Merge pull request #23 from jorainer/devel

refactor: add extractByIndex method

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MsBackendRawFileReader
 Type: Package
 Title: Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
-Version: 1.11.5
+Version: 1.11.6
 Authors@R: c(person(given = "Christian",
     family = "Panse", email = "[email protected]", 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 = "[email protected]", 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,

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)

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 

R/MsBackendRawFileReader.R

@@ -144,9 +144,18 @@ 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