R/AllGenerics.R

In LTLA/SingleCellExperiment: S4 Classes for Single Cell Data

########################################
# Getters/setters for linearEmbedding.

#' @export
setGeneric("sampleFactors", function(x, ...) standardGeneric("sampleFactors"))

#' @export
setGeneric("sampleFactors<-", function(x, ..., value) standardGeneric("sampleFactors<-"))

#' @export
setGeneric("featureLoadings", function(x, ..., withDimnames=TRUE) standardGeneric("featureLoadings"))

#' @export
setGeneric("featureLoadings<-", function(x, ..., value) standardGeneric("featureLoadings<-"))

#' @export
setGeneric("factorData", function(x, ..., withDimnames=TRUE) standardGeneric("factorData"))

#' @export
setGeneric("factorData<-", function(x, ..., value) standardGeneric("factorData<-"))

########################################
# Getter/setters for reducedDim.

#' @export
setGeneric("reducedDim", function(x, type, ...) standardGeneric("reducedDim"))

#' @export
setGeneric("reducedDim<-", function(x, type, withDimnames=TRUE, ..., value) standardGeneric("reducedDim<-"))

#' @export
setGeneric("reducedDimNames", function(x) standardGeneric("reducedDimNames"))

#' @export
setGeneric("reducedDimNames<-", function(x, value) standardGeneric("reducedDimNames<-"))

#' @export
setGeneric("reducedDims", function(x, ...) standardGeneric("reducedDims"))

#' @export
setGeneric("reducedDims<-", function(x, withDimnames=TRUE, ..., value) standardGeneric("reducedDims<-"))

########################################
# Hidden getter/setters for internal slots.

#' @export
setGeneric("int_elementMetadata", function(x) standardGeneric("int_elementMetadata"))

#' @export
setGeneric("int_elementMetadata<-", function(x, value) standardGeneric("int_elementMetadata<-"))

#' @export
setGeneric("int_colData", function(x) standardGeneric("int_colData"))

#' @export
setGeneric("int_colData<-", function(x, value) standardGeneric("int_colData<-"))

#' @export
setGeneric("int_metadata", function(x) standardGeneric("int_metadata"))

#' @export
setGeneric("int_metadata<-", function(x, value) standardGeneric("int_metadata<-"))

########################################
# Miscellaneous methods.

#' @export
setGeneric("colLabels", function(x, ...) standardGeneric("colLabels"))

#' @export
setGeneric("colLabels<-", function(x, ..., value) standardGeneric("colLabels<-"))

#' @export
setGeneric("rowSubset", function(x, ...) standardGeneric("rowSubset"))

#' @export
setGeneric("rowSubset<-", function(x, ..., value) standardGeneric("rowSubset<-"))

#' @export
setGeneric("objectVersion", function(x) standardGeneric("objectVersion"))

########################################
# Alternative experiment getter/setters.

#' @export
setGeneric("altExp", function(x, e, ...) standardGeneric("altExp"))

#' @export
setGeneric("altExps", function(x, ...) standardGeneric("altExps"))

#' @export
setGeneric("altExpNames", function(x, ...) standardGeneric("altExpNames"))

#' @export
setGeneric("altExp<-", function(x, e, withDimnames=TRUE, withColData=FALSE, ..., value) standardGeneric("altExp<-"))

#' @export
setGeneric("altExps<-", function(x, withDimnames=TRUE, withColData=FALSE, ..., value) standardGeneric("altExps<-"))

#' @export
setGeneric("altExpNames<-", function(x, ..., value) standardGeneric("altExpNames<-"))

#' @export
setGeneric("mainExpName", function(x) standardGeneric("mainExpName"))

#' @export
setGeneric("mainExpName<-", function(x, value) standardGeneric("mainExpName<-"))

########################################
# Pairing getter/setters.

#' @export
setGeneric("colPair", function(x, type, ...) standardGeneric("colPair"))

#' @export
setGeneric("colPairs", function(x, ...) standardGeneric("colPairs"))

#' @export
setGeneric("colPairNames", function(x, ...) standardGeneric("colPairNames"))

#' @export
setGeneric("colPair<-", function(x, type, ..., value) standardGeneric("colPair<-"))

#' @export
setGeneric("colPairs<-", function(x, ..., value) standardGeneric("colPairs<-"))

#' @export
setGeneric("colPairNames<-", function(x, ..., value) standardGeneric("colPairNames<-"))

#' @export
setGeneric("rowPair", function(x, type, ...) standardGeneric("rowPair"))

#' @export
setGeneric("rowPairs", function(x, ...) standardGeneric("rowPairs"))

#' @export
setGeneric("rowPairNames", function(x, ...) standardGeneric("rowPairNames"))

#' @export
setGeneric("rowPair<-", function(x, type, ..., value) standardGeneric("rowPair<-"))

#' @export
setGeneric("rowPairs<-", function(x, ..., value) standardGeneric("rowPairs<-"))

#' @export
setGeneric("rowPairNames<-", function(x, ..., value) standardGeneric("rowPairNames<-"))

########################################
# Convenience assay getter/setters.

#' @export
setGeneric("normcounts", function(object, ...) standardGeneric("normcounts"))

#' @export
setGeneric("normcounts<-", function(object, ..., value) standardGeneric("normcounts<-"))

#' @export
setGeneric("logcounts", function(object, ...) standardGeneric("logcounts"))

#' @export
setGeneric("logcounts<-", function(object, ..., value) standardGeneric("logcounts<-"))

#' @export
setGeneric("cpm", function(object, ...) standardGeneric("cpm"))

#' @export
setGeneric("cpm<-", function(object, ..., value) standardGeneric("cpm<-"))

#' @export
setGeneric("tpm", function(object, ...) standardGeneric("tpm"))

#' @export
setGeneric("tpm<-", function(object, ..., value) standardGeneric("tpm<-"))

#' @export
setGeneric("weights<-", function(object, ..., value) standardGeneric("weights<-"))