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> 
   42 #include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h> 
  109     double calcXcorrCoelutionScore();
 
  112     double calcXcorrShape_score();
 
  115     double calcXcorrShape_score_weighted(
const std::vector<double>& normalized_library_intensity);
 
  118     double calcXcorrCoelutionScore_weighted(
const std::vector<double>& normalized_library_intensity);
 
  121     static void calcLibraryScore(
OpenSwath::IMRMFeature* mrmfeature, 
const std::vector<TransitionType>& transitions,
 
  122                                  double& correlation, 
double& rmsd, 
double& manhattan, 
double& dotprod);
 
  125     static double calcRTScore(
const PeptideType& peptide, 
double normalized_experimental_rt);
 
  130     static double calcSNScore(
OpenSwath::IMRMFeature* mrmfeature, std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
 
  145 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_MRMSCORING_H 
OpenSwath::LightPeptide PeptideType
Definition: MRMScoring.h:91
std::string String
Definition: MRMScoring.h:87
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
std::vector< std::vector< XCorrArrayType > > XCorrMatrixType
Cross Correlation matrix. 
Definition: MRMScoring.h:85
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor. 
Definition: ITransition.h:65
Definition: TransitionExperiment.h:99
OpenSwath::SpectrumPtr SpectrumType
Definition: MRMScoring.h:89
boost::shared_ptr< OpenSwath::IFeature > FeatureType
Definition: MRMScoring.h:94
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227
Definition: TransitionExperiment.h:46
Definition: ITransition.h:56
OpenSwath::LightTransition TransitionType
Definition: MRMScoring.h:90
OpenSwath::LightProtein ProteinType
Definition: MRMScoring.h:92
Definition: TransitionExperiment.h:114