R/methods_Annotated.R

In pepkit/BiocProject: Bioconductor Management with Portable Encapsulated Project (PEP) Objects

setGeneric(".is.project", function(.Object) standardGeneric(".is.project"))

setMethod(".is.project", "Annotated", 
          function(.Object) {
              mData = S4Vectors::metadata(.Object)
              result = tryCatch(expr = {
                  mData$PEP
              }, error = function(e) {
                  FALSE
              })
              is(result, "Project")
          })
#' Extract the object of \code{\link[pepr]{Project-class}} from 
#' the \code{\link[S4Vectors]{Annotated-class}} 
#'
#' This method can be used to extract the project metadata from objects of 
#' \code{\link[S4Vectors]{Annotated-class}} 
#'
#' @param .Object an object of \code{\link[S4Vectors]{Annotated-class}} 
#'
#' @return an object of \code{\link[pepr]{Project-class}}
#' 
#' @examples
#' projectConfig = system.file('extdata', 'example_peps-master',
#' 'example_BiocProject', 'project_config.yaml', package='BiocProject')
#' p=BiocProject(projectConfig)
#' getProject(p)
#'
#' @import S4Vectors
#' @exportMethod getProject
setGeneric("getProject", function(.Object) standardGeneric("getProject"))

#' @describeIn getProject extracts \code{\link[pepr]{Project-class}} 
#' from the \code{\link[S4Vectors]{Annotated-class}}
setMethod("getProject", "Annotated", 
          function(.Object) {
              if (.is.project(.Object)) {
                  S4Vectors::metadata(.Object)$PEP
              } else {
                  stop(.Object)
                  stop("This object does not have PEP in the metadata slot.")
              }
          })
#' View samples in the objects of \code{\link[pepr]{Project-class}} 
#'
#' This method can be used to view the samples slot
#' of the \code{\link[pepr]{Project-class}} 
#' or \code{\link[S4Vectors]{Annotated-class}} 
#'
#' @param object an object of \code{\link[pepr]{Project-class}}
#'
#' @return a data.table with the with metadata about samples
#' @examples
#' projectConfig = system.file('extdata', 'example_peps-master',
#' 'example_BiocProject', 'project_config.yaml', package='BiocProject')
#' p=BiocProject(projectConfig)
#' sampleTable(p)
#' @import pepr
#' @export
setMethod(f = "sampleTable", signature = "Annotated", 
          definition = function(object) {
              pepr::sampleTable(getProject(object))
          })

#' View PEP config of the object of \code{\link[pepr]{Project-class}}
#'
#' This method can be used to view the config slot of
#' the \code{\link[pepr]{Project-class}}
#'  or \code{\link[S4Vectors]{Annotated-class}} 
#'
#' @param object an object of \code{\link[pepr]{Project-class}}
#'
#' @return a list with the config file
#'
#' @examples
#' projectConfig = system.file('extdata', 'example_peps-master',
#' 'example_BiocProject', 'project_config.yaml', package='BiocProject')
#' p=BiocProject(projectConfig)
#' config(p)
#'
#' @import pepr
#' @export
setMethod(f = "config", signature = "Annotated", 
          definition = function(object) {
              pepr::config(getProject(object))
          })
setGeneric("is", package = "methods")

#' Is an Object from a Class?
#' 
#' Functions to test inheritance relationships between an object and a class 
#' or between two classes. It uses the generic is function but overrides its 
#' behavior for objects of class \code{\link[S4Vectors]{Annotated-class}} when 
#' testing for inheritance from \code{\link[pepr]{Project-class}} class.
#' 
#' see the \code{\link[methods]{is}} for more details
#' 
#' @param object the object to be tested
#' @param class2 the class name to test the object against
#' 
#' @return a logical 
#' @examples
#' object = S4Vectors::List(test='test')
#' is(object,'Annotated')
#' 
#' @import methods
#' @export
setMethod("is", "Annotated", definition = function(object, 
                                                   class2) {
    if (class2 == "Project" & .is.project(object)) {
        TRUE
    } else {
        methods::extends(class(object), 
                         class2)
    }
})