Scoring.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
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#pragma once
 
#include <numeric>
#include <map>
#include <vector>
 
#include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
 
namespace OpenSwath
{
 
  namespace Scoring
  {
    typedef std::pair<int, double> XCorrEntry;
    struct XCorrArrayType 
    {
public:
    std::vector<XCorrEntry> data;
 
    // Access functions
    typedef std::vector<XCorrEntry>::iterator iterator;
    typedef std::vector<XCorrEntry>::const_iterator const_iterator;
 
    iterator begin() {return data.begin();}
    const_iterator begin() const {return data.begin();}
    iterator end() {return data.end();}
    const_iterator end() const {return data.end();}
    };
 
    OPENSWATHALGO_DLLAPI double NormalizedManhattanDist(double x[], double y[], int n);
 
    OPENSWATHALGO_DLLAPI double RootMeanSquareDeviation(double x[], double y[], int n);
 
    OPENSWATHALGO_DLLAPI double SpectralAngle(double x[], double y[], int n);
 
    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);                                                                   
 
    OPENSWATHALGO_DLLAPI XCorrArrayType calculateCrossCorrelation(const std::vector<double>& data1,
                                                                  const std::vector<double>& data2, const int maxdelay, const int lag);
 
    OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator xcorrArrayGetMaxPeak(const XCorrArrayType & array);
 
    OPENSWATHALGO_DLLAPI void standardize_data(std::vector<double>& data);
 
    OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n);
 
    OPENSWATHALGO_DLLAPI void computeAndAppendRank(const std::vector<double>& v, std::vector<unsigned int>& ranks);
 
    OPENSWATHALGO_DLLAPI void 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);
 
 
  }
}