R/AllClasses.R

In rols: An R interface to the Ontology Lookup Service

setClassUnion("NullOrChar", c("NULL", "character"))
setClassUnion("NullOrList", c("NULL", "list"))

## a param is [CV label, accession, name|synonym, value]
.CVParam <- setClass("CVParam",
                     representation = representation(
                         label = "character",
                         accession = "character",
                         name = "character",
                         value = "character",
                         user = "logical"),
                     contains = "Versioned",
                     prototype = prototype(
                         user = FALSE,
                         new("Versioned", versions=c(CVParam="0.2.0"))),
                     validity = function(object) {
                         msg <- validMsg(NULL, NULL)
                         if (object@user) {
                             if (!all(c(object@label, object@accession) == ""))
                                 msg <- "Label and accession must be empty in UserParams."
                         } else {
                             x <- c(object@label, object@accession,
                                    object@name, object@value) == ""
                             if (!all(x)) {
                                 ._term <- term(object@label, object@accession)
                                 ._label <- termLabel(._term)
                                 ._synonyms <- termSynonym(._term)
                                 if (!(object@name %in% c(._label, ._synonyms)))
                                     msg <- paste0("CVParam accession and name/synomyms do not match. Got [",
                                                   paste(c(._label, ._synonyms), collapse = ", "),
                                                   "], expected '", object@name, "'.")
                             }
                         }
                         if (is.null(msg)) TRUE else msg
                     })


.Ontology <- setClass("Ontology",
                      slots = c(loaded = "NullOrChar",
                                updated = "NullOrChar",
                                status = "NullOrChar",
                                message = "NullOrChar",
                                version = "NullOrChar",
                                numberOfTerms = "integer",
                                numberOfProperties = "integer",
                                numberOfIndividuals = "integer",
                                config = "list"
                                ))

.Ontologies <- setClass("Ontologies", slots = c(x = "list"))

.Term <- setClass("Term",
                  slots = c(iri = "character",
                            label = "character",
                            description = "NullOrList",
                            annotation = "list",
                            synonym = "NullOrList",
                            ontology_name = "character",
                            ontology_prefix = "character",
                            ontology_iri = "character",
                            is_obsolete = "logical",
                            is_defining_ontology = "logical",
                            has_children = "logical",
                            is_root = "logical",
                            short_form = "character",
                            obo_id = "NullOrChar",
                            links = "list"))

Terms <- setClass("Terms", slots = c(x = "list"))

.OlsSearch <- setClass("OlsSearch",
                       slots = c(q = "character",
                                 ontology = "character",
                                 type = "character",
                                 slim = "character",
                                 fieldList = "character",
                                 queryFields = "character",
                                 exact = "logical",
                                 groupField = "logical",
                                 obsoletes = "logical",
                                 local = "character",
                                 childrenOf = "character",
                                 rows = "integer",
                                 start = "integer",
                                 url = "character",
                                 numFound = "integer",
                                 response = "data.frame"))

.Property <- setClass("Property",
                      contains = "Term")
Properties <- setClass("Properties", contains = "Terms")