This class implements different scores for peaks found in SRM/MRM. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMScoring.h>

Public Types
typedef OpenSwath::Scoring::XCorrArrayType	XCorrArrayType
	Type definitions.

typedef OpenMS::Matrix< XCorrArrayType >	XCorrMatrixType
	Cross Correlation matrix.

typedef OpenSwath::SpectrumPtr	SpectrumType

typedef OpenSwath::LightTransition	TransitionType

typedef OpenSwath::LightCompound	PeptideType

typedef OpenSwath::LightProtein	ProteinType

typedef std::shared_ptr< OpenSwath::IFeature >	FeatureType

Public Member Functions
Accessors
const XCorrMatrixType &	getXCorrMatrix () const
	non-mutable access to the cross-correlation matrix

const XCorrMatrixType &	getXCorrContrastMatrix () const
	non-mutable access to the cross-correlation contrast matrix

const XCorrMatrixType &	getXCorrPrecursorContrastMatrix () const
	non-mutable access to the cross-correlation precursor contrast matrix

const XCorrMatrixType &	getXCorrPrecursorCombinedMatrix () const
	non-mutable access to the cross-correlation precursor contrast matrix

Private Attributes
Members
XCorrMatrixType	xcorr_matrix_
	the precomputed cross correlation matrix

OpenMS::Matrix< int >	xcorr_matrix_max_peak_
	contains max Peaks from xcorr_matrix_

OpenMS::Matrix< double >	xcorr_matrix_max_peak_sec_

XCorrMatrixType	xcorr_contrast_matrix_
	the precomputed contrast cross correlation

OpenMS::Matrix< int >	xcorr_contrast_matrix_max_peak_
	contains max Peaks from xcorr_contrast_matrix_

OpenMS::Matrix< double >	xcorr_contrast_matrix_max_peak_sec_

XCorrMatrixType	xcorr_precursor_matrix_
	the precomputed cross correlation matrix of the MS1 trace

OpenMS::Matrix< int >	xcorr_precursor_matrix_max_peak_
	contains max peaks from xcorr_precursor_matrix_

OpenMS::Matrix< double >	xcorr_precursor_matrix_max_peak_sec_

XCorrMatrixType	xcorr_precursor_contrast_matrix_
	the precomputed cross correlation against the MS1 trace

OpenMS::Matrix< int >	xcorr_precursor_contrast_matrix_max_peak_
	contains max peaks from xcorr_precursor_contrast_matrix_

OpenMS::Matrix< double >	xcorr_precursor_contrast_matrix_max_peak_sec_

XCorrMatrixType	xcorr_precursor_combined_matrix_
	the precomputed cross correlation with the MS1 trace

OpenMS::Matrix< int >	xcorr_precursor_combined_matrix_max_peak_
	contains max peaks from xcorr_precursor_combined_matrix_

OpenMS::Matrix< double >	xcorr_precursor_combined_matrix_max_peak_sec_

OpenMS::Matrix< double >	mi_matrix_
	the precomputed mutual information matrix

OpenMS::Matrix< double >	mi_contrast_matrix_
	the precomputed contrast mutual information matrix

OpenMS::Matrix< double >	mi_precursor_matrix_
	the precomputed mutual information matrix of the MS1 trace

OpenMS::Matrix< double >	mi_precursor_contrast_matrix_
	the precomputed contrast mutual information matrix against the MS1 trace

OpenMS::Matrix< double >	mi_precursor_combined_matrix_
	the precomputed contrast mutual information matrix with the MS1 trace

Scores
void	initializeXCorrMatrix (const std::vector< std::vector< double > > &data)
	Initialize the scoring object and building the cross-correlation matrix.

void	initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
	Initialize the scoring object and building the cross-correlation 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.g. identification transitions) vs set2 (e.g. detection transitions)

void	initializeXCorrPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
	Initialize the scoring object and building the cross-correlation matrix.

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 isotopes vs transitions.

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 isotopes vs transitions.

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 isotopes and transitions.

void	initializeXCorrPrecursorMatrices (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
	Build the transition, precursor, precursor contrast and precursor combined cross-correlation matrices at once.

double	calcXcorrCoelutionScore ()
	Calculate the cross-correlation coelution score.

double	calcXcorrCoelutionWeightedScore (const std::vector< double > &normalized_library_intensity)
	Calculate the weighted cross-correlation coelution score.

std::vector< double >	calcSeparateXcorrContrastCoelutionScore ()
	calculate the separate cross-correlation contrast score

double	calcXcorrPrecursorCoelutionScore ()
	calculate the precursor cross-correlation contrast score

double	calcXcorrPrecursorContrastCoelutionScore ()
	Calculate the precursor cross-correlation contrast score against the transitions.

double	calcXcorrPrecursorContrastSumFragCoelutionScore ()

double	calcXcorrPrecursorCombinedCoelutionScore ()
	calculate the precursor cross-correlation coelution score including the transitions

double	calcXcorrShapeScore ()
	Calculate the cross-correlation shape score.

double	calcXcorrShapeWeightedScore (const std::vector< double > &normalized_library_intensity)
	Calculate the weighted cross-correlation shape score.

double	calcXcorrContrastShapeScore ()
	calculate the cross-correlation contrast shape score

std::vector< double >	calcSeparateXcorrContrastShapeScore ()
	calculate the separate cross-correlation contrast shape score

double	calcXcorrPrecursorShapeScore ()
	calculate the precursor cross-correlation shape score

double	calcXcorrPrecursorContrastShapeScore ()
	calculate the precursor cross-correlation shape score against the transitions

double	calcXcorrPrecursorContrastSumFragShapeScore ()

double	calcXcorrPrecursorCombinedShapeScore ()
	calculate the precursor cross-correlation shape score including the transitions

const OpenMS::Matrix< double > &	getMIMatrix () const
	non-mutable access to the MI matrix

const OpenMS::Matrix< double > &	getMIContrastMatrix () const
	non-mutable access to the MI contrast matrix

const OpenMS::Matrix< double > &	getMIPrecursorContrastMatrix () const
	non-mutable access to the MI precursor contrast matrix

const OpenMS::Matrix< double > &	getMIPrecursorCombinedMatrix () const
	non-mutable access to the MI precursor combined matrix

void	initializeMIMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
	Initialize the scoring object and building the MI matrix.

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.g. identification transitions) vs set2 (e.g. detection transitions)

void	initializeMIPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
	Initialize the scoring object and building the MI 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.

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.

void	initializeMIPrecursorMatrices (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
	Build the transition, precursor, precursor contrast and precursor combined MI matrices at once.

double	calcMIScore ()

double	calcMIWeightedScore (const std::vector< double > &normalized_library_intensity)

double	calcMIPrecursorScore ()

double	calcMIPrecursorContrastScore ()

double	calcMIPrecursorCombinedScore ()

std::vector< double >	calcSeparateMIContrastScore ()

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

static double	calcRTScore (const PeptideType &peptide, double normalized_experimental_rt)
	calculate the retention time correlation score

static double	calcSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
	calculate the Signal to Noise ratio

static std::vector< double >	calcSeparateSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)

Detailed Description

This class implements different scores for peaks found in SRM/MRM.

It uses scores based on different parameters of the peaks from the individual transitions and stores them individually. The idea and the scores are based on the following paper: Reiter L, Rinner O, Picotti P, Huettenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011 May;8(5):430-5. Epub 2011 Mar 20.

The currently implemented scores include:

xcorr_coelution: Cross-correlation of the different transitions
xcorr_shape: Cross-correlation shape score (whether the maximal Cross-correlation coincides with the maximal intensity)
library_rmsd: normalized RMSD of the measured intensities to the expected intensities
library_correlation: correlation of the measured intensities to the expected intensities
rt_score: deviation from the expected retention time
elution_fit_score: how well the elution profile fits a theoretical elution profile

Member Typedef Documentation

◆ FeatureType

typedef std::shared_ptr<OpenSwath::IFeature> FeatureType

◆ PeptideType

typedef OpenSwath::LightCompound PeptideType

◆ ProteinType

typedef OpenSwath::LightProtein ProteinType

◆ SpectrumType

typedef OpenSwath::SpectrumPtr SpectrumType

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

◆ XCorrArrayType

typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType

Type definitions.

Cross Correlation array

◆ XCorrMatrixType

typedef OpenMS::Matrix<XCorrArrayType> XCorrMatrixType

Cross Correlation matrix.

Member Function Documentation

◆ calcLibraryScore()

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
	)

static

calculate the library correlation score

◆ calcMIPrecursorCombinedScore()

double calcMIPrecursorCombinedScore ( )

◆ calcMIPrecursorContrastScore()

double calcMIPrecursorContrastScore ( )

◆ calcMIPrecursorScore()

double calcMIPrecursorScore ( )

◆ calcMIScore()

double calcMIScore ( )

◆ calcMIWeightedScore()

double calcMIWeightedScore ( const std::vector< double > & normalized_library_intensity )

◆ calcRTScore()

static double calcRTScore	(	const PeptideType &	peptide,
		double	normalized_experimental_rt
	)

static

calculate the retention time correlation score

◆ calcSeparateMIContrastScore()

std::vector< double > calcSeparateMIContrastScore ( )

◆ calcSeparateSNScore()

static std::vector< double > calcSeparateSNScore	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators
	)

static

◆ calcSeparateXcorrContrastCoelutionScore()

std::vector< double > calcSeparateXcorrContrastCoelutionScore ( )

calculate the separate cross-correlation contrast score

◆ calcSeparateXcorrContrastShapeScore()

std::vector< double > calcSeparateXcorrContrastShapeScore ( )

calculate the separate cross-correlation contrast shape score

◆ calcSNScore()

static double calcSNScore	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators
	)

static

calculate the Signal to Noise ratio

◆ calcXcorrCoelutionScore()

double calcXcorrCoelutionScore ( )

Calculate the cross-correlation coelution score.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrCoelutionWeightedScore()

double calcXcorrCoelutionWeightedScore ( const std::vector< double > & normalized_library_intensity )

Calculate the weighted cross-correlation coelution score.

The score is a distance where zero indicates perfect coelution. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.

◆ calcXcorrContrastShapeScore()

double calcXcorrContrastShapeScore ( )

calculate the cross-correlation contrast shape score

◆ calcXcorrPrecursorCoelutionScore()

double calcXcorrPrecursorCoelutionScore ( )

calculate the precursor cross-correlation contrast score

◆ calcXcorrPrecursorCombinedCoelutionScore()

double calcXcorrPrecursorCombinedCoelutionScore ( )

calculate the precursor cross-correlation coelution score including the transitions

◆ calcXcorrPrecursorCombinedShapeScore()

double calcXcorrPrecursorCombinedShapeScore ( )

calculate the precursor cross-correlation shape score including the transitions

◆ calcXcorrPrecursorContrastCoelutionScore()

double calcXcorrPrecursorContrastCoelutionScore ( )

Calculate the precursor cross-correlation contrast score against the transitions.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorContrastShapeScore()

double calcXcorrPrecursorContrastShapeScore ( )

calculate the precursor cross-correlation shape score against the transitions

◆ calcXcorrPrecursorContrastSumFragCoelutionScore()

double calcXcorrPrecursorContrastSumFragCoelutionScore ( )

  @brief Calculate the precursor cross-correlation contrast score against the sum of transitions

implemented the same as calcXcorrPrecursorCoelutionScore(), however assertion is different.

  The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorContrastSumFragShapeScore()

double calcXcorrPrecursorContrastSumFragShapeScore ( )

  @brief Calculate the precursor cross-correlation contrast score against the sum of transitions

implemented the same as calcXcorrPrecursorContrastShapeScore(), however assertion is different.

  The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorShapeScore()

double calcXcorrPrecursorShapeScore ( )

calculate the precursor cross-correlation shape score

◆ calcXcorrShapeScore()

double calcXcorrShapeScore ( )

Calculate the cross-correlation shape score.

The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation.

◆ calcXcorrShapeWeightedScore()

double calcXcorrShapeWeightedScore ( const std::vector< double > & normalized_library_intensity )

Calculate the weighted cross-correlation shape score.

The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.

◆ getMIContrastMatrix()

const OpenMS::Matrix< double > & getMIContrastMatrix ( ) const

non-mutable access to the MI contrast matrix

◆ getMIMatrix()

const OpenMS::Matrix< double > & getMIMatrix ( ) const

non-mutable access to the MI matrix

◆ getMIPrecursorCombinedMatrix()

const OpenMS::Matrix< double > & getMIPrecursorCombinedMatrix ( ) const

non-mutable access to the MI precursor combined matrix

◆ getMIPrecursorContrastMatrix()

const OpenMS::Matrix< double > & getMIPrecursorContrastMatrix ( ) const

non-mutable access to the MI precursor contrast matrix

◆ getXCorrContrastMatrix()

const XCorrMatrixType & getXCorrContrastMatrix ( ) const

non-mutable access to the cross-correlation contrast matrix

◆ getXCorrMatrix()

const XCorrMatrixType & getXCorrMatrix ( ) const

non-mutable access to the cross-correlation matrix

◆ getXCorrPrecursorCombinedMatrix()

const XCorrMatrixType & getXCorrPrecursorCombinedMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ getXCorrPrecursorContrastMatrix()

const XCorrMatrixType & getXCorrPrecursorContrastMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ initializeMIContrastMatrix()

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.g. identification transitions) vs set2 (e.g. detection transitions)

◆ initializeMIMatrix()

void initializeMIMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	native_ids
	)

Initialize the scoring object and building the MI matrix.

◆ initializeMIPrecursorCombinedMatrix()

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.

◆ initializeMIPrecursorContrastMatrix()

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.

◆ initializeMIPrecursorMatrices()

void initializeMIPrecursorMatrices	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	precursor_ids,
		const std::vector< std::string > &	native_ids
	)

Build the transition, precursor, precursor contrast and precursor combined MI matrices at once.

The same matrices as initializeMIMatrix(), initializeMIPrecursorMatrix(), initializeMIPrecursorContrastMatrix() and initializeMIPrecursorCombinedMatrix(), but every chromatogram is read and ranked once and the mutual information of every pair of chromatograms is computed once.

◆ initializeMIPrecursorMatrix()

void initializeMIPrecursorMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	precursor_ids
	)

Initialize the scoring object and building the MI matrix.

◆ initializeXCorrContrastMatrix()

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.g. identification transitions) vs set2 (e.g. detection transitions)

◆ initializeXCorrMatrix() [1/2]

void initializeXCorrMatrix ( const std::vector< std::vector< double > > & data )

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrMatrix() [2/2]

void initializeXCorrMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	native_ids
	)

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrPrecursorCombinedMatrix()

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 isotopes and transitions.

◆ initializeXCorrPrecursorContrastMatrix() [1/2]

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 isotopes vs transitions.

◆ initializeXCorrPrecursorContrastMatrix() [2/2]

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 isotopes vs transitions.

◆ initializeXCorrPrecursorMatrices()

void initializeXCorrPrecursorMatrices	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	precursor_ids,
		const std::vector< std::string > &	native_ids
	)

Build the transition, precursor, precursor contrast and precursor combined cross-correlation matrices at once.

The same matrices as initializeXCorrMatrix(mrmfeature, native_ids), initializeXCorrPrecursorMatrix(), initializeXCorrPrecursorContrastMatrix() and initializeXCorrPrecursorCombinedMatrix(), but every chromatogram is read and standardized once and every pair of chromatograms is correlated once: the combined matrix consists of the entries of the other three.

◆ initializeXCorrPrecursorMatrix()

void initializeXCorrPrecursorMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< std::string > &	precursor_ids
	)

Initialize the scoring object and building the cross-correlation matrix.

Member Data Documentation

◆ mi_contrast_matrix_

OpenMS::Matrix<double> mi_contrast_matrix_

private

the precomputed contrast mutual information matrix

◆ mi_matrix_

OpenMS::Matrix<double> mi_matrix_

private

the precomputed mutual information matrix

◆ mi_precursor_combined_matrix_

OpenMS::Matrix<double> mi_precursor_combined_matrix_

private

the precomputed contrast mutual information matrix with the MS1 trace

◆ mi_precursor_contrast_matrix_

OpenMS::Matrix<double> mi_precursor_contrast_matrix_

private

the precomputed contrast mutual information matrix against the MS1 trace

◆ mi_precursor_matrix_

OpenMS::Matrix<double> mi_precursor_matrix_

private

the precomputed mutual information matrix of the MS1 trace

◆ xcorr_contrast_matrix_

XCorrMatrixType xcorr_contrast_matrix_

private

the precomputed contrast cross correlation

◆ xcorr_contrast_matrix_max_peak_

OpenMS::Matrix<int> xcorr_contrast_matrix_max_peak_

private

contains max Peaks from xcorr_contrast_matrix_

◆ xcorr_contrast_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_contrast_matrix_max_peak_sec_

private

◆ xcorr_matrix_

XCorrMatrixType xcorr_matrix_

private

the precomputed cross correlation matrix

◆ xcorr_matrix_max_peak_

OpenMS::Matrix<int> xcorr_matrix_max_peak_

private

contains max Peaks from xcorr_matrix_

◆ xcorr_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_matrix_max_peak_sec_

private

◆ xcorr_precursor_combined_matrix_

XCorrMatrixType xcorr_precursor_combined_matrix_

private

the precomputed cross correlation with the MS1 trace

◆ xcorr_precursor_combined_matrix_max_peak_

OpenMS::Matrix<int> xcorr_precursor_combined_matrix_max_peak_

private

contains max peaks from xcorr_precursor_combined_matrix_

◆ xcorr_precursor_combined_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_precursor_combined_matrix_max_peak_sec_

private

◆ xcorr_precursor_contrast_matrix_

XCorrMatrixType xcorr_precursor_contrast_matrix_

private

the precomputed cross correlation against the MS1 trace

◆ xcorr_precursor_contrast_matrix_max_peak_

OpenMS::Matrix<int> xcorr_precursor_contrast_matrix_max_peak_

private

contains max peaks from xcorr_precursor_contrast_matrix_

◆ xcorr_precursor_contrast_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_precursor_contrast_matrix_max_peak_sec_

private

◆ xcorr_precursor_matrix_

XCorrMatrixType xcorr_precursor_matrix_

private

the precomputed cross correlation matrix of the MS1 trace

◆ xcorr_precursor_matrix_max_peak_

OpenMS::Matrix<int> xcorr_precursor_matrix_max_peak_

private

contains max peaks from xcorr_precursor_matrix_

◆ xcorr_precursor_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_precursor_matrix_max_peak_sec_

private

Public Types

Public Member Functions

Private Attributes

Scores

Detailed Description

Member Typedef Documentation

◆ FeatureType

◆ PeptideType

◆ ProteinType

◆ SpectrumType

◆ TransitionType

◆ XCorrArrayType

◆ XCorrMatrixType

Member Function Documentation

◆ calcLibraryScore()

◆ calcMIPrecursorCombinedScore()

◆ calcMIPrecursorContrastScore()

◆ calcMIPrecursorScore()

◆ calcMIScore()

◆ calcMIWeightedScore()

◆ calcRTScore()

◆ calcSeparateMIContrastScore()

◆ calcSeparateSNScore()

◆ calcSeparateXcorrContrastCoelutionScore()

◆ calcSeparateXcorrContrastShapeScore()

◆ calcSNScore()

◆ calcXcorrCoelutionScore()

◆ calcXcorrCoelutionWeightedScore()

◆ calcXcorrContrastShapeScore()

◆ calcXcorrPrecursorCoelutionScore()

◆ calcXcorrPrecursorCombinedCoelutionScore()

◆ calcXcorrPrecursorCombinedShapeScore()

◆ calcXcorrPrecursorContrastCoelutionScore()

◆ calcXcorrPrecursorContrastShapeScore()

◆ calcXcorrPrecursorContrastSumFragCoelutionScore()

◆ calcXcorrPrecursorContrastSumFragShapeScore()

◆ calcXcorrPrecursorShapeScore()

◆ calcXcorrShapeScore()

◆ calcXcorrShapeWeightedScore()

◆ getMIContrastMatrix()

◆ getMIMatrix()

◆ getMIPrecursorCombinedMatrix()

◆ getMIPrecursorContrastMatrix()

◆ getXCorrContrastMatrix()

◆ getXCorrMatrix()

◆ getXCorrPrecursorCombinedMatrix()

◆ getXCorrPrecursorContrastMatrix()

◆ initializeMIContrastMatrix()

◆ initializeMIMatrix()

◆ initializeMIPrecursorCombinedMatrix()

◆ initializeMIPrecursorContrastMatrix()

◆ initializeMIPrecursorMatrices()

◆ initializeMIPrecursorMatrix()

◆ initializeXCorrContrastMatrix()

◆ initializeXCorrMatrix() [1/2]

◆ initializeXCorrMatrix() [2/2]

◆ initializeXCorrPrecursorCombinedMatrix()

◆ initializeXCorrPrecursorContrastMatrix() [1/2]

◆ initializeXCorrPrecursorContrastMatrix() [2/2]

◆ initializeXCorrPrecursorMatrices()

◆ initializeXCorrPrecursorMatrix()

Member Data Documentation

◆ mi_contrast_matrix_

◆ mi_matrix_

◆ mi_precursor_combined_matrix_

◆ mi_precursor_contrast_matrix_

◆ mi_precursor_matrix_

◆ xcorr_contrast_matrix_

◆ xcorr_contrast_matrix_max_peak_

◆ xcorr_contrast_matrix_max_peak_sec_

◆ xcorr_matrix_

◆ xcorr_matrix_max_peak_

◆ xcorr_matrix_max_peak_sec_

◆ xcorr_precursor_combined_matrix_

◆ xcorr_precursor_combined_matrix_max_peak_

◆ xcorr_precursor_combined_matrix_max_peak_sec_

◆ xcorr_precursor_contrast_matrix_

◆ xcorr_precursor_contrast_matrix_max_peak_

◆ xcorr_precursor_contrast_matrix_max_peak_sec_

◆ xcorr_precursor_matrix_