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

 Type: Package

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

        (mass spectrometry data)

-Version: 2.19.3

+Version: 2.19.4

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

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

 	    Laurent Gatto <lg390@cam.ac.uk>,

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 2.19.4

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

+ o Add header columns scanWindowLowerLimit and scanWindowUpperLimit

+

 CHANGES IN VERSION 2.19.3

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

  o use ProtGenerics::tolerance generic <2019-08-16 Fri>

@@ -41,7 +41,9 @@

                   ionMobilityDriftTime = "numeric",

                   isolationWindowTargetMZ = "numeric",

                   isolationWindowLowerOffset = "numeric",

-                  isolationWindowUpperOffset = "numeric"

+                  isolationWindowUpperOffset = "numeric",

+                  scanWindowLowerLimit = "numeric",

+                  scanWindowUpperLimit = "numeric"

                   )

     if (!is.data.frame(x))

         return("'x' is supposed to be a data.frame")

@@ -53,6 +55,10 @@

         x$isolationWindowLowerOffset <- NA_real_

     if (!any(colnames(x) == "isolationWindowUpperOffset"))

         x$isolationWindowUpperOffset <- NA_real_

+    if (!any(colnames(x) == "scanWindowLowerLimit"))

+        x$scanWindowLowerLimit <- NA_real_

+    if (!any(colnames(x) == "scanWindowUpperLimit"))

+        x$scanWindowUpperLimit <- 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 = ", ")))

@@ -82,6 +82,8 @@ setMethod("header",

             result$isolationWindowTargetMZ <- NA_real_

             result$isolationWindowLowerOffset <- NA_real_

             result$isolationWindowUpperOffset <- NA_real_

+            result$scanWindowLowerLimit <- NA_real_

+            result$scanWindowUpperLimit <- NA_real_

             return(result)

           })

@@ -51,6 +51,8 @@ setMethod("header",

               res$isolationWindowTargetMZ <- NA_real_

               res$isolationWindowLowerOffset <- NA_real_

               res$isolationWindowUpperOffset <- NA_real_

+              res$scanWindowLowerLimit <- NA_real_

+              res$scanWindowUpperLimit <- NA_real_

               res

 })

@@ -71,6 +73,8 @@ setMethod("header",

               res$isolationWindowTargetMZ <- NA_real_

               res$isolationWindowLowerOffset <- NA_real_

               res$isolationWindowUpperOffset <- NA_real_

+              res$scanWindowLowerLimit <- NA_real_

+              res$scanWindowUpperLimit <- NA_real_

               res

           })

@@ -77,7 +77,8 @@ setMethod("isolationWindow", "character",

             "precursorIsolationWindowTargetMZ",

             "precursorIsolationWindowLowerOffset",

             "precursorIsolationWindowUpperOffset",

-            "precursorCollisionEnergy", "productIsolationWindowTargetMZ",

+            "precursorCollisionEnergy",

+            "productIsolationWindowTargetMZ",

             "productIsolationWindowLowerOffset",

             "productIsolationWindowUpperOffset")

     data.frame(matrix(nrow = 0, ncol = length(cn),

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

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

   h <- header(cdf)

-  checkEquals(ncol(h), 26)

+  checkEquals(ncol(h), 28)

   checkEquals(nrow(h), 1278)

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

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

@@ -74,12 +74,17 @@ test_header <- function() {

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

   checkEquals(h$spectrumId, paste0("scan=", h$acquisitionNum))

+  checkTrue(any(colnames(h) == "scanWindowLowerLimit"))

+  checkTrue(any(colnames(h) == "scanWindowUpperLimit"))

+  checkTrue(all(is.na(h$scanWindowLowerLimit)))

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

+

   h <- header(cdf, 1)

-  checkEquals(ncol(h), 26)

+  checkEquals(ncol(h), 28)

   checkEquals(nrow(h), 1)

   h <- header(cdf, 2:3)

-  checkEquals(ncol(h), 26)

+  checkEquals(ncol(h), 28)

   checkEquals(nrow(h), 2)

   close(cdf)

@@ -15,13 +15,17 @@ test_mzXML <- function() {

     hdr <- header(mzxml)

     checkTrue(any(colnames(hdr) == "spectrumId"))

     checkTrue(all(hdr$centroided))

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

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

+    checkTrue(all(is.na(hdr$scanWindowLowerLimit)))

+    checkTrue(all(is.na(hdr$scanWindowUpperLimit)))

     hdr <- header(mzxml,1)

     checkTrue(is.list(hdr))

     hdr <- header(mzxml, 2:3)

     checkTrue(is.data.frame(hdr))

     checkTrue(nrow(hdr) == 2)

     fileName(mzxml)

-    close(mzxml)    

+    close(mzxml)

 }

 test_mzML <- function() {

@@ -40,6 +44,10 @@ test_mzML <- function() {

     checkTrue(any(colnames(hdr) == "spectrumId"))

     checkTrue(all(hdr$centroided))

     checkEquals(hdr$spectrumId, paste0("spectrum=", hdr$acquisitionNum))

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

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

+    checkTrue(all(!is.na(hdr$scanWindowLowerLimit)))

+    checkTrue(all(!is.na(hdr$scanWindowUpperLimit)))

     hdr <- header(mzml,1)

     checkTrue(is.list(hdr))

     hdr <- header(mzml, 2:3)

@@ -76,7 +84,8 @@ test_getScanHeaderInfo <- function() {

     ## Read single scan header.

     scan_3 <- header(mzml, scans = 3)

     cn <- names(scan_3)

-    cn <- cn[cn != "spectrumId"]

+    cn <- cn[!(cn %in% c("spectrumId", "scanWindowLowerLimit",

+                         "scanWindowUpperLimit"))]

     scan_3_ramp <- header(ramp, scans = 3)

     ## Ramp does not read polarity

     scan_3$polarity <- 0

@@ -19,6 +19,10 @@ test_mzXML <- function() {

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

     checkTrue(any(colnames(hdr) == "ionMobilityDriftTime"))

     checkTrue(all(is.na(hdr$ionMobilityDriftTime)))

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

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

+    checkTrue(all(is.na(hdr$scanWindowLowerLimit)))

+    checkTrue(all(is.na(hdr$scanWindowUpperLimit)))

     close(mzxml)

 }

@@ -41,6 +45,10 @@ test_mzML <- function() {

     header(mzml,2:3)

     checkTrue(any(colnames(hdr) == "ionMobilityDriftTime"))

     checkTrue(all(is.na(hdr$ionMobilityDriftTime)))

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

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

+    checkTrue(all(is.na(hdr$scanWindowLowerLimit)))

+    checkTrue(all(is.na(hdr$scanWindowUpperLimit)))

     checkTrue(ncol(header(mzml))>4)

     checkTrue(length(header(mzml,1))>4)

@@ -186,7 +186,9 @@ test_copyWriteMSData <- function() {

     checkEquals(hdr_mod[, rt_col], hdr_new[, rt_col], tolerance = 0.01)

     cn <- colnames(hdr)[!(colnames(hdr) %in% c("injectionTime", "retentionTime",

                                                "filterString", "spectrumId",

-                                               "isolationWindowTargetMZ"))]

+                                               "isolationWindowTargetMZ",

+                                               "scanWindowLowerLimit",

+                                               "scanWindowUpperLimit"))]

     checkEquals(hdr_mod[, cn], hdr_new[, cn])

     ## checkEquals(ii, ii_new)

@@ -245,7 +247,9 @@ test_copyWriteMSData <- function() {

                                                        "retentionTime",

                                                        "filterString",

                                                        "spectrumId",

-                                                       "isolationWindowTargetMZ"))]

+                                                       "isolationWindowTargetMZ",

+                                                       "scanWindowLowerLimit",

+                                                       "scanWindowUpperLimit"))]

     checkEquals(hdr_sub[, cn], hdr_new[, cn])    

     ## Other mzML:

@@ -279,8 +283,9 @@ test_copyWriteMSData <- function() {

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

     mzR::close(in_file)

-    checkEquals(hdr[, colnames(hdr) != "spectrumId"],

-                hdr_2[, colnames(hdr_2) != "spectrumId"])

+    cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")

+    checkEquals(hdr[, !(colnames(hdr) %in% cn)],

+                hdr_2[, !(colnames(hdr_2) %in% cn)])

     checkEquals(pks, pks_2)

     checkEquals(ii, ii_2)

 }

@@ -444,7 +449,9 @@ test_writeMSData <- function() {

                                                        "injectionTime",

                                                        "filterString",

                                                        "spectrumId",

-                                                       "isolationWindowTargetMZ"))]

+                                                       "isolationWindowTargetMZ",

+                                                       "scanWindowLowerLimit",

+                                                       "scanWindowUpperLimit"))]

     checkEquals(hdr_mod[, cn], hdr_2[, cn])

     ## Subset. These checks ensure that the scan - precursor scan are mapped

@@ -512,7 +519,9 @@ test_writeMSData <- function() {

                                                        "retentionTime",

                                                        "filterString",

                                                        "spectrumId",

-                                                       "isolationWindowTargetMZ"))]

+                                                       "isolationWindowTargetMZ",

+                                                       "scanWindowLowerLimit",

+                                                       "scanWindowUpperLimit"))]

     checkEquals(hdr_sub[, cn], hdr_new[, cn])

     ## Other mzML:

@@ -545,9 +554,10 @@ test_writeMSData <- function() {

     pks_2 <- peaks(in_file)

     mzR::close(in_file)

     checkEquals(pks, pks_2)

-    checkEquals(hdr[, colnames(hdr_2) != "spectrumId"],

-                hdr_2[, colnames(hdr_2) != "spectrumId"])

-

+    cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")

+    checkEquals(hdr[, !(colnames(hdr_2) %in% cn)],

+                hdr_2[, !(colnames(hdr_2) %in% cn)])

+    

     ## mzData:

     test_file <- system.file("iontrap", "extracted.mzData", package = "msdata")

     in_file <- openMSfile(test_file, backend = "Ramp")

@@ -124,8 +124,9 @@

   or profile mode; only for pwiz backend), \code{injectionTime} (ion

   injection time, in milliseconds), \code{ionMobilityDriftTime} (in

   milliseconds), \code{isolationWindowTargetMZ},

-  \code{isolationWindowLowerOffset} and

-  \code{isolationWindowUpperOffset}. If multiple scans are queried, a

+  \code{isolationWindowLowerOffset},

+  \code{isolationWindowUpperOffset}, \code{scanWindowLowerLimit} and

+  \code{scanWindowUpperLimit}. If multiple scans are queried, a

   \code{data.frame} is returned with the scans reported along the

   rows.

@@ -210,6 +210,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       Rcpp::NumericVector isolationWindowTargetMZ(N_scans);

       Rcpp::NumericVector isolationWindowLowerOffset(N_scans);

       Rcpp::NumericVector isolationWindowUpperOffset(N_scans);

+      Rcpp::NumericVector scanWindowLowerLimit(N_scans);

+      Rcpp::NumericVector scanWindowUpperLimit(N_scans);

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

 	{

@@ -228,6 +230,14 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

 	  ionInjectionTime[i] = (scan.cvParam(MS_ion_injection_time).timeInSeconds() * 1000);

 	  filterString[i] = scan.cvParam(MS_filter_string).value.empty() ? NA_STRING : Rcpp::String(scan.cvParam(MS_filter_string).value);

 	  ionMobilityDriftTime[i] = scan.cvParam(MS_ion_mobility_drift_time).value.empty() ? NA_REAL : (scan.cvParam(MS_ion_mobility_drift_time).timeInSeconds() * 1000);

+

+	  if (!scan.scanWindows.empty()) {

+	    scanWindowLowerLimit[i] = scan.scanWindows[0].cvParam(MS_scan_window_lower_limit).valueAs<double>();

+	    scanWindowUpperLimit[i] = scan.scanWindows[0].cvParam(MS_scan_window_upper_limit).valueAs<double>();

+	  } else {

+	    scanWindowLowerLimit[i] = NA_REAL;

+	    scanWindowUpperLimit[i] = NA_REAL;

+	  }

 	  if (!sp->precursors.empty()) {

 	    IsolationWindow iwin = sp->precursors[0].isolationWindow;

@@ -270,7 +280,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       delete adapter;

       adapter = NULL;

-      Rcpp::List header(29);

+      Rcpp::List header(31);

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

       int i = 0;

       names.push_back("seqNum");

@@ -331,6 +341,10 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

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

       names.push_back("isolationWindowUpperOffset");

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

+      names.push_back("scanWindowLowerLimit");

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

+      names.push_back("scanWindowUpperLimit");

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

       header.attr("names") = names;

       return header;

@@ -651,6 +665,8 @@ void RcppPwiz::addSpectrumList(MSData& msd,

   Rcpp::NumericVector isolationWindowTargetMZ = spctr_header["isolationWindowTargetMZ"];

   Rcpp::NumericVector isolationWindowLowerOffset = spctr_header["isolationWindowLowerOffset"];

   Rcpp::NumericVector isolationWindowUpperOffset = spctr_header["isolationWindowUpperOffset"];

+  Rcpp::NumericVector scanWindowLowerLimit = spctr_header["scanWindowLowerLimit"];

+  Rcpp::NumericVector scanWindowUpperLimit = spctr_header["scanWindowUpperLimit"];

   // From MSnbase::Spectrum        Column in the header

   // msLevel integer               $msLevel

@@ -727,7 +743,11 @@ void RcppPwiz::addSpectrumList(MSData& msd,

     if (ionMobilityDriftTime[i] != NA_REAL)

       spct_scan.set(MS_ion_mobility_drift_time, ionMobilityDriftTime[i],

 		    UO_millisecond);

-    

+

+    // scanWindow

+    if (scanWindowLowerLimit[i] != NA_REAL && scanWindowUpperLimit[i] != NA_REAL) {

+      spct_scan.scanWindows.push_back(ScanWindow(scanWindowLowerLimit[i], scanWindowUpperLimit[i], MS_m_z));

+    }

     // MSn - precursor:

     if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {

       // Fill precursor data. This preserves the precursor data even if the

@@ -834,7 +854,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )

 Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichChrom)

 {

   if (msd != NULL) {

-    CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this...

+    CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd);

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     if (clp.get() == 0) {

       Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");

@@ -874,8 +894,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh

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

       if (!ch->precursor.empty()) {

 	precursorIsolationWindowTargetMZ[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_target_m_z).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_target_m_z).valueAs<double>();

-	precursorIsolationWindowLowerOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? 0 : ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>();

-	precursorIsolationWindowUpperOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? 0 : ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>();

+	precursorIsolationWindowLowerOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>();

+	precursorIsolationWindowUpperOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>();

 	precursorCollisionEnergy[i] = ch->precursor.activation.cvParam(MS_collision_energy).value.empty() ? NA_REAL : ch->precursor.activation.cvParam(MS_collision_energy).valueAs<double>(); 

       } else {

 	precursorIsolationWindowTargetMZ[i] = NA_REAL;

@@ -885,8 +905,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh

       }

       if (!ch->product.empty()) {

 	productIsolationWindowTargetMZ[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_target_m_z).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_target_m_z).valueAs<double>();

-	productIsolationWindowLowerOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? 0 : ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>();

-	productIsolationWindowUpperOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? 0 : ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>();

+	productIsolationWindowLowerOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>();

+	productIsolationWindowUpperOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>();

       } else {

 	productIsolationWindowTargetMZ[i] = NA_REAL;

 	productIsolationWindowLowerOffset[i] = NA_REAL;