ProteoWizard
SpectrumList_Waters.hpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
6//
7// Copyright 2009 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
31#include <boost/thread.hpp>
32
33
34using boost::shared_ptr;
35
36
37namespace pwiz {
38namespace msdata {
39namespace detail {
40
41
42//
43// SpectrumList_Waters
44//
46{
47 public:
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
#define PWIZ_API_DECL
Definition Export.hpp:32
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet &msLevelsToCentroid) const
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 bool canConvertIonMobilityAndCCS() const
virtual double ccsToIonMobility(double ccs, double mz, int charge) const
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
virtual size_t find(const string &id) const
find id in the spectrum index (returns size() on failure)
virtual double ionMobilityToCCS(double ionMobility, double mz, int charge) const
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual pwiz::analysis::Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set< double > &driftTimeRanges) const
virtual size_t size() const
returns the number of spectra
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
retrieve a spectrum by index
virtual pair< int, int > sonarMzToDriftBinRange(int function, float precursorMz, float precursorTolerance) const
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
boost::shared_ptr< Spectrum3D > Spectrum3DPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
Reader configuration.
Definition Reader.hpp:45
Identifying information for a spectrum.
Definition MSData.hpp:471