R/findNeighbors-methods.R

In BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

##############
# S4 Factory #
##############

#' @importFrom BiocParallel SerialParam
.FINDNEIGHBORS_GENERATOR <- function(FUN, ARGS=spill_args) {
    function(X, threshold, ..., BNINDEX, BNPARAM) {
        do.call(FUN, c(list(X=X, threshold=threshold, ...), ARGS(BNPARAM)))
    }
}

#' @importFrom BiocParallel SerialParam
.FINDNEIGHBORS_GENERATOR_NOX <- function(FUN) {
    function(X, threshold, ..., BNINDEX, BNPARAM) {
        FUN(threshold=threshold, ..., precomputed=BNINDEX)
    }
}

####################
# Default dispatch #
####################

#' @export
setMethod("findNeighbors", c("missing", "missing"), .FINDNEIGHBORS_GENERATOR(findNeighbors, .default_param))

####################
# Specific methods #
####################

#' @export
setMethod("findNeighbors", c("missing", "KmknnParam"), .FINDNEIGHBORS_GENERATOR(rangeFindKmknn))

#' @export
setMethod("findNeighbors", c("KmknnIndex", "missing"), .FINDNEIGHBORS_GENERATOR_NOX(rangeFindKmknn))

#' @export
setMethod("findNeighbors", c("KmknnIndex", "KmknnParam"), .FINDNEIGHBORS_GENERATOR_NOX(rangeFindKmknn))

#' @export
setMethod("findNeighbors", c("missing", "VptreeParam"), .FINDNEIGHBORS_GENERATOR(rangeFindVptree))

#' @export
setMethod("findNeighbors", c("VptreeIndex", "missing"), .FINDNEIGHBORS_GENERATOR_NOX(rangeFindVptree))

#' @export
setMethod("findNeighbors", c("VptreeIndex", "VptreeParam"), .FINDNEIGHBORS_GENERATOR_NOX(rangeFindVptree))