Precursor.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// 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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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,                      
      PQD,                      
      TRAP,                     
      HCD,                     
      INSOURCE,                 
      LIFT,                     
      SIZE_OF_ACTIVATIONMETHOD
    };
    static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];
    static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD];

    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;    
    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