From 6bcbc94241cb84fb5793075dbcdc3719311b5e53 Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Wed, 18 Dec 2024 14:12:01 +0100
Subject: [PATCH] refactor: import extractByIndex from ProtGenerics

---
 DESCRIPTION     | 4 ++--
 NAMESPACE       | 1 +
 NEWS.md         | 4 ++++
 R/AllGenerics.R | 2 --
 R/MsBackend.R   | 2 ++
 5 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bda18ab1..b355aa2d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.17.3
+Version: 1.17.4
 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
@@ -42,7 +42,7 @@ Depends:
     S4Vectors,
     BiocParallel
 Imports:
-    ProtGenerics (>= 1.37.1),
+    ProtGenerics (>= 1.39.1),
     methods,
     IRanges,
     MsCoreUtils (>= 1.7.5),
diff --git a/NAMESPACE b/NAMESPACE
index d70ef776..c3dd72ab 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -257,6 +257,7 @@ importMethodsFrom(ProtGenerics,compareSpectra)
 importMethodsFrom(ProtGenerics,dataOrigin)
 importMethodsFrom(ProtGenerics,dataStorage)
 importMethodsFrom(ProtGenerics,estimatePrecursorIntensity)
+importMethodsFrom(ProtGenerics,extractByIndex)
 importMethodsFrom(ProtGenerics,filterAcquisitionNum)
 importMethodsFrom(ProtGenerics,filterDataOrigin)
 importMethodsFrom(ProtGenerics,filterDataStorage)
diff --git a/NEWS.md b/NEWS.md
index 6fd58890..d9088114 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # Spectra 1.17
 
+## Change in 1.17.4
+
+- Import `extractByIndex()` from *ProtGenerics*.
+
 ## Change in 1.17.3
 
 - Fix `cbind2()` unit test for backends that fails if the number of spectra in
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 856cb69e..5ac35fc9 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -21,8 +21,6 @@ setGeneric("entropy", function(object, ...)
   standardGeneric("entropy"))
 setGeneric("export", function(object, ...)
     standardGeneric("export"))
-setGeneric("extractByIndex", function(object, i)
-    standardGeneric("extractByIndex"))
 setGeneric("filterFourierTransformArtefacts", function(object, ...)
     standardGeneric("filterFourierTransformArtefacts"))
 setGeneric("neutralLoss", function(object, param, ...)
diff --git a/R/MsBackend.R b/R/MsBackend.R
index 6b66fef1..10dffd8a 100644
--- a/R/MsBackend.R
+++ b/R/MsBackend.R
@@ -1171,6 +1171,8 @@ setMethod("dropNaSpectraVariables", "MsBackend", function(object) {
 #'
 #' @importFrom methods existsMethod
 #'
+#' @importMethodsFrom ProtGenerics extractByIndex
+#'
 #' @export
 setMethod("extractByIndex", c("MsBackend", "ANY"), function(object, i) {
     if (existsMethod("[", class(object)[1L]))