Restructure classes and their responsibilities

R/method.R

@@ -0,0 +1,67 @@
+#' Describe a new method for analyzing gene position data.
+#'
+#' @param id Unique identifier for the method.
+#' @param name Human readable name.
+#' @param description Slightly longer description.
+#' @param func Function to apply the method. The function should accept two
+#'   parameters: an object of class `geposan_preset` as input and a function to
+#'   report progress information to as a numeric value. The return value should
+#'   be an object of class `geposan_result`.
+#'
+#' @return An object of class `geposan_method`.
+#'
+#' @export
+method <- function(id, name, description, func) {
+    stopifnot(is.character(id) & length(id) == 1)
+    stopifnot(is.character(name) & length(name) == 1)
+    stopifnot(is.character(description) & length(description) == 1)
+    stopifnot(is.function(func))
+
+    structure(
+        list(
+            id = id,
+            name = name,
+            description = description,
+            func = func
+        ),
+        class = "geposan_method"
+    )
+}
+
+#' Get a list of all available methods.
+#'
+#' @export
+all_methods <- function() {
+    list(
+        clustering(),
+        correlation(),
+        neural(),
+        adjacency(),
+        proximity()
+    )
+}
+
+#' Print a method object.
+#'
+#' @param x The method to print.
+#' @param ... Other parameters.
+#'
+#' @seealso [method()]
+#'
+#' @export
+print.geposan_method <- function(x, ...) {
+    cat(sprintf(
+        paste0(
+            "geposan method:",
+            "\n  Method ID: %s",
+            "\n  Name: %s",
+            "\n  Description: %s",
+            "\n"
+        ),
+        x$id,
+        x$name,
+        x$description
+    ))
+
+    invisible(x)
+}