add BPCellsBasicSeed class

Yunuuuu · Jan 30, 2024 · 6867ad2 · 6867ad2
1 parent d1c7913
commit 6867ad2
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Showing 7 changed files with 42 additions and 25 deletions.
diff --git a/R/Class-BPCellsMatrix.R b/R/Class-BPCellsMatrix.R
@@ -53,5 +53,3 @@ methods::setMethod(
 methods::setMethod("matrixClass", "BPCellsArray", function(x) {
     "BPCellsMatrix"
 })
-
-methods::setMethod("entity", "BPCellsMatrix", function(x) x@seed)
diff --git a/R/Class-BPCellsSeed.R b/R/Class-BPCellsSeed.R
@@ -22,6 +22,7 @@ methods::setClass("BPCellsSeed",
 )
 methods::setClass("BPCellsUnaryOpsSeed", contains = c("BPCellsSeed", "VIRTUAL"))
 methods::setClass("BPCellsNaryOpsSeed", contains = c("BPCellsSeed", "VIRTUAL"))
+methods::setClass("BPCellsBasicSeed", contains = c("BPCellsSeed", "VIRTUAL"))
 
 #' @export
 #' @rdname BPCellsSeed
@@ -38,7 +39,7 @@ methods::setMethod("BPCellsSeed", "BPCellsSeed", function(x) {
 #############################################################
 # used to extract the actual entity of `BPCellsSeed` objet.
 methods::setGeneric("entity", function(x, ...) standardGeneric("entity"))
-methods::setMethod("entity", "BPCellsSeed", function(x) x)
+methods::setMethod("entity", "BPCellsBasicSeed", function(x) x)
 methods::setMethod("entity", "BPCellsUnaryOpsSeed", function(x) {
     x@matrix
 })
@@ -55,7 +56,7 @@ methods::setMethod("entity", "BPCellsUnaryOpsSeed", function(x) {
 ############################################################
 # Iterable_dgCMatrix_wrapper
 methods::setClass("BPCellsdgCMatrixSeed",
-    contains = c("BPCellsSeed", get_class("Iterable_dgCMatrix_wrapper"))
+    contains = c("BPCellsBasicSeed", get_class("Iterable_dgCMatrix_wrapper"))
 )
 
 #' @noRd

diff --git a/R/Class-Dir.R b/R/Class-Dir.R
@@ -1,5 +1,5 @@
 methods::setClass("BPCellsDirSeed",
-    contains = c("BPCellsSeed", get_class("MatrixDir"))
+    contains = c("BPCellsBasicSeed", get_class("MatrixDir"))
 )
 
 BPCellsDirSeed <- function(x) methods::as(x, "BPCellsDirSeed")

diff --git a/R/Class-HDF5.R b/R/Class-HDF5.R
@@ -2,7 +2,7 @@
 # - add method of subset: Method-subset.R
 # - add method of showtree: showtree.R
 methods::setClass("BPCellsHDF5Seed",
-    contains = c("BPCellsSeed", get_class("MatrixH5"))
+    contains = c("BPCellsBasicSeed", get_class("MatrixH5"))
 )
 
 BPCellsHDF5Seed <- function(x) methods::as(x, "BPCellsHDF5Seed")

diff --git a/R/Class-Mem.R b/R/Class-Mem.R
@@ -15,7 +15,7 @@
 #' @noRd
 NULL
 
-methods::setClass("BPCellsMemSeed", contains = "BPCellsSeed")
+methods::setClass("BPCellsMemSeed", contains = c("BPCellsBasicSeed", "VIRTUAL"))
 methods::setClass("BPCellsPackedMemSeed",
     contains = c("BPCellsMemSeed", get_class("PackedMatrixMemBase"))
 )

diff --git a/R/runSVD.R b/R/runSVD.R
@@ -73,7 +73,8 @@ methods::setMethod(
 )
 
 methods::setMethod("SpectraSVD", "BPCellsMatrix", function(x, ...) {
-    SpectraSVD(x = entity(x), ...)
+    x <- x@seed
+    methods::callGeneric()
 })
 
 methods::setMethod(

diff --git a/R/showtree.R b/R/showtree.R
@@ -82,21 +82,24 @@ showtree <- function(object) {
 #' @export
 #' @rdname showtree
 methods::setMethod("nseed", "BPCellsMatrix", function(x) {
-    nseed(entity(x))
+    x <- x@seed
+    methods::callGeneric()
 })
 
 #' @importFrom DelayedArray seed
 #' @export
 #' @rdname showtree
 methods::setMethod("seed", "BPCellsMatrix", function(x) {
-    seed(entity(x))
+    x <- x@seed
+    methods::callGeneric()
 })
 
 #' @importFrom DelayedArray path
 #' @export
 #' @rdname showtree
 methods::setMethod("path", "BPCellsMatrix", function(object, ...) {
-    path(entity(object), ...)
+    object <- object@seed
+    methods::callGeneric()
 })
 
 #' @importFrom DelayedArray seed<-
@@ -144,11 +147,11 @@ methods::setMethod("path", "BPCellsHDF5Seed", function(object, ...) object@path)
 
 #' @export
 #' @rdname showtree
-methods::setMethod("seed", "BPCellsSeed", function(x) x)
+methods::setMethod("seed", "BPCellsBasicSeed", function(x) x)
 
 #' @export
 #' @rdname showtree
-methods::setMethod("nseed", "BPCellsSeed", function(x) 1L)
+methods::setMethod("nseed", "BPCellsBasicSeed", function(x) 1L)
 
 # Five DelayedUnaryOp-like seeds ------------------------------------
 ###########################################################
@@ -201,20 +204,34 @@ methods::setMethod("nseed", "BPCellsNaryOpsSeed", function(x) {
 
 # Don't use this, we directly use `seed` function to return all seeds
 # this is different with what the DelayedArray does.
-new_seedApply <- function(x, .fn, ...) {
-    if (methods::is(x, "BPCellsMatrix")) {
-        x <- entity(x)
+methods::setGeneric("new_seedApply",
+    signature = "x", function(x, .fn, ...) {
+        standardGeneric("new_seedApply")
     }
-    if (methods::is(x, "BPCellsUnaryOpsSeed")) {
-        return(Recall(entity(x), .fn, ...))
-    }
-    if (methods::is(x, "BPCellsNaryOpsSeed")) {
+)
+
+methods::setMethod("new_seedApply", "BPCellsMatrix", function(x, .fn, ...) {
+    x <- x@seed
+    methods::callGeneric()
+})
+
+methods::setMethod(
+    "new_seedApply", "BPCellsUnaryOpsSeed",
+    function(x, .fn, ...) {
         x <- entity(x)
+        methods::callGeneric()
     }
-    if (is.list(x)) {
+)
+
+methods::setMethod(
+    "new_seedApply", "BPCellsNaryOpsSeed",
+    function(x, .fn, ...) {
+        x <- entity(x)
         ans <- lapply(x, FUN = new_seedApply, .fn = .fn, ...)
-        return(unlist(ans, recursive = FALSE, use.names = FALSE))
-    } else {
-        list(.fn(x, ...))
+        unlist(ans, recursive = FALSE, use.names = FALSE)
     }
-}
+)
+
+methods::setMethod("new_seedApply", "BPCellsBasicSeed", function(x, .fn, ...) {
+    list(.fn(x, ...))
+})