IonizationSimulation.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 2002-2012.
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// $Maintainer: Chris Bielow$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_IONIZATIONSIMULATION_H
#define OPENMS_SIMULATION_IONIZATIONSIMULATION_H

#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(const SimRandomNumberGenerator &);

    IonizationSimulation(const IonizationSimulation & source);

    virtual ~IonizationSimulation();

    IonizationSimulation & operator=(const IonizationSimulation & source);

    void ionize(FeatureMapSim & features, ConsensusMap & charge_consensus, MSSimExperiment & experiment);

private:
    IonizationSimulation();

    class CompareCmpByEF_;

    void ionizeEsi_(FeatureMapSim &, ConsensusMap & charge_consensus);

    void ionizeMaldi_(FeatureMapSim &, ConsensusMap & charge_consensus);

    inline bool isFeatureValid_(const Feature & feature);

    void setFeatureProperties_(Feature & f,
                               const DoubleReal & adduct_mass,
                               const String & adduct_formula,
                               const SimChargeType charge,
                               const SimIntensityType new_intensity,
                               const Size parent_index);

    void setDefaultParams_();

    void updateMembers_();

    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_;

    DoubleReal esi_probability_;

    // important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)
    std::vector<double> esi_impurity_probabilities_;


    Adduct::AdductsType esi_adducts_;

    Size max_adduct_charge_;

    // important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)
    std::vector<double> maldi_probabilities_;

    SimCoordinateType maximal_mz_measurement_limit_;
    SimCoordinateType minimal_mz_measurement_limit_;

protected:
    SimRandomNumberGenerator const * rnd_gen_;
  };

}

#endif