R/findFilesTodo.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

###########################################################################/**
# @RdocGeneric findFilesTodo
# @alias findFilesTodo.AromaSeqTransform
# @alias findFilesTodo.TotalCnBinnedCounting
#
# @title "Identifies which files are not yet processed"
#
# \description{
#   @get "title".
# }
#
# \usage{
#  @usage findFilesTodo,AromaSeqTransform
#  @usage findFilesTodo,TotalCnBinnedCounting
# }
#
# \arguments{
#  \item{...}{Not used.}
# }
#
# \value{
#   Returns a @vector of named indices.
# }
#
# \seealso{
#   Internally \code{getOutputDataSet(..., onMissing="NA")} is utilized.
# }
#
# @author "HB"
#
# @keyword internal
#*/###########################################################################
setMethodS3("findFilesTodo", "TotalCnBinnedCounting", function(this, ...) {
  res <- getOutputDataSet(this, onMissing="NA")
  isFile <- unlist(sapply(res, FUN=isFile), use.names=FALSE)
  todo <- !isFile
  todo <- which(todo)
  if (length(todo) > 0L) {
    ds <- getInputDataSet(this)
    names(todo) <- getNames(ds[todo])
  }
  todo
})