OpenMS  3.0.0
FragmentMassError.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Patricia Scheil, Swenja Wagner$
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34 
35 #pragma once
36 
38 #include <OpenMS/QC/QCBase.h>
39 #include <vector>
40 
41 namespace OpenMS
42 {
43  class FeatureMap;
44  class MSExperiment;
45  class PeptideIdentification;
46  class WindowMower;
47 
48  class OPENMS_DLLAPI FragmentMassError : public QCBase
49  {
50  public:
52  FragmentMassError() = default;
53 
55  virtual ~FragmentMassError() = default;
56 
60  struct Statistics
61  {
62  double average_ppm = 0;
63  double variance_ppm = 0;
64  };
65 
88  void compute(FeatureMap& fmap, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, ToleranceUnit tolerance_unit = ToleranceUnit::AUTO, double tolerance = 20);
89 
113  void compute(std::vector<PeptideIdentification>& pep_ids, const ProteinIdentification::SearchParameters& search_params, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, ToleranceUnit tolerance_unit = ToleranceUnit::AUTO, double tolerance = 20);
114 
116  const String& getName() const override;
117 
119  const std::vector<Statistics>& getResults() const;
120 
121 
126  QCBase::Status requires() const override;
127 
128  private:
130  std::vector<Statistics> results_;
131 
132  static void calculateFME_(PeptideIdentification& pep_id, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, bool& print_warning, double tolerance, FragmentMassError::ToleranceUnit tolerance_unit, double& accumulator_ppm, UInt32& counter_ppm, WindowMower& window_mower_filter);
133 
134  static void calculateVariance_(FragmentMassError::Statistics& result, const PeptideIdentification& pep_id, const UInt num_ppm);
135  };
136 
137 } //namespace OpenMS
OpenMS::FragmentMassError::results_
std::vector< Statistics > results_
container that stores results
Definition: FragmentMassError.h:130
OpenMS::UInt32
OPENMS_UINT32_TYPE UInt32
Unsigned integer type (32bit)
Definition: Types.h:63
OpenMS::WindowMower
WindowMower augments the highest peaks in a sliding or jumping window.
Definition: WindowMower.h:54
OpenMS::FragmentMassError
Definition: FragmentMassError.h:48
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
ProteinIdentification.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FragmentMassError::Statistics
Structure for storing results: average and variance of all FragmentMassErrors in ppm.
Definition: FragmentMassError.h:60
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::FlagSet
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:53
OpenMS::QCBase::ToleranceUnit
ToleranceUnit
Definition: QCBase.h:75
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
QCBase.h