35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
39 #include <boost/math/special_functions/fpclassify.hpp>
40 #include <boost/numeric/conversion/cast.hpp>
99 const XCorrMatrixType& getXCorrMatrix()
const;
109 void initializeMS1XCorr(
OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids, std::string precursor_id);
112 double calcXcorrCoelutionScore();
115 double calcXcorrShape_score();
118 double calcXcorrShape_score_weighted(
const std::vector<double>& normalized_library_intensity);
121 double calcXcorrCoelutionScore_weighted(
const std::vector<double>& normalized_library_intensity);
124 double calcMS1XcorrCoelutionScore();
127 double calcMS1XcorrShape_score();
131 const std::vector<TransitionType>& transitions,
double& correlation,
132 double& norm_manhattan,
double& manhattan,
double& dotprod,
133 double& spectral_angle,
double& rmsd);
136 static double calcRTScore(
const PeptideType& peptide,
double normalized_experimental_rt);
142 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
150 XCorrMatrixType xcorr_matrix_;
160 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H
OpenSwath::LightPeptide PeptideType
Definition: MRMScoring.h:91
std::string String
Definition: MRMScoring.h:87
std::vector< XCorrArrayType > ms1_xcorr_vector_
the precomputed cross correlation with the MS1 trace
Definition: MRMScoring.h:154
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:232
std::vector< std::vector< XCorrArrayType > > XCorrMatrixType
Cross Correlation matrix.
Definition: MRMScoring.h:85
Definition: TransitionExperiment.h:101
OpenSwath::SpectrumPtr SpectrumType
Definition: MRMScoring.h:89
Definition: MRMScoring.h:51
boost::shared_ptr< OpenSwath::IFeature > FeatureType
Definition: MRMScoring.h:94
Definition: TransitionExperiment.h:47
Definition: ITransition.h:56
OpenSwath::LightTransition TransitionType
Definition: MRMScoring.h:90
OpenSwath::LightProtein ProteinType
Definition: MRMScoring.h:92
#define OPENSWATHALGO_DLLAPI
Definition: OpenSwathAlgoConfig.h:15
Definition: TransitionExperiment.h:119