Scoring.h File Reference

#include <numeric>
#include <map>
#include <vector>
#include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>

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Classes
struct	pair_hash
	Simple hash function for Scoring::pos2D. More...
struct	XCorrArrayType

Namespaces
namespace	OpenSwath
namespace	OpenSwath::Scoring
	Scoring functions used by MRMScoring.

Typedefs
Type defs and helper structures
typedef std::pair< unsigned int, unsigned int >	pos2D
typedef std::pair< int, double >	XCorrEntry
	Cross Correlation array contains (lag,correlation) pairs.

Functions
Helper functions
OPENSWATHALGO_DLLAPI double	NormalizedManhattanDist (double x[], double y[], int n)
	Calculate the normalized Manhattan distance between two arrays.
OPENSWATHALGO_DLLAPI double	RootMeanSquareDeviation (double x[], double y[], int n)
	Calculate the RMSD (root means square deviation)
OPENSWATHALGO_DLLAPI double	SpectralAngle (double x[], double y[], int n)
	Calculate the Spectral angle (acosine of the normalized dotproduct)
OPENSWATHALGO_DLLAPI XCorrArrayType	calcxcorr_legacy_mquest_ (std::vector< double > &data1, std::vector< double > &data2, bool normalize)
OPENSWATHALGO_DLLAPI XCorrArrayType	normalizedCrossCorrelation (std::vector< double > &data1, std::vector< double > &data2, const int maxdelay, const int lag)
OPENSWATHALGO_DLLAPI XCorrArrayType	normalizedCrossCorrelationPost (std::vector< double > &normalized_data1, std::vector< double > &normalized_data2, const int maxdelay, const int lag)
	Calculate crosscorrelation on std::vector data that is already normalized.
OPENSWATHALGO_DLLAPI XCorrArrayType	calculateCrossCorrelation (const std::vector< double > &data1, const std::vector< double > &data2, const int maxdelay, const int lag)
	Calculate crosscorrelation on std::vector data without normalization.
OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator	xcorrArrayGetMaxPeak (const XCorrArrayType &array)
	Find best peak in an cross-correlation (highest apex)
OPENSWATHALGO_DLLAPI void	standardize_data (std::vector< double > &data)
	Standardize a vector (subtract mean, divide by standard deviation)
OPENSWATHALGO_DLLAPI void	normalize_sum (double x[], unsigned int n)
	Divide each element of x by the sum of the vector.
OPENSWATHALGO_DLLAPI unsigned int	computeAndAppendRank (const std::vector< double > &v, std::vector< unsigned int > &ranks)
OPENSWATHALGO_DLLAPI std::vector< unsigned int >	computeRankVector (const std::vector< std::vector< double > > &intensity, std::vector< std::vector< unsigned int > > &ranks)
OPENSWATHALGO_DLLAPI double	rankedMutualInformation (std::vector< unsigned int > &ranked_data1, std::vector< unsigned int > &ranked_data2, const unsigned int max_rank1, const unsigned int max_rank2)