spatialdataR/R/AllClasses.R at d2884fa9fe9537fea8b040635106458b829a2863 · HelenaLC/spatialdataR · GitHub

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#' @importFrom S4Vectors SimpleList
#' @importFrom methods new setClass setClassUnion setOldClass

.sdLayerList <- setClass(
    Class="sdLayerList",
    contains="SimpleList",
    slots=c(metadata="list"),
    prototype=prototype(metadata=list()))

.sdImageList <- setClass(
    Class="sdImageList",
    contains="sdLayerList",
    prototype=prototype(elementType="SpatialDataImage"))

.sdLabelList <- setClass(
    Class="sdLabelList",
    contains="sdLayerList",
    prototype=prototype(elementType="SpatialDataLabel"))

.sdPointList <- setClass(
    Class="sdPointList",
    contains="sdLayerList",
    prototype=prototype(elementType="SpatialDataPoint"))

.sdShapeList <- setClass(
    Class="sdShapeList",
    contains="sdLayerList",
    prototype=prototype(elementType="SpatialDataShape"))

.sdTableList <- setClass(
    Class="sdTableList",
    contains="sdLayerList",
    prototype=prototype(elementType="SingleCellExperiment"))

.sl <- S4Vectors:::new_SimpleList_from_list
.ok <- \(x) length(x) == 1L && (is.list(x[[1L]]) || is(x[[1L]], "SimpleList"))

sdImageList <- \(...) {
    x <- list(...)
    if (.ok(x)) x <- x[[1L]]
    .sl("sdImageList", as.list(x))
}

sdLabelList <- \(...) {
    x <- list(...)
    if (.ok(x)) x <- x[[1L]]
    .sl("sdLabelList", as.list(x))
}

sdPointList <- \(...) {
    x <- list(...)
    if (.ok(x)) x <- x[[1L]]
    .sl("sdPointList", as.list(x))
}

sdShapeList <- \(...) {
    x <- list(...)
    if (.ok(x)) x <- x[[1L]]
    .sl("sdShapeList", as.list(x))
}

sdTableList <- \(...) {
    x <- list(...)
    if (.ok(x)) x <- x[[1L]]
    .sl("sdTableList", as.list(x))
}

#' @export
#' @rdname SpatialData
.SpatialData <- setClass(
    Class="SpatialData",
    contains=c("list", "Annotated"),
    representation(
        images="sdImageList",
        labels="sdLabelList",
        points="sdPointList",
        shapes="sdShapeList",
        tables="sdTableList"))

.LAYERS <- `names<-`(. <- c("images","labels","points","shapes","tables"), .)
.SpatialDataAttrs <- setClass("SpatialDataAttrs", contains="list")
setOldClass("duckspatial_df")

setClass("SpatialDataArray",
    contains=c("Annotated", "VIRTUAL"),
    slots=list(data="list", meta="SpatialDataAttrs"))

setClass("SpatialDataFrame",
    contains=c("Annotated", "VIRTUAL"),
    slots=list(data="duckspatial_df", meta="SpatialDataAttrs"))

.SpatialDataImage <- setClass("SpatialDataImage", contains="SpatialDataArray")
.SpatialDataLabel <- setClass("SpatialDataLabel", contains="SpatialDataArray")

.SpatialDataPoint <- setClass("SpatialDataPoint", contains="SpatialDataFrame")
.SpatialDataShape <- setClass("SpatialDataShape", contains="SpatialDataFrame")

setClassUnion("SpatialDataElement", c(
    "SpatialDataImage", "SpatialDataLabel",
    "SpatialDataPoint", "SpatialDataShape"))