From fb19acc5d1d39d3788552bc076d98e62fd66d179 Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Mon, 30 Sep 2024 14:07:03 +0200
Subject: [PATCH] refactor: add extractByIndex method

---
 DESCRIPTION                          |  6 +++---
 NAMESPACE                            |  2 ++
 R/MsBackendRawFileReader-functions.R |  7 +------
 R/MsBackendRawFileReader.R           | 11 ++++++++++-
 man/hidden_aliases.Rd                |  3 +++
 5 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8da7581..77a7e59 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MsBackendRawFileReader
 Type: Package
 Title: Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
-Version: 1.11.2
+Version: 1.11.3
 Authors@R: c(person(given = "Christian",
     family = "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"),
     comment = c(ORCID = "0000-0003-1975-3064")),
@@ -11,7 +11,7 @@ Authors@R: c(person(given = "Christian",
     person(given = "Roger", family = "Gine Bertomeu",
       email = "roger.gine@iispv.cat", role = "ctb",
       comment = c(ORCID = "0000-0003-0288-9619")))
-Depends: R (>= 4.1), methods, Spectra (>= 1.5.8)
+Depends: R (>= 4.1), methods, Spectra (>= 1.15.10)
 Imports:
     ProtGenerics (>= 1.35.3),
     MsCoreUtils,
@@ -41,7 +41,7 @@ BugReports: https://github.com/fgcz/MsBackendRawFileReader/issues
 Encoding: UTF-8
 NeedsCompilation: yes
 biocViews: MassSpectrometry, Proteomics, Metabolomics
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 License: GPL-3
 SystemRequirements: mono-runtime 4.x or higher (including System.Data library)
     on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows.
diff --git a/NAMESPACE b/NAMESPACE
index b0315fc..7e0f33f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,7 @@ export(MsBackendRawFileReader)
 export(ioBenchmark)
 exportClasses(MsBackendRawFileReader)
 exportMethods("[")
+exportMethods(extractByIndex)
 exportMethods(filterScan)
 exportMethods(intensity)
 exportMethods(mz)
@@ -30,3 +31,4 @@ importMethodsFrom(ProtGenerics,intensity)
 importMethodsFrom(ProtGenerics,mz)
 importMethodsFrom(ProtGenerics,peaksData)
 importMethodsFrom(ProtGenerics,scanIndex)
+importMethodsFrom(Spectra,extractByIndex)
diff --git a/R/MsBackendRawFileReader-functions.R b/R/MsBackendRawFileReader-functions.R
index cfe3842..bd40b3d 100644
--- a/R/MsBackendRawFileReader-functions.R
+++ b/R/MsBackendRawFileReader-functions.R
@@ -148,12 +148,7 @@ NULL
 #' @importFrom S4Vectors extractROWS
 #' @importFrom MsCoreUtils i2index
 #' @importFrom methods slot<-
-.subset_backend_MsBackendRawFileReader <- function(x, i) {
-  if (missing(i))
-    return(x)
-  idx <- i
-  i <- MsCoreUtils::i2index(i, length(x), rownames(x@spectraData))
-  
+.subset_backend_MsBackendRawFileReader <- function(x, i = integer()) {
   slot(x, "spectraData", check = FALSE) <- S4Vectors::extractROWS(x@spectraData, i)
   
   # check if item is complete otherwise retrieval of data through using 
diff --git a/R/MsBackendRawFileReader.R b/R/MsBackendRawFileReader.R
index 86ca07b..af8ffb5 100644
--- a/R/MsBackendRawFileReader.R
+++ b/R/MsBackendRawFileReader.R
@@ -143,9 +143,18 @@ setMethod("peaksData", "MsBackendRawFileReader",
 #' @importFrom IRanges NumericList
 #' @exportMethod [
 setMethod("[", "MsBackendRawFileReader", function(x, i, j, ..., drop = FALSE) {
-  .subset_backend_MsBackendRawFileReader(x, i)
+    i <- MsCoreUtils::i2index(i, length(x), rownames(x@spectraData))
+    extractByIndex(x, i)
 })
 
+#' @rdname hidden_aliases
+#' @importMethodsFrom Spectra extractByIndex
+#' @export
+setMethod("extractByIndex", c("MsBackendRawFileReader", "ANY"),
+          function(object, i) {
+              .subset_backend_MsBackendRawFileReader(object, i)
+          })
+
 #' @importClassesFrom IRanges NumericList
 #' @rdname hidden_aliases
 #' @importMethodsFrom ProtGenerics intensity
diff --git a/man/hidden_aliases.Rd b/man/hidden_aliases.Rd
index d60640d..7468273 100644
--- a/man/hidden_aliases.Rd
+++ b/man/hidden_aliases.Rd
@@ -10,6 +10,7 @@
 \alias{backendInitialize,MsBackendRawFileReader-method}
 \alias{show,MsBackendRawFileReader-method}
 \alias{peaksData,MsBackendRawFileReader-method}
+\alias{extractByIndex,MsBackendRawFileReader,ANY-method}
 \alias{intensity,MsBackendRawFileReader-method}
 \alias{mz,MsBackendRawFileReader-method}
 \title{Internal page for hidden aliases}
@@ -24,6 +25,8 @@ scanType(object, ...)
 
 \S4method{peaksData}{MsBackendRawFileReader}(object, ..., BPPARAM = bpparam())
 
+\S4method{extractByIndex}{MsBackendRawFileReader,ANY}(object, i)
+
 \S4method{intensity}{MsBackendRawFileReader}(object, ..., BPPARAM = bpparam())
 
 \S4method{mz}{MsBackendRawFileReader}(object, ..., BPPARAM = bpparam())