38 #include <boost/math/special_functions/fpclassify.hpp> 39 #include <boost/numeric/conversion/cast.hpp> 41 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h> 97 const XCorrMatrixType& getXCorrMatrix()
const;
102 const XCorrMatrixType& getXCorrContrastMatrix()
const;
106 const XCorrMatrixType& getXCorrPrecursorContrastMatrix()
const;
110 const XCorrMatrixType& getXCorrPrecursorCombinedMatrix()
const;
115 void initializeXCorrMatrix(
const std::vector< std::vector< double > >& data);
122 void initializeXCorrContrastMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& native_ids_set1,
const std::vector<String>& native_ids_set2);
125 void initializeXCorrPrecursorMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& precursor_ids);
128 void initializeXCorrPrecursorContrastMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& precursor_ids,
const std::vector<String>& native_ids);
131 void initializeXCorrPrecursorContrastMatrix(
const std::vector< std::vector< double > >& data_precursor,
const std::vector< std::vector< double > >& data_fragments);
134 void initializeXCorrPrecursorCombinedMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& precursor_ids,
const std::vector<String>& native_ids);
141 double calcXcorrCoelutionScore();
150 double calcXcorrCoelutionWeightedScore(
const std::vector<double>& normalized_library_intensity);
153 double calcXcorrContrastCoelutionScore();
156 std::vector<double> calcSeparateXcorrContrastCoelutionScore();
159 double calcXcorrPrecursorCoelutionScore();
166 double calcXcorrPrecursorContrastCoelutionScore();
169 double calcXcorrPrecursorCombinedCoelutionScore();
177 double calcXcorrShapeScore();
187 double calcXcorrShapeWeightedScore(
const std::vector<double>& normalized_library_intensity);
190 double calcXcorrContrastShapeScore();
193 std::vector<double> calcSeparateXcorrContrastShapeScore();
196 double calcXcorrPrecursorShapeScore();
199 double calcXcorrPrecursorContrastShapeScore();
202 double calcXcorrPrecursorCombinedShapeScore();
206 const std::vector<TransitionType>& transitions,
double& correlation,
207 double& norm_manhattan,
double& manhattan,
double& dotprod,
208 double& spectral_angle,
double& rmsd);
211 static double calcRTScore(
const PeptideType& peptide,
double normalized_experimental_rt);
217 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
220 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
223 const std::vector< std::vector<double> > & getMIMatrix()
const;
227 const std::vector< std::vector<double> > & getMIContrastMatrix()
const;
231 const std::vector< std::vector<double> > & getMIPrecursorContrastMatrix()
const;
235 const std::vector< std::vector<double> > & getMIPrecursorCombinedMatrix()
const;
242 void initializeMIContrastMatrix(
OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids_set1, std::vector<String> native_ids_set2);
248 void initializeMIPrecursorContrastMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& precursor_ids,
const std::vector<String>& native_ids);
251 void initializeMIPrecursorCombinedMatrix(
OpenSwath::IMRMFeature* mrmfeature,
const std::vector<String>& precursor_ids,
const std::vector<String>& native_ids);
253 double calcMIScore();
254 double calcMIWeightedScore(
const std::vector<double>& normalized_library_intensity);
255 double calcMIPrecursorScore();
256 double calcMIPrecursorContrastScore();
257 double calcMIPrecursorCombinedScore();
258 std::vector<double> calcSeparateMIContrastScore();
266 XCorrMatrixType xcorr_matrix_;
Definition: TransitionExperiment.h:46
XCorrMatrixType xcorr_precursor_combined_matrix_
the precomputed cross correlation with the MS1 trace
Definition: MRMScoring.h:281
std::vector< std::vector< double > > mi_precursor_matrix_
the precomputed mutual information matrix of the MS1 trace
Definition: MRMScoring.h:291
Definition: TransitionExperiment.h:149
This class implements different scores for peaks found in SRM/MRM.
Definition: MRMScoring.h:73
Definition: TransitionExperiment.h:201
Definition: MRMScoring.h:49
OpenSwath::LightCompound PeptideType
Definition: MRMScoring.h:89
XCorrMatrixType xcorr_precursor_matrix_
the precomputed cross correlation matrix of the MS1 trace
Definition: MRMScoring.h:274
std::vector< std::vector< double > > mi_precursor_combined_matrix_
the precomputed contrast mutual information matrix with the MS1 trace
Definition: MRMScoring.h:298
OpenSwath::LightTransition TransitionType
Definition: MRMScoring.h:88
OpenSwath::LightProtein ProteinType
Definition: MRMScoring.h:90
XCorrMatrixType xcorr_contrast_matrix_
the precomputed contrast cross correlation
Definition: MRMScoring.h:270
std::vector< std::vector< double > > mi_contrast_matrix_
the precomputed contrast mutual information matrix
Definition: MRMScoring.h:288
XCorrMatrixType xcorr_precursor_contrast_matrix_
the precomputed cross correlation against the MS1 trace
Definition: MRMScoring.h:277
OpenSwath::SpectrumPtr SpectrumType
Definition: MRMScoring.h:87
std::vector< std::vector< double > > mi_precursor_contrast_matrix_
the precomputed contrast mutual information matrix against the MS1 trace
Definition: MRMScoring.h:294
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
std::string String
Definition: MRMScoring.h:85
boost::shared_ptr< OpenSwath::IFeature > FeatureType
Definition: MRMScoring.h:92
std::vector< std::vector< double > > mi_matrix_
the precomputed mutual information matrix
Definition: MRMScoring.h:285
Definition: ITransition.h:56
std::vector< std::vector< XCorrArrayType > > XCorrMatrixType
Cross Correlation matrix.
Definition: MRMScoring.h:83