OpenMS  2.8.0
MRMScoring.h
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34 
35 #pragma once
36 
37 #include <string>
38 
40 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
41 
47 
48 namespace OpenSwath
49 {
50 
72  class OPENMS_DLLAPI MRMScoring
73  {
74 
75  public:
77 
82 
87 
88  typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType;
90 
96 
100 
104 
108 
111 
113  void initializeXCorrMatrix(const std::vector< std::vector< double > >& data);
114 
116  void initializeXCorrMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids);
117 
119  void initializeXCorrContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids_set1, const std::vector<std::string>& native_ids_set2);
120 
122  void initializeXCorrPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids);
123 
125  void initializeXCorrPrecursorContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);
126 
128  void initializeXCorrPrecursorContrastMatrix(const std::vector< std::vector< double > >& data_precursor, const std::vector< std::vector< double > >& data_fragments);
129 
131  void initializeXCorrPrecursorCombinedMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);
132 
139 
147  double calcXcorrCoelutionWeightedScore(const std::vector<double>& normalized_library_intensity);
148 
151 
154 
157 
164 
167 
175 
184  double calcXcorrShapeWeightedScore(const std::vector<double>& normalized_library_intensity);
185 
188 
190  std::vector<double> calcSeparateXcorrContrastShapeScore();
191 
194 
197 
200 
202  static void calcLibraryScore(OpenSwath::IMRMFeature* mrmfeature,
203  const std::vector<TransitionType>& transitions, double& correlation,
204  double& norm_manhattan, double& manhattan, double& dotprod,
205  double& spectral_angle, double& rmsd);
206 
208  static double calcRTScore(const PeptideType& peptide, double normalized_experimental_rt);
209 
211  // using a vector of SignalToNoiseEstimatorMedian that were calculated for
212  // each chromatogram of the transition_group.
213  static double calcSNScore(OpenSwath::IMRMFeature* mrmfeature,
214  std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
215 
216  static std::vector<double> calcSeparateSNScore(OpenSwath::IMRMFeature* mrmfeature,
217  std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
218 
222 
226 
230 
234 
236  void initializeMIMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids);
237 
239  void initializeMIContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids_set1, const std::vector<std::string>& native_ids_set2);
240 
242  void initializeMIPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids);
243 
245  void initializeMIPrecursorContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);
246 
248  void initializeMIPrecursorCombinedMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);
249 
250  double calcMIScore();
251  double calcMIWeightedScore(const std::vector<double>& normalized_library_intensity);
255  std::vector<double> calcSeparateMIContrastScore();
256 
258 
259  private:
264 
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299 
303  };
304 }
Definition: ITransition.h:57
This class implements different scores for peaks found in SRM/MRM.
Definition: MRMScoring.h:73
const XCorrMatrixType & getXCorrContrastMatrix() const
non-mutable access to the cross-correlation contrast matrix
const OpenMS::Matrix< double > & getMIMatrix() const
non-mutable access to the MI matrix
double calcMIPrecursorCombinedScore()
double calcXcorrCoelutionWeightedScore(const std::vector< double > &normalized_library_intensity)
Calculate the weighted cross-correlation coelution score.
XCorrMatrixType xcorr_precursor_combined_matrix_
the precomputed cross correlation with the MS1 trace
Definition: MRMScoring.h:284
OpenSwath::LightProtein ProteinType
Definition: MRMScoring.h:86
void initializeMIPrecursorMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
Initialize the scoring object and building the MI matrix.
double calcMIPrecursorContrastScore()
OpenMS::Matrix< double > mi_precursor_contrast_matrix_
the precomputed contrast mutual information matrix against the MS1 trace
Definition: MRMScoring.h:297
void initializeXCorrMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
Initialize the scoring object and building the cross-correlation matrix.
OpenMS::Matrix< double > xcorr_contrast_matrix_max_peak_sec_
contains max Peaks from xcorr_contrast_matrix_
Definition: MRMScoring.h:274
const OpenMS::Matrix< double > & getMIPrecursorCombinedMatrix() const
non-mutable access to the MI precursor combined matrix
OpenMS::Matrix< double > mi_precursor_matrix_
the precomputed mutual information matrix of the MS1 trace
Definition: MRMScoring.h:294
const XCorrMatrixType & getXCorrMatrix() const
non-mutable access to the cross-correlation matrix
OpenMS::Matrix< XCorrArrayType > XCorrMatrixType
Cross Correlation matrix.
Definition: MRMScoring.h:81
const OpenMS::Matrix< double > & getMIPrecursorContrastMatrix() const
non-mutable access to the MI precursor contrast matrix
void initializeXCorrPrecursorCombinedMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor...
OpenMS::Matrix< int > xcorr_matrix_max_peak_
contains max Peaks from xcorr_matrix_
Definition: MRMScoring.h:266
std::vector< double > calcSeparateMIContrastScore()
void initializeXCorrPrecursorContrastMatrix(const std::vector< std::vector< double > > &data_precursor, const std::vector< std::vector< double > > &data_fragments)
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor...
XCorrMatrixType xcorr_matrix_
the precomputed cross correlation matrix
Definition: MRMScoring.h:263
static std::vector< double > calcSeparateSNScore(OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
boost::shared_ptr< OpenSwath::IFeature > FeatureType
Definition: MRMScoring.h:88
double calcMIWeightedScore(const std::vector< double > &normalized_library_intensity)
double calcXcorrContrastShapeScore()
calculate the cross-correlation contrast shape score
std::vector< double > calcSeparateXcorrContrastCoelutionScore()
calculate the separate cross-correlation contrast score
OpenSwath::LightCompound PeptideType
Definition: MRMScoring.h:85
OpenMS::Matrix< double > mi_matrix_
the precomputed mutual information matrix
Definition: MRMScoring.h:289
const OpenMS::Matrix< double > & getMIContrastMatrix() const
non-mutable access to the MI contrast matrix
void initializeXCorrContrastMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2)
Initialize the scoring object and building the cross-correlation matrix of chromatograms of set1 (e....
double calcXcorrPrecursorShapeScore()
calculate the precursor cross-correlation shape score
double calcXcorrShapeWeightedScore(const std::vector< double > &normalized_library_intensity)
Calculate the weighted cross-correlation shape score.
double calcXcorrCoelutionScore()
Calculate the cross-correlation coelution score.
void initializeMIContrastMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2)
Initialize the scoring object and building the MI matrix of chromatograms of set1 (e....
double calcXcorrPrecursorCombinedCoelutionScore()
calculate the precursor cross-correlation coelution score including the transitions
std::vector< double > calcSeparateXcorrContrastShapeScore()
calculate the separate cross-correlation contrast shape score
void initializeXCorrPrecursorContrastMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor...
OpenSwath::LightTransition TransitionType
Definition: MRMScoring.h:84
XCorrMatrixType xcorr_precursor_contrast_matrix_
the precomputed cross correlation against the MS1 trace
Definition: MRMScoring.h:280
OpenSwath::SpectrumPtr SpectrumType
Definition: MRMScoring.h:83
XCorrMatrixType xcorr_precursor_matrix_
the precomputed cross correlation matrix of the MS1 trace
Definition: MRMScoring.h:277
double calcXcorrPrecursorCoelutionScore()
calculate the precursor cross-correlation contrast score
void initializeMIMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
Initialize the scoring object and building the MI matrix.
double calcMIPrecursorScore()
double calcXcorrPrecursorContrastShapeScore()
calculate the precursor cross-correlation shape score against the transitions
double calcXcorrShapeScore()
Calculate the cross-correlation shape score.
double calcXcorrPrecursorCombinedShapeScore()
calculate the precursor cross-correlation shape score including the transitions
void initializeXCorrMatrix(const std::vector< std::vector< double > > &data)
Initialize the scoring object and building the cross-correlation matrix.
const XCorrMatrixType & getXCorrPrecursorCombinedMatrix() const
non-mutable access to the cross-correlation precursor contrast matrix
void initializeMIPrecursorContrastMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
Initialize the mutual information vector against the MS1 trace.
static double calcSNScore(OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
calculate the Signal to Noise ratio
OpenMS::Matrix< double > mi_contrast_matrix_
the precomputed contrast mutual information matrix
Definition: MRMScoring.h:291
OpenMS::Matrix< double > xcorr_matrix_max_peak_sec_
Definition: MRMScoring.h:267
XCorrMatrixType xcorr_contrast_matrix_
the precomputed contrast cross correlation
Definition: MRMScoring.h:270
double calcXcorrContrastCoelutionScore()
calculate the cross-correlation contrast score
OpenMS::Matrix< double > mi_precursor_combined_matrix_
the precomputed contrast mutual information matrix with the MS1 trace
Definition: MRMScoring.h:301
void initializeXCorrPrecursorMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
Initialize the scoring object and building the cross-correlation matrix.
static double calcRTScore(const PeptideType &peptide, double normalized_experimental_rt)
calculate the retention time correlation score
void initializeMIPrecursorCombinedMatrix(OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
Initialize the mutual information vector with the MS1 trace.
static void calcLibraryScore(OpenSwath::IMRMFeature *mrmfeature, const std::vector< TransitionType > &transitions, double &correlation, double &norm_manhattan, double &manhattan, double &dotprod, double &spectral_angle, double &rmsd)
calculate the library correlation score
double calcXcorrPrecursorContrastCoelutionScore()
Calculate the precursor cross-correlation contrast score against the transitions.
const XCorrMatrixType & getXCorrPrecursorContrastMatrix() const
non-mutable access to the cross-correlation precursor contrast matrix
Definition: Scoring.h:44
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:291
Definition: TransitionExperiment.h:201
Definition: TransitionExperiment.h:149
Definition: TransitionExperiment.h:46
Definition: Scoring.h:60