OpenMS  3.0.0
Scoring.h File Reference
#include <numeric>
#include <map>
#include <vector>
#include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
Include dependency graph for Scoring.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes

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

Namespaces

 OpenSwath
 
 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, doubleXCorrEntry
 Cross Correlation array contains (lag,correlation) pairs. More...
 

Functions

Helper functions
OPENSWATHALGO_DLLAPI double NormalizedManhattanDist (double x[], double y[], int n)
 Calculate the normalized Manhattan distance between two arrays. More...
 
OPENSWATHALGO_DLLAPI double RootMeanSquareDeviation (double x[], double y[], int n)
 Calculate the RMSD (root means square deviation) More...
 
OPENSWATHALGO_DLLAPI double SpectralAngle (double x[], double y[], int n)
 Calculate the Spectral angle (acosine of the normalized dotproduct) More...
 
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. More...
 
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. More...
 
OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator xcorrArrayGetMaxPeak (const XCorrArrayType &array)
 Find best peak in an cross-correlation (highest apex) More...
 
OPENSWATHALGO_DLLAPI void standardize_data (std::vector< double > &data)
 Standardize a vector (subtract mean, divide by standard deviation) More...
 
OPENSWATHALGO_DLLAPI void normalize_sum (double x[], unsigned int n)
 Divide each element of x by the sum of the vector. More...
 
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)