export methods

Yunuuuu · Feb 26, 2024 · 6d99b18 · 6d99b18
1 parent d789dd0
commit 6d99b18
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Showing 8 changed files with 200 additions and 14 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -70,10 +70,14 @@ exportMethods(colSums)
 exportMethods(colVars)
 exportMethods(convert_mode)
 exportMethods(crossprod)
+exportMethods(dim)
+exportMethods(dimnames)
 exportMethods(expm1)
 exportMethods(expm1_slow)
 exportMethods(extract_array)
 exportMethods(extract_sparse_array)
+exportMethods(is_noop)
+exportMethods(is_sparse)
 exportMethods(log1p)
 exportMethods(log1p_single)
 exportMethods(mask_matrix)
@@ -166,6 +170,5 @@ importMethodsFrom(BPCells,t)
 importMethodsFrom(DelayedArray,OLD_extract_sparse_array)
 importMethodsFrom(DelayedArray,dim)
 importMethodsFrom(DelayedArray,dimnames)
-importMethodsFrom(DelayedArray,drop)
 importMethodsFrom(DelayedArray,extract_array)
 importMethodsFrom(DelayedArray,is_sparse)
diff --git a/R/Class-BPCellsMatrix.R b/R/Class-BPCellsMatrix.R
@@ -175,13 +175,18 @@ array_call_DelayedArray_method <- function(..., Array = "object", type = "S4") {
 
 # hepler function to call BPCells method for `BPCellsArray`
 # running order
-# (before - delayed - to_BPCells) - method - (body - DelayedArray - after)
+# 1. before - extract seed_form - to_BPCells
+# 2. method
+# 3. body - DelayedArray - after
 #' @include utils.R
 array_call_BPCells_method <- function(..., before = NULL, method = NULL, body = NULL, after = NULL, Arrays = "object") {
     method <- method %||% quote(methods::callGeneric())
     Arrays <- rlang::syms(Arrays)
-    # extract whether should be delayed, always respect the first Array
-    seed_form <- substitute(seed_form <- Array@SeedForm, list(Array = Arrays[[1L]]))
+    # extract seed_form, always respect the first Array
+    seed_form <- substitute(
+        seed_form <- Array@SeedForm,
+        list(Array = Arrays[[1L]])
+    )
     before <- c(
         before, list(seed_form),
         # transform all Arrays into BPCells object
@@ -210,10 +215,6 @@ methods::setAs("BPCellsMatrix", "dgCMatrix", function(from) {
 })
 
 # Default drop use `as.array` and `aperm` methods
-#' @importMethodsFrom DelayedArray drop
-#' @noRd
-NULL
-
 ### S3/S4 combo for aperm.BPCellsMatrix
 # list_methods("DelayedAperm")
 aperm.BPCellsMatrix <- array_call_DelayedArray_method(

diff --git a/R/Class-BPCellsSeed.R b/R/Class-BPCellsSeed.R
@@ -1,6 +1,6 @@
 #' Seed Contract methods for `IterableMatrix`
 #'
-#' @param x A `IterableMatrix` object.
+#' @param x A `IterableMatrix` or `BPCellsDelayedOp` object.
 #' @include utils-BPCells.R
 #' @aliases IterableMatrix
 #' @name BPCellsSeed-class
@@ -108,6 +108,8 @@ methods::setMethod(
     }
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "IterableMatrix", function(x) TRUE)
 
 #' @return

diff --git a/R/Class-BindMatrix.R b/R/Class-BindMatrix.R
@@ -9,22 +9,33 @@ mould_BPCells("BPCellsDelayedAbind", "ColBindMatrices",
 ### list_methods("DelayedAbind")
 ### Seed contract
 ### here: we override the `DelayedAbind` methods
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dim", "BPCellsDelayedAbind",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedAbind",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsDelayedAbind", function(x) TRUE)
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_array", "BPCellsDelayedAbind",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "OLD_extract_sparse_array", "BPCellsDelayedAbind",
     delayedop_call_BPCells_method(x = , index = , Array = "x")

diff --git a/R/Class-Delayed.R b/R/Class-Delayed.R
@@ -27,6 +27,7 @@ methods::setGeneric("to_BPCells", function(object, ...) {
 
 methods::setMethod("to_BPCells", "IterableMatrix", function(object) object)
 
+#' @importClassesFrom DelayedArray DelayedOp
 methods::setMethod("to_BPCells", "DelayedOp", function(object) {
     cli::cli_abort(
         "You cannot mix {.pkg BPCells} method with {.pkg DelayedArray} method"
@@ -94,30 +95,48 @@ methods::setMethod(
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsDelayedOp", function(x) TRUE)
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_array", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "OLD_extract_sparse_array", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_sparse_array", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dim", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
 #' @importMethodsFrom BPCells t
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "t", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(
@@ -126,6 +145,10 @@ methods::setMethod(
         Array = "x"
     )
 )
+
+#' @importFrom DelayedArray chunkdim
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "chunkdim", "BPCellsDelayedOp",
     delayedop_call_BPCells_method(x = , Array = "x")
@@ -149,6 +172,8 @@ methods::setMethod(
 
 ### list_methods("DelayedUnaryOp")
 ### Seed contract
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "chunkdim", "BPCellsDelayedUnaryOp",
     delayedop_call_BPCells_method(x = , Array = "x")
@@ -163,22 +188,33 @@ methods::setClass("BPCellsDelayedUnaryIsoOp",
 ### list_methods("DelayedUnaryIsoOp")
 ### Seed contract
 ### here: we override the `DelayedNaryIsoOp` methods
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dim", "BPCellsDelayedUnaryIsoOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedUnaryIsoOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsDelayedUnaryIsoOp", function(x) TRUE)
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_array", "BPCellsDelayedUnaryIsoOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "OLD_extract_sparse_array", "BPCellsDelayedUnaryIsoOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
@@ -201,22 +237,33 @@ methods::setClass("BPCellsDelayedNaryIsoOp",
 ### list_methods("DelayedNaryIsoOp")
 ### Seed contract
 ### here: we override the `DelayedNaryIsoOp` methods
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dim", "BPCellsDelayedNaryIsoOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedNaryIsoOp",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsDelayedNaryIsoOp", function(x) TRUE)
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_array", "BPCellsDelayedNaryIsoOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "OLD_extract_sparse_array", "BPCellsDelayedNaryIsoOp",
     delayedop_call_BPCells_method(x = , index = , Array = "x")

diff --git a/R/Class-RenameDims.R b/R/Class-RenameDims.R
@@ -12,8 +12,12 @@ mould_BPCells("BPCellsDelayedRenameDims", "RenameDims",
 ### Seed contract
 ### here: we override the `DelayedSetDimnames` methods
 #' @importFrom DelayedArray is_noop
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_noop", "BPCellsDelayedRenameDims", function(x) FALSE)
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedRenameDims",
     delayedop_call_BPCells_method(x = , Array = "x")

diff --git a/R/Class-Subset.R b/R/Class-Subset.R
@@ -11,29 +11,44 @@ mould_BPCells("BPCellsDelayedSubset", "MatrixSubset",
 ### list_methods("DelayedSubset")
 ### Seed contract
 ### here: we override the `DelayedSubset` methods
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dim", "BPCellsDelayedSubset",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "dimnames", "BPCellsDelayedSubset",
     delayedop_call_BPCells_method(x = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsDelayedSubset", function(x) TRUE)
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "extract_array", "BPCellsDelayedSubset",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "OLD_extract_sparse_array", "BPCellsDelayedSubset",
     delayedop_call_BPCells_method(x = , index = , Array = "x")
 )
 
 #' @importFrom DelayedArray is_noop
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod("is_noop", "BPCellsDelayedSubset", function(x) FALSE)
+
+#' @export
+#' @rdname BPCellsSeed-class
 methods::setMethod(
     "chunkdim", "BPCellsDelayedSubset",
     delayedop_call_BPCells_method(x = , Array = "x")