Merge pull request #337 from rformassspectrometry/jomain

feat: add precursorMz<- replacement method (issue #336)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.12
+Version: 1.15.13
 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

NAMESPACE

@@ -60,6 +60,7 @@ exportMethods("msLevel<-")
 exportMethods("mz<-")
 exportMethods("peaksData<-")
 exportMethods("polarity<-")
+exportMethods("precursorMz<-")
 exportMethods("rtime<-")
 exportMethods("smoothed<-")
 exportMethods("spectraData<-")
@@ -237,6 +238,7 @@ importMethodsFrom(ProtGenerics,"msLevel<-")
 importMethodsFrom(ProtGenerics,"mz<-")
 importMethodsFrom(ProtGenerics,"peaksData<-")
 importMethodsFrom(ProtGenerics,"polarity<-")
+importMethodsFrom(ProtGenerics,"precursorMz<-")
 importMethodsFrom(ProtGenerics,"rtime<-")
 importMethodsFrom(ProtGenerics,"smoothed<-")
 importMethodsFrom(ProtGenerics,"spectraData<-")

NEWS.md

@@ -1,5 +1,9 @@
 # Spectra 1.15
 
+## Changes in 1.15.13
+
+- Add `precursorMz<-` method [issue #336](https://github.com/rformassspectrometry/Spectra/issues/336).
+
 ## Changes in 1.15.12
 
 - Add generic `backendRequiredSpectraVariables()` to allow definition of

R/MsBackend.R

@@ -1699,6 +1699,18 @@ setMethod("precursorMz", "MsBackend", function(object) {
     stop("Not implemented for ", class(object), ".")
 })
 
+#' @exportMethod precursorMz<-
+#'
+#' @importMethodsFrom ProtGenerics precursorMz<-
+#'
+#' @rdname MsBackend
+#'
+#' @export
+setReplaceMethod("precursorMz", "MsBackend", function(object, ..., value) {
+    object$precursorMz <- value
+    object
+})
+
 #' @exportMethod peaksData<-
 #'
 #' @importMethodsFrom ProtGenerics peaksData<-

R/MsBackendCached.R

@@ -464,7 +464,6 @@ setMethod("centroided", "MsBackendCached", function(object) {
 #' @rdname MsBackendCached
 setReplaceMethod("centroided", "MsBackendCached", function(object, value) {
     object$centroided <- value
-    validObject(object)
     object
 })
 
@@ -476,7 +475,6 @@ setMethod("collisionEnergy", "MsBackendCached", function(object) {
 #' @rdname MsBackendCached
 setReplaceMethod("collisionEnergy", "MsBackendCached", function(object, value) {
     object$collisionEnergy <- value
-    validObject(object)
     object
 })
 
@@ -488,7 +486,6 @@ setMethod("dataOrigin", "MsBackendCached", function(object) {
 #' @rdname MsBackendCached
 setReplaceMethod("dataOrigin", "MsBackendCached", function(object, value) {
     object$dataOrigin <- value
-    validObject(object)
     object
 })
 
@@ -525,7 +522,6 @@ setMethod("isolationWindowLowerMz", "MsBackendCached", function(object) {
 setReplaceMethod("isolationWindowLowerMz", "MsBackendCached",
                  function(object, value) {
                      object$isolationWindowLowerMz <- value
-                     validObject(object)
                      object
                  })
 
@@ -538,7 +534,6 @@ setMethod("isolationWindowTargetMz", "MsBackendCached", function(object) {
 setReplaceMethod("isolationWindowTargetMz", "MsBackendCached",
                  function(object, value) {
                      object$isolationWindowTargetMz <- value
-                     validObject(object)
                      object
                  })
 
@@ -551,7 +546,6 @@ setMethod("isolationWindowUpperMz", "MsBackendCached", function(object) {
 setReplaceMethod("isolationWindowUpperMz", "MsBackendCached",
                  function(object, value) {
                      object$isolationWindowUpperMz <- value
-                     validObject(object)
                      object
                  })
 
@@ -574,7 +568,6 @@ setMethod("polarity", "MsBackendCached", function(object) {
 setReplaceMethod("polarity", "MsBackendCached", function(object, value) {
     if (is.numeric(value)) value <- as.integer(value)
     object$polarity <- value
-    validObject(object)
     object
 })
 
@@ -601,7 +594,6 @@ setMethod("rtime", "MsBackendCached", function(object) {
 #' @rdname MsBackendCached
 setReplaceMethod("rtime", "MsBackendCached", function(object, value) {
     object$rtime <- value
-    validObject(object)
     object
 })
 
@@ -618,6 +610,5 @@ setMethod("smoothed", "MsBackendCached", function(object) {
 #' @rdname MsBackendCached
 setReplaceMethod("smoothed", "MsBackendCached", function(object, value) {
     object$smoothed <- value
-    validObject(object)
     object
 })

R/Spectra.R

@@ -1244,6 +1244,12 @@ setMethod("precursorMz", "Spectra", function(object) {
     precursorMz(object@backend)
 })
 
+#' @rdname spectraData
+setReplaceMethod("precursorMz", "Spectra", function(object, ..., value) {
+    precursorMz(object@backend) <- value
+    object
+})
+
 #' @rdname spectraData
 setMethod("rtime", "Spectra", function(object) {
     rtime(object@backend)

tests/testthat/test_MsBackend.R

@@ -58,6 +58,7 @@ test_that("MsBackend methods throw errors", {
     expect_error(dm$a <- "a", "implemented for")
     expect_error(extractByIndex(dm, 1), "implemented for")
     expect_equal(backendRequiredSpectraVariables(dm), character())
+    expect_error(precursorMz(dm) <- 12.3, "implemented for")
 })
 
 test_that("extractByIndex not implemented fallback", {

tests/testthat/test_MsBackendCached.R

@@ -302,3 +302,10 @@ test_that("lengths,MsBackendCached works", {
     res <- lengths(be)
     expect_true(all(res == 0))
 })
+
+test_that("precursorMz<-,MsBackendCached works", {
+    be <- backendInitialize(MsBackendCached(), nspectra = 4)
+    expect_true(all(is.na(precursorMz(be))))
+    precursorMz(be) <- c(1.1, 1.2, 1.3, 1.34)
+    expect_equal(precursorMz(be), c(1.1, 1.2, 1.3, 1.34))
+})

tests/testthat/test_MsBackendMzR.R

@@ -603,3 +603,9 @@ test_that("backendRequiredSpectraVariables,MsBackendMzR works", {
     expect_equal(backendRequiredSpectraVariables(tmp),
                  c("dataStorage", "scanIndex"))
 })
+
+test_that("precursorMz<-,MsbackendMzR works", {
+    a <- sciex_mzr[1:3]
+    precursorMz(a) <- c(12.2, 1.2, 1.4)
+    expect_equal(precursorMz(a), c(12.2, 1.2, 1.4))
+})

tests/testthat/test_Spectra.R

@@ -1986,3 +1986,9 @@ test_that("estimatePrecursorIntensity works", {
     res_both <- estimatePrecursorIntensity(both)
     expect_equal(res_second, res_both[510:length(res_both)])
 })
+
+test_that("precursorMz<-,Spectra works", {
+    a <- sps_dda[1:3]
+    precursorMz(a) <- c(12.3, 1.1, 34.3)
+    expect_equal(precursorMz(a), c(12.3, 1.1, 34.3))
+})

vignettes/MsBackend.Rmd

@@ -1677,6 +1677,21 @@ This method thus retrieves first the MS levels of all spectra and then calls
 operation by selecting the unique MS levels directly using an SQL call.
 
 
+### `precursorMz<-`
+
+Replace the values for the *precursor m/z* spectra
+variable. Parameter `value` has to be of type `numeric` (`NA_real_` missing
+values are supported, e.g. for MS1 spectra). The default implementation uses the
+`$<-` method:
+
+```{r}
+setReplaceMethod("precursorMz", "MsBackend", function(object, ..., value) {
+    object$precursorMz <- value
+    object
+})
+```
+
+
 ### `ionCount()`
 
 The `ionCount()` method should return a `numeric` (length equal to the number of