R/AllGenerics.R

In GSEABase: Gene set enrichment data structures and methods

## many generics are constructed in code; see AAA.R and methods-* 

## union generic from graph

## GeneIdentifierType

setGeneric("mapIdentifiers",
           function(what, to, from, ..., verbose=FALSE)
           standardGeneric("mapIdentifiers"),
           signature=c("what", "to", "from"),
           useAsDefault=function(what, to, from, ..., verbose=FALSE) {
               if (geneIdType(from) == geneIdType(to)) {
                   warning(sprintf("map from '%s' to '%s': identical types",
                                   geneIdType(from), geneIdType(to)))
                   what
               } else {
                   stop(sprintf("cannot map from '%s' to '%s' on object of class '%s'",
                                geneIdType(from), geneIdType(to),
                                class(what)))
               }
           })

## goSlim

setGeneric("goSlim",
           function(idSrc, slimCollection, ontology, ..., verbose=FALSE)
           standardGeneric("goSlim"),
           signature=c("idSrc", "slimCollection"))

## toGmt

setGeneric("toGmt",
           function(x, con=stdout(), ...)
           standardGeneric("toGmt"),
           signature=c("x"))

## GeneSet

setGeneric("geneIds",
           function(object, ...) standardGeneric("geneIds"))

setGeneric("geneIds<-",
           function(object, value) standardGeneric("geneIds<-"))

setGeneric("ontology",
           function(object) standardGeneric("ontology"))

setGeneric("details",
           function(object) standardGeneric("details"))

setGeneric("geneIdType<-",
           function(object, verbose=FALSE, value)
           standardGeneric("geneIdType<-"),
           signature=c("object", "value"))

setGeneric("intersect",
           function(x, y) standardGeneric("intersect"))

setGeneric("setdiff",
           function(x, y) standardGeneric("setdiff"))

setGeneric("incidence",
           function(x, ...) standardGeneric("incidence"))

## GeneColorSet

setGeneric("coloring",
           function(object, ...) standardGeneric("coloring"))

setGeneric("coloring<-",
           function(object, ..., value) standardGeneric("coloring<-"))

## GeneSetCollection

setGeneric("GeneSetCollection",
           function(object, ..., idType, setType)
           standardGeneric("GeneSetCollection"))

## OBOCollection

setGeneric("subsets",
           function(object, ...)  standardGeneric("subsets"))