FeatureFinderAlgorithmMetaboIdent.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg, Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/CHEMISTRY/AdductInfo.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
 
#include <map>
#include <vector>
 
namespace OpenMS
{
class IsotopeDistribution;
  
class OPENMS_DLLAPI FeatureFinderAlgorithmMetaboIdent :
  public DefaultParamHandler
{
public:
  struct OPENMS_DLLAPI FeatureFinderMetaboIdentCompound
  {
    FeatureFinderMetaboIdentCompound(const std::string& _name,
        const std::string& _formula,
        double _mass,
        const std::vector<int>& _charges,
        const std::vector<double>& _rts,
        const std::vector<double>& _rt_ranges,
        const std::vector<double>& _iso_distrib,
        const std::vector<double>& _ion_mobilities = {},
        const std::string& _adduct = ""):
      name_(_name),
      formula_(_formula),
      mass_(_mass),
      charges_(_charges),
      rts_(_rts),
      rt_ranges_(_rt_ranges),
      iso_distrib_(_iso_distrib),
      ion_mobilities_(_ion_mobilities),
      adduct_(_adduct)
      {
      }
 
    private:
      std::string name_;                          
      std::string formula_;                       
      double mass_;                          
      std::vector<int> charges_;             
      std::vector<double> rts_;              
      std::vector<double> rt_ranges_;        
      std::vector<double> iso_distrib_;      
      std::vector<double> ion_mobilities_;   
      std::string adduct_;                        
 
    public:
      const std::string& getName() const {
        return name_;
      }
 
      const std::string& getFormula() const {
        return formula_;
      }
 
      double getMass() const {
        return mass_;
      }
 
      const std::vector<int>& getCharges() const {
        return charges_;
      }
 
      const std::vector<double>& getRTs() const {
        return rts_;
      }
 
      const std::vector<double>& getRTRanges() const {
        return rt_ranges_;
      }
 
      const std::vector<double>& getIsotopeDistribution() const {
        return iso_distrib_;
      }
 
      const std::vector<double>& getIonMobilities() const {
        return ion_mobilities_;
      }
 
      const std::string& getAdduct() const {
        return adduct_;
      }
  };
 
  FeatureFinderAlgorithmMetaboIdent();
 
  void run(const std::vector<FeatureFinderMetaboIdentCompound>& metaboIdentTable, FeatureMap& features, const std::string& spectra_file = "");
 
  PeakMap& getMSData() { return ms_data_; }
  const PeakMap& getMSData() const { return ms_data_; }
 
  void setMSData(const PeakMap& m); // needed because pyOpenMS can't wrap the non-const reference version
 
  void setMSData(PeakMap&& m); // moves peak data and saves the copy. Note that getMSData() will give back a processed/modified version.
 
  const PeakMap& getChromatograms() const { return chrom_data_; }
  PeakMap& getChromatograms() { return chrom_data_; }
 
  const TargetedExperiment& getLibrary() const { return library_; }
  
  const TransformationDescription& getTransformations() const { return trafo_; }
 
  size_t getNShared() const  { return n_shared_; }
 
  static std::string prettyPrintCompound(const TargetedExperiment::Compound& compound);
protected:
 
  struct MassTraceBounds
  {
    Size sub_index;
    double rt_min, rt_max, mz_min, mz_max;
  };
 
  typedef std::map<UInt64, std::vector<MassTraceBounds> > FeatureBoundsMap;
 
  typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace;
  typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces;
 
  typedef std::vector<Feature*> FeatureGroup; 
 
  struct FeatureFilterQuality
  {
    bool operator()(const Feature& feature)
    {
      return feature.metaValueExists("FFMetId_remove");
    }
  } feature_filter_;
 
  struct FeatureCompare
  {
    bool operator()(const Feature& f1, const Feature& f2)
    {
      const std::string ref1 = StringUtils::toStr(f1.getMetaValue("PeptideRef"));
      const std::string ref2 = StringUtils::toStr(f2.getMetaValue("PeptideRef"));
      if (ref1 == ref2)
      {
        return f1.getRT() < f2.getRT();
      }
      return ref1 < ref2;
    }
  } feature_compare_;
 
 
  void extractTransformations_(const FeatureMap& features);
 
  void addTargetToLibrary_(const std::string& name, const std::string& formula,
                           double mass, const std::vector<Int>& charges,
                           const std::vector<double>& rts,
                           std::vector<double> rt_ranges,
                           const std::vector<double>& iso_distrib,
                           const std::vector<double>& ion_mobilities = {},
                           const std::string& adduct = "");
 
  Size addTargetAnnotations_(FeatureMap& features);
 
  void addTargetRT_(TargetedExperiment::Compound& target, double rt);
 
  double calculateMZ_(double mass, Int charge) const;
 
  void generateTransitions_(const std::string& target_id, double mz, Int charge,
                            const IsotopeDistribution& iso_dist);
 
  void annotateFeatures_(FeatureMap& features);
 
  void ensureConvexHulls_(Feature& feature) const;
 
  void selectFeaturesFromCandidates_(FeatureMap& features);
 
  void runSingleGroup_(const std::vector<FeatureFinderMetaboIdentCompound>& metaboIdentTable,
                       FeatureMap& features,
                       const std::string& spectra_file);
 
  double rt_window_; 
  double mz_window_; 
  bool mz_window_ppm_; 
  double im_window_; 
 
  double isotope_pmin_; 
  Size n_isotopes_; 
 
  double peak_width_;
  double min_peak_width_;
  double signal_to_noise_;
 
  std::string elution_model_;
 
  // output file (before filtering)
  std::string candidates_out_;
 
  Size debug_level_;
 
  void updateMembers_() override;
 
  PeakMap ms_data_; 
  PeakMap chrom_data_; 
 
  MRMFeatureFinderScoring feat_finder_; 
 
  TargetedExperiment library_; 
  
  TransformationDescription trafo_;
  
  CoarseIsotopePatternGenerator iso_gen_; 
  std::map<std::string, double> isotope_probs_; 
  std::map<std::string, double> target_rts_; 
  
  size_t n_shared_ = 0;
};
 
} // namespace OpenMS