From a1f45335a3308b0935fdecf51220cb689a225165 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 21 Dec 2023 08:15:57 +0000
Subject: [PATCH] fix: change dispatch method to S3 instead of custom

---
 NAMESPACE                             |  4 ++++
 R/methods-get_filter_call.R           | 28 +++++++++------------------
 man/default_filter_panel_internals.Rd | 16 +++++++--------
 3 files changed, 21 insertions(+), 27 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 809f5e380..ff3d28908 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,10 @@ S3method(as.list,teal_slices)
 S3method(c,teal_slices)
 S3method(format,teal_slice)
 S3method(format,teal_slices)
+S3method(get_filter_call,MultiAssayExperiment)
+S3method(get_filter_call,SummarizedExperiment)
+S3method(get_filter_call,array.Matrix)
+S3method(get_filter_call,data.frame)
 S3method(get_filter_call,default)
 S3method(get_filter_overview,default)
 S3method(get_slice_variable,default)
diff --git a/R/methods-get_filter_call.R b/R/methods-get_filter_call.R
index e7b7e5660..1286a576c 100644
--- a/R/methods-get_filter_call.R
+++ b/R/methods-get_filter_call.R
@@ -13,22 +13,12 @@ get_filter_call <- function(data, states_list) {
 #' @rdname get_filter_call
 #' @export
 get_filter_call.default <- function(data, states_list) {
-  if (inherits(data, "data.frame")) {
-    get_filter_call_data.frame(data, states_list)
-  } else if (inherits(data, c("array", "Matrix"))) {
-    get_filter_call_array(data, states_list)
-  } else if (inherits(data, "SummarizedExperiment")) {
-    get_filter_call_SummarizedExperiment(data, states_list)
-  } else if (inherits(data, "MultiAssayExperiment")) {
-    get_filter_call_MultiAssayExperiment(data, states_list)
-  } else {
-    stop("get_filter_call not implemented for class ", class(data), call. = FALSE)
-  }
+  stop("get_filter_call not implemented for class ", class(data), call. = FALSE)
 }
 
 #' @rdname default_filter_panel_internals
-#' @keywords internal
-get_filter_call_data.frame <- function(data, states_list) {
+#' @export
+get_filter_call.data.frame <- function(data, states_list) {
   dataname_lang <- str2lang(states_list[[1L]]$get_state()$dataname)
   states_predicate <- lapply(states_list, function(state) state$get_call())
   combined_predicate <- calls_combine_by(states_predicate, "&")
@@ -41,8 +31,8 @@ get_filter_call_data.frame <- function(data, states_list) {
 }
 
 #' @rdname default_filter_panel_internals
-#' @keywords internal
-get_filter_call_array <- function(data, states_list) {
+#' @export
+get_filter_call.array.Matrix <- function(data, states_list) {
   dataname_lang <- str2lang(states_list[[1L]]$get_state()$dataname)
   states_predicate <- lapply(states_list, function(state) state$get_call())
   combined_predicate <- calls_combine_by(states_predicate, "&")
@@ -55,8 +45,8 @@ get_filter_call_array <- function(data, states_list) {
 }
 
 #' @rdname default_filter_panel_internals
-#' @keywords internal
-get_filter_call_MultiAssayExperiment <- function(data, states_list) {
+#' @export
+get_filter_call.MultiAssayExperiment <- function(data, states_list) {
   states_grouped <- split(
     states_list,
     sapply(states_list, function(x) if (is.null(x$get_state()$experiment)) "_subjects_" else x$get_state()$experiment)
@@ -96,8 +86,8 @@ get_filter_call_MultiAssayExperiment <- function(data, states_list) {
 }
 
 #' @rdname default_filter_panel_internals
-#' @keywords internal
-get_filter_call_SummarizedExperiment <- function(data, states_list) {
+#' @export
+get_filter_call.SummarizedExperiment <- function(data, states_list) {
   state_list_grouped <- split(
     states_list,
     sapply(states_list, function(x) x$get_state()$arg)
diff --git a/man/default_filter_panel_internals.Rd b/man/default_filter_panel_internals.Rd
index 94d7c88ad..30275923c 100644
--- a/man/default_filter_panel_internals.Rd
+++ b/man/default_filter_panel_internals.Rd
@@ -5,10 +5,10 @@
 %   R/methods-module_overview.R
 \name{default_filter_panel_internals}
 \alias{default_filter_panel_internals}
-\alias{get_filter_call_data.frame}
-\alias{get_filter_call_array}
-\alias{get_filter_call_MultiAssayExperiment}
-\alias{get_filter_call_SummarizedExperiment}
+\alias{get_filter_call.data.frame}
+\alias{get_filter_call.array.Matrix}
+\alias{get_filter_call.MultiAssayExperiment}
+\alias{get_filter_call.SummarizedExperiment}
 \alias{get_merge_call}
 \alias{get_slice_variable_array}
 \alias{get_slice_variable_MultiAssayExperiment}
@@ -31,13 +31,13 @@
 \alias{get_filter_overview_SummarizedExperiment}
 \title{Default methods for supported datasets}
 \usage{
-get_filter_call_data.frame(data, states_list)
+\method{get_filter_call}{data.frame}(data, states_list)
 
-get_filter_call_array(data, states_list)
+\method{get_filter_call}{array.Matrix}(data, states_list)
 
-get_filter_call_MultiAssayExperiment(data, states_list)
+\method{get_filter_call}{MultiAssayExperiment}(data, states_list)
 
-get_filter_call_SummarizedExperiment(data, states_list)
+\method{get_filter_call}{SummarizedExperiment}(data, states_list)
 
 get_merge_call(join_keys)