R/AllGenerics.R

In LTLA/BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

#' @export
#' @rdname buildIndex
setGeneric("buildIndex", signature=c("X", "BNPARAM"), function(X, transposed=FALSE, ..., BNPARAM=NULL) standardGeneric("buildIndex"))

#' @export
#' @rdname defineBuilder 
setGeneric("defineBuilder", signature="BNPARAM", function(BNPARAM) standardGeneric("defineBuilder"))

# This is explicitly a S4 generic so that developers can extend it at the R
# level, not at the C++ level. We need to support dispatch on both X and
# BNPARAM as X could be an arbitrary index structure (i.e., not an external
# pointer). If we only dispatched on BNPARAM, a user could call the method with
# a prebuilt X that doesn't match the BNPARAM. This means that the developer of
# the BNPARAM method would be responsible for figuring out what to do with a X
# that they don't know anything about, which is pretty weird.

#' @export
#' @rdname findKNN
setGeneric("findKNN", signature=c("X", "BNPARAM"), function(X, k, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, ..., BNPARAM=NULL) {
    standardGeneric("findKNN")
})

#' @export
#' @rdname queryKNN
setGeneric("queryKNN", signature=c("X", "BNPARAM"), function(X, query, k, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, transposed=FALSE, ..., BNPARAM=NULL) {
    standardGeneric("queryKNN")
})

#' @export
#' @rdname findNeighbors
setGeneric("findNeighbors", signature=c("X", "BNPARAM"), function(X, threshold, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, ..., BNPARAM=NULL) {
    standardGeneric("findNeighbors")
})

#' @export
#' @rdname queryNeighbors
setGeneric("queryNeighbors", signature=c("X", "BNPARAM"), function(X, query, threshold, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, transposed=FALSE, ..., BNPARAM=NULL) {
    standardGeneric("queryNeighbors")
})

#' @export
#' @rdname findDistance
setGeneric("findDistance", signature=c("X", "BNPARAM"), function(X, k, num.threads=1, subset=NULL, ..., BNPARAM=NULL) {
    standardGeneric("findDistance")
})

#' @export
#' @rdname queryDistance
setGeneric("queryDistance", signature=c("X", "BNPARAM"), function(X, query, k, num.threads=1, subset=NULL, transposed=FALSE, ..., BNPARAM=NULL) {
    standardGeneric("queryDistance")
})