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31 #include <boost/thread.hpp>
34 using boost::shared_ptr;
53 virtual size_t size()
const;
55 virtual size_t find(
const string&
id)
const;
76 #ifdef PWIZ_READER_WATERS
94 mutable vector<IndexEntry> index_;
95 mutable map<string, size_t> idToIndexMap_;
96 mutable boost::container::flat_map<double, vector<pair<int, int> > > scanTimeToFunctionAndBlockMap_;
98 void initializeCoefficients()
const;
99 double calibrate(
const double &
mz)
const;
100 mutable vector<double> calibrationCoefficients_;
101 mutable vector<double> imsCalibratedMasses_;
102 mutable vector<float> imsMasses_;
103 mutable vector<int> massIndices_;
104 mutable vector<float> imsIntensities_;
105 mutable boost::mutex readMutex;
108 #endif // PWIZ_READER_WATERS
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual double ionMobilityToCCS(double ionMobility, double mz, int charge) const
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet &msLevelsToCentroid) const
Identifying information for a spectrum.
pwiz::util::IntegerSet msLevelsToCentroid
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual size_t size() const
returns the number of spectra
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const
retrieve a spectrum by index
virtual bool hasSonarFunctions() const
returns true if any functions are SONAR-enabled
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual pwiz::analysis::Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set< double > &driftTimeRanges) const
virtual size_t find(const string &id) const
find id in the spectrum index (returns size() on failure)
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
boost::shared_ptr< Spectrum > SpectrumPtr
double mz(double neutralMass, int protonDelta, int electronDelta=0, int neutronDelta=0)
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
retrieve a spectrum by index
boost::shared_ptr< Spectrum3D > Spectrum3DPtr
virtual bool hasIonMobility() const
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
virtual bool canConvertIonMobilityAndCCS() const
virtual double ccsToIonMobility(double ccs, double mz, int charge) const
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
virtual pair< int, int > sonarMzToDriftBinRange(int function, float precursorMz, float precursorTolerance) const