@@ -133,7 +133,7 @@ setMethod("writeMSData", signature(object = "list", file = "character"),

               ## Check software_processing:

               software_processing <- .check_software_processing(software_processing)

               ## Add mzR processing:

-              mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."))

+              mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

               if (outformat == "mzml")

                   mzR <- c(mzR, "MS:1000544")

               if (outformat == "mzxml")

@@ -114,7 +114,7 @@

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

   \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)

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

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

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

   rows.

@@ -2,12 +2,12 @@

 RcppPwiz::RcppPwiz()

 {

-    msd = NULL;

-    instrumentInfo = Rcpp::List::create();

-    chromatogramsInfo = Rcpp::DataFrame::create();

-    isInCacheInstrumentInfo = FALSE;

-    allScanHeaderInfo = Rcpp::List::create();

-    isInCacheAllScanHeaderInfo = FALSE;

+  msd = NULL;

+  instrumentInfo = Rcpp::List::create();

+  chromatogramsInfo = Rcpp::DataFrame::create();

+  isInCacheInstrumentInfo = FALSE;

+  allScanHeaderInfo = Rcpp::List::create();

+  isInCacheAllScanHeaderInfo = FALSE;

 }

 /* Destructor*/

 RcppPwiz::~RcppPwiz()

@@ -18,8 +18,8 @@ RcppPwiz::~RcppPwiz()

 void RcppPwiz::open(const string& fileName)

 {

-    filename = fileName;

-    msd = new MSDataFile(fileName);

+  filename = fileName;

+  msd = new MSDataFile(fileName);

 }

@@ -76,98 +76,98 @@ void RcppPwiz::close()

 string RcppPwiz::getFilename() {

-    return filename;

+  return filename;

 }

 int RcppPwiz::getLastScan() const {

-    if (msd != NULL) {

-      SpectrumListPtr slp = msd->run.spectrumListPtr;

-      return slp->size();

-    }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

-    return -1;

+  if (msd != NULL) {

+    SpectrumListPtr slp = msd->run.spectrumListPtr;

+    return slp->size();

+  }

+  Rprintf("Warning: pwiz not yet initialized.\n ");

+  return -1;

 }

 int RcppPwiz::getLastChrom() const {

-    if (msd != NULL) {

-      ChromatogramListPtr clp = msd->run.chromatogramListPtr;

-      return clp->size();

-    }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

-    return -1;

+  if (msd != NULL) {

+    ChromatogramListPtr clp = msd->run.chromatogramListPtr;

+    return clp->size();

+  }

+  Rprintf("Warning: pwiz not yet initialized.\n ");

+  return -1;

 }

 Rcpp::List RcppPwiz::getInstrumentInfo ( )

 {

-    if (msd != NULL)

+  if (msd != NULL)

     {

-        if (!isInCacheInstrumentInfo)

+      if (!isInCacheInstrumentInfo)

         {

-            vector<InstrumentConfigurationPtr> icp = msd->instrumentConfigurationPtrs; // NULL for mzData	    

-            if (icp.size() != 0)

+	  vector<InstrumentConfigurationPtr> icp = msd->instrumentConfigurationPtrs; // NULL for mzData	    

+	  if (icp.size() != 0)

             {

-                CVTranslator cvTranslator;

-                LegacyAdapter_Instrument adapter(*icp[0], cvTranslator);

-                vector<SoftwarePtr> sp = msd->softwarePtrs;

-                std::vector<SamplePtr> sample = msd->samplePtrs;

-                std::vector<ScanSettingsPtr> scansetting = msd->scanSettingsPtrs;

-		std::string ionisation = "";

-		std::string analyzer = "";

-		std::string detector = "";

-		// Fix issue #113

-		// if (icp[0]->componentList.size() > 0)

-		// That does still not mean we have a ionisation available.

-		// Could be that either analyzer or detector or ionisation is

-		// defined.

-		// Have to use try-catch

-		try {

-		  ionisation = std::string(adapter.ionisation());		  

-		} catch(...) {}

-		try {

-		  analyzer = std::string(adapter.analyzer());		  

-		} catch(...) {}

-		try {

-		  detector = std::string(adapter.detector());		  

-		} catch(...) {}

-                instrumentInfo = Rcpp::List::create(

-                                     Rcpp::_["manufacturer"]  = std::string(adapter.manufacturer()),

-                                     Rcpp::_["model"]         = std::string(adapter.model()),

-                                     Rcpp::_["ionisation"]    = ionisation,

-                                     Rcpp::_["analyzer"]      = analyzer,

-                                     Rcpp::_["detector"]      = detector,

-                                     Rcpp::_["software"]      = (sp.size()>0?sp[0]->id + " " + sp[0]->version:""),

-                                     Rcpp::_["sample"]		  = (sample.size()>0?sample[0]->name+sample[0]->id:""),

-                                     Rcpp::_["source"]        = (scansetting.size()>0?scansetting[0]->sourceFilePtrs[0]->location:"")

-                                 ) ;

+	      CVTranslator cvTranslator;

+	      LegacyAdapter_Instrument adapter(*icp[0], cvTranslator);

+	      vector<SoftwarePtr> sp = msd->softwarePtrs;

+	      std::vector<SamplePtr> sample = msd->samplePtrs;

+	      std::vector<ScanSettingsPtr> scansetting = msd->scanSettingsPtrs;

+	      std::string ionisation = "";

+	      std::string analyzer = "";

+	      std::string detector = "";

+	      // Fix issue #113

+	      // if (icp[0]->componentList.size() > 0)

+	      // That does still not mean we have a ionisation available.

+	      // Could be that either analyzer or detector or ionisation is

+	      // defined.

+	      // Have to use try-catch

+	      try {

+		ionisation = std::string(adapter.ionisation());		  

+	      } catch(...) {}

+	      try {

+		analyzer = std::string(adapter.analyzer());		  

+	      } catch(...) {}

+	      try {

+		detector = std::string(adapter.detector());		  

+	      } catch(...) {}

+	      instrumentInfo = Rcpp::List::create(

+						  Rcpp::_["manufacturer"]  = std::string(adapter.manufacturer()),

+						  Rcpp::_["model"]         = std::string(adapter.model()),

+						  Rcpp::_["ionisation"]    = ionisation,

+						  Rcpp::_["analyzer"]      = analyzer,

+						  Rcpp::_["detector"]      = detector,

+						  Rcpp::_["software"]      = (sp.size()>0?sp[0]->id + " " + sp[0]->version:""),

+						  Rcpp::_["sample"]		  = (sample.size()>0?sample[0]->name+sample[0]->id:""),

+						  Rcpp::_["source"]        = (scansetting.size()>0?scansetting[0]->sourceFilePtrs[0]->location:"")

+						  ) ;

             }

-            else

+	  else

             {

-                instrumentInfo = Rcpp::List::create(

-                                     Rcpp::_["manufacturer"]  = "",

-                                     Rcpp::_["model"]         = "",

-                                     Rcpp::_["ionisation"]    = "",

-                                     Rcpp::_["analyzer"]      = "",

-                                     Rcpp::_["detector"]      = "",

-                                     Rcpp::_["software"]      = "",

-                                     Rcpp::_["sample"]		  = "",

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

-                                 ) ;

+	      instrumentInfo = Rcpp::List::create(

+						  Rcpp::_["manufacturer"]  = "",

+						  Rcpp::_["model"]         = "",

+						  Rcpp::_["ionisation"]    = "",

+						  Rcpp::_["analyzer"]      = "",

+						  Rcpp::_["detector"]      = "",

+						  Rcpp::_["software"]      = "",

+						  Rcpp::_["sample"]		  = "",

+						  Rcpp::_["source"]		  = ""

+						  ) ;

             }

-            isInCacheInstrumentInfo = TRUE;

+	  isInCacheInstrumentInfo = TRUE;

         }

-        return(instrumentInfo);

+      return(instrumentInfo);

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

-    return instrumentInfo;

+  Rprintf("Warning: pwiz not yet initialized.\n ");

+  return instrumentInfo;

 }

 Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

 {

-    if (msd != NULL)

+  if (msd != NULL)

     {

       SpectrumListPtr slp = msd->run.spectrumListPtr;

       int N = slp->size();

@@ -220,8 +220,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

 	  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();

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

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

 	  peaksCount[i] = scanHeader.peaksCount;

@@ -307,64 +306,64 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       return header;

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

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

+  Rprintf("Warning: pwiz not yet initialized.\n ");

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

 }

 Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( )

 {

-    if (msd != NULL)

+  if (msd != NULL)

     {

-        if (!isInCacheAllScanHeaderInfo)

+      if (!isInCacheAllScanHeaderInfo)

         {

-            SpectrumListPtr slp = msd->run.spectrumListPtr;

-            int N = slp->size();

+	  SpectrumListPtr slp = msd->run.spectrumListPtr;

+	  int N = slp->size();

-            allScanHeaderInfo = getScanHeaderInfo(Rcpp::seq(1, N));

-            isInCacheAllScanHeaderInfo = TRUE;	    

+	  allScanHeaderInfo = getScanHeaderInfo(Rcpp::seq(1, N));

+	  isInCacheAllScanHeaderInfo = TRUE;	    

         }

-        return allScanHeaderInfo ;

+      return allScanHeaderInfo ;

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

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

+  Rprintf("Warning: pwiz not yet initialized.\n ");

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

 }

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

 {

-    if (msd != NULL)

+  if (msd != NULL)

     {

-        SpectrumListPtr slp = msd->run.spectrumListPtr;

+      SpectrumListPtr slp = msd->run.spectrumListPtr;

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

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

         {

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

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

+	  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);

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

+      vector<MZIntensityPair> pairs;

+      s->getMZIntensityPairs(pairs);

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

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

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

+      if(pairs.size()!=0)

         {

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

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

             {

-                MZIntensityPair p = pairs.at(i);

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

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

+	      MZIntensityPair p = pairs.at(i);

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

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

             }

         }

-        return Rcpp::List::create(

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

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

-               ) ;

+      return Rcpp::List::create(

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

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

+				) ;

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

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

+  Rprintf("Warning: pwiz not yet initialized.\n ");

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

 }

 /**

@@ -651,6 +650,11 @@ void RcppPwiz::addSpectrumList(MSData& msd,

     spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));

     Spectrum& spct = *spectrumList->spectra[i];

     spct.set(MS_ms_level, msLevel[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);

     // [X] polarity

     if (polarity[i] == 0)

       spct.set(MS_negative_scan);

@@ -660,16 +664,12 @@ void RcppPwiz::addSpectrumList(MSData& msd,

       spct.set(MS_MS1_spectrum);

     else

       spct.set(MS_MSn_spectrum);

-    spct.set(MS_lowest_observed_m_z, lowMZ[i]);

-    spct.set(MS_highest_observed_m_z, highMZ[i]);

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

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

+    spct.set(MS_lowest_observed_m_z, lowMZ[i], MS_m_z);

+    spct.set(MS_highest_observed_m_z, highMZ[i], MS_m_z);

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

+    spct.set(MS_base_peak_intensity, basePeakIntensity[i],

+	     MS_number_of_detector_counts);

     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?

@@ -681,15 +681,12 @@ void RcppPwiz::addSpectrumList(MSData& msd,

     spct.scanList.scans.push_back(Scan());

     spct.scanList.set(MS_no_combination);

     Scan &spct_scan = spct.scanList.scans.back();

-    if (rtime_seconds) {

+    if (rtime_seconds)

       spct_scan.set(MS_scan_start_time, retentionTime[i], UO_second);

-      if (ionInjectionTime[i] > 0)

-	spct_scan.set(MS_ion_injection_time, ionInjectionTime[i], UO_second);

-    } else {

+    else

       spct_scan.set(MS_scan_start_time, retentionTime[i], UO_minute);

-      if (ionInjectionTime[i] > 0)

-	spct_scan.set(MS_ion_injection_time, ionInjectionTime[i], UO_minute);

-    }

+    if (ionInjectionTime[i] > 0)

+      spct_scan.set(MS_ion_injection_time, ionInjectionTime[i], UO_millisecond);

     if (!Rcpp::StringVector::is_na(filterString[i]))

       spct_scan.set(MS_filter_string, filterString[i]);

@@ -756,38 +753,38 @@ void RcppPwiz::addSpectrumList(MSData& msd,

 Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )

 {

-    if (msd != NULL) {

-      ChromatogramListPtr clp = msd->run.chromatogramListPtr;

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

-	Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;

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

-      } else if (clp->size() == 0) {

-	Rcpp::Rcerr << "No available chromatogram info." << std::endl;

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

-      } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {

-	Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);

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

-      } else {

-	std::vector<double> time;

-	std::vector<double> intensity;

-	ChromatogramPtr c = clp->chromatogram(whichChrom, true);

-	vector<TimeIntensityPair> pairs;

-	c->getTimeIntensityPairs (pairs);

-

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

-	  TimeIntensityPair p = pairs.at(i);

-	  time.push_back(p.time);

-	  intensity.push_back(p.intensity);

-	}

+  if (msd != NULL) {

+    ChromatogramListPtr clp = msd->run.chromatogramListPtr;

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

+      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;

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

+    } else if (clp->size() == 0) {

+      Rcpp::Rcerr << "No available chromatogram info." << std::endl;

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

+    } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {

+      Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);

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

+    } else {

+      std::vector<double> time;

+      std::vector<double> intensity;

+      ChromatogramPtr c = clp->chromatogram(whichChrom, true);

+      vector<TimeIntensityPair> pairs;

+      c->getTimeIntensityPairs (pairs);

+

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

+	TimeIntensityPair p = pairs.at(i);

+	time.push_back(p.time);

+	intensity.push_back(p.intensity);

+      }

-	chromatogramsInfo = Rcpp::DataFrame::create(Rcpp::_["time"] = time,

-						    Rcpp::_[c->id]  = intensity);

+      chromatogramsInfo = Rcpp::DataFrame::create(Rcpp::_["time"] = time,

+						  Rcpp::_[c->id]  = intensity);

-      }

-      return(chromatogramsInfo);

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

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

+    return(chromatogramsInfo);

+  }

+  Rprintf("Warning: pwiz not yet initialized.\n ");

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

 }

 // get the header info for chromatograms.

@@ -897,53 +894,53 @@ Rcpp::DataFrame RcppPwiz::getAllChromatogramHeaderInfo ( ) {

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

 {

-    if (msd != NULL)

+  if (msd != NULL)

     {

-        SpectrumListPtr slp = msd->run.spectrumListPtr;

-        double f = 1 / resMz;

-        int low = round(whichMzLow * f);

-        int high = round(whichMzHigh * f);

-        int dmz = high - low + 1;

-        int drt = scanNumbers.size();

+      SpectrumListPtr slp = msd->run.spectrumListPtr;

+      double f = 1 / resMz;

+      int low = round(whichMzLow * f);

+      int high = round(whichMzHigh * f);

+      int dmz = high - low + 1;

+      int drt = scanNumbers.size();

-        Rcpp::NumericMatrix map3d(drt, dmz);

+      Rcpp::NumericMatrix map3d(drt, dmz);

-        for (int i = 0; i < drt; i++)

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

         {

-            for (int j = 0; j < dmz; j++)

+	  for (int j = 0; j < dmz; j++)

             {

-                map3d(i,j) = 0.0;

+	      map3d(i,j) = 0.0;

             }

         }

-        int j=0;

-        Rprintf("%d\n",1);

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

+      int j=0;

+      Rprintf("%d\n",1);

+      for (int i = 0; i < scanNumbers.size(); i++)

         {

-            SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);

-            vector<MZIntensityPair> pairs;

-            s->getMZIntensityPairs(pairs);

+	  SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);

+	  vector<MZIntensityPair> pairs;

+	  s->getMZIntensityPairs(pairs);

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

+	  for (int k=0; k < pairs.size(); k++)

             {

-                MZIntensityPair p = pairs.at(k);

-                j = round(p.mz * f) - low;

-                if ((j >= 0) & (j < dmz))

+	      MZIntensityPair p = pairs.at(k);

+	      j = round(p.mz * f) - low;

+	      if ((j >= 0) & (j < dmz))

                 {

-                    if (p.intensity > map3d(i,j))

+		  if (p.intensity > map3d(i,j))

                     {

-                        map3d(i,j) = p.intensity;

+		      map3d(i,j) = p.intensity;

                     }

                 }

             }

         }

-        return(map3d);

+      return(map3d);

     }

-    Rprintf("Warning: pwiz not yet initialized.\n ");

-    return Rcpp::NumericMatrix(0,0);

+  Rprintf("Warning: pwiz not yet initialized.\n ");

+  return Rcpp::NumericMatrix(0,0);

 }

 string RcppPwiz::getRunStartTimeStamp() {