@@ -1,6 +1,7 @@

 CHANGES IN VERSION 2.11.3

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

- o Nothing yet

+ o Read ion injection time from mzML files and add it to the data.frame returned

+   by the header function.

 CHANGES IN VERSION 2.11.2

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

@@ -91,7 +91,8 @@ setMethod("header",

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

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

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

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

+                            mergedResultEndScanNum=rep(-1, length(scans)),

+                            injectionTime = rep(-1, length(scans)))

             return(result)

           })

@@ -40,15 +40,15 @@ test_header <- function() {

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

   h <- header(cdf)

-  checkEquals(ncol(h), 19)

+  checkEquals(ncol(h), 20)

   checkEquals(nrow(h), 1278)

   h <- header(cdf, 1)

-  checkEquals(ncol(h), 19)

+  checkEquals(ncol(h), 20)

   checkEquals(nrow(h), 1)

   h <- header(cdf, 2:3)

-  checkEquals(ncol(h), 19)

+  checkEquals(ncol(h), 20)

   checkEquals(nrow(h), 2)

   close(cdf)

new file mode 100644

@@ -0,0 +1,40 @@

+test_injection_time <- function() {

+    library(msdata)

+    library(mzR)

+    library(RUnit)

+    ## mzXML

+    fl <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",

+                      package = "msdata")

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

+    hdr <- header(mzxml)

+    mzR::close(mzxml)

+    checkTrue(all(hdr$injectionTime == 0))

+    checkTrue(any(colnames(hdr) == "injectionTime"))

+    fl <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",

+                      package = "msdata")

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

+    hdr <- header(mzxml)

+    mzR::close(mzxml)

+    checkTrue(all(hdr$injectionTime == 0))

+    checkTrue(any(colnames(hdr) == "injectionTime"))

+

+    ## CDF

+    fl <- system.file("cdf", "ko15.CDF",

+                      package = "msdata")

+    mzxml <- openMSfile(fl, backend = "netCDF")

+    hdr <- header(mzxml)

+    mzR::close(mzxml)

+    checkTrue(all(hdr$injectionTime == -1))

+    checkTrue(any(colnames(hdr) == "injectionTime"))

+

+    ## mzML - with injection time present.

+    fl <- system.file("proteomics",

+                      "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz",

+                      package = "msdata")

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

+    hdr <- header(mzxml)

+    mzR::close(mzxml)

+    checkTrue(all(hdr$injectionTime != 0))

+    checkTrue(any(colnames(hdr) == "injectionTime"))

+    

+}

@@ -124,20 +124,23 @@ test_getScanHeaderInfo <- function() {

     ## Read single scan header.

     scan_3 <- header(mzml, scans = 3)

     scan_3_ramp <- header(ramp, scans = 3)

-    ## Ramp does not read polarity

+    ## Ramp does not read polarity or injectionTime

     scan_3$polarity <- 0

+    scan_3$injectionTime <- 0

     checkEquals(scan_3, scan_3_ramp)

     ## Read all scan header

     all_scans <- header(mzml)

     all_scans_ramp <- header(ramp)

     all_scans$polarity <- 0

+    all_scans$injectionTime <- 0

     checkEquals(all_scans, all_scans_ramp)

     ## passing the index of all scan headers should return the same

     all_scans_2 <- header(mzml, scans = 1:nrow(all_scans))

     all_scans_ramp_2 <- header(ramp, scans = 1:nrow(all_scans))

     all_scans_2$polarity <- 0

+    all_scans_2$injectionTime <- 0

     checkEquals(all_scans, all_scans_2)

     checkEquals(as.list(all_scans[3, ]), scan_3)

     checkEquals(all_scans_2, all_scans_ramp_2)

@@ -147,6 +150,7 @@ test_getScanHeaderInfo <- function() {

     scan_3_ramp <- header(ramp, scans = c(3, 1, 14))

     ## Ramp does not read polarity

     scan_3$polarity <- 0

+    scan_3$injectionTime <- 0

     checkEquals(scan_3, scan_3_ramp)

     close(mzml)

@@ -97,7 +97,8 @@

   \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},

   \code{precursorIntensity}, \code{mergedScan},

   \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and

-  \code{mergedResultEndScanNum}, when available in the original file. If

+  \code{mergedResultEndScanNum}, \code{injectionTime} (ion injection

+  time) when available in the original file. If

   multiple scans are queried, a \code{data.frame} is returned with the

   scans reported along the rows.

@@ -186,6 +186,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       Rcpp::IntegerVector mergedResultScanNum(N_scans); /* scan number of the resultant merged scan */

       Rcpp::IntegerVector mergedResultStartScanNum(N_scans); /* smallest scan number of the scanOrigin for merged scan */

       Rcpp::IntegerVector mergedResultEndScanNum(N_scans); /* largest scan number of the scanOrigin for merged scan */

+      Rcpp::NumericVector ionInjectionTime(N_scans); /* The time spent filling an ion trapping device*/

       for (int i = 0; i < N_scans; i++)

 	{

@@ -196,9 +197,13 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

 	  msLevel[i] = scanHeader.msLevel;

 	  SpectrumPtr sp = slp->spectrum(current_scan-1, false); // Is TRUE neccessary here ? 

+	  Scan dummy;

+	  Scan& scan = sp->scanList.scans.empty() ? dummy : sp->scanList.scans[0];

 	  CVParam param = sp->cvParamChild(MS_scan_polarity);

 	  polarity[i] = (param.cvid==MS_negative_scan ? 0 : (param.cvid==MS_positive_scan ? +1 : -1 ) );

-	  

+	  // ionInjectionTime[i] = sp->cvParam(MS_ion_injection_time).valueAs<double>();

+	  ionInjectionTime[i] = scan.cvParam(MS_ion_injection_time).timeInSeconds();

+

 	  peaksCount[i] = scanHeader.peaksCount;

 	  totIonCurrent[i] = scanHeader.totIonCurrent;

 	  retentionTime[i] = scanHeader.retentionTime;

@@ -221,7 +226,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       delete adapter;

       adapter = NULL;

-      Rcpp::List header(21);

+      Rcpp::List header(22);

       std::vector<std::string> names;

       int i = 0;

       names.push_back("seqNum");

@@ -266,6 +271,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       header[i++] = Rcpp::wrap(mergedResultStartScanNum);

       names.push_back("mergedResultEndScanNum");

       header[i++] = Rcpp::wrap(mergedResultEndScanNum);

+      names.push_back("injectionTime");

+      header[i++] = Rcpp::wrap(ionInjectionTime);

       header.attr("names") = names;

@@ -148,7 +148,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )

         delete info;

         std::vector<std::string> names;

-        Rcpp::List header(21);

+        Rcpp::List header(22);

         int i = 0;

         names.push_back("seqNum");

@@ -193,6 +193,8 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )

         header[i++] = Rcpp::wrap(data.mergedResultStartScanNum);

         names.push_back("mergedResultEndScanNum");

         header[i++] = Rcpp::wrap(data.mergedResultEndScanNum);

+        names.push_back("injectionTime");

+        header[i++] = 0;

         header.attr("names") = names;

@@ -260,7 +262,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )

                 mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;

             }

-            Rcpp::List header(21);

+            Rcpp::List header(22);

             std::vector<std::string> names;

             int i = 0;

@@ -306,6 +308,8 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )

             header[i++] =Rcpp::wrap(mergedResultStartScanNum);

             names.push_back("mergedResultEndScanNum");

             header[i++] =Rcpp::wrap(mergedResultEndScanNum);

+            names.push_back("injectionTime");

+            header[i++] = 0;

 			header.attr("names") = names;