- remove not used allowNoMatch argument in getMzShift()

- more tests for getMzShift()
CeMOS-Mannheim · Sep 4, 2024 · 81a6a11 · 81a6a11
1 parent 40dcdce
commit 81a6a11
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/R/getMzShift.R b/R/getMzShift.R
@@ -49,9 +49,6 @@ getMzShift <- function(peaks,
   mzShift <- na.omit(mzShift)
 
   if (!all(allIdx %in% specIdx)) {
-    if (!allowNoMatch) {
-      stop("Could not find ", targetMz, " for all spectra! Consider adjusting tol.\n")
-    }
     warning("Could not find ", targetMz, " in spectrum ", paste(which(!(allIdx %in% specIdx)), collapse = ", "), ".\n")
     specIdx <- sort(which(allIdx %in% specIdx))
   } else {

diff --git a/man/isMALDIassay.Rd b/man/isMALDIassay.Rd
diff --git a/tests/testthat/test-getMzShift.R b/tests/testthat/test-getMzShift.R
@@ -33,7 +33,20 @@ test_that("getMzShift stops if a single condition gets filtered completly", {
   MALDIquant::mass(dummyPeaks[[1]]) <- c(1:4, 6, 7:11)
   names(dummyPeaks) <- 1:3
 
-  expect_error(suppressWarnings(getMzShift(dummyPeaks, targetMz = 5.1, tol = 0.15, verbose = TRUE)))
+  expect_error(suppressWarnings(getMzShift(dummyPeaks,
+                                           targetMz = 5.1, 
+                                           tol = 0.15, 
+                                           verbose = TRUE)))
+})
+
+test_that("getMzShift stops if targetMz can't be found in any spectrum", {
+  dummyPeaks <- peakListConstructor()
+  names(dummyPeaks) <- 1:3
+
+  expect_error(suppressWarnings(getMzShift(dummyPeaks, 
+                                           targetMz = 12, 
+                                           tol = 0.15, 
+                                           verbose = TRUE)))
 })
 
 test_that("getMzShift finds mass shift correctly", {