ProteoWizard
SpectrumInfo.hpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Darren Kessner <darren@proteowizard.org>
6 //
7 // Copyright 2008 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
11 // you may not use this file except in compliance with the License.
12 // You may obtain a copy of the License at
13 //
14 // http://www.apache.org/licenses/LICENSE-2.0
15 //
16 // Unless required by applicable law or agreed to in writing, software
17 // distributed under the License is distributed on an "AS IS" BASIS,
18 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 // See the License for the specific language governing permissions and
20 // limitations under the License.
21 //
22 
23 
24 #ifndef _SPECTRUMINFO_HPP_
25 #define _SPECTRUMINFO_HPP_
26 
27 
29 #include "MSData.hpp"
30 
31 
32 namespace pwiz {
33 namespace msdata {
34 
35 
36 /// simple structure for holding Spectrum info
38 {
39  /// structure for Precursor info
41  {
42  size_t index;
43  double mz;
44  double intensity;
45  double charge;
46 
47  PrecursorInfo() : index((size_t)-1), mz(0), intensity(0), charge(0) {}
48  };
49 
50  size_t index;
51  std::string id;
54  int scanEvent;
55  int msLevel;
56  bool isZoomScan;
57  double retentionTime; // seconds
58  std::string filterString;
59  double mzLow;
60  double mzHigh;
61  double basePeakMZ;
66  std::vector<PrecursorInfo> precursors;
67  size_t dataSize;
68  std::vector<MZIntensityPair> data;
69 
71  SpectrumInfo(const Spectrum& spectrum);
72 
73  void update(const Spectrum& spectrum, bool getBinaryData = false);
75 
76  // some helper functions
77  std::string massAnalyzerTypeAbbreviation() const;
78  double mzFromFilterString() const;
79 };
80 
81 
82 } // namespace msdata
83 } // namespace pwiz
84 
85 
86 #endif // _SPECTRUMINFO_HPP_
87 
pwiz::msdata::SpectrumInfo
simple structure for holding Spectrum info
Definition: SpectrumInfo.hpp:38
pwiz::msdata::SpectrumInfo::SpectrumInfo
SpectrumInfo(const Spectrum &spectrum)
pwiz::msdata::SpectrumInfo::basePeakMZ
double basePeakMZ
Definition: SpectrumInfo.hpp:61
pwiz::msdata::Spectrum
The structure that captures the generation of a peak list (including the underlying acquisitions)
Definition: MSData.hpp:506
pwiz
Definition: ChromatogramList_Filter.hpp:36
MSData.hpp
pwiz::msdata::SpectrumInfo::massAnalyzerType
CVID massAnalyzerType
Definition: SpectrumInfo.hpp:53
pwiz::msdata::SpectrumInfo::dataSize
size_t dataSize
Definition: SpectrumInfo.hpp:67
pwiz::msdata::SpectrumInfo::index
size_t index
Definition: SpectrumInfo.hpp:50
pwiz::msdata::SpectrumInfo::basePeakIntensity
double basePeakIntensity
Definition: SpectrumInfo.hpp:62
pwiz::msdata::SpectrumInfo::msLevel
int msLevel
Definition: SpectrumInfo.hpp:55
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::msdata::SpectrumInfo::isZoomScan
bool isZoomScan
Definition: SpectrumInfo.hpp:56
pwiz::msdata::SpectrumInfo::retentionTime
double retentionTime
Definition: SpectrumInfo.hpp:57
pwiz::msdata::SpectrumInfo::id
std::string id
Definition: SpectrumInfo.hpp:51
Export.hpp
pwiz::msdata::SpectrumInfo::clearBinaryData
void clearBinaryData()
pwiz::msdata::SpectrumInfo::PrecursorInfo::index
size_t index
Definition: SpectrumInfo.hpp:42
pwiz::msdata::SpectrumInfo::PrecursorInfo
structure for Precursor info
Definition: SpectrumInfo.hpp:41
pwiz::msdata::SpectrumInfo::filterString
std::string filterString
Definition: SpectrumInfo.hpp:58
pwiz::msdata::SpectrumInfo::mzLow
double mzLow
Definition: SpectrumInfo.hpp:59
pwiz::msdata::SpectrumInfo::PrecursorInfo::intensity
double intensity
Definition: SpectrumInfo.hpp:44
pwiz::msdata::SpectrumInfo::SpectrumInfo
SpectrumInfo()
pwiz::msdata::SpectrumInfo::scanNumber
int scanNumber
Definition: SpectrumInfo.hpp:52
pwiz::msdata::SpectrumInfo::scanEvent
int scanEvent
Definition: SpectrumInfo.hpp:54
pwiz::msdata::SpectrumInfo::PrecursorInfo::mz
double mz
Definition: SpectrumInfo.hpp:43
pwiz::msdata::SpectrumInfo::thermoMonoisotopicMZ
double thermoMonoisotopicMZ
Definition: SpectrumInfo.hpp:64
pwiz::chemistry::Ion::mz
double mz(double neutralMass, int protonDelta, int electronDelta=0, int neutronDelta=0)
Definition: Ion.hpp:78
pwiz::msdata::SpectrumInfo::precursors
std::vector< PrecursorInfo > precursors
Definition: SpectrumInfo.hpp:66
pwiz::msdata::SpectrumInfo::PrecursorInfo::charge
double charge
Definition: SpectrumInfo.hpp:45
pwiz::msdata::SpectrumInfo::totalIonCurrent
double totalIonCurrent
Definition: SpectrumInfo.hpp:63
pwiz::msdata::SpectrumInfo::mzHigh
double mzHigh
Definition: SpectrumInfo.hpp:60
pwiz::msdata::SpectrumInfo::massAnalyzerTypeAbbreviation
std::string massAnalyzerTypeAbbreviation() const
pwiz::msdata::SpectrumInfo::data
std::vector< MZIntensityPair > data
Definition: SpectrumInfo.hpp:68
pwiz::msdata::SpectrumInfo::mzFromFilterString
double mzFromFilterString() const
pwiz::msdata::SpectrumInfo::PrecursorInfo::PrecursorInfo
PrecursorInfo()
Definition: SpectrumInfo.hpp:47
pwiz::msdata::SpectrumInfo::update
void update(const Spectrum &spectrum, bool getBinaryData=false)
pwiz::msdata::SpectrumInfo::ionInjectionTime
double ionInjectionTime
Definition: SpectrumInfo.hpp:65