Merge pull request #1 from jorainer/adafede

Make electronBeamEnergy an optional header column for export

Author: Adafede

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mzR
 Type: Package
 Title: parser for netCDF, mzXML and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.43.1
+Version: 2.43.3
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
 Authors@R: c(
     person("Steffen", "Neumann", email="[email protected]", role=c("aut","cre")),

NEWS

@@ -1,3 +1,11 @@
+CHANGES IN VERSION 2.43.3
+
+o Make electronBeamEnergy an optional header field.
+
+CHANGES IN VERSION 2.43.2
+-------------------------
+o More fixes around NaN
+
 CHANGES IN VERSION 2.43.1
 -------------------------
 o Update CV, adds multiple terms

R/functions-utils.R

@@ -60,6 +60,8 @@
         x$scanWindowLowerLimit <- NA_real_
     if (!any(colnames(x) == "scanWindowUpperLimit"))
         x$scanWindowUpperLimit <- NA_real_
+    if (!any(colnames(x) == "electronBeamEnergy"))
+        x$electronBeamEnergy <- NA_real_
     if (!(all(names(req_cols) %in% colnames(x))))
         return(paste0("'x' is missing one or more required columns: ",
                       paste(names(req_cols), collapse = ", ")))

inst/unitTests/test_cdf.R

@@ -64,7 +64,7 @@ test_header <- function() {
   cdf <- openMSfile(file, backend="netCDF")        
 
   h <- header(cdf)
-  checkEquals(ncol(h), 31)
+  checkEquals(ncol(h), 32)
   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), 31)
+  checkEquals(ncol(h), 32)
   checkEquals(nrow(h), 1)
 
   h <- header(cdf, 2:3)
-  checkEquals(ncol(h), 31)
+  checkEquals(ncol(h), 32)
   checkEquals(nrow(h), 2)
 
   close(cdf)

inst/unitTests/test_header.R

@@ -18,7 +18,8 @@ test_header_all <- function() {
                           "mergedResultScanNum", "mergedResultStartScanNum", "mergedResultEndScanNum",  
                           "injectionTime", "filterString", "spectrumId", "centroided",  
                           "ionMobilityDriftTime", "isolationWindowTargetMZ", "isolationWindowLowerOffset",  
-                          "isolationWindowUpperOffset", "scanWindowLowerLimit", "scanWindowUpperLimit" )
+                          "isolationWindowUpperOffset", "scanWindowLowerLimit", "scanWindowUpperLimit",
+                          "electronBeamEnergy")
 
     checkTrue( all(neededCdfHeaders %in% colnames(header_cdf)) )
     checkTrue( all(neededCdfHeaders %in% colnames(header_pwiz)) )