-update Sciex Data API to 1.5.1.391 (May 2024)

pwiz/data/msdata/MSData.hpp

@@ -745,7 +745,7 @@ class PWIZ_API_DECL SpectrumList
     // (as with msconvert's --ignoreCalibrationScans flag)
     virtual bool calibrationSpectraAreOmitted() const;
 
-    virtual ~SpectrumList(){} 
+    virtual ~SpectrumList(){}
 };
 
 

pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.hpp

@@ -45,7 +45,7 @@ class PWIZ_API_DECL ChromatogramList_ABI : public ChromatogramListBase
     virtual size_t find(const std::string& id) const;
     virtual ChromatogramPtr chromatogram(size_t index, bool getBinaryData) const;
     virtual ChromatogramPtr chromatogram(size_t index, DetailLevel detailLevel) const;
-    
+
 #ifdef PWIZ_READER_ABI
     ChromatogramList_ABI(const MSData& msd, WiffFilePtr wifffile, const ExperimentsMap& experimentsMap, int sample, const Reader::Config& config);
 

pwiz/data/vendor_readers/ABI/SpectrumList_ABI.hpp

@@ -50,8 +50,8 @@ class PWIZ_API_DECL SpectrumList_ABI : public SpectrumListBase
     virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const;
     virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const;
     virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
-    virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
-    
+    virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
+
 #ifdef PWIZ_READER_ABI
     SpectrumList_ABI(const MSData& msd, WiffFilePtr wifffile,
                      const ExperimentsMap& experimentsMap, int sample,

pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp

@@ -37,6 +37,7 @@ using namespace System::Collections::Generic;
 
 using namespace SCIEX::Apis::Data::v1;
 using namespace SCIEX::Apis::Data::v1::Contracts;
+using namespace SCIEX::Apis::Data::v1::Types;
 
 namespace pwiz {
 namespace vendor_api {
@@ -48,10 +49,13 @@ class WiffFile2Impl : public WiffFile
     WiffFile2Impl(const std::string& wiffpath);
     ~WiffFile2Impl()
     {
-        auto dataReader = DataReader();
-        if (dataReader != nullptr)
-            dataReader->CloseFile(((IList<ISample^>^) allSamples)[0]->Sources[0]);
-        System::GC::Collect();
+        auto dataReader = DataReader();
+	    if (dataReader != nullptr)
+	    {
+	        System::GC::Collect();
+	        dataReader->CloseFile(((IList<ISample^>^) allSamples)[0]->Sources[0]);
+	    }
+	    System::GC::Collect();
     }
 
     ISampleDataApi^ DataReader() const
@@ -93,7 +97,7 @@ class WiffFile2Impl : public WiffFile
     virtual ExperimentPtr getExperiment(int sample, int period, int experiment) const;
     virtual SpectrumPtr getSpectrum(int sample, int period, int experiment, int cycle) const;
     virtual SpectrumPtr getSpectrum(ExperimentPtr experiment, int cycle) const;
-
+    
     virtual int getADCTraceCount(int sampleIndex) const { return 0; }
     virtual std::string getADCTraceName(int sampleIndex, int traceIndex) const { throw std::out_of_range("WIFF2 does not support ADC traces"); }
     virtual void getADCTrace(int sampleIndex, int traceIndex, ADCTrace& trace) const { throw std::out_of_range("WIFF2 does not support ADC traces"); }
@@ -249,6 +253,7 @@ struct Spectrum2Impl : public Spectrum
             spectrumRequest->Range->Start = scanTime;
             spectrumRequest->Range->End = scanTime;
             spectrumRequest->ConvertToCentroid = doCentroid;
+        	spectrumRequest->CentroidOption = CentroidOptions::IntensitySumAbove50Percent;
             spectrumRequest->AddFramingZeros = addZeros;
 
             auto spectraReader = experiment->wiffFile_->DataReader()->GetSpectra(spectrumRequest);