@@ -2,7 +2,7 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.25.1

+Version: 2.25.2

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,

 	    Laurent Gatto <laurent.gatto@uclouvain.be>,

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 2.25.2

+-------------------------

+ o Fix issue #238: ensure `header` call returns the same columns for all

+   backends.

+

 CHANGES IN VERSION 2.25.1

 -------------------------

  o Bump version to trigger new build using latest Rcpp

@@ -51,41 +51,44 @@ setMethod("header",

           signature=c("mzRnetCDF","missing"),

           function(object) return(header(object, 1:length(object))))

-setMethod("header",

-          signature=c("mzRnetCDF","numeric"),

-          function(object, scans) {

-            empty_val <- rep(-1, length(scans))

-            result <- data.frame(seqNum=scans,

-                            acquisitionNum=scans,

-                            msLevel=rep(1, length(scans)),

-                            peaksCount=rep(1, length(scans)),

-                            totIonCurrent=netCDFVarDouble(object@backend, "total_intensity")[scans],

-                            retentionTime=netCDFVarDouble(object@backend, "scan_acquisition_time")[scans], 

-                            basePeakMZ = empty_val,

-                            basePeakIntensity = empty_val,

-                            collisionEnergy = empty_val,

-                            ionisationEnergy = empty_val,

-                            highMZ = empty_val,

-                            precursorScanNum = empty_val,

-                            precursorMZ = empty_val,

-                            precursorCharge = empty_val,

-                            precursorIntensity = empty_val,

-                            mergedScan = empty_val,

-                            mergedResultScanNum = empty_val,

-                            mergedResultStartScanNum = empty_val,

-                            mergedResultEndScanNum = empty_val,

-                            injectionTime = empty_val,

-                            spectrumId = paste0("scan=", scans),

-                            centroided = NA,

-                            ionMobilityDriftTime = empty_val,

-                            stringsAsFactors = FALSE)

-            result$isolationWindowTargetMZ <- NA_real_

-            result$isolationWindowLowerOffset <- NA_real_

-            result$isolationWindowUpperOffset <- NA_real_

-            result$scanWindowLowerLimit <- NA_real_

-            result$scanWindowUpperLimit <- NA_real_

-            return(result)

-          })

+setMethod("header", c("mzRnetCDF", "numeric"), function(object, scans) {

+    ls <- length(scans)

+    empty_val <- rep(-1, ls)

+    na_real <- rep(NA_real_, ls)

+    result <- data.frame(

+        seqNum=scans,

+        acquisitionNum=scans,

+        msLevel = rep(1L, length(scans)),

+        polarity = -1L,

+        peaksCount=rep(1, length(scans)),

+        totIonCurrent=netCDFVarDouble(object@backend, "total_intensity")[scans],

+        retentionTime=netCDFVarDouble(object@backend, "scan_acquisition_time")[scans],

+        basePeakMZ = empty_val,

+        basePeakIntensity = empty_val,

+        collisionEnergy = empty_val,

+        ionisationEnergy = empty_val,

+        lowMZ = empty_val,

+        highMZ = empty_val,

+        precursorScanNum = empty_val,

+        precursorMZ = empty_val,

+        precursorCharge = empty_val,

+        precursorIntensity = empty_val,

+        mergedScan = empty_val,

+        mergedResultScanNum = empty_val,

+        mergedResultStartScanNum = empty_val,

+        mergedResultEndScanNum = empty_val,

+        injectionTime = empty_val,

+        filterString = NA_character_,

+        spectrumId = paste0("scan=", scans),

+        centroided = NA,

+        ionMobilityDriftTime = empty_val,

+        isolationWindowTargetMZ = na_real,

+        isolationWindowLowerOffset = na_real,

+        isolationWindowUpperOffset = na_real,

+        scanWindowLowerLimit = na_real,

+        scanWindowUpperLimit = na_real)

+    return(result)

+})

 setMethod("close", 

           signature="mzRnetCDF",

@@ -1,4 +1,4 @@

-BUILT_RCPP_VERSION = package_version("0.12.19")

+BUILT_RCPP_VERSION = package_version("1.0.2")

 .onLoad <-

     function(libname, pkgname) {

@@ -64,7 +64,7 @@ test_header <- function() {

   cdf <- openMSfile(file, backend="netCDF")        

   h <- header(cdf)

-  checkEquals(ncol(h), 28)

+  checkEquals(ncol(h), 31)

   checkEquals(nrow(h), 1278)

   checkTrue(any(colnames(h) == "centroided"))

   checkTrue(all(is.na(h$centroided)))

@@ -80,11 +80,11 @@ test_header <- function() {

   checkTrue(all(is.na(h$scanWindowUpperLimit)))

   h <- header(cdf, 1)

-  checkEquals(ncol(h), 28)

+  checkEquals(ncol(h), 31)

   checkEquals(nrow(h), 1)

   h <- header(cdf, 2:3)

-  checkEquals(ncol(h), 28)

+  checkEquals(ncol(h), 31)

   checkEquals(nrow(h), 2)

   close(cdf)

new file mode 100644

@@ -0,0 +1,20 @@

+test_header_all <- function() {

+    ## Check that the header call returns the same columns irrespectively of the

+    ## backend. Issue #238

+    file <- system.file('cdf/ko15.CDF', package = "msdata")

+    cdf <- openMSfile(file, backend="netCDF")

+    header_cdf <- header(cdf)

+    close(cdf)

+

+    file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML", package = "msdata")

+    mzxml <- openMSfile(file, backend="pwiz")

+    header_pwiz <- header(mzxml)

+    close(mzxml)

+

+    mzxml <- openMSfile(file, backend="Ramp")

+    header_ramp <- header(mzxml)

+    close(mzxml)

+

+    checkEquals(colnames(header_cdf), colnames(header_pwiz))

+    checkEquals(colnames(header_ramp), colnames(header_pwiz))

+}