IonizationSimulation.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/Adduct.h>
#include <OpenMS/SIMULATION/SimTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
 
// STL includes
#include <set>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI IonizationSimulation :
    public DefaultParamHandler,
    public ProgressLogger
  {
 
public:
    typedef enum
    {
      MALDI,
      ESI
    } IonizationType;
 
    IonizationSimulation();
 
    explicit IonizationSimulation(SimTypes::MutableSimRandomNumberGeneratorPtr);
 
    IonizationSimulation(const IonizationSimulation& source);
 
    ~IonizationSimulation() override;
 
    IonizationSimulation& operator=(const IonizationSimulation& source);
 
    void ionize(SimTypes::FeatureMapSim& features, ConsensusMap& charge_consensus, SimTypes::MSSimExperiment& experiment);
 
private:
    class CompareCmpByEF_;
 
    void ionizeEsi_(SimTypes::FeatureMapSim&, ConsensusMap& charge_consensus);
 
    void ionizeMaldi_(SimTypes::FeatureMapSim&, ConsensusMap& charge_consensus);
 
    inline bool isFeatureValid_(const Feature& feature) const;
 
    void setFeatureProperties_(Feature& f,
                               const double& adduct_mass,
                               const String& adduct_formula,
                               const SimTypes::SimChargeType charge,
                               const SimTypes::SimIntensityType new_intensity,
                               const Size parent_index);
 
    void setDefaultParams_();
 
    void updateMembers_() override;
 
    UInt countIonizedResidues_(const AASequence&) const;
 
 
    // Members //
 
    IonizationType ionization_type_;
 
    /*
 @brief List of residues that are counted as basic during execution of countBasicResidues_
*/
    std::set<String> basic_residues_;
 
    double esi_probability_;
 
    std::vector<double> esi_impurity_probabilities_;
 
 
    Adduct::AdductsType esi_adducts_;
 
    Size max_adduct_charge_;
 
    std::vector<double> maldi_probabilities_;
 
    SimTypes::SimCoordinateType maximal_mz_measurement_limit_;
    SimTypes::SimCoordinateType minimal_mz_measurement_limit_;
 
protected:
    SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_;
  };
 
}