qualifiedmassspectrum.h

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/*******************************************************************************
 * Copyright (c) 2015 Olivier Langella <olivier.langella@u-psud.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms++ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
#pragma once
 
/////////////////////// StdLib includes
#include <memory>
 
 
/////////////////////// Qt includes
 
 
/////////////////////// Local includes
#include "../exportinmportconfig.h"
#include "../types.h"
#include "massspectrum.h"
#include "massspectrumid.h"
 
 
namespace pappso
{
 
// Forward declaration.
class QualifiedMassSpectrum;
 
typedef std::shared_ptr<QualifiedMassSpectrum> QualifiedMassSpectrumSPtr;
typedef std::shared_ptr<const QualifiedMassSpectrum>
  QualifiedMassSpectrumCstSPtr;
 
enum class QualifiedMassSpectrumParameter
{
 
  OneOverK0,      ///< 1/kO of a simple scan
  OneOverK0begin, ///< 1/kO of first acquisition for composite pasef MS/MS
                  ///< spectrum
  OneOverK0end, ///< 1/k0 of last acquisition for composite pasef MS/MS spectrum
  IsolationMz,  ///< isolation window
  IsolationWidth,       ///< isolation window width
  CollisionEnergy,      ///< Bruker's Tims tof collision energy
  BrukerPrecursorIndex, ///< Bruker's Tims tof precursor index
  last
};
 
//! Class representing a fully specified mass spectrum.
/*!
 * The member data that qualify the MassSpectrum \c msp_massSpectrum member
 * allow to unambiguously characterize the mass spectrum.
 * \sa MassSpectrum
 */
class PMSPP_LIB_DECL QualifiedMassSpectrum
{
  public:
  QualifiedMassSpectrum();
  QualifiedMassSpectrum(const MassSpectrumId &id);
  QualifiedMassSpectrum(MassSpectrumSPtr mass_spectrum_SPtr);
  QualifiedMassSpectrum(const QualifiedMassSpectrum &other);
  ~QualifiedMassSpectrum();
 
 
  QualifiedMassSpectrumSPtr makeQualifiedMassSpectrumSPtr() const;
  QualifiedMassSpectrumCstSPtr makeQualifiedMassSpectrumCstSPtr() const;
 
  void setMassSpectrumId(const MassSpectrumId &iD);
  const MassSpectrumId &getMassSpectrumId() const;
 
  void setMassSpectrumSPtr(MassSpectrumSPtr massSpectrum);
  MassSpectrumSPtr getMassSpectrumSPtr() const;
  MassSpectrumCstSPtr getMassSpectrumCstSPtr() const;
 
  void setEmptyMassSpectrum(bool is_empty_mass_spectrum);
  bool isEmptyMassSpectrum() const;
 
  void setPrecursorCharge(uint precursor_charge);
  uint getPrecursorCharge() const;
 
  void setPrecursorMz(pappso_double precursor_mz);
  pappso_double getPrecursorMz() const;
 
  void setMsLevel(uint ms_level);
  uint getMsLevel() const;
 
  void setPrecursorSpectrumIndex(std::size_t precursor_scan_num);
  std::size_t getPrecursorSpectrumIndex() const;
 
  void setPrecursorNativeId(const QString &native_id);
  const QString &getPrecursorNativeId() const;
 
  void setRtInSeconds(pappso_double rt);
  pappso_double getRtInSeconds() const;
  pappso_double getRtInMinutes() const;
 
  void setDtInMilliSeconds(pappso_double rt);
  pappso_double getDtInMilliSeconds() const;
 
  void setPrecursorIntensity(pappso_double intensity);
  pappso_double getPrecursorIntensity() const;
 
  void setParameterValue(QualifiedMassSpectrumParameter parameter,
                         const QVariant &value);
  const QVariant
  getParameterValue(QualifiedMassSpectrumParameter parameter) const;
 
  std::size_t size() const;
 
  QString toString() const;
 
  protected:
  //! Shared pointer to the mass spectrum.
  MassSpectrumSPtr msp_massSpectrum = nullptr;
 
  //! Id of the mass spectrum.
  MassSpectrumId m_massSpectrumId;
 
  bool m_isEmptyMassSpectrum = false;
 
  //! Mass spectrometry level of this mass spectrum.
  unsigned int m_msLevel = 0;
 
  //! Retention time (in seconds) at which this mass spectrum was acquired.
  pappso_double m_rt = -1;
 
  //! Drift time (in milliseconds) at which this mass spectrum was acquired.
  pappso_double m_dt = -1;
 
  //! Index of the spectrum of the precusor ion that was fragmented to yield
  // this mass spectrum.
  std::size_t m_precursorSpectrumIndex =
    std::numeric_limits<std::size_t>::max();
 
  //! Native XML id of the spectrum relative to the mz data native file
  QString m_precursorNativeId;
 
  //! m/z ratio of the precursor that was fragmented to yield this mass
  //! spectrum.
  pappso_double m_precursorMz = std::numeric_limits<double>::max();
 
  //! Charge of the precursor that was fragmented to yield this mass spectrum.
  unsigned int m_precursorCharge = std::numeric_limits<unsigned int>::max();
 
  //! Intensity of the precursor that was fragmented to yield this mass
  //! spectrum.
  pappso_double m_precursorIntensity = std::numeric_limits<double>::max();
 
  //! map containing any parameter value for this spectrum
  std::map<QualifiedMassSpectrumParameter, QVariant> m_params;
};
 
 
} // namespace pappso