OpenMS  3.0.0
Ms2IdentificationRate.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Patricia Scheil, Swenja Wagner$
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
38 #include "OpenMS/QC/QCBase.h"
39 #include <string>
40 #include <vector>
41 
42 namespace OpenMS
43 {
44  class FeatureMap;
45  class MSExperiment;
46  class MzTabMetaData;
47  class PeptideIdentification;
48 
56  class OPENMS_DLLAPI Ms2IdentificationRate : public QCBase
57  {
58  public:
61  {
62  Size num_peptide_identification = 0;
63  Size num_ms2_spectra = 0;
64  double identification_rate = 0.;
65  };
66 
67  private:
69  const String name_ = "Ms2IdentificationRate";
70 
72  std::vector<IdentificationRateData> rate_result_;
73 
75  Size getMS2Count_(const MSExperiment& exp);
76 
77  /*
78  * @brief Checks pepID for target/decoy
79  *
80  * Only checks the first (!) hit, all other hits are ignored
81  * Is static so that it can be used with MapUtilities::applyFunctionOnPeptideIDs() without creating a new object for each ID
82  *
83  * @param id pepID to be checked
84  * @param all_targets always returns true (if the hits aren't empty)
85  * @return true/false
86  * @throws MissingInformation if target/decoy annotation is missing
87  */
88  static bool isTargetPeptide_(const PeptideIdentification& id, bool all_targets);
89 
90  /*
91  * @brief Calculates id-rate and writes the result into a IdentificationRateData object which is appended to rate_result_
92  *
93  * @param ms2_spectra_count number of found ms2 spectra
94  * @param pep_ids_count number of found (target) peptide identifications
95  */
96  void writeResults_(Size pep_ids_count, Size ms2_spectra_count);
97 
98  public:
100  Ms2IdentificationRate() = default;
101 
103  virtual ~Ms2IdentificationRate() = default;
104 
118  void compute(const FeatureMap& feature_map, const MSExperiment& exp, bool assume_all_target = false);
119 
133  void compute(const std::vector<PeptideIdentification>& pep_ids, const MSExperiment& exp, bool assume_all_target = false);
134 
136  const String& getName() const override;
137 
139  const std::vector<IdentificationRateData>& getResults() const;
140 
145  QCBase::Status requires() const override;
146 
147  void addMetaDataMetricsToMzTab(MzTabMetaData& meta) const;
148  };
149 
150 } // namespace OpenMS
OpenMS::Ms2IdentificationRate::rate_result_
std::vector< IdentificationRateData > rate_result_
container that stores results
Definition: Ms2IdentificationRate.h:72
OpenMS::Ms2IdentificationRate::IdentificationRateData
Structure for storing results.
Definition: Ms2IdentificationRate.h:60
Types.h
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::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MzTabMetaData
all meta data of a mzTab file. Please refer to specification for documentation.
Definition: MzTab.h:140
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
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::Ms2IdentificationRate
This class is a metric for the QualityControl-ToppTool.
Definition: Ms2IdentificationRate.h:56
QCBase.h