initial testthat #2

DESCRIPTION

@@ -11,6 +11,7 @@ Authors@R: c(person(given = "Christian",
 Depends: R (>= 3.6),
   IRanges,
 	methods,
+	S4Vectors,
 	Spectra,
 	rDotNet (>= 0.9)
 Suggests:

NAMESPACE

@@ -3,6 +3,7 @@
 export(MsBackendRawFileReader)
 importClassesFrom(Spectra,MsBackendDataFrame)
 importFrom(IRanges,NumericList)
+importFrom(S4Vectors,DataFrame)
 importFrom(methods,callNextMethod)
 importFrom(methods,new)
 importFrom(rDotNet,.cinit)

R/MsBackendRawFileReader-functions.R

@@ -18,6 +18,7 @@ MsBackendRawFileReader <- function() {
 #' adapted from the MsBackendMzR-function.R file by Johannes Rainer
 #'
 #' @return `DataFrame` with the header.
+#' @importFrom S4Vectors DataFrame
 #' @noRd
 .MsBackendRawFileReader_header <- function(x) {
     stopifnot(class(x) == "rDotNet")
@@ -27,10 +28,10 @@ MsBackendRawFileReader <- function() {
     first <- x$getFirstScanNumber()
     last <- x$getLastScanNumber()
 
-    S4Vectors::DataFrame(
+    DataFrame(
       scanIndex = first:last,
       msLevel = vapply(first:last, FUN=function(z){x$GetMsLevel(z)}, FUN.VALUE = as.integer(1)),
-      precursorMz = vapply(first:last, FUN=function(z){x$GetPepmass(z)}, FUN.VALUE = as.double(1.0)),
+      precursorMz = vapply(first:last, FUN=function(z){x$GetPrecursorMz(z)}, FUN.VALUE = as.double(1.0)),
       precursorCharge = as.integer(vapply(first:last, FUN=function(z){x$GetCharge(z)}, FUN.VALUE = as.character(1.0))),
       rtime =   vapply(first:last, FUN=function(z){x$GetRTinSeconds(z)}, FUN.VALUE = as.double(1.0))
     )

R/MsBackendRawFileReader.R

@@ -3,9 +3,9 @@ NULL
 
 
 #' @title RawFileReader-based backend
-#'
+#' @aliases MsBackendRawFileReader
 #' @description
-#'
+
 #' The `MsBackendRawFileReader` inherits all slots and methods from the base
 #' `MsBackendDataFrame` (in-memory) backend. It overrides the base `mz` and
 #' `intensity` methods as well as `peaks` to read the respective data from
@@ -23,7 +23,6 @@ NULL
 #' adapted from the MsBackendMzR.R file by Johannes Rainer
 #' 
 #' @importClassesFrom Spectra MsBackendDataFrame 
-#' @rdname hidden_aliases
 setClass("MsBackendRawFileReader",
          contains = "MsBackendDataFrame",
          prototype = prototype(version = "0.1",

src/MsBackendRawFileReader.cs

@@ -96,9 +96,16 @@ public string GetTitle(int scanNumber)
             return s;
         }
 
-        public double GetPepmass(int scanNumber)
+        public double GetPrecursorMz(int scanNumber)
         {
+
+
+            var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
+
+            if (scanFilter.MSOrder.ToString() == "Ms") return 0.0;
+
             var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
+
             try
             {
                 var reaction0 = scanEvent.GetReaction(0);
@@ -110,13 +117,6 @@ public double GetPepmass(int scanNumber)
             }
         }
 
-        public double[] GetPepmasss()
-        {
-            var pepmass = new double[this.getLastScanNumber()];
-            foreach (int scan in this.scans) pepmass[scan] = GetPepmass(scan);
-            return pepmass;
-        }
-
 
         public string GetScanType(int scanNumber)
         {

tests/testthat.R

@@ -0,0 +1,17 @@
+library("testthat")
+library("MsBackendRawFileReader")
+library("Spectra")
+
+sample_raw_file <- file.path(path.package(package = 'MsBackendRawFileReader'),
+                                'extdata', 'sample.raw')
+
+sample_mzXML_file <- file.path(path.package(package = 'MsBackendRawFileReader'),
+                                'extdata', 'sample.mzXML')
+
+
+sample_raw <-  backendInitialize(MsBackendRawFileReader(), files = sample_raw_file)
+sample_mzr <-  backendInitialize(MsBackendMzR(), files = sample_mzXML_file)
+
+
+
+test_check("MsBackendRawFileReader")

tests/testthat/test_MsBackendMzR_MsBackendRawFileReader.R

@@ -0,0 +1,31 @@
+test_that("msLevel", {
+	expect_identical(msLevel(sample_raw), msLevel(sample_mzr))
+})
+
+
+test_that("rtime", {
+  expect_equal(rtime(sample_raw), rtime(sample_mzr), tolerance = 1E-4)
+})
+
+test_that("precursorMz", {
+  expect_equal(precursorMz(sample_raw), precursorMz(sample_mzr), tolerance = 1E-5)
+})
+
+test_that("precursorCharge", {
+  expect_identical(precursorCharge(sample_raw), precursorCharge(sample_mzr))
+})
+
+
+test_that("peaks", {
+
+  sample_peaks_raw <- peaks(sample_raw)
+  sample_peaks_mzr <- peaks(sample_mzr)
+
+  n <- length(sample_peaks_raw )
+  expect_true(n == 574)
+
+  rv <- lapply(1:n, function(i){
+    expect_identical(sample_peaks_raw[[i]] , sample_peaks_mzr[[i]])
+  })
+
+})