Merge branch 'devel' into devel

fgcz · Sep 30, 2024 · 6cbef4c · 6cbef4c
2 parents fb19acc + cc1c4f2
commit 6cbef4c
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Showing 4 changed files with 15 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MsBackendRawFileReader
 Type: Package
 Title: Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
-Version: 1.11.3
+Version: 1.11.6
 Authors@R: c(person(given = "Christian",
     family = "Panse", email = "[email protected]", role = c("aut", "cre"),
     comment = c(ORCID = "0000-0003-1975-3064")),
@@ -17,7 +17,7 @@ Imports:
     MsCoreUtils,
     S4Vectors,
     IRanges,
-    rawrr (>= 1.10.1),
+    rawrr (>= 1.13.1),
     utils,
     BiocParallel
 Suggests:

diff --git a/R/MsBackendRawFileReader-functions.R b/R/MsBackendRawFileReader-functions.R
@@ -74,7 +74,7 @@ NULL
   hdr_full <- .get_spectrum_metadata(x)
 
   hdr <- cbind(hdr, hdr_full)
-  
+
   ## Remove core spectra variables that contain only `NA`
   hdr <- S4Vectors::DataFrame(hdr[, !(MsCoreUtils::vapply1l(hdr, function(z) all(is.na(z))) &
                                       colnames(hdr) %in%

diff --git a/R/MsBackendRawFileReader.R b/R/MsBackendRawFileReader.R
@@ -106,18 +106,19 @@ setMethod("peaksData", "MsBackendRawFileReader",
                                                                          scanIndex, BPPARAM=BPPARAM)
 
               rv <- lapply(pls, function(p){
-                if (all(c("centroid.mz", "centroid.intensity", "noises",
-                          "resolutions", "baselines") %in% colnames(p))){
+                if (all(c("centroid.mZ", "centroid.intensity", "noises",
+                          "resolutions", "baselines") %in% names(p))){
 
                   m <- as.matrix(cbind(p$centroid.mZ,
-                                       p$centroid.intensity,
-                                       p$noises,
-                                       p$resolutions,
-                                       p$baselines))
+                                       p$centroid.intensity))
+## TODO(cp): add it 
+                                       #p$noises,
+                                       #p$resolutions,
+                                       #p$baselines))
 
-                  colnames(m) <- c("mz", "intensity",
-                                   "noises", "resolutions", "baselines")
-                }else if (all(c("centroid.mz", "centroid.intensity") %in% colnames(p) )){
+                  colnames(m) <- c("mz", "intensity")
+                            #       "noises", "resolutions", "baselines")
+                }else if (all(c("centroid.mZ", "centroid.intensity") %in% names(p) )){
                   m <- as.matrix(cbind(p$centroid.mZ, p$centroid.intensity))
                   colnames(m) <- c("mz", "intensity")
                 }else if (length(p$mZ) > 0){
@@ -126,7 +127,7 @@ setMethod("peaksData", "MsBackendRawFileReader",
                   colnames(m) <- c("mz", "intensity")
                 }
                 else{
-                  warning(paste0("Scan ", p$scan, " has an empyt peaklist!"))
+                  warning(paste0("Scan ", p$scan, " has an empty peaklist!"))
                   m <- matrix(, 0, 2)
                   colnames(m) <- c("mz", "intensity")
                 }
@@ -171,7 +172,6 @@ setMethod("mz", "MsBackendRawFileReader", function(object, ..., BPPARAM = bppara
   IRanges::NumericList(lapply(peaksData(object, BPPARAM = BPPARAM), "[", , 1), compress = FALSE)
 })
 
-
 #' @exportMethod filterScan
 #' @rdname MsBackendRawFileReader
 #' @param object MsBackendRawFileReader object

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -37,6 +37,7 @@ be <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(
                                  files = c(sample_raw_file))
 
 ## Run the MsBackend spectra variable test suite
+
 test_suite <- system.file("test_backends", "test_MsBackend",
                           package = "Spectra")