InternalCalibration.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 2002-2018.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/CalibrationData.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/FILTERING/CALIBRATION/MZTrafoModel.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <vector>

namespace OpenMS
{
  
  class FeatureMap;
    
  class OPENMS_DLLAPI InternalCalibration
    : public ProgressLogger
  {
  public:

    InternalCalibration();

    ~InternalCalibration(){}

    struct LockMass
    {
      double mz; 
      unsigned int ms_level;   
      int charge;     

      LockMass(double mz_, int lvl_, int charge_)
        : mz(mz_),
         ms_level(lvl_),
         charge(charge_)
      {}
    };

  

    Size fillCalibrants(const PeakMap exp,
                        const std::vector<InternalCalibration::LockMass>& ref_masses,
                        double tol_ppm,
                        bool lock_require_mono,
                        bool lock_require_iso,
                        CalibrationData& failed_lock_masses,
                        bool verbose = true);

    Size fillCalibrants(const FeatureMap& fm, double tol_ppm);

    Size fillCalibrants(const std::vector<PeptideIdentification>& pep_ids, double tol_ppm);

    const CalibrationData& getCalibrationPoints() const;

    bool calibrate(PeakMap& exp, 
                   const IntList& target_mslvl,
                   MZTrafoModel::MODELTYPE model_type,
                   double rt_chunk,
                   bool use_RANSAC,
                   double post_ppm_median,
                   double post_ppm_MAD,
                   const String& file_models = "",
                   const String& file_models_plot = "",
                   const String& file_residuals = "",
                   const String& file_residuals_plot = "",
                   const String& rscript_executable = "Rscript");

    /*
      @brief Transform a precursor's m/z

      Calibrate m/z of precursors.

      @param pcs Uncalibrated Precursors
      @param trafo The calibration function to apply
    */
    static void applyTransformation(std::vector<Precursor>& pcs, const MZTrafoModel& trafo);

    /*
      @brief Transform a spectrum (data+precursor)

      See applyTransformation(MSExperiment, ...) for details.

      @param spec Uncalibrated MSSpectrum
      @param target_mslvl List (can be unsorted) of MS levels to calibrate
      @param trafo The calibration function to apply
    */
    static void applyTransformation(PeakMap::SpectrumType& spec, const IntList& target_mslvl, const MZTrafoModel& trafo);

    /*
      @brief Transform spectra from a whole map (data+precursor)

      All data peaks and precursor information (if present) are calibrated in m/z.

      Only spectra whose MS-level is contained in 'target_mslvl' are calibrated.
      In addition, if a fragmentation spectrum's precursor information originates from an MS level in 'target_mslvl',
      the precursor (not the spectrum itself) is also subjected to calibration.
      E.g., If we only have MS and MS/MS spectra: for 'target_mslvl' = {1} then all MS1 spectra and MS2 precursors are calibrated.
      If 'target_mslvl' = {2}, only MS2 spectra (not their precursors) are calibrated.
      If 'target_mslvl' = {1,2} all spectra and precursors are calibrated.
            

      @param exp Uncalibrated peak map
      @param target_mslvl List (can be unsorted) of MS levels to calibrate
      @param trafo The calibration function to apply
    */
    static void applyTransformation(PeakMap& exp, const IntList& target_mslvl, const MZTrafoModel& trafo);
  
  protected:
    void fillIDs_( const std::vector<PeptideIdentification>& pep_ids, double tol_ppm );

    /*
     @brief Calibrate m/z of a spectrum, ignoring precursors!

     This method is not exposed as public, because its easy to be misused on spectra while forgetting about the precursors of high-level spectra.
    */
    static void applyTransformation_(PeakMap::SpectrumType& spec, const MZTrafoModel& trafo);

  private:
    CalibrationData cal_data_;


  }; // class InternalCalibration
  
} // namespace OpenMS