Precursor.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $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 <set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI Precursor :
    public CVTermList,
    public Peak1D
  {
 
public:
 
    enum ActivationMethod
    {
      CID,                      
      PSD,                      
      PD,                       
      SID,                      
      BIRD,                     
      ECD,                      
      IMD,                      
      SORI,                     
      HCID,                     
      LCID,                     
      PHD,                      
      ETD,                      
      PQD,                      
      SIZE_OF_ACTIVATIONMETHOD
    };
 
    enum DriftTimeUnit
    {
      NONE,                        
      MILLISECOND,                 
      VSSC,                        
      FAIMS_COMPENSATION_VOLTAGE,  
      SIZE_OF_DRIFTTIMEUNIT
    };
 
 
    static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];
    static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD];
 
    Precursor();
    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;
 
    Precursor & operator=(const Precursor &) = default;
    Precursor& operator=(Precursor&&) & = default;
 
    bool operator==(const Precursor & rhs) const;
    bool operator!=(const Precursor & rhs) const;
 
    const std::set<ActivationMethod> & getActivationMethods() const;
    std::set<ActivationMethod> & getActivationMethods();
    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_;
    double drift_window_low_;
    double drift_window_up_;
    DriftTimeUnit drift_time_unit_;
    Int charge_;
    std::vector<Int> possible_charge_states_;
  };
} // namespace OpenMS