IonMobilityScoring.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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(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(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(OpenSwath::SpectrumPtr spectrum, 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);
  };
}