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#' @export
#' @importFrom methods show
setMethod("show", "BiocNeighborIndex", function(object) {
cat(sprintf("class: %s\n", class(object)))
cat(sprintf("dim: %i %i\n", nrow(object), ncol(object)))
cat(sprintf("distance: %s\n", bndistance(object)))
})
#' @export
setMethod("bndistance", "BiocNeighborIndex", function(x) x@distance)
#' @export
setMethod("dimnames", "BiocNeighborIndex", function(x) {
list(x@NAMES, NULL)
})
#' @export
setMethod("bndata", "BiocNeighborIndex", function(x) x@data)
#' @export
setMethod("dim", "BiocNeighborIndex", function(x) rev(dim(bndata(x))) ) # reversed, as matrix was transposed.
#' @importFrom S4Vectors setValidity2
setValidity2("BiocNeighborIndex", function(object) {
msg <- character(0)
NAMES <- rownames(object)
if (!is.null(NAMES) && length(NAMES)!=nrow(object)) {
msg <- c(msg, "length of non-NULL 'NAMES' is not equal to the number of rows")
}
if (length(bndistance(object))!=1L) {
msg <- c(msg, "'distance' must be a string")
}
if (length(msg)) return(msg)
return(TRUE)
})
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