R/AbstractIndexSet.R

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

###########################################################################/**
# @RdocClass AbstractIndexSet
# @aliasmethod getDefaultFilePatterns
#
# @title "The AbstractIndexSet class"
#
# \description{
#  @classhierarchy
#
#  An AbstractIndexSet object represents a set of @see "AbstractIndexFile":s.
# }
#
# @synopsis
#
# \arguments{
#   \item{files}{A @list of @see "AbstractIndexFile":s.}
#   \item{...}{Arguments passed to @see "R.filesets::GenericDataFileSet".}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author "HB"
#
# @keyword internal
#*/###########################################################################
setConstructorS3("AbstractIndexSet", function(files=NULL, ...) {
  extend(GenericDataFileSet(files=files, ...), "AbstractIndexSet")
})


setMethodS3("as.character", "AbstractIndexSet", function(x, ...) {
  this <- x
  s <- NextMethod("as.character")
  s <- c(s, sprintf("Index prefix: %s", getIndexPrefix(this)))
  s <- c(s, sprintf("Organism: %s", getOrganism(this)))
  s <- c(s, sprintf("Complete: %s", isComplete(this)))
  s
}, protected=TRUE)


setMethodS3("getOrganism", "AbstractIndexSet", function(this, ...) {
  path <- getPath(this)
  path <- dirname(path)
  organism <- basename(path)
  organism
})


setMethodS3("getDefaultFilePatterns", "AbstractIndexSet", function(static, prefix, ...) {
  sprintf("%s[.]([^.]+)$", basename(prefix))
}, static=TRUE, protected=TRUE)


setMethodS3("byPrefix", "AbstractIndexSet", function(static, prefix, pattern=NULL, ..., verbose=FALSE) {
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enterf(verbose, "Locating %s by prefix", class(static)[1])

  if (is.null(pattern)) pattern <- getDefaultFilePatterns(static, prefix=prefix)
  verbose && cat(verbose, "Pattern: ", pattern)

  path <- getParent(prefix)
  verbose && cat(verbose, "Path: ", path)

  res <- byPath(static, path=path, pattern=pattern, ..., verbose=verbose)

  verbose && exit(verbose)

  res
}, static=TRUE)


setMethodS3("getIndexPrefix", "AbstractIndexSet", function(this, ...) {
  df <- getOneFile(this)
  getIndexPrefix(df, ...)
})


setMethodS3("getFastaReferenceFile", "AbstractIndexSet", function(this, ...) {
  organism <- getOrganism(this)
  prefix <- getIndexPrefix(this)
  fullname <- basename(prefix)
  fa <- FastaReferenceFile$byOrganism(organism, prefix=fullname)

  # Assert compatibility
  isCompatibleWith(fa, this, mustWork=TRUE)

  fa
})


setMethodS3("isComplete", "AbstractIndexSet", abstract=TRUE)