@@ -36,7 +36,8 @@

                   mergedResultStartScanNum = "numeric",

                   mergedResultEndScanNum = "numeric",

                   injectionTime = "numeric",

-                  filterString = "character"

+                  filterString = "character",

+                  centroided = "logical"

                   )

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

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

@@ -94,6 +94,7 @@ setMethod("header",

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

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

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

+                            centroided = NA,

                             stringsAsFactors = FALSE)

             return(result)

@@ -46,6 +46,7 @@ setMethod("header",

               res <- object@backend$getAllScanHeaderInfo()

               res$filterString <- NA_character_

               res$spectrumId <- paste0("scan=", res$acquisitionNum)

+              res$centroided <- NA

               res

 })

@@ -61,6 +62,7 @@ setMethod("header",

               }

               res$filterString <- NA_character_

               res$spectrumId <- paste0("scan=", res$acquisitionNum)

+              res$centroided <- NA

               res

           })

@@ -40,18 +40,20 @@ test_header <- function() {

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

   h <- header(cdf)

-  checkEquals(ncol(h), 21)

+  checkEquals(ncol(h), 22)

   checkEquals(nrow(h), 1278)

-

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

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

+  

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

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

   h <- header(cdf, 1)

-  checkEquals(ncol(h), 21)

+  checkEquals(ncol(h), 22)

   checkEquals(nrow(h), 1)

   h <- header(cdf, 2:3)

-  checkEquals(ncol(h), 21)

+  checkEquals(ncol(h), 22)

   checkEquals(nrow(h), 2)

   close(cdf)

@@ -7,16 +7,21 @@ test_mzXML <- function() {

     length(mzxml)

     runInfo(mzxml)

     instrumentInfo(mzxml)

-    peaks(mzxml)

-    peaks(mzxml,1)

-    peaks(mzxml, 2:3)

+    checkTrue(is.list(peaks(mzxml)))

+    checkTrue(is.matrix(peaks(mzxml,1)))

+    pks <- peaks(mzxml, 2:3)

+    checkTrue(length(pks) == 2)

     peaksCount(mzxml)

     hdr <- header(mzxml)

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

-    header(mzxml,1)

-    header(mzxml, 2:3)

+    checkTrue(all(hdr$centroided))

+    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() {

@@ -33,9 +38,13 @@ test_mzML <- function() {

     peaksCount(mzml)

     hdr <- header(mzml)

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

+    checkTrue(all(hdr$centroided))

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

-    header(mzml,1)

-    header(mzml,2:3)

+    hdr <- header(mzxml,1)

+    checkTrue(is.list(hdr))

+    hdr <- header(mzxml, 2:3)

+    checkTrue(is.data.frame(hdr))

+    checkTrue(nrow(hdr) == 2)

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

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

@@ -46,6 +55,15 @@ test_mzML <- function() {

     fileName(mzml)

     close(mzml)

+

+    file <- system.file("proteomics", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz",

+                        package = "msdata")

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

+    checkTrue(class(mzml)=="mzRpwiz")

+    hdr <- header(mzml)

+    checkTrue(hdr$centroided[2])

+    checkTrue(!hdr$centroided[1])

+    close(mzml)

 }

 ## Test the new implementation of the getScanHeaderInfo

@@ -62,18 +80,21 @@ test_getScanHeaderInfo <- function() {

     scan_3_ramp <- header(ramp, scans = 3)

     ## Ramp does not read polarity

     scan_3$polarity <- 0

+    scan_3$centroided <- NA

     checkEquals(scan_3[cn], scan_3_ramp[cn])

     ## Read all scan header

     all_scans <- header(mzml)

     all_scans_ramp <- header(ramp)

     all_scans$polarity <- 0

+    all_scans$centroided <- NA

     checkEquals(all_scans[, cn], all_scans_ramp[, cn])

     ## 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$centroided <- NA

     checkEquals(all_scans, all_scans_2)

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

     checkEquals(all_scans_2[, cn], all_scans_ramp_2[, cn])

@@ -83,6 +104,7 @@ test_getScanHeaderInfo <- function() {

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

     ## Ramp does not read polarity

     scan_3$polarity <- 0

+    scan_3$centroided <- NA

     checkEquals(scan_3[, cn], scan_3_ramp[, cn])

     close(mzml)

@@ -95,11 +117,13 @@ test_getScanHeaderInfo <- function() {

     ramp <- openMSfile(file, backend = "Ramp")

     ## Read single scan header.

     scan_3 <- header(mzml, scans = 3)

+    scan_3$centroided <- NA

     scan_3_ramp <- header(ramp, scans = 3)

     checkEquals(scan_3[cn], scan_3_ramp[cn])

     ## Read all scan header

     all_scans <- header(mzml)

+    all_scans$centroided <- NA

     all_scans_ramp <- header(ramp)

     ## Ramp unable to read precursorScanNum from an mzXML file.

     all_scans$precursorScanNum <- 0

@@ -107,6 +131,7 @@ test_getScanHeaderInfo <- function() {

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

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

+    all_scans_2$centroided <- NA

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

     all_scans_2$precursorScanNum <- 0

     checkEquals(all_scans, all_scans_2)

@@ -117,6 +142,7 @@ test_getScanHeaderInfo <- function() {

     scan_3 <- header(mzml, scans = c(3, 1, 14))

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

     scan_3$precursorScanNum <- 0

+    scan_3$centroided <- NA

     checkEquals(scan_3[, cn], scan_3_ramp[, cn])

     close(mzml)

@@ -134,6 +160,7 @@ test_getScanHeaderInfo <- function() {

     scan_3$polarity <- 0

     scan_3$injectionTime <- 0

     scan_3$filterString <- NA_character_

+    scan_3$centroided <- NA

     checkEquals(scan_3[cn], scan_3_ramp[cn])

     ## Read all scan header

@@ -143,6 +170,7 @@ test_getScanHeaderInfo <- function() {

     all_scans$polarity <- 0

     all_scans$injectionTime <- 0

     all_scans$filterString <- NA_character_

+    all_scans$centroided <- NA

     checkEquals(all_scans[, cn], all_scans_ramp[, cn])

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

@@ -152,6 +180,7 @@ test_getScanHeaderInfo <- function() {

     all_scans_2$polarity <- 0

     all_scans_2$injectionTime <- 0

     all_scans_2$filterString <- NA_character_

+    all_scans_2$centroided <- NA

     checkEquals(all_scans[, cn], all_scans_2[, cn])

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

     checkEquals(all_scans_2[, cn], all_scans_ramp_2[, cn])

@@ -163,6 +192,7 @@ test_getScanHeaderInfo <- function() {

     scan_3$polarity <- 0

     scan_3$injectionTime <- 0

     scan_3$filterString <- NA_character_

+    scan_3$centroided <- NA

     checkEquals(scan_3[, cn], scan_3_ramp[, cn])

     close(mzml)

@@ -14,6 +14,9 @@ test_mzXML <- function() {

     header(mzxml,1)

     header(mzxml,2:3)

     fileName(mzxml)

+    hdr <- header(mzxml)

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

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

     close(mzxml)

 }

@@ -1,9 +1,6 @@

 ## Testing to write stuff.

 test_copyWriteMSData <- function() {

-    library(msdata)

-    library(mzR)

-    library(RUnit)

     test_folder = tempdir()

     ## INPUT: mzXML

@@ -77,11 +74,12 @@ test_copyWriteMSData <- function() {

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

     hdr_new <- header(mzml_new)

-    mzR::close(mzml_new)

     rownames(hdr_new) <- NULL

     rownames(hdr_sub) <- NULL

     checkEquals(pks_new, pks_sub)

     checkEquals(hdr_new, hdr_sub)

+    checkEquals(peaks(mzml_new, 2), pks[[3]])

+    mzR::close(mzml_new)

     ## mzXML

     mzR::copyWriteMSData(file = fnew, original_file = orig_file,

                          header = hdr_sub, object = pks_sub, backend = "pwiz",

@@ -149,11 +147,12 @@ test_copyWriteMSData <- function() {

     pks_new <- peaks(mzml_new)

     hdr_new <- header(mzml_new)

     ii_new <- mzR::instrumentInfo(mzml_new)

-    mzR::close(mzml_new)

     checkEquals(pks_new, pks)

     checkEquals(hdr_new, hdr)  ## polarity is OK here

     checkEquals(ii, ii_new)

-    

+

+    checkEquals(peaks(mzml_new, 12), pks[[12]])

+    mzR::close(mzml_new)

     ## OUTPUT: mzXML

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

     suppressWarnings(

@@ -276,11 +275,7 @@ test_copyWriteMSData <- function() {

     checkEquals(ii, ii_2)

 }

-test_writeMSData <- function() {

-    

-    library(msdata)

-    library(mzR)

-    library(RUnit)

+test_writeMSData <- function() {    

     test_folder = tempdir()

     ## Input: mzXML

     test_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",

@@ -296,9 +291,10 @@ test_writeMSData <- function() {

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

-    mzR::close(in_file)

     checkEquals(hdr, hdr_2)

     checkEquals(pks, pks_2)

+    checkEquals(peaks(in_file, 13), pks[[13]])

+    mzR::close(in_file)

     ## Test subsetting.

     hdr_sub <- hdr[c(1, 3, 5), ]

@@ -308,8 +304,9 @@ test_writeMSData <- function() {

     in_file <- openMSfile(out_file)

     hdr_sub_2 <- header(in_file)

     pks_sub_2 <- peaks(in_file)

-    mzR::close(in_file)

     checkEquals(pks_sub, pks_sub_2)

+    checkEquals(peaks(in_file, 3), pks[[5]])

+    mzR::close(in_file)

     ## mzXML does not support spectrumId, thus acquisitionNum, precursorScanNum

     ## and spectrumId will be different, but their order and mapping has to be

     ## the same.

@@ -395,8 +392,10 @@ test_writeMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_write.mzXML")

-    writeMSData(file = out_file, header = hdr, object = pks,

-                outformat = "mzXML")

+    suppressWarnings(

+        writeMSData(file = out_file, header = hdr, object = pks,

+                    outformat = "mzXML")

+    )

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -456,8 +455,10 @@ test_writeMSData <- function() {

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     pks_sub <- pks[idx]

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

-    writeMSData(file = fnew, header = hdr_sub, object = pks_sub,

-                backend = "pwiz", outformat = "mzxml")

+    suppressWarnings(

+        writeMSData(file = fnew, header = hdr_sub, object = pks_sub,

+                    backend = "pwiz", outformat = "mzxml")

+    )

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -535,5 +536,6 @@ test_writeMSData <- function() {

     pks_2 <- peaks(in_file)

     mzR::close(in_file)

     checkEquals(pks, pks_2)

+    hdr$centroided <- FALSE

     checkEquals(hdr, hdr_2)

 }

@@ -112,9 +112,10 @@

   \code{precursorCharge}, \code{precursorIntensity},

   \code{mergedScan}, \code{mergedResultScanNum},

   \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},

-  \code{spectrumId} and

-  \code{injectionTime} (ion injection time, in seconds) when available

-  in the original file. If multiple scans are queried, a

+  \code{spectrumId}, \code{centroided} (\code{logical} whether the data

+  of the spectrum is in centroid mode or profile mode; only for pwiz

+  backend) and \code{injectionTime} (ion injection time, in seconds)

+  when available in the original file. If multiple scans are queried, a

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

   rows.

@@ -205,6 +205,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

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

       Rcpp::StringVector filterString(N_scans);

       Rcpp::StringVector spectrumId(N_scans);

+      Rcpp::LogicalVector centroided(N_scans);

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

 	{

@@ -241,12 +242,14 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

 	  mergedResultStartScanNum[i] = scanHeader.mergedResultStartScanNum;

 	  mergedResultEndScanNum[i] = scanHeader.mergedResultEndScanNum;

 	  spectrumId[i] = sp->id;

+	  CVParam prm = sp->cvParamChild(MS_spectrum_representation);

+	  centroided[i] = (prm.cvid==MS_centroid_spectrum ? TRUE : (prm.cvid==MS_profile_spectrum ? FALSE : NA_LOGICAL));

 	}

       // delete adapter issue #64

       delete adapter;

       adapter = NULL;

-      Rcpp::List header(24);

+      Rcpp::List header(25);

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

       int i = 0;

       names.push_back("seqNum");

@@ -297,6 +300,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

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

       names.push_back("spectrumId");

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

+      names.push_back("centroided");

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

       header.attr("names") = names;

@@ -610,6 +615,7 @@ void RcppPwiz::addSpectrumList(MSData& msd,

   Rcpp::NumericVector ionInjectionTime = spctr_header["injectionTime"];

   Rcpp::StringVector filterString = spctr_header["filterString"];

   Rcpp::StringVector spectrumId = spctr_header["spectrumId"];

+  Rcpp::LogicalVector centroided = spctr_header["centroided"];

   // From MSnbase::Spectrum        Column in the header

   // msLevel integer               $msLevel

@@ -656,6 +662,11 @@ void RcppPwiz::addSpectrumList(MSData& msd,

     spct.set(MS_base_peak_m_z, basePeakMZ[i]);

     spct.set(MS_base_peak_intensity, basePeakIntensity[i]);

     spct.set(MS_total_ion_current, totIonCurrent[i]);

+    // centroided

+    if (centroided[i] != NA_LOGICAL && centroided[i] == TRUE)

+      spct.set(MS_centroid_spectrum);

+    if (centroided[i] != NA_LOGICAL && centroided[i] == FALSE)

+      spct.set(MS_profile_spectrum);

     // TODO:

     // [X] seqNum: number observed in file.

     spct.index = seqNum[i] - 1;	// Or just i?