R/getAromaFullNameTranslatorSet.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

# NOW:
# (1) annotationData/dataSets/<dataSet>/<chipType>/
# (2) annotationData/dataSets/<dataSet>/
#
# PROBABLY BETTER/MORE SPECIFIC (THINK OO DESIGN):
# (1) <rootPath>/<dataSet>/<chipType>/
# (2) <rootPath>/<dataSet>/
# (3) annotationData/dataSets/<dataSet>/<chipType>/
# (4) annotationData/dataSets/<dataSet>/
# (5) annotationData/dataSets/ [?!?]
setMethodS3("getAromaFullNameTranslatorSet", "character", function(dataSet, ..., chipType=NULL, paths=c("annotationData/dataSets/"), verbose=FALSE) {
  # Find existing dataset directory
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Arguments 'dataSet':
  dataSet <- Arguments$getCharacter(dataSet)

  # Arguments 'chipType':
  if (!is.null(dataSet)) {
    chipType <- Arguments$getCharacter(chipType)
  }

  # Arguments 'paths':
  paths <- Arguments$getCharacters(paths)

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


  verbose && enter(verbose, "Locating fullname TabularTextFileSet:s")
  verbose && cat(verbose, "Data set: ", dataSet)
  verbose && cat(verbose, "Chip type: ", chipType)

  subdirs <- c(chipType, ".")
  res <- getFullNameTranslatorSet(dataSet, ..., subdirs=subdirs, 
                                    paths=paths, verbose=less(verbose, 5))
  verbose && print(verbose, res)

  verbose && exit(verbose)

  res
}, protected=TRUE) # getAromaFullNameTranslatorSet()


setMethodS3("getAromaFullNameTranslatorSet", "AromaMicroarrayDataSet", function(this, ...) {
  getAromaFullNameTranslatorSet(getFullName(this), tags=NULL, chipType=getChipType(this, fullname=FALSE), ...)
}, protected=TRUE)

setMethodS3("getAromaFullNameTranslatorSet", "AromaUnitSignalBinarySet", function(this, ...) {
  getAromaFullNameTranslatorSet(getFullName(this), tags=NULL, chipType=getChipType(this, fullname=FALSE), ...)
}, protected=TRUE)




setMethodS3("getFullNameTranslatorSet", "character", function(dataSet, ..., firstOnly=FALSE, verbose=FALSE) {
  # Find existing dataset directory
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Arguments 'dataSet':
  dataSet <- Arguments$getCharacter(dataSet)

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


  verbose && enter(verbose, "Locating fullname TabularTextFileSet:s")
  verbose && cat(verbose, "Data set: ", dataSet)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Find all existing search paths
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  paths <- GenericDataFileSet$findByName(dataSet, ..., firstOnly=firstOnly,
                                mustExist=FALSE, verbose=less(verbose, 5))

  verbose && cat(verbose, "Existing search paths:")
  verbose && print(verbose, paths)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Scan for existing fullname translator files
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Allocate empty result
  res <- TabularTextFileSet()

  for (path in paths) {
    ds <- TabularTextFileSet$byPath(path, pattern=",fullnames[.]txt$")
    append(res, ds)
  } # for (path ...)

  verbose && print(verbose, res)

  verbose && exit(verbose)

  res
}, protected=TRUE) # getFullNameTranslatorSet()




# NOT USED. /HB 2010-05-26
setMethodS3("getFullNameTranslatorSet", "GenericDataFileSet", function(this, subdirs=c("*"), paths=getParent(getPath(this)), ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Arguments 'dirs':
  subdirs <- Arguments$getCharacters(subdirs)

  # Arguments 'paths':
  paths <- Arguments$getCharacters(paths)

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


  verbose && enter(verbose, "Locating fullname TabularTextFileSet:s")
  dataSet <- getFullName(this)
  verbose && cat(verbose, "Argument 'dataSet': ", dataSet)
  verbose && cat(verbose, "Argument 'subdirs': ")
  verbose && print(verbose, subdirs)
  verbose && cat(verbose, "Argument 'paths':")
  verbose && print(verbose, paths)

  res <- getFullNameTranslatorSet(dataSet, subdirs=subdirs, paths=paths,
                                           ..., verbose=less(verbose, 1))

  verbose && exit(verbose)

  res
}, protected=TRUE)