SONARScoring.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 2002-2023.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SONARScoring :
    public DefaultParamHandler
  {
public:
 
 
    SONARScoring();
 
    ~SONARScoring() override {}
    //
 
    void computeSonarScores(OpenSwath::IMRMFeature* imrmfeature,
                            const std::vector<OpenSwath::LightTransition> & transitions,
                            const std::vector<OpenSwath::SwathMap>& swath_maps,
                            OpenSwath_Scores & scores) const;
 
private:
 
    void computeXCorr_(std::vector<std::vector<double> >& sonar_profiles,
                       double& xcorr_coelution_score, double& xcorr_shape_score) const;
 
    SONARScoring(const SONARScoring& rhs);
 
    SONARScoring& operator=(const SONARScoring& rhs);
 
    void updateMembers_() override;
 
    double dia_extract_window_;
    bool dia_centroided_;
    bool dia_extraction_ppm_;
 
  };
}