cat(verbose, "Chip type: ", chipType)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locate Affymetrix CDF file
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (is.null(unf)) {
    verbose && enter(verbose, "Locating UnitNamesFile")
    cdf <- AffymetrixCdfFile$byChipType(chipType)
    unf <- cdf
    verbose && exit(verbose)
  }

  verbose && print(verbose, "Target UnitNamesFile:")
  verbose && print(verbose, unf)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Check for cached results
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  key <- list(method="mapToUnitNamesFile", class=class(this)[1], chipType=chipType, unf=list(platform=getPlatform(unf), chipType=getChipType(unf), nbrOfUnits=nbrOfUnits(unf), fullName=getFullName(unf), fileSize=getFileSize(unf)))
  dirs <- c("aroma.affymetrix", "dChip", chipType)
  if (!force) {
    units <- loadCache(key=key, dirs=dirs)
    if (!is.null(units)) {
      verbose && cat(verbose, "Found cached results.")
      verbose && exit(verbose)
      return(units)
    }
  }

  verbose && enter(verbose, "Reading unit names from CDF.bin")
  verbose && cat(verbose, "Number of units: ", nbrOfUnits(this))
  unitNames <- getUnitNames(this)
  verbose && str(verbose, unitNames)
  verbose && exit(verbose)

  verbose && enter(verbose, "Querying target UnitNamesFile")
  units <- indexOf(unf, names=unitNames)
  # Not needed anymore
  unitNames <- NULL
  verbose && str(verbose, units)
  verbose && exit(verbose)

  saveCache(units, key=key, dirs=dirs)
 
  verbose && exit(verbose)

  units
}, protected=TRUE)