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## Functions related to EnsDb objects.
#' @title Globally filter an EnsDb database
#'
#' @description \code{.addFilter} globally filters the provided
#' \code{EnsDb} database, i.e. it returns a \code{EnsDb} object with the
#' provided filter permanently set and active.
#'
#' @details Adding a filter to an \code{EnsDb} object causes this filter to be
#' permanently active. The filter will be used for all queries to the
#' databases and is added to all additional filters passed to the methods.
#'
#' @param x An \code{EnsDb} object on which the filter(s) should be set.
#'
#' @param filter An \code{\link[AnnotationFilter]{AnnotationFilterList}},
#' \code{\link[AnnotationFulter]{AnnotationFilter}} object or a filter
#' expression providing the filter(s) to be set.
#'
#' @return For \code{.addFilter}: the \code{EnsDb} object with the filter
#' globally added and enabled.
#'
#' For \code{.dropFilter}: the \code{EnsDb} object with all filters removed.
#'
#' For \code{.activeFilter}: an \code{}
#'
#' @author Johannes Rainer
#'
#' @noRd
.addFilter <- function(x, filter = AnnotationFilterList()) {
if (length(filter) == 0)
stop("No filter provided")
filter <- .processFilterParam(filter, x)
## Now, if there was no error, filter is an AnnotationFilterList
got_filter <- getProperty(x, "FILTER")
if (is(got_filter, "AnnotationFilter") |
is(got_filter, "AnnotationFilterList")) {
## Append the new filter.
filter <- AnnotationFilterList(got_filter, filter)
} else {
if (!is.na(got_filter))
stop("Globally set filter is not an 'AnnotationFilter' or ",
"'AnnotationFilterList'")
}
x@.properties$FILTER <- filter
x
}
#' @description \code{.dropFilter} drops all (globally) added filters from the
#' submitted \code{EnsDb} object.
#'
#' @noRd
.dropFilter <- function(x) {
dropProperty(x, "FILTER")
}
#' @description \code{.activeFilter} lists the globally set and active filter(s)
#' of an \code{EnsDb} object.
#'
#' @noRd
.activeFilter <- function(x) {
getProperty(x, "FILTER")
}
#' @aliases filter
#'
#' @description \code{filter} filters an \code{EnsDb} object. \code{filter} is
#' an alias for the \code{addFilter} function.
#'
#' @rdname global-filters
filter <- function(x, filter = AnnotationFilterList()) {
if (is(x, "EnsDb"))
addFilter(x, filter)
else
stop("ensembldb::filter requires an 'EnsDb' object as input. To call ",
"the filter function from the stats or dplyr package use ",
"stats::filter and dplyr::filter instead.")
}
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