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Merge pull request #239 from jorainer/master

fix: ensure header returns the same columns for all backends

Laurent Gatto authored on 03/02/2021 13:13:32 • GitHub committed on 03/02/2021 13:13:32
Showing6 changed files

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@@ -2,7 +2,7 @@ Package: mzR
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 Type: Package
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 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
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        (mass spectrometry data)
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-Version: 2.25.1
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+Version: 2.25.2
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 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
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 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
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 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
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@@ -1,3 +1,8 @@
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+CHANGES IN VERSION 2.25.2
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+-------------------------
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+ o Fix issue #238: ensure `header` call returns the same columns for all
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+   backends.
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+
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 CHANGES IN VERSION 2.25.1
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 -------------------------
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  o Bump version to trigger new build using latest Rcpp
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@@ -51,41 +51,44 @@ setMethod("header",
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           signature=c("mzRnetCDF","missing"),
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           function(object) return(header(object, 1:length(object))))
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-setMethod("header",
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-          signature=c("mzRnetCDF","numeric"),
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-          function(object, scans) {
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-            empty_val <- rep(-1, length(scans))
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-            result <- data.frame(seqNum=scans,
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-                            acquisitionNum=scans,
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-                            msLevel=rep(1, length(scans)),
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-                            peaksCount=rep(1, length(scans)),
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-                            totIonCurrent=netCDFVarDouble(object@backend, "total_intensity")[scans],
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-                            retentionTime=netCDFVarDouble(object@backend, "scan_acquisition_time")[scans], 
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-                            basePeakMZ = empty_val,
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-                            basePeakIntensity = empty_val,
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-                            collisionEnergy = empty_val,
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-                            ionisationEnergy = empty_val,
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-                            highMZ = empty_val,
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-                            precursorScanNum = empty_val,
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-                            precursorMZ = empty_val,
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-                            precursorCharge = empty_val,
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-                            precursorIntensity = empty_val,
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-                            mergedScan = empty_val,
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-                            mergedResultScanNum = empty_val,
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-                            mergedResultStartScanNum = empty_val,
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-                            mergedResultEndScanNum = empty_val,
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-                            injectionTime = empty_val,
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-                            spectrumId = paste0("scan=", scans),
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-                            centroided = NA,
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-                            ionMobilityDriftTime = empty_val,
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-                            stringsAsFactors = FALSE)
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-            result$isolationWindowTargetMZ <- NA_real_
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-            result$isolationWindowLowerOffset <- NA_real_
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-            result$isolationWindowUpperOffset <- NA_real_
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-            result$scanWindowLowerLimit <- NA_real_
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-            result$scanWindowUpperLimit <- NA_real_
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-            return(result)
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-          })
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+setMethod("header", c("mzRnetCDF", "numeric"), function(object, scans) {
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+    ls <- length(scans)
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+    empty_val <- rep(-1, ls)
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+    na_real <- rep(NA_real_, ls)
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+    result <- data.frame(
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+        seqNum=scans,
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+        acquisitionNum=scans,
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+        msLevel = rep(1L, length(scans)),
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+        polarity = -1L,
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+        peaksCount=rep(1, length(scans)),
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+        totIonCurrent=netCDFVarDouble(object@backend, "total_intensity")[scans],
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+        retentionTime=netCDFVarDouble(object@backend, "scan_acquisition_time")[scans],
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+        basePeakMZ = empty_val,
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+        basePeakIntensity = empty_val,
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+        collisionEnergy = empty_val,
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+        ionisationEnergy = empty_val,
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+        lowMZ = empty_val,
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+        highMZ = empty_val,
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+        precursorScanNum = empty_val,
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+        precursorMZ = empty_val,
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+        precursorCharge = empty_val,
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+        precursorIntensity = empty_val,
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+        mergedScan = empty_val,
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+        mergedResultScanNum = empty_val,
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+        mergedResultStartScanNum = empty_val,
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+        mergedResultEndScanNum = empty_val,
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+        injectionTime = empty_val,
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+        filterString = NA_character_,
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+        spectrumId = paste0("scan=", scans),
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+        centroided = NA,
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+        ionMobilityDriftTime = empty_val,
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+        isolationWindowTargetMZ = na_real,
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+        isolationWindowLowerOffset = na_real,
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+        isolationWindowUpperOffset = na_real,
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+        scanWindowLowerLimit = na_real,
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+        scanWindowUpperLimit = na_real)
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+    return(result)
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+})
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 setMethod("close", 
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           signature="mzRnetCDF",
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@@ -1,4 +1,4 @@
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-BUILT_RCPP_VERSION = package_version("0.12.19")
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+BUILT_RCPP_VERSION = package_version("1.0.2")
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 .onLoad <-
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     function(libname, pkgname) {
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@@ -64,7 +64,7 @@ test_header <- function() {
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   cdf <- openMSfile(file, backend="netCDF")        
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   h <- header(cdf)
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-  checkEquals(ncol(h), 28)
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+  checkEquals(ncol(h), 31)
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   checkEquals(nrow(h), 1278)
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   checkTrue(any(colnames(h) == "centroided"))
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   checkTrue(all(is.na(h$centroided)))
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@@ -80,11 +80,11 @@ test_header <- function() {
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   checkTrue(all(is.na(h$scanWindowUpperLimit)))
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   h <- header(cdf, 1)
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-  checkEquals(ncol(h), 28)
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+  checkEquals(ncol(h), 31)
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   checkEquals(nrow(h), 1)
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   h <- header(cdf, 2:3)
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-  checkEquals(ncol(h), 28)
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+  checkEquals(ncol(h), 31)
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   checkEquals(nrow(h), 2)
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   close(cdf)
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new file mode 100644
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@@ -0,0 +1,20 @@
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+test_header_all <- function() {
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+    ## Check that the header call returns the same columns irrespectively of the
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+    ## backend. Issue #238
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+    file <- system.file('cdf/ko15.CDF', package = "msdata")
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+    cdf <- openMSfile(file, backend="netCDF")
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+    header_cdf <- header(cdf)
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+    close(cdf)
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+
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+    file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML", package = "msdata")
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+    mzxml <- openMSfile(file, backend="pwiz")
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+    header_pwiz <- header(mzxml)
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+    close(mzxml)
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+
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+    mzxml <- openMSfile(file, backend="Ramp")
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+    header_ramp <- header(mzxml)
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+    close(mzxml)
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+
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+    checkEquals(colnames(header_cdf), colnames(header_pwiz))
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+    checkEquals(colnames(header_ramp), colnames(header_pwiz))
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+}