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MRMScoring.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
37 
38 #include <string>
39 #include <boost/math/special_functions/fpclassify.hpp> // for isnan
40 #include <boost/numeric/conversion/cast.hpp>
41 
42 #include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>
43 
49 //#include "OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/ALGO/DIAHelpers.h"
50 
51 namespace OpenSwath
52 {
53 
75  class OPENSWATHALGO_DLLAPI MRMScoring
76  {
77 
78 public:
79 
81 
82  typedef std::map<int, double> XCorrArrayType;
85  typedef std::vector<std::vector<XCorrArrayType> > XCorrMatrixType;
86 
87  typedef std::string String;
88 
93 
94  typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType;
96 
99  const XCorrMatrixType& getXCorrMatrix() const;
102 
105  void initializeXCorrMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids);
107 
109  void initializeMS1XCorr(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids, std::string precursor_id);
110 
112  void initializeXCorrIdMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids_identification, std::vector<String> native_ids_detection);
113 
115  double calcXcorrCoelutionScore();
116  std::string calcIndXcorrIdCoelutionScore();
117 
119  double calcXcorrShape_score();
120  std::string calcIndXcorrIdShape_score();
121 
123  double calcXcorrShape_score_weighted(const std::vector<double>& normalized_library_intensity);
124 
126  double calcXcorrCoelutionScore_weighted(const std::vector<double>& normalized_library_intensity);
127 
129  double calcMS1XcorrCoelutionScore();
130 
132  double calcMS1XcorrShape_score();
133 
135  static void calcLibraryScore(OpenSwath::IMRMFeature* mrmfeature,
136  const std::vector<TransitionType>& transitions, double& correlation,
137  double& norm_manhattan, double& manhattan, double& dotprod,
138  double& spectral_angle, double& rmsd);
139 
141  static double calcRTScore(const PeptideType& peptide, double normalized_experimental_rt);
142 
144  // using a vector of SignalToNoiseEstimatorMedian that were calculated for
145  // each chromatogram of the transition_group.
146  static double calcSNScore(OpenSwath::IMRMFeature* mrmfeature,
147  std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
148  static std::string calcIndSNScore(OpenSwath::IMRMFeature* mrmfeature,
149  std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
150 
152 
153 private:
154 
157  XCorrMatrixType xcorr_matrix_;
159 
161  std::vector<XCorrArrayType> ms1_xcorr_vector_;
163 
164  };
165 }
166 
167 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
std::string String
Definition: MRMScoring.h:87
std::vector< XCorrArrayType > ms1_xcorr_vector_
the precomputed cross correlation with the MS1 trace
Definition: MRMScoring.h:161
std::map< int, double > XCorrArrayType
Cross Correlation array.
Definition: Scoring.h:57
This class implements different scores for peaks found in SRM/MRM.
Definition: MRMScoring.h:75
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:244
std::vector< std::vector< XCorrArrayType > > XCorrMatrixType
Cross Correlation matrix.
Definition: MRMScoring.h:85
OpenSwath::SpectrumPtr SpectrumType
Definition: MRMScoring.h:89
Definition: MRMScoring.h:51
boost::shared_ptr< OpenSwath::IFeature > FeatureType
Definition: MRMScoring.h:94
Definition: TransitionExperiment.h:150
Definition: TransitionExperiment.h:47
Definition: ITransition.h:56
OpenSwath::LightTransition TransitionType
Definition: MRMScoring.h:90
OpenSwath::LightCompound PeptideType
Definition: MRMScoring.h:91
OpenSwath::LightProtein ProteinType
Definition: MRMScoring.h:92
Definition: TransitionExperiment.h:189

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13