ProteoWizard
SpectrumList_Waters.hpp
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5 // Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
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7 // Copyright 2009 Vanderbilt University - Nashville, TN 37232
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21 
22 
25 #include "Reader_Waters_Detail.hpp"
31 #include <boost/thread.hpp>
32 
33 
34 using boost::shared_ptr;
35 
36 
37 namespace pwiz {
38 namespace msdata {
39 namespace detail {
40 
41 
42 //
43 // SpectrumList_Waters
44 //
46 {
47  public:
49  {
51 
52  };
53  virtual size_t size() const;
54  virtual const SpectrumIdentity& spectrumIdentity(size_t index) const;
55  virtual size_t find(const string& id) const;
56  virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const;
57  virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const;
58 
59  // TODO: convert vendor-specific parameters to a single config struct, but all non-vendor wrappers are going to have to pass it along :(
60  virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
61  virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
62  virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
63  virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
64 
65  virtual pwiz::analysis::Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set<double>& driftTimeRanges) const;
66 
67  /// returns true if any functions are SONAR-enabled
68  virtual bool hasSonarFunctions() const;
69  virtual pair<int, int> sonarMzToDriftBinRange(int function, float precursorMz, float precursorTolerance) const;
70 
71  virtual bool hasIonMobility() const;
72  virtual bool canConvertIonMobilityAndCCS() const;
73  virtual double ionMobilityToCCS(double ionMobility, double mz, int charge) const;
74  virtual double ccsToIonMobility(double ccs, double mz, int charge) const;
75 
76 #ifdef PWIZ_READER_WATERS
77  SpectrumList_Waters(MSData& msd, RawDataPtr rawdata, const Reader::Config& config);
78 
79  private:
80 
81  MSData& msd_;
82  RawDataPtr rawdata_;
83  size_t size_;
84  Reader::Config config_;
85 
86  struct IndexEntry : public SpectrumIdentity
87  {
88  int function;
89  int process;
90  int scan;
91  int block; // block < 0 is not ion mobility
92  };
93 
94  mutable vector<IndexEntry> index_;
95  mutable map<string, size_t> idToIndexMap_;
96  mutable boost::container::flat_map<double, vector<pair<int, int> > > scanTimeToFunctionAndBlockMap_;
97 
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;
106 
107  void createIndex();
108 #endif // PWIZ_READER_WATERS
109 };
110 
111 } // detail
112 } // msdata
113 } // pwiz
pwiz::msdata::Reader::Config
Reader configuration.
Definition: Reader.hpp:45
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
pwiz::msdata::detail::SpectrumList_Waters::ionMobilityToCCS
virtual double ionMobilityToCCS(double ionMobility, double mz, int charge) const
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet &msLevelsToCentroid) const
pwiz::msdata::SpectrumIdentity
Identifying information for a spectrum.
Definition: MSData.hpp:471
pwiz::msdata::detail::SpectrumList_Waters::VendorOptions::msLevelsToCentroid
pwiz::util::IntegerSet msLevelsToCentroid
Definition: SpectrumList_Waters.hpp:50
pwiz
Definition: ChromatogramList_Filter.hpp:36
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
pwiz::msdata::detail::SpectrumList_Waters::size
virtual size_t size() const
returns the number of spectra
Container.hpp
Export.hpp
pwiz::msdata::detail::SpectrumList_Waters
Definition: SpectrumList_Waters.hpp:46
SpectrumList_3D.hpp
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const
retrieve a spectrum by index
SpectrumListBase.hpp
pwiz::msdata::detail::SpectrumList_Waters::hasSonarFunctions
virtual bool hasSonarFunctions() const
returns true if any functions are SONAR-enabled
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet &msLevelsToCentroid) const
pwiz::msdata::detail::SpectrumList_Waters::spectrum3d
virtual pwiz::analysis::Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set< double > &driftTimeRanges) const
pwiz::msdata::detail::SpectrumList_Waters::find
virtual size_t find(const string &id) const
find id in the spectrum index (returns size() on failure)
pwiz::msdata::detail::SpectrumList_Waters::spectrumIdentity
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
String.hpp
pwiz::msdata::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: MSData.hpp:573
Stream.hpp
pwiz::chemistry::Ion::mz
double mz(double neutralMass, int protonDelta, int electronDelta=0, int neutronDelta=0)
Definition: Ion.hpp:78
Reader_Waters_Detail.hpp
pwiz::msdata::detail::SpectrumList_Waters::spectrum
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
retrieve a spectrum by index
pwiz::analysis::Spectrum3DPtr
boost::shared_ptr< Spectrum3D > Spectrum3DPtr
Definition: SpectrumList_3D.hpp:36
pwiz::msdata::detail::SpectrumList_Waters::hasIonMobility
virtual bool hasIonMobility() const
pwiz::msdata::MSData
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition: MSData.hpp:850
pwiz::msdata::DetailLevel
DetailLevel
Definition: MSData.hpp:631
Reader.hpp
pwiz::msdata::detail::SpectrumList_Waters::canConvertIonMobilityAndCCS
virtual bool canConvertIonMobilityAndCCS() const
pwiz::msdata::SpectrumListIonMobilityBase
Definition: SpectrumListBase.hpp:75
pwiz::msdata::detail::SpectrumList_Waters::ccsToIonMobility
virtual double ccsToIonMobility(double ccs, double mz, int charge) const
pwiz::util::IntegerSet
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
Definition: IntegerSet.hpp:38
pwiz::msdata::detail::SpectrumList_Waters::sonarMzToDriftBinRange
virtual pair< int, int > sonarMzToDriftBinRange(int function, float precursorMz, float precursorTolerance) const
pwiz::msdata::detail::SpectrumList_Waters::VendorOptions
Definition: SpectrumList_Waters.hpp:49