Merge pull request #51 from rformassspectrometry/jomain

feat: add extractByIndex method

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendMassbank
 Title: Mass Spectrometry Data Backend for MassBank record Files
-Version: 1.13.0
+Version: 1.13.1
 Authors@R:
     c(person(given = "RforMassSpectrometry Package Maintainer",
              email = "maintainer@rformassspectrometry.org",
@@ -25,7 +25,7 @@ Description: Mass spectrometry (MS) data backend supporting import and
 	     adds MassBank support to the Spectra package.
 Depends:
     R (>= 4.0),
-    Spectra (>= 1.9.12)
+    Spectra (>= 1.15.10)
 Imports:
     BiocParallel,
     S4Vectors,
@@ -50,7 +50,7 @@ BugReports: /~https://github.com/RforMassSpectrometry/MsBackendMassbank/issues
 URL: /~https://github.com/RforMassSpectrometry/MsBackendMassbank
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'hidden_aliases.R'
     'MsBackendMassbank.R'

NAMESPACE

@@ -14,6 +14,7 @@ exportMethods(backendInitialize)
 exportMethods(compounds)
 exportMethods(dataStorage)
 exportMethods(export)
+exportMethods(extractByIndex)
 exportMethods(peaksData)
 exportMethods(precScanNum)
 exportMethods(reset)
@@ -71,6 +72,7 @@ importMethodsFrom(Spectra,"$<-")
 importMethodsFrom(Spectra,"spectraData<-")
 importMethodsFrom(Spectra,backendBpparam)
 importMethodsFrom(Spectra,export)
+importMethodsFrom(Spectra,extractByIndex)
 importMethodsFrom(Spectra,precScanNum)
 importMethodsFrom(Spectra,reset)
 importMethodsFrom(Spectra,spectraData)

NEWS.md

@@ -1,3 +1,9 @@
+# MsBackendMassbank 1.13
+
+## Changes in 1.13.1
+
+- Add `extractByIndex()` method.
+
 # MsBackendMassbank 1.11
 
 ## Changes in 1.11.2

R/MsBackendMassbankSql.R

@@ -477,11 +477,21 @@ setMethod("[", "MsBackendMassbankSql", 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 MsBackendMassbankSql
+#'
+#' @importMethodsFrom Spectra extractByIndex
+#'
+#' @export
+setMethod("extractByIndex", c("MsBackendMassbankSql", "ANY"),
+          function(object, i) {
+              slot(object, "spectraIds", check = FALSE) <- object@spectraIds[i]
+              callNextMethod(object, i = i)
+          })
+
 #' @rdname MsBackendMassbankSql
 #'
 #' @importFrom ProtGenerics compounds

tests/testthat/test_MsBackendMassbankSql.R

@@ -218,9 +218,23 @@ test_that("selectSpectraVariables,MsBackendMassbankSql works", {
         unique(c(names(Spectra:::.SPECTRA_DATA_COLUMNS)), "rtime"))
 })
 
+test_that("extractByIndex,MsBackendMassbankSql works", {
+    be <- backendInitialize(MsBackendMassbankSql(), dbc)
+
+    res <- extractByIndex(be, 2:3)
+    expect_true(length(res) == 2)
+    expect_equal(res@spectraIds, be@spectraIds[2:3])
+    expect_equal(res@spectraIds, res$spectrum_id)
+    expect_equal(be$mz[2:3], res$mz)
+
+})
+
 test_that("[,MsBackendMassbankSql works", {
     be <- backendInitialize(MsBackendMassbankSql(), dbc)
 
+    res <- be[]
+    expect_equal(res, be)
+
     res <- be[2:3]
     expect_true(length(res) == 2)
     expect_equal(res@spectraIds, be@spectraIds[2:3])