libopenms-dev 1.11.1-3 / usr / include / OpenMS / METADATA / Precursor.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Mathias Walzer $
// $Authors: Marc Sturm, Mathias Walzer $
// --------------------------------------------------------------------------

#ifndef OPENMS_METADATA_PRECURSOR_H
#define OPENMS_METADATA_PRECURSOR_H

#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/CONCEPT/Constants.h>

#include <set>

namespace OpenMS
{
  /**
      @brief Precursor meta information.

      This class contains precursor information:
  - isolation window
  - activation
  - selected ion (m/z, intensity, charge, possible charge states)

      @ingroup Metadata
  */
  class OPENMS_DLLAPI Precursor :
    public CVTermList,
    public Peak1D
  {

public:

    /// Method of activation
    enum ActivationMethod
    {
      CID,                      ///< Collision-induced dissociation
      PSD,                      ///< Post-source decay
      PD,                       ///< Plasma desorption
      SID,                      ///< Surface-induced dissociation
      BIRD,                             ///< Blackbody infrared radiative dissociation
      ECD,                              ///< Electron capture dissociation
      IMD,                              ///< Infrared multiphoton dissociation
      SORI,                             ///< Sustained off-resonance irradiation
      HCID,                             ///< High-energy collision-induced dissociation
      LCID,                             ///< Low-energy collision-induced dissociation
      PHD,                              ///< Photodissociation
      ETD,                              ///< Electron transfer dissociation
      PQD,                              ///< Pulsed q dissociation
      SIZE_OF_ACTIVATIONMETHOD
    };
    /// Names of activation methods
    static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];

    /// Constructor
    Precursor();
    /// Copy constructor
    Precursor(const Precursor & source);
    /// Destructor
    virtual ~Precursor();

    /// Assignment operator
    Precursor & operator=(const Precursor & source);

    /// Equality operator
    bool operator==(const Precursor & rhs) const;
    /// Equality operator
    bool operator!=(const Precursor & rhs) const;

    /// returns a const reference to the activation methods
    const std::set<ActivationMethod> & getActivationMethods() const;
    /// returns a mutable reference to the activation methods
    std::set<ActivationMethod> & getActivationMethods();
    /// sets the activation methods
    void setActivationMethods(const std::set<ActivationMethod> & activation_methods);

    /// returns the activation energy (in electronvolt)
    DoubleReal getActivationEnergy() const;
    /// sets the activation energy (in electronvolt)
    void setActivationEnergy(DoubleReal activation_energy);

    /// returns the lower offset from the target m/z
    DoubleReal getIsolationWindowLowerOffset() const;
    /// sets the lower offset from the target m/z
    void setIsolationWindowLowerOffset(DoubleReal bound);

    /// returns the upper offset from the target m/z
    DoubleReal getIsolationWindowUpperOffset() const;
    /// sets the upper offset from the target m/z
    void setIsolationWindowUpperOffset(DoubleReal bound);

    /// Non-mutable access to the charge
    Int getCharge() const;
    /// Mutable access to the charge
    void setCharge(Int charge);

    ///Mutable access to possible charge states
    std::vector<Int> & getPossibleChargeStates();
    ///Non-mutable access to possible charge states
    const std::vector<Int> & getPossibleChargeStates() const;
    ///Sets the possible charge states
    void setPossibleChargeStates(const std::vector<Int> & possible_charge_states);

    /// Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged
    inline DoubleReal 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_;
    DoubleReal activation_energy_;
    DoubleReal window_low_;
    DoubleReal window_up_;
    Int charge_;
    std::vector<Int> possible_charge_states_;
  };
} // namespace OpenMS

#endif // OPENMS_METADATA_PRECURSOR_H