R/genomic_ressource.R

In ViSEAGO: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

#' @title genomic_ressource class object definition.
#' @description This class stores the annotations and associated metadata obtained by \code{\link{Bioconductor2GO}},
#' \code{\link{EntrezGene2GO}}, \code{\link{Ensembl2GO}}, or \code{\link{Uniprot2GO}} .
#' @family genomic_ressource
#' @slot db name of database used (Bioconductor, EntrezGene, Ensembl, or Uniprot).
#' @slot stamp date of stamp (for Bioconductor, EntrezGene, and Uniprot), or annotation version for Ensembl database.
#' @slot data GO annotations from \code{\link{EntrezGene2GO}} method.
#' @slot organisms informations about species/datasets availables.
#' @slot mart Ensembl mart from \code{\link{Ensembl2GO}} method.
setClass(
    "genomic_ressource",
    slots=c(
        db="character",
        stamp="character",
        data="data.table",
        organisms="data.table",
        mart="list"
    )
)

#' @aliases genomic_ressource
setMethod(
    "show",
    signature="genomic_ressource",
    function(object){

        # cat some text
        cat("- object class: genomic_ressource",
            "\n- database: ",slot(object,"db"),
            "\n- stamp/version: ",slot(object,"stamp"),
            "\n- available organisms: ",nrow(slot(object,"organisms")),
            sep=""
        )
    }
)