feat: add extractByIndex method

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CompoundDb
 Type: Package
 Title: Creating and Using (Chemical) Compound Annotation Databases
-Version: 1.9.4
+Version: 1.9.5
 Authors@R: c(person(given = "Jan", family = "Stanstrup",
                     email = "[email protected]",
 		    role = c("aut"),
@@ -52,7 +52,7 @@ Imports:
     ProtGenerics (>= 1.35.3),
     xml2,
     IRanges,
-    Spectra (>= 1.9.12),
+    Spectra (>= 1.15.10),
     MsCoreUtils,
     MetaboCoreUtils,
     BiocParallel
@@ -69,6 +69,7 @@ VignetteBuilder: knitr
 License: Artistic-2.0
 RoxygenNote: 7.3.2
 Roxygen: list(markdown=TRUE)
+Encoding: UTF-8
 Collate:
     'AllGenerics.R'
     'AnnotationFilters.R'

NAMESPACE

@@ -60,6 +60,7 @@ exportMethods(dbconn)
 exportMethods(deleteCompound)
 exportMethods(deleteIon)
 exportMethods(deleteSpectra)
+exportMethods(extractByIndex)
 exportMethods(insertCompound)
 exportMethods(insertIon)
 exportMethods(insertSpectra)
@@ -161,4 +162,5 @@ importMethodsFrom(ProtGenerics,tic)
 importMethodsFrom(S4Vectors,metadata)
 importMethodsFrom(Spectra,Spectra)
 importMethodsFrom(Spectra,backendBpparam)
+importMethodsFrom(Spectra,extractByIndex)
 importMethodsFrom(Spectra,precScanNum)

NEWS.md

@@ -1,5 +1,9 @@
 # CompoundDb version 1.9
 
+## Changes in version 1.9.5
+
+- Add new `extractByIndex()` method.
+
 ## Changes in version 1.9.4
 
 - `compound_tbl_lipidblast` supports now parallel processing and extracts more

R/MsBackendCompDb.R

@@ -304,9 +304,17 @@ setMethod("[", "MsBackendCompDb", function(x, i, j, ..., drop = FALSE) {
     if (missing(i))
         return(x)
     i <- i2index(i, length(x), x@spectraIds)
-    slot(x, "spectraIds", check = FALSE) <- x@spectraIds[i]
-    x <- callNextMethod(x, i = i)
-    x
+    extractByIndex(x, i)
+})
+
+#' @rdname MsBackendCompDb
+#'
+#' @importMethodsFrom Spectra extractByIndex
+#'
+#' @export
+setMethod("extractByIndex", c("MsBackendCompDb", "ANY"), function(object, i) {
+    slot(object, "spectraIds", check = FALSE) <- object@spectraIds[i]
+    callNextMethod(object, i = i)
 })
 
 #' @rdname MsBackendCompDb

tests/testthat/test_MsBackendCompDb.R

@@ -142,8 +142,21 @@ test_that("$<-,MsBackendCompDb works", {
     expect_error(be$mz <- be$mz, "not supported")
 })
 
+test_that("extractByIndex,MsBackendCompDb works", {
+    be <- backendInitialize(MsBackendCompDb(), cmp_spctra_db)
+    res <- extractByIndex(be, c(2, 4))
+    expect_true(length(res) == 2)
+    expect_equal(res$polarity, be$polarity[c(2, 4)])
+    expect_equal(res@spectraIds, be@spectraIds[c(2, 4)])
+    expect_equal(res$mz, be$mz[c(2, 4)])
+
+})
+
 test_that("[,MsBackendCompDb works", {
     be <- backendInitialize(MsBackendCompDb(), cmp_spctra_db)
+    res <- be[]
+    expect_equal(res, be)
+
     res <- be[c(2, 4)]
     expect_true(length(res) == 2)
     expect_equal(res$polarity, be$polarity[c(2, 4)])