refactor: import method generics from ProtGenerics

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendMgf
 Title: Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
-Version: 1.11.1
+Version: 1.11.2
 Authors@R:
     c(person(given = "RforMassSpectrometry Package Maintainer",
              email = "[email protected]",
@@ -34,6 +34,7 @@ Depends:
     R (>= 4.0),
     Spectra (>= 1.5.14)
 Imports:
+    ProtGenerics (>= 1.35.3),
     BiocParallel,
     S4Vectors,
     IRanges,
@@ -54,7 +55,7 @@ BugReports: https://github.com/RforMassSpectrometry/MsBackendMgf/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendMgf
 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics, DataImport
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'hidden_aliases.R'
     'MsBackendMgf.R'

NAMESPACE

@@ -19,12 +19,12 @@ importFrom(methods,new)
 importFrom(methods,validObject)
 importFrom(stats,setNames)
 importMethodsFrom(BiocParallel,bplapply)
+importMethodsFrom(ProtGenerics,backendInitialize)
+importMethodsFrom(ProtGenerics,peaksData)
 importMethodsFrom(Spectra,"$")
 importMethodsFrom(Spectra,"$<-")
 importMethodsFrom(Spectra,"spectraData<-")
-importMethodsFrom(Spectra,backendInitialize)
 importMethodsFrom(Spectra,export)
-importMethodsFrom(Spectra,peaksData)
 importMethodsFrom(Spectra,spectraData)
 importMethodsFrom(Spectra,spectraNames)
 importMethodsFrom(Spectra,spectraVariableMapping)

NEWS.md

@@ -1,5 +1,10 @@
 # MsBackendMgf 1.11
 
+## Changes in 1.11.2
+
+- Import generic methods from `ProtGenerics`. Requires `ProtGenerics` version
+  1.35.3.
+
 ## Changes in 1.11.1
 
 - Small runtime improvements in MGF importer.

R/MsBackendMgf.R

@@ -150,10 +150,12 @@ setClass("MsBackendMgf",
                                readonly = FALSE,
                                version = "0.1"))
 
-#' @importMethodsFrom Spectra backendInitialize spectraData<- $<- $
+#' @importMethodsFrom Spectra spectraData<- $<- $
 #'
 #' @importFrom BiocParallel SerialParam
 #'
+#' @importMethodsFrom ProtGenerics backendInitialize
+#'
 #' @importMethodsFrom BiocParallel bplapply
 #'
 #' @importFrom methods validObject

R/functions-mgf.R

@@ -248,7 +248,9 @@ readMgfSplit <- function(f, msLevel = 2L,
 #'
 #' @author Johannes Rainer
 #'
-#' @importMethodsFrom Spectra spectraVariables spectraNames peaksData spectraData
+#' @importMethodsFrom Spectra spectraVariables spectraNames spectraData
+#'
+#' @importMethodsFrom ProtGenerics peaksData
 #'
 #' @noRd
 #'