diff --git a/DESCRIPTION b/DESCRIPTION index 61c6c54..bf43112 100644 --- a/DESCRIPTION +++ b/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 = "maintainer@rformassspectrometry.org", @@ -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' diff --git a/NAMESPACE b/NAMESPACE index 5df8485..0547ab6 100644 --- a/NAMESPACE +++ b/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) diff --git a/NEWS.md b/NEWS.md index da505c5..6cddc7a 100644 --- a/NEWS.md +++ b/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. diff --git a/R/MsBackendMgf.R b/R/MsBackendMgf.R index df91b68..17666b6 100644 --- a/R/MsBackendMgf.R +++ b/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 diff --git a/R/functions-mgf.R b/R/functions-mgf.R index e84b3a4..2dc0d5b 100644 --- a/R/functions-mgf.R +++ b/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 #'