IonMobilityScoring.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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
{
 
  struct RangeMobility;
  struct RangeMZ;
 
  class OPENMS_DLLAPI IonMobilityScoring
  {
    typedef OpenSwath::LightCompound CompoundType;
    typedef OpenSwath::LightTransition TransitionType;
 
    struct MobilityPeak
    {
      double im;
      double intensity;
      MobilityPeak ();
      MobilityPeak (double im_, double int_) :
        im(im_),
        intensity(int_)
      {}
    };
    typedef std::vector< MobilityPeak > IonMobilogram;
 
  public:
 
    IonMobilityScoring();
 
    ~IonMobilityScoring();
 
    static void driftScoring(const SpectrumSequence& spectra,
                             const std::vector<TransitionType> & transitions,
                             OpenSwath_Scores & scores,
                             const double drift_target,
                             RangeMobility im_range,
                             const double dia_extraction_window_,
                             const bool dia_extraction_ppm_,
                             const bool use_spline,
                             const double drift_extra);
 
    static void driftScoringMS1(const SpectrumSequence& spectra,
                                const std::vector<TransitionType> & transitions,
                                OpenSwath_Scores & scores,
                                const double drift_target,
                                RangeMobility im_range,
                                const double dia_extraction_window_,
                                const bool dia_extraction_ppm_,
                                const bool use_spline,
                                const double drift_extra);
 
    static void driftScoringMS1Contrast(const SpectrumSequence& spectra, const SpectrumSequence& ms1spectrum,
                                        const std::vector<TransitionType> & transitions,
                                        OpenSwath_Scores & scores,
                                        RangeMobility im_range,
                                        const double dia_extraction_window_,
                                        const bool dia_extraction_ppm_,
                                        const double drift_extra);
 
    static void computeIonMobilogram(const SpectrumSequence& spectra,
                              const RangeMZ & mz_range,
                              const RangeMobility & im_range,
                              double & im,
                              double & intensity,
                              IonMobilogram& res,
                              double eps);
 
 
  private:
    static std::vector<double> computeGrid_(const std::vector< IonMobilogram >& mobilograms, double eps);
 
 
    /*
     @brief Extracts ion mobility values projected onto a grid
 
     For a given ion mobility profile and a grid, compute an ion mobilogram
     across the grid for each ion mobility data point. Returns two data arrays
     for the ion mobilogram: intensity (y) and ion mobility (x). Zero values are
     inserted if no data point was found for a given grid value.
 
     @param profile The ion mobility data
     @param im_grid The grid to be used
     @param al_int_values The intensity vector (y)
     @param al_im_values The ion mobility vector (x)
     @param eps Epsilon used for computing the ion mobility grid
     @param max_peak_idx The grid position of the maximum
    */
    static void alignToGrid_(const IonMobilogram& profile,
                 const std::vector<double>& im_grid,
                 std::vector< double >& al_int_values,
                 std::vector< double >& al_im_values,
                 double eps,
                 Size & max_peak_idx);
 
  };
}