Add matchAll methods

DESCRIPTION

@@ -2,7 +2,7 @@ Package: AcidBase
 Title: Acid Genomics Base Functions
 Description: Low-level base functions imported by Acid Genomics packages.
 Version: 0.7.3.9000
-Date: 2023-12-12
+Date: 2023-12-15
 Authors@R: c(
     person(
         "Michael", "Steinbaugh",
@@ -22,17 +22,17 @@ License: AGPL-3
 Encoding: UTF-8
 Depends: R (>= 4.3)
 Imports:
-    AcidGenerics (>= 0.7.3),
-    BiocGenerics (>= 0.46.0),
-    S4Vectors (>= 0.38.0),
-    goalie (>= 0.7.5),
+    AcidGenerics (>= 0.7.6),
+    BiocGenerics (>= 0.48.0),
+    S4Vectors (>= 0.40.0),
+    goalie (>= 0.7.7),
     methods
 Suggests:
     AcidCLI (>= 0.3.0),
     AcidTest (>= 0.9.0),
     memuse (>= 4.2.3),
-    processx (>= 3.8.2),
-    testthat (>= 3.2.0),
+    processx (>= 3.8.3),
+    testthat (>= 3.2.1),
     withr (>= 2.5.2),
     parallel,
     stats,

NAMESPACE

@@ -31,6 +31,7 @@ export(lanePattern)
 export(logRatioToFoldChange)
 export(majorMinorVersion)
 export(majorVersion)
+export(matchAll)
 export(matchNested)
 export(metadataDenylist)
 export(methodFormals)
@@ -80,6 +81,7 @@ exportMethods(headtail)
 exportMethods(intersectionMatrix)
 exportMethods(keepOnlyAtomicCols)
 exportMethods(logRatioToFoldChange)
+exportMethods(matchAll)
 exportMethods(matchNested)
 exportMethods(rankedMatrix)
 exportMethods(sem)
@@ -97,6 +99,7 @@ importFrom(AcidGenerics,intersectAll)
 importFrom(AcidGenerics,intersectionMatrix)
 importFrom(AcidGenerics,keepOnlyAtomicCols)
 importFrom(AcidGenerics,logRatioToFoldChange)
+importFrom(AcidGenerics,matchAll)
 importFrom(AcidGenerics,matchNested)
 importFrom(AcidGenerics,rankedMatrix)
 importFrom(AcidGenerics,sem)

R/AllGenerics.R

@@ -52,6 +52,12 @@ NULL
 #' @usage logRatioToFoldChange(object, ...)
 NULL
 
+#' @rdname matchAll
+#' @name matchAll
+#' @export
+#' @usage matchAll(x, table, ...)
+NULL
+
 #' @rdname matchNested
 #' @name matchNested
 #' @export

R/matchAll-methods.R

@@ -0,0 +1,95 @@
+#' @name matchAll
+#' @inherit AcidGenerics::matchAll
+#'
+#' @note Updated 2023-12-15.
+#'
+#' @inheritParams AcidRoxygen::params
+#' @param ... Additional arguments.
+#'
+#' @param simplify `logical(1)`.
+#' Unlist match list into a positional vector.
+#'
+#' @examples
+#' ## vector ====
+#' x <- c("c", "b", "a")
+#' table <- c("a", "b", "c", "a", "b", "c")
+#' i <- matchAll(x = x, table = table, simplify = FALSE)
+#' print(i)
+#' i <- matchAll(x = x, table = table, simplify = TRUE)
+#' print(i)
+NULL
+
+
+
+## Updated 2023-12-15.
+`matchAll,vector` <- # nolint
+    function(x, table, simplify = FALSE) {
+        assert(
+            hasLength(x),
+            hasNoDuplicates(x),
+            hasLength(table),
+            isFlag(simplify)
+        )
+        out <- lapply(
+            X = x,
+            FUN = function(x, table) {
+                lgl <- table %in% x
+                assert(
+                    any(lgl),
+                    msg = sprintf("Failed to match {.var %s}.", x)
+                )
+                which(lgl)
+            },
+            table = table
+        )
+        if (isTRUE(simplify)) {
+            out <- unlist(x = out, recursive = FALSE, use.names = FALSE)
+        }
+        out
+    }
+
+
+
+`matchAll,character` <- # nolint
+    `matchAll,vector`
+
+`matchAll,factor` <- # nolint
+    `matchAll,vector`
+
+`matchAll,numeric` <- # nolint
+    `matchAll,vector`
+
+
+
+#' @rdname matchAll
+#' @export
+setMethod(
+    f = "matchAll",
+    signature = signature(
+        x = "character",
+        table = "character"
+    ),
+    definition = `matchAll,character`
+)
+
+#' @rdname matchAll
+#' @export
+setMethod(
+    f = "matchAll",
+    signature = signature(
+        x = "factor",
+        table = "factor"
+    ),
+    definition = `matchAll,factor`
+)
+
+#' @rdname matchAll
+#' @export
+setMethod(
+    f = "matchAll",
+    signature = signature(
+        x = "numeric",
+        table = "numeric"
+    ),
+    definition = `matchAll,numeric`
+)

R/package.R

@@ -20,7 +20,7 @@ NULL
 
 #' @importFrom AcidGenerics coerceToList euclidean foldChangeToLogRatio
 #' geometricMean headtail intersectAll intersectionMatrix keepOnlyAtomicCols
-#' logRatioToFoldChange matchNested rankedMatrix sem showHeader zscore
+#' logRatioToFoldChange matchAll matchNested rankedMatrix sem showHeader zscore
 #' @importFrom BiocGenerics dims do.call duplicated grep grepl match unlist
 #' unique unlist
 #' @importFrom S4Vectors head metadata metadata<- na.omit tail