refactor: address Phili's comments

R/AlabasterParam.R

@@ -189,7 +189,9 @@
 #'
 #' @examples
 #'
+#' ########
 #' ## Export and import a `MsBackendMzR` object:
+#' ####
 #'
 #' library(Spectra)
 #' library(msdata)
@@ -216,7 +218,9 @@
 #' all.equal(mz(be), mz(be_in))
 #'
 #'
+#' ########
 #' ## Export and import of `Spectra` objects:
+#' ####
 #'
 #' ## Create a `Spectra` object with a `MsBackendMzR` backend.
 #' s <- Spectra(fl)
@@ -238,8 +242,10 @@
 #' be_in
 #'
 #'
-#'
+#' ########
 #' ## Export and import of `MsExperiment` objects:
+#' ####
+#'
 #' library(MsExperiment)
 #'
 #' ## Create a new `MsExperiment` with sample data and our previously defined
@@ -261,8 +267,10 @@
 #' m_in
 #'
 #'
-#'
+#' ########
 #' ## Export and import of `XcmsExperiment` objects:
+#' ####
+#'
 #' ## `XcmsExperiment` objects extend `MsExperiment` to represent all
 #' ## data of an MS experiment and contain in addition the results
 #' ## of the preprocessing of the data with the *xcms* package. Below

R/MsBackendMzR.R

@@ -52,15 +52,15 @@ setMethod("readMsObject", signature(object = "MsBackendMzR",
                   rownames(data) <- NULL
                   object@spectraData <- DataFrame(data)
                   if (length(spectraPath) > 0) {
-                      object <- .mz_backend_mzr_update_storage_path(
+                      object <- .ms_backend_mzr_update_storage_path(
                           object, spectraPath)
                   }
               }
               validObject(object)
               object
           })
 
-.mz_backend_mzr_update_storage_path <- function(x, spectraPath = character()) {
+.ms_backend_mzr_update_storage_path <- function(x, spectraPath = character()) {
     if (!length(x)) return(x)
     old <- common_path(dataStorage(x))
     dataStoragePaths <- dataStorage(x)
@@ -110,7 +110,7 @@ setMethod("saveObject", "MsBackendMzR", function(x, path, ...) {
 #' @importFrom alabaster.base registerValidateObjectFunction
 #'
 #' @noRd
-validateAlabasterMzBackendMzR <- function(path = character(),
+validateAlabasterMsBackendMzR <- function(path = character(),
                                           metadata = list()) {
     .check_directory_content(path, c("spectra_data", "peaks_variables"))
 }
@@ -124,19 +124,19 @@ validateAlabasterMzBackendMzR <- function(path = character(),
 #' @export readObject
 #'
 #' @noRd
-readAlabasterMzBackendMzR <- function(path = character(), metadata = list(),
+readAlabasterMsBackendMzR <- function(path = character(), metadata = list(),
                                       spectraPath = character()) {
     if (!requireNamespace("Spectra", quietly = TRUE))
         stop("Required package 'Spectra' missing. Please install ",
              "and try again.", call. = FALSE)
-    validateAlabasterMzBackendMzR(path, metadata)
+    validateAlabasterMsBackendMzR(path, metadata)
     sdata <- altReadObject(file.path(path, "spectra_data"))
     pvars <- altReadObject(file.path(path, "peaks_variables"))
     be <- Spectra::MsBackendMzR()
     be@spectraData <- sdata
     be@peaksVariables <- pvars
     if (length(spectraPath) > 0)
-        be <- .mz_backend_mzr_update_storage_path(be, spectraPath)
+        be <- .ms_backend_mzr_update_storage_path(be, spectraPath)
     validObject(be)
     be
 }
@@ -156,6 +156,6 @@ setMethod("saveMsObject", signature(object = "MsBackendMzR",
 setMethod("readMsObject", signature(object = "MsBackendMzR",
                                    param = "AlabasterParam"),
           function(object, param, spectraPath = character()) {
-              readAlabasterMzBackendMzR(path = param@path,
+              readAlabasterMsBackendMzR(path = param@path,
                                         spectraPath = spectraPath)
           })

R/zzz.R

@@ -1,8 +1,8 @@
 .onLoad <- function(libname, pkgname) {
     ## requireNamespace("alabaster.base", quietly = TRUE)
     registerValidateObjectFunction("ms_backend_mz_r",
-                                   validateAlabasterMzBackendMzR)
-    registerReadObjectFunction("ms_backend_mz_r", readAlabasterMzBackendMzR)
+                                   validateAlabasterMsBackendMzR)
+    registerReadObjectFunction("ms_backend_mz_r", readAlabasterMsBackendMzR)
     registerValidateObjectFunction("spectra", validateAlabasterSpectra)
     registerReadObjectFunction("spectra", readAlabasterSpectra)
     registerValidateObjectFunction("ms_experiment_files",

tests/testthat/test_MsBackendMzR.R

@@ -57,15 +57,15 @@ test_that("saveObject,readObject,MsBackendMzR works", {
     expect_true(length(res) > 0)
     expect_true(all(c("OBJECT", "spectra_data", "peaks_variables") %in% res))
 
-    ## validateAlabasterMzBackendMzR
-    expect_error(validateAlabasterMzBackendMzR("some_path"),
+    ## validateAlabasterMsBackendMzR
+    expect_error(validateAlabasterMsBackendMzR("some_path"),
                  "required file/directory")
-    expect_silent(validateAlabasterMzBackendMzR(pth))
+    expect_silent(validateAlabasterMsBackendMzR(pth))
 
-    ## readAlabasterMzBackendMzR
-    expect_error(readAlabasterMzBackendMzR("some_path"),
+    ## readAlabasterMsBackendMzR
+    expect_error(readAlabasterMsBackendMzR("some_path"),
                  "required file/directory")
-    res <- readAlabasterMzBackendMzR(pth)
+    res <- readAlabasterMsBackendMzR(pth)
     expect_s4_class(res, "MsBackendMzR")
     expect_equal(length(b), length(res))
 
@@ -100,9 +100,9 @@ test_that("saveObject,readObject,MsBackendMzR works", {
     }
 })
 
-test_that(".mz_backend_mzr_update_storage_path works", {
+test_that(".ms_backend_mzr_update_storage_path works", {
     x <- sciex_mzr
-    res <- .mz_backend_mzr_update_storage_path(x, "/new/path")
+    res <- .ms_backend_mzr_update_storage_path(x, "/new/path")
     expect_true(all(grepl("/new/path", res$dataStorage)))
     expect_error(validObject(res), "not found")
 })