InternalCalibration.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#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:
 
    struct CalibrantStats_
    {
      CalibrantStats_(const double tol_ppm)
        : tol_ppm_(tol_ppm)
      {};
      Size cnt_empty = 0; 
      Size cnt_nomz = 0; 
      Size cnt_nort = 0; 
      Size cnt_decal = 0; 
      Size cnt_total = 0; 
 
      void print() const
      {
        if (cnt_empty > 0) OPENMS_LOG_WARN << "Warning: " << cnt_empty << "/" << cnt_total << " calibrations points were skipped, since they have no peptide sequence!" << std::endl;
        if (cnt_nomz > 0) OPENMS_LOG_WARN << "Warning: " << cnt_nomz << "/" << cnt_total << " calibrations points were skipped, since they have no m/z value!" << std::endl;
        if (cnt_nort > 0) OPENMS_LOG_WARN << "Warning: " << cnt_nort << "/" << cnt_total << " calibrations points were skipped, since they have no RT value!" << std::endl;
        if (cnt_decal > 0) OPENMS_LOG_WARN << "Warning: " << cnt_decal << "/" << cnt_total << " calibrations points were skipped, since their theoretical weight is more than " << tol_ppm_ << " ppm away from their measured mass!" << std::endl;
      }
 
      private:
      const double tol_ppm_; 
    };
 
    void fillID_( const PeptideIdentification& pep_id, const double tol_ppm, CalibrantStats_& stats);
 
    void fillIDs_(const std::vector<PeptideIdentification>& pep_ids, const double tol_ppm, CalibrantStats_& stats);
 
    bool isDecalibrated_(const PeptideIdentification& pep_id, const double mz_obs, const double tol_ppm, CalibrantStats_& stats, double& mz_ref);
 
    /*
     @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