R/coxpresdbr_CoxpresDbAccessor.R

In russHyde/coxpresdbr: Parses and Summarises Data from coxpresdb.jp

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#' Template for \code{CoxpresDbAccessor} class
#'
#' `CoxpresDbAccessor` is a virtual class, to construct an object of this
#' class, use `CoxpresDbArchiveAccessor` or `CoxpresDbDataframeAccessor`.
#'
#' @name         CoxpresDbAccessor-class
#' @rdname       CoxpresDbAccessor-class
#'
#' @exportClass       CoxpresDbAccessor
#'
methods::setClass("CoxpresDbAccessor")

#' Constructor for the concrete class `CoxpresDbArchiveAccessor`
#'
#' This is a datastructure that stores the location of a CoxpresDb archive and
#' the relative paths of all subfiles within that archive. If the archive is
#' compressed, on construction of \code{CoxpresDbAccessor} a temporary copy of
#' the uncompressed archive is constructed. So construction may take a couple
#' of minutes depending on the size of the archive. You may want to wrap a call
#' to this function in a \code{future()} block.
#'
#' @param        archive       The path to a CoxpresDb archive (either .tar.bz2
#'   or .tar).
#' @param        archive_uncompressed   The path to an uncompressed copy of the
#'   CoxpresDb archive.
#' @param        file_paths    The relative paths of all file present in
#'   subdirectories of the archive. As a data-frame of `gene_id` -> `file_path`
#'   pairs.
#'
#' @name         CoxpresDbArchiveAccessor-class
#' @rdname       CoxpresDbArchiveAccessor-class
#'
methods::setClass(
  "CoxpresDbArchiveAccessor",
  slots = list(
    archive = "character",
    archive_uncompressed = "character",
    file_paths = "data.frame"
  ),
  contains = "CoxpresDbAccessor"
)

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.validity_coxpresdb_df_accessor <- function(object) {
  if (
    !all(c("source_id", "target_id", "mutual_rank") %in% colnames(object@df))
  ) {
    return(
      paste(
        "`data.frame` should have a `source_id`, `target_id`, `mutual_rank`",
        "column in a `CoxpresDbDataframeAccessor`"
      )
    )
  }
}

#' Constructor for the concrete class `CoxpresDbDataframeAccessor`
#'
#' @param        df            A dataframe.
#'
#' @name         CoxpresDbDataframeAccessor-class
#' @rdname       CoxpresDbDataframeAccessor-class
#'
methods::setClass(
  "CoxpresDbDataframeAccessor",
  slots = list(
    df = "data.frame"
  ),
  contains = "CoxpresDbAccessor",
  # Note that we use `validity = function(object) some_f(object)` rather than
  # `validity = some_f`; we do this to ensure that .validity_cox... is ran
  # during `covr` tests of test coverage
  validity = function(object) .validity_coxpresdb_df_accessor(object)
)

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