From 561ecde02ca2c1ac30f3e8102a9cb721e51a511a Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Tue, 25 Feb 2025 14:56:15 +0100
Subject: [PATCH 1/2] feat: add spectraVariableMapping<- generic

---
 DESCRIPTION                   |  2 +-
 NAMESPACE                     |  1 +
 NEWS.md                       |  4 ++++
 R/AllGenerics.R               | 10 ++++++++++
 man/spectraVariableMapping.Rd |  5 +++++
 5 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ff7d9bb5..be854e05 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.17.6
+Version: 1.17.7
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different
diff --git a/NAMESPACE b/NAMESPACE
index fa354178..5318a751 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("spectraVariableMapping<-")
 export(MsBackendCached)
 export(MsBackendDataFrame)
 export(MsBackendHdf5Peaks)
diff --git a/NEWS.md b/NEWS.md
index 4c044a68..e8abe9c0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # Spectra 1.17
 
+## Change in 1.17.7
+
+- Add the `spectraVariableMapping<-` generic method.
+
 ## Change in 1.17.6
 
 - Add new `fillCoreSpectraVariables()` function that allows to add eventually
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 5ac35fc9..68b6a657 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -55,12 +55,22 @@ setGeneric("Spectra", function(object, ...) standardGeneric("Spectra"))
 #'
 #' @param ... Optional parameters.
 #'
+#' @param value For `spectraVariableMapping<-`: a named `character` vector.
+#'
 #' @return A named `character` with names being spectra variable names (use
 #'     [spectraVariables()] for a list of supported names) and values being the
 #'     data field names.
 #'
 #' @author Johannes Rainer
 #'
+#' @name spectraVariableMapping
+#'
 #' @export
 setGeneric("spectraVariableMapping", function(object, ...)
     standardGeneric("spectraVariableMapping"))
+
+#' @rdname spectraVariableMapping
+#'
+#' @export
+setGeneric("spectraVariableMapping<-", function(object, ..., value)
+    standardGeneric("spectraVariableMapping<-"))
diff --git a/man/spectraVariableMapping.Rd b/man/spectraVariableMapping.Rd
index 9cf49ced..edff3a67 100644
--- a/man/spectraVariableMapping.Rd
+++ b/man/spectraVariableMapping.Rd
@@ -2,14 +2,19 @@
 % Please edit documentation in R/AllGenerics.R
 \name{spectraVariableMapping}
 \alias{spectraVariableMapping}
+\alias{spectraVariableMapping<-}
 \title{Mapping between spectra variables and data file fields}
 \usage{
 spectraVariableMapping(object, ...)
+
+spectraVariableMapping(object, ...) <- value
 }
 \arguments{
 \item{object}{An instance of an object extending \code{\link[=MsBackend]{MsBackend()}}.}
 
 \item{...}{Optional parameters.}
+
+\item{value}{For \verb{spectraVariableMapping<-}: a named \code{character} vector.}
 }
 \value{
 A named \code{character} with names being spectra variable names (use

From a7b73b0937f198477ad415d3ff4ea0dcf0452b39 Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Tue, 25 Feb 2025 15:05:08 +0100
Subject: [PATCH 2/2] refactor: fix exports

---
 NAMESPACE       | 4 ++--
 R/AllGenerics.R | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 5318a751..a5f9d4a1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("spectraVariableMapping<-")
 export(MsBackendCached)
 export(MsBackendDataFrame)
 export(MsBackendHdf5Peaks)
@@ -33,7 +32,6 @@ export(ppm)
 export(processingLog)
 export(reduceSpectra)
 export(scalePeaks)
-export(spectraVariableMapping)
 exportClasses(MsBackend)
 exportClasses(MsBackendCached)
 exportClasses(MsBackendDataFrame)
@@ -64,6 +62,7 @@ exportMethods("rtime<-")
 exportMethods("smoothed<-")
 exportMethods("spectraData<-")
 exportMethods("spectraNames<-")
+exportMethods("spectraVariableMapping<-")
 exportMethods(Spectra)
 exportMethods(acquisitionNum)
 exportMethods(addProcessing)
@@ -144,6 +143,7 @@ exportMethods(smooth)
 exportMethods(smoothed)
 exportMethods(spectraData)
 exportMethods(spectraNames)
+exportMethods(spectraVariableMapping)
 exportMethods(spectraVariables)
 exportMethods(spectrapply)
 exportMethods(split)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 68b6a657..3c4f5c8e 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -65,12 +65,12 @@ setGeneric("Spectra", function(object, ...) standardGeneric("Spectra"))
 #'
 #' @name spectraVariableMapping
 #'
-#' @export
+#' @exportMethod spectraVariableMapping
 setGeneric("spectraVariableMapping", function(object, ...)
     standardGeneric("spectraVariableMapping"))
 
 #' @rdname spectraVariableMapping
 #'
-#' @export
+#' @exportMethod spectraVariableMapping<-
 setGeneric("spectraVariableMapping<-", function(object, ..., value)
     standardGeneric("spectraVariableMapping<-"))