IonMobilityScoring.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 2002-2022.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

// data access
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>

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

// scoring
#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>

#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI IonMobilityScoring
  {
    typedef OpenSwath::LightCompound CompoundType;
    typedef OpenSwath::LightTransition TransitionType;

  public:

    IonMobilityScoring();

    ~IonMobilityScoring();

    static void driftScoring(const OpenSwath::SpectrumPtr& spectrum,
                             const std::vector<TransitionType> & transitions,
                             OpenSwath_Scores & scores,
                             const double drift_lower,
                             const double drift_upper,
                             const double drift_target,
                             const double dia_extraction_window_,
                             const bool dia_extraction_ppm_,
                             const bool use_spline,
                             const double drift_extra);

    static void driftScoringMS1(const OpenSwath::SpectrumPtr& spectrum,
                                const std::vector<TransitionType> & transitions,
                                OpenSwath_Scores & scores,
                                const double drift_lower,
                                const double drift_upper,
                                const double drift_target,
                                const double dia_extract_window_,
                                const bool dia_extraction_ppm_,
                                const bool use_spline,
                                const double drift_extra);

    static void driftScoringMS1Contrast(const OpenSwath::SpectrumPtr& spectrum, const OpenSwath::SpectrumPtr& ms1spectrum,
                                        const std::vector<TransitionType> & transitions,
                                        OpenSwath_Scores & scores,
                                        const double drift_lower,
                                        const double drift_upper,
                                        const double dia_extract_window_,
                                        const bool dia_extraction_ppm_,
                                        const double drift_extra);
  };
}