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 2002-2018.
//
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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);

    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_;
  };

}