feat: add a function to coerce from Spectra to MSnbase::MSpectra

- Add backward compatibility: support changing from a `Spectra` object to a
  `MSnbase::MSpectra` object using the `as()` method.
- Add unit tests conditional to the installation of the *MSnbase* package.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.7
+Version: 1.15.8
 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
@@ -66,6 +66,8 @@ Suggests:
     vdiffr (>= 1.0.0),
     msentropy,
     patrick
+Enhances:
+    MSnbase
 License: Artistic-2.0
 LazyData: false
 VignetteBuilder: knitr

NEWS.md

@@ -1,5 +1,10 @@
 # Spectra 1.15
 
+## Changes in 1.15.8
+
+- Add backward compatibility by supporting to change from a `Spectra` to a
+  *MSnbase* `MSpectra` object using `as()`.
+
 ## Changes in 1.15.7
 
 - Change `estimatePrecursorIntensity()` to a method to avoid overrides/clashes

R/Spectra-functions.R

@@ -1292,3 +1292,62 @@ filterPeaksRanges <- function(object, ..., keep = TRUE) {
         "user-provided ranges for ", length(variables), " variables")
     object
 }
+
+#' Coercion method from `Spectra` to `MSnbase::MSpectra`.
+#'
+#' @noRd
+.spectra_to_spectrum_list <- function(x, chunkSize = 100) {
+    requireNamespace("MSnbase", quietly = TRUE)
+    spectrapply(x, function(z) {
+        msl <- msLevel(z)
+        r <- vector("list", length = length(msl))
+        i <- which(msl == 1L)
+        j <- which(msl > 1L)
+        if (length(i)) {
+            z_1 <- z[i]
+            mzs <- mz(z_1)
+            ints <- intensity(z_1)
+            l <- lengths(mzs)
+            r[i] <- MSnbase:::Spectra1_mz_sorted(
+                                  peaksCount = l,
+                                  rt = rtime(z_1),
+                                  acquisitionNum = acquisitionNum(z_1),
+                                  scanIndex = scanIndex(z_1),
+                                  tic = sum(ints),
+                                  mz = unlist(mzs),
+                                  intensity = unlist(ints),
+                                  fromFile = rep(NA_integer_, length(i)),
+                                  centroided = centroided(z_1),
+                                  smoothed = smoothed(z_1),
+                                  polarity = polarity(z_1),
+                                  nvalues = l)
+        }
+        if (length(j)) {
+            z_2 <- z[j]
+            mzs <- mz(z_2)
+            ints <- intensity(z_2)
+            l <- lengths(mzs)
+            r[j] <- MSnbase:::Spectra2_mz_sorted(
+                                  msLevel = msl[j],
+                                  peaksCount = l,
+                                  rt = rtime(z_2),
+                                  acquisitionNum = acquisitionNum(z_2),
+                                  scanIndex = scanIndex(z_2),
+                                  tic = sum(ints),
+                                  mz = unlist(mzs),
+                                  intensity = unlist(intensity(z_2)),
+                                  fromFile = rep(NA_integer_, length(j)),
+                                  centroided = centroided(z_2),
+                                  smoothed = smoothed(z_2),
+                                  polarity = polarity(z_2),
+                                  merged = rep(1, length(j)),
+                                  precScanNum = precScanNum(z_2),
+                                  precursorMz = precursorMz(z_2),
+                                  precursorIntensity = precursorIntensity(z_2),
+                                  precursorCharge = precursorCharge(z_2),
+                                  collisionEnergy = collisionEnergy(z_2),
+                                  nvalues = l)
+        }
+        r
+    }, chunkSize = chunkSize)
+}

R/Spectra.R

@@ -6,6 +6,7 @@ NULL
 #' @aliases Spectra-class [,Spectra-method
 #' @aliases uniqueMsLevels uniqueMsLevels,Spectra-method
 #' @aliases combinePeaks
+#' @aliases msLevel
 #'
 #' @name Spectra
 #'
@@ -55,6 +56,7 @@ NULL
 #'
 #' See also [this issue](https://github.com/lgatto/MSnbase/issues/525).
 #'
+#'
 #' @section Creation of objects, conversion, changing the backend and export:
 #'
 #' `Spectra` classes can be created with the `Spectra()` constructor function
@@ -146,6 +148,7 @@ NULL
 #' that were moved to another file system or computer, these functions allow to
 #' adjust/adapt the base file path.
 #'
+#'
 #' @section Accessing spectra data:
 #'
 #' - `$`, `$<-`: gets (or sets) a spectra variable for all spectra in `object`.
@@ -331,6 +334,7 @@ NULL
 #' - `uniqueMsLevels()`: get the unique MS levels available in `object`. This
 #'   function is supposed to be more efficient than `unique(msLevel(object))`.
 #'
+#'
 #' @section Filter spectra data:
 #'
 #' Filter a `Spectra` object based on the spectra data. This includes subset
@@ -799,6 +803,13 @@ NULL
 #'   level(s).
 #'
 #'
+#' @section Backward compatibility:
+#'
+#' `Spectra` objects can be coerced to the older `MSpectra` objects from the
+#' *MSnbase* package using the `as()` function (e.g. `as(sps, "MSpectra")`
+#' where `sps` is a `Spectra` object).
+#'
+#'
 #' @return See individual method description for the return value.
 #'
 #' @param acquisitionNum for `filterPrecursorScan()`: `integer` with the
@@ -1788,6 +1799,10 @@ setAs("Spectra", "SimpleList", function(from, to) {
     peaksData(from)
 })
 
+setAs("Spectra", "MSpectra", function(from) {
+    MSnbase::MSpectra(.spectra_to_spectrum_list(from, chunkSize = 1000))
+})
+
 #' @rdname Spectra
 setMethod("centroided", "Spectra", function(object) {
     centroided(object@backend)

tests/testthat/test_Spectra-functions.R

@@ -923,3 +923,13 @@ test_that("filterPeaksRanges,Spectra works", {
     a <- peaksData(res)[[2L]]
     expect_true(nrow(a) == 0)
 })
+
+test_that(".spectra_to_spectrum_list works", {
+    ## With MSnbase in Enhances we would need to call it like below.
+    if (requireNamespace("MSnbase", quietly = TRUE)) {
+        ## library(MSnbase) # MSnbase needs to be in Suggests
+        a <- .spectra_to_spectrum_list(sps_dda, chunkSize = 5000)
+        expect_true(is.list(a))
+        expect_equal(length(a), length(sps_dda))
+    }
+})

tests/testthat/test_Spectra.R

@@ -1939,3 +1939,13 @@ test_that("estimatePrecursorIntensity works", {
     res_both <- estimatePrecursorIntensity(both)
     expect_equal(res_second, res_both[510:length(res_both)])
 })
+
+test_that("coersion from Spectra to MSpectra works", {
+    ## With MSnbase in Enhances we would need to call it like below
+    if (requireNamespace("MSnbase", quietly = TRUE)) {
+        ## library(MSnbase) # MSnbase needs to be in Suggests
+        a <- as(sps_dda, "MSpectra")
+        expect_s4_class(a, "MSpectra")
+        expect_equal(unname(msLevel(a)), msLevel(sps_dda))
+    }
+})