refactor: import filterSpectra from ProtGenerics

- Import `filterSpectra` from `ProtGenerics`.
- Address Laurent's review comments.

DESCRIPTION

@@ -26,7 +26,7 @@ Authors@R: c(person(given = "Laurent", family = "Gatto",
                     role = "aut"))
 Depends:
     R (>= 4.2),
-    ProtGenerics (>= 1.9.1),
+    ProtGenerics (>= 1.35.2),
 Imports:
     methods,
     S4Vectors,
@@ -53,7 +53,7 @@ VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/MsExperiment/issues
 URL: https://github.com/RforMassSpectrometry/MsExperiment
 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics, ExperimentalDesign, DataImport
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown=TRUE)
 Encoding: UTF-8
 Collate:

NAMESPACE

@@ -9,7 +9,6 @@ export(MsExperimentFiles)
 export(dbWriteSampleData)
 export(existMsExperimentFiles)
 export(experimentFiles)
-export(filterSpectra)
 export(linkSampleData)
 export(otherData)
 export(qdata)
@@ -53,6 +52,7 @@ importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importMethodsFrom(BiocGenerics,dbconn)
 importMethodsFrom(ProtGenerics,"spectra<-")
+importMethodsFrom(ProtGenerics,filterSpectra)
 importMethodsFrom(S4Vectors,"mcols<-")
 importMethodsFrom(S4Vectors,"metadata<-")
 importMethodsFrom(S4Vectors,mcols)

NEWS.md

@@ -3,7 +3,7 @@
 ## MsExperiment 1.5.3
 
 - Add `filterSpectra` method to allow filtering of `Spectra` within an
-  `MsExperiment` while keeping eventually present relationships between samples
+  `MsExperiment` while keeping possibly present relationships between samples
   and spectra consistent.
 
 ## MsExperiment 1.5.2

R/MsExperiment.R

@@ -164,7 +164,7 @@
 #' - `filterSpectra`: subsets the `Spectra` within an `MsExperiment` using a
 #'   provided filter function (parameter `filter`). Parameters for the filter
 #'   function can be passed with parameter `...`. Any of the filter functions
-#'   of a [Spectra()] object can be passed with parameter `filter`. Eventually
+#'   of a [Spectra()] object can be passed with parameter `filter`. Possibly
 #'   present relationships between samples and spectra (*links*, see also
 #'   `linkSampleData`) are updated. Filtering affects only the spectra data
 #'   of the object, none of the other slots and data (e.g. `sampleData`) are
@@ -577,19 +577,15 @@ setMethod("[", "MsExperiment", function(x, i, j, ..., drop = FALSE) {
     .extractSamples(x, i, newx = x)
 })
 
-#' @rdname MsExperiment
-#'
-#' @export
-setGeneric("filterSpectra", def = function(object, filter, ...)
-    standardGeneric("filterSpectra"))
-
 #' @rdname MsExperiment
 #'
 #' @importMethodsFrom Spectra selectSpectraVariables
 #'
 #' @importMethodsFrom Spectra spectraVariables
 #'
 #' @importMethodsFrom Spectra peaksVariables
+#'
+#' @importMethodsFrom ProtGenerics filterSpectra
 setMethod(
     "filterSpectra", c("MsExperiment", "function"),
     function(object, filter, ...) {