R/FastaReferenceSet.R

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

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

setMethodS3("getDepth", "FastaReferenceSet", function(this, ...) {
  1L
}, protected=TRUE)


setMethodS3("byPath", "FastaReferenceSet", function(static, ..., pattern="[.](fa|fasta)(|[.]gz)$") {
  NextMethod("byPath", pattern=pattern)
}, static=TRUE)

setMethodS3("getOrganism", "FastaReferenceSet", function(this, ...) {
  aFile <- this[[1L]]
  getOrganism(aFile, ...)
})