@@ -2,6 +2,8 @@ CHANGES IN VERSION 2.19.5

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

  o header for the pwiz backend returns NA instead of 0 for not defined or

    missing information <2019-09-24 Tue>.

+ o peaks for pwiz backend rewritten (small performance improvement)

+   <2019-09-26 Thu>.

 CHANGES IN VERSION 2.19.4

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

@@ -81,19 +81,12 @@ setMethod("spectra", "mzRpwiz",

 setMethod("peaksCount", c("mzRpwiz", "numeric"),

           function(object, scans) {

-            if (length(scans) == 1) {

-              return(object@backend$getPeakList(scans)$peaksCount)

-            } else {

-                return(sapply(scans,

-                              function(x)

-                                  object@backend$getPeakList(x)$peaksCount))

-            }

+              lengths(object@backend$getPeakList(scans))/2

           })

 setMethod("peaksCount", c("mzRpwiz", "missing"),

           function(object) {

-            n <- length(object)

-            return(peaksCount(object, 1:n))

+            peaksCount(object, seq_along(object))

           })

 setMethod("runInfo", "mzRpwiz",

@@ -18,18 +18,18 @@ setMethod("length",

           function(x) return(x@backend$getLastScan()))

 setMethod("peaks", "mzRramp",

-          function(object, scans) .peaks(object, scans))

+          function(object, scans) .peaks_ramp(object, scans))

 setMethod("spectra", "mzRramp",

-          function(object, scans) .peaks(object, scans))

+          function(object, scans) .peaks_ramp(object, scans))

 setMethod("peaksCount",

           signature=c("mzRramp","numeric"),

           function(object,scans) {

               if (length(scans)==1) {

-                  return(object@backend$getPeakList(scans)$peaksCount)

+                  object@backend$getPeakList(scans)$peaksCount

               } else {

-                  return(sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount))

+                  sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount)

               }

           })

@@ -1,20 +1,26 @@

 .peaks <- function(object, scans) {

+    if (missing(scans))

+        scans <- 1:length(object)

+    res <- object@backend$getPeakList(scans)

+    if (length(res) == 1)

+        res[[1]]

+    else res

+}

+

+.peaks_ramp <- function(object, scans) {

     if (missing(scans))

         scans <- 1:length(object)

     if (length(scans) == 1) {

-        return(object@backend$getPeakList(scans)$peaks)

+        object@backend$getPeakList(scans)$peaks

     } else {

-        return(sapply(scans,

-                      function(x) object@backend$getPeakList(x)$peaks,

-                      simplify = FALSE))

+        sapply(scans, function(x) object@backend$getPeakList(x)$peaks,

+               simplify = FALSE)

     }

 }

-

 setMethod("isolationWindow", "character",

           function(object, ...) .isolationWindow(object, ...))

-

 .isolationWindow <- function(x, unique. = TRUE, simplify = TRUE) {

     stopifnot(all(file.exists(x)))

     if (!requireNamespace("XML"))

@@ -128,7 +128,7 @@

   \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.

+  rows. For missing or not defined spectrum variables \code{NA} is reported.

   The \code{get3Dmap} function performs a simple resampling between

   \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix

@@ -38,43 +38,6 @@ void RcppPwiz::close()

     }

 }

-

-// void RcppPwiz::writeMSfile(const string& file, const string& format)

-// {

-//     if (msd != NULL)

-//     {

-//         if(format == "mgf")

-//         {

-//             std::ofstream* mgfOutFileP = new std::ofstream(file.c_str());

-//             Serializer_MGF serializerMGF;

-//             serializerMGF.write(*mgfOutFileP, *msd);

-//             mgfOutFileP->flush();

-//             mgfOutFileP->close();

-//         }

-//         else if(format == "mzxml")

-//         {

-//             std::ofstream mzXMLOutFileP(file.c_str());

-//             Serializer_mzXML::Config config;

-//             config.binaryDataEncoderConfig.compression = BinaryDataEncoder::Compression_Zlib;

-//             Serializer_mzXML serializerMzXML(config);

-//             serializerMzXML.write(mzXMLOutFileP, *msd);

-//         }

-//         else if(format == "mzml")

-//         {

-//             std::ofstream mzXMLOutFileP(file.c_str());

-//             Serializer_mzML::Config config;

-//             config.binaryDataEncoderConfig.compression = BinaryDataEncoder::Compression_Zlib;

-//             Serializer_mzML mzmlSerializer(config);

-//             mzmlSerializer.write(mzXMLOutFileP, *msd);

-//         }

-//         else

-//             Rcpp::Rcerr << format << " format not supported! Please try mgf, mzML, mzXML or mz5." << std::endl;

-//     }

-//     else

-//         Rcpp::Rcerr << "No pwiz object available! Please open a file first!" << std::endl;

-// }

-

-

 string RcppPwiz::getFilename() {

   return filename;

 }

@@ -400,34 +363,43 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( ) {

   return Rcpp::DataFrame::create( );

 }

-Rcpp::List RcppPwiz::getPeakList (int whichScan) {

+Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector whichScan) {

   if (msd != NULL) {

     SpectrumListPtr slp = msd->run.spectrumListPtr;

-    if ((whichScan <= 0) || (whichScan > slp->size())) {

-      Rprintf("Index whichScan out of bounds [1 ... %d].\n", slp->size());

-      return Rcpp::List::create( );

-    }

-    SpectrumPtr s = slp->spectrum(whichScan - 1, true);

-    vector<MZIntensityPair> pairs;

-    s->getMZIntensityPairs(pairs);

-

-    Rcpp::NumericMatrix peaks(pairs.size(), 2);

-

-    if(pairs.size()!=0) {

-      for (int i = 0; i < pairs.size(); i++) {

-	MZIntensityPair p = pairs.at(i);

-	peaks(i,0) = p.mz;

-	peaks(i,1) = p.intensity;

+    int n_scans = slp->size();

+    int n_want = whichScan.size();

+    int current_scan;

+    SpectrumPtr sp;

+    BinaryDataArrayPtr mzs,ints;

+    std::vector<double> data;

+    Rcpp::NumericVector data_matrix;

+    Rcpp::List res(n_want);

+    for (int i = 0; i < n_want; i++) {

+      current_scan = whichScan[i];

+      if (current_scan < 1 || current_scan > n_scans) {

+	Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);

+	return Rcpp::List::create( );

       }

+      sp = slp->spectrum(current_scan - 1, true);

+      mzs = sp->getMZArray();

+      ints = sp->getIntensityArray();

+      if (!mzs.get() || !ints.get()) {

+	Rcpp::NumericMatrix pks(0, 2);

+	res[i] = pks;

+	continue;

+      }

+      if (mzs->data.size() != ints->data.size())

+	Rcpp::Rcerr << "Sizes of mz and intensity arrays don't match." << std::endl;

+      data = mzs->data;

+      data.insert(data.end(), ints->data.begin(), ints->data.end());

+      data_matrix = Rcpp::wrap(data);

+      data_matrix.attr("dim") = Rcpp::Dimension(ints->data.size(), 2);

+      res[i] = data_matrix;

     }

-

-    return Rcpp::List::create(

-			      Rcpp::_["peaksCount"]  = pairs.size(),

-			      Rcpp::_["peaks"]  = peaks

-			      ) ;

+    return res;

   }

   Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

-  return Rcpp::List::create( );

+  return Rcpp::List::create();

 }

 /**

@@ -98,7 +98,7 @@ public:

     Rcpp::DataFrame getAllChromatogramHeaderInfo();

-    Rcpp::List getPeakList(int whichScan);

+    Rcpp::List getPeakList(Rcpp::IntegerVector whichScan);

     Rcpp::NumericMatrix get3DMap(std::vector<int> scanNumbers, double whichMzLow, double whichMzHigh, double resMz);