Precursor.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: Mathias Walzer $
// $Authors: Marc Sturm, Mathias Walzer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/IONMOBILITY/IMTypes.h>
 
#include <set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI Precursor :
    public CVTermList,
    public Peak1D
  {
 
public:
    Precursor() = default;
    Precursor(const Precursor&) = default;
 
    // note: we implement the move constructor ourselves due to a bug in MSVS
    // 2015/2017 which cannot produce a default move constructor for classes
    // that contain STL containers (other than vector).
 
    Precursor(Precursor&&) noexcept;
    ~Precursor() override = default;
 
    Precursor& operator=(const Precursor&) = default;
    Precursor& operator=(Precursor&&) & = default;
 
    enum ActivationMethod
    {
      CID,                      
      PSD,                      
      PD,                       
      SID,                      
      BIRD,                     
      ECD,                      
      IMD,                      
      SORI,                     
      HCID,                     
      LCID,                     
      PHD,                      
      ETD,                      
      ETciD,                    
      EThcD,                    
      PQD,                      
      TRAP,                     
      HCD,                      
      INSOURCE,                 
      LIFT,                     
      SIZE_OF_ACTIVATIONMETHOD
    };
    static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];
    static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD];
 
    static StringList getAllNamesOfActivationMethods();
    static StringList getAllShortNamesOfActivationMethods();
 
    bool operator==(const Precursor & rhs) const;
    bool operator!=(const Precursor & rhs) const;
  
    const std::set<ActivationMethod>& getActivationMethods() const;
    std::set<ActivationMethod>& getActivationMethods();
    
    StringList getActivationMethodsAsString() const;    
    StringList getActivationMethodsAsShortString() const;
 
    void setActivationMethods(const std::set<ActivationMethod> & activation_methods);
 
    double getActivationEnergy() const;
    void setActivationEnergy(double activation_energy);
 
    double getIsolationWindowLowerOffset() const;
    void setIsolationWindowLowerOffset(double bound);
 
    double getIsolationWindowUpperOffset() const;
    void setIsolationWindowUpperOffset(double bound);
 
    double getDriftTime() const;
    void setDriftTime(double drift_time);
 
    DriftTimeUnit getDriftTimeUnit() const;
 
    void setDriftTimeUnit(DriftTimeUnit dt);
 
 
    double getDriftTimeWindowLowerOffset() const;
    void setDriftTimeWindowLowerOffset(double drift_time);
 
    double getDriftTimeWindowUpperOffset() const;
    void setDriftTimeWindowUpperOffset(double drift_time);
 
    Int getCharge() const;
    void setCharge(Int charge);
 
    std::vector<Int>& getPossibleChargeStates();
    const std::vector<Int>& getPossibleChargeStates() const;
    void setPossibleChargeStates(const std::vector<Int> & possible_charge_states);
 
    inline double getUnchargedMass() const
    {
      int c = charge_;
      (c == 0) ? c = 2 : c = charge_;
      return getMZ() * c - c * Constants::PROTON_MASS_U;
    }
 
protected:
 
    std::set<ActivationMethod> activation_methods_;
    double activation_energy_{};
    double window_low_{};
    double window_up_{};
    double drift_time_{-1};
    double drift_window_low_{};
    double drift_window_up_{};
    DriftTimeUnit drift_time_unit_{DriftTimeUnit::NONE};
    Int charge_{};
    std::vector<Int> possible_charge_states_;
  };
} // namespace OpenMS