Merge pull request #303 from jorainer/devel

feat: extract electronBeamEnergy MS term

Author: sneumann

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mzR
 Type: Package
 Title: parser for netCDF, mzXML and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.41.1
+Version: 2.41.2
 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 +1,7 @@
+CHANGES IN VERSION 2.41.2
+-------------------------
+o Report also electron beam energy (MS:1003410) for EAD data.
+
 CHANGES IN VERSION 2.41.1
 -------------------------
 o Fix compilation error with stricter compiler checks

inst/unitTests/test_pwiz.R

@@ -20,6 +20,8 @@ test_mzXML <- function() {
     checkTrue(any(colnames(hdr) == "scanWindowUpperLimit"))
     checkTrue(all(!is.na(hdr$scanWindowLowerLimit)))
     checkTrue(all(!is.na(hdr$scanWindowUpperLimit)))
+    checkTrue(any(colnames(hdr) == "electronBeamEnergy"))
+    checkTrue(all(is.na(hdr$electronBeamEnergy)))
     hdr <- header(mzxml,1)
     checkTrue(is.list(hdr))
     hdr <- header(mzxml, 2:3)

src/RcppPwiz.cpp

@@ -200,7 +200,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
     Rcpp::NumericVector isolationWindowUpperOffset(N_scans);
     Rcpp::NumericVector scanWindowLowerLimit(N_scans);
     Rcpp::NumericVector scanWindowUpperLimit(N_scans);
-
+    Rcpp::NumericVector electronBeamEnergy(N_scans);
+    
     for (size_t i = 0; i < N_scans; i++) {
       int current_scan = whichScan[i];
       size_t current_index = static_cast<size_t>(current_scan - 1);
@@ -262,6 +263,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
 	const Precursor& precursor = sp->precursors[0];
 	// collisionEnergy
 	collisionEnergy[i] = precursor.activation.cvParam(MS_collision_energy).valueAs<double>();
+	// electronBeamEnergy - for EAD
+	electronBeamEnergy[i] = precursor.activation.cvParam(MS_electron_beam_energy).value.empty() ? NA_REAL : precursor.activation.cvParam(MS_electron_beam_energy).valueAs<double>();	
 	// precursorScanNum
 	size_t precursorIndex = slp->find(precursor.spectrumID);
 	if (precursorIndex < N) {
@@ -288,6 +291,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
 	}
       } else {
 	collisionEnergy[i] = NA_REAL;
+	electronBeamEnergy[i] = NA_REAL;
 	precursorScanNum[i] = NA_INTEGER;
 	precursorMZ[i] = NA_REAL;
 	precursorCharge[i] = NA_INTEGER;
@@ -302,7 +306,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
       }
     }
 
-    Rcpp::List header(31);
+    Rcpp::List header(32);
     std::vector<std::string> names;
     size_t i = 0;
     names.push_back("seqNum");
@@ -367,6 +371,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
     header[i++] = Rcpp::wrap(scanWindowLowerLimit);
     names.push_back("scanWindowUpperLimit");
     header[i++] = Rcpp::wrap(scanWindowUpperLimit);
+    names.push_back("electronBeamEnergy");
+    header[i++] = Rcpp::wrap(electronBeamEnergy);
     header.attr("names") = names;
 
     return header;