pwizmsrunreader.h

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/**
 * \file pappsomspp/msrun/private/pwizmsrunreader.h
 * \date 29/05/2018
 * \author Olivier Langella
 * \brief MSrun file reader base on proteowizard library
 */
 
/*******************************************************************************
 * Copyright (c) 2018 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/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
 *implementation
 ******************************************************************************/
 
 
#pragma once
 
#include <pwiz/data/msdata/MSData.hpp>
#include <pwiz/data/msdata/MSDataFile.hpp>
 
#include "../../types.h"
#include "pappsomspp/core/massspectrum/massspectrumid.h"
#include "pappsomspp/core/msfile/msfileaccessor.h"
 
 
namespace pappso
{
 
class PMSPP_LIB_DECL PwizMsRunReader : public MsRunReader
{
  friend class MsFileAccessor;
 
  public:
  PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
  virtual ~PwizMsRunReader();
 
  const pwiz::msdata::MSDataPtr getMsDataPtr() const;
 
  virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override;
  virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override;
 
  virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index,
                                                      bool want_binary_data = true) const override;
 
  virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
 
  virtual void readSpectrumCollection2(const MsRunReadConfig &config,
                                       SpectrumCollectionHandlerInterface &handler) override;
 
  virtual pappso::XicCoordSPtr
  newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index,
                                   pappso::PrecisionPtr precision) const override;
 
  virtual pappso::XicCoordSPtr
  newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum,
                                           pappso::PrecisionPtr precision) const override;
 
 
  virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
                                               unsigned int ms_level) override;
 
 
  virtual std::size_t spectrumListSize() const override;
 
  virtual bool hasScanNumbers() const override;
 
  virtual bool releaseDevice() override;
 
  virtual bool acquireDevice() override;
 
 
  /** @brief get OboPsiModTerm corresponding to the nativeID format format of mz
   * data
   */
  const OboPsiModTerm getOboPsiModTermNativeIDFormat() const;
 
  virtual std::size_t
  spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override;
 
  protected:
  virtual void
  readSpectrumCollectionWithMsrunReadConfig(const MsRunReadConfig &config,
                                            SpectrumCollectionHandlerInterface &handler);
 
  virtual void initialize() override;
  virtual bool accept(const QString &file_name) const override;
 
  bool processRetentionTime(pwiz::msdata::Spectrum *spectrum_p,
                            QualifiedMassSpectrum &qualified_mass_spectrum) const;
  bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p,
                        QualifiedMassSpectrum &qualified_mass_spectrum) const;
 
  QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(std::size_t spectrum_index,
                                                            bool want_binary_data,
                                                            bool &ok) const;
 
  QualifiedMassSpectrum
  qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId,
                                           pwiz::msdata::Spectrum *spectrum_p,
                                           bool want_binary_data,
                                           bool &ok) const;
 
  pwiz::msdata::SpectrumPtr getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list,
                                               std::size_t spectrum_index,
                                               bool want_binary_data) const;
 
  static std::string setGlobalLocaleToEnglish();
 
  static void setGlobalLocaleToCurrentOs(const std::string &environment_locale);
 
  virtual const OboPsiModTerm getOboPsiModTermInstrumentModelName() const override;
 
  void checkNativeId(const pwiz::msdata::Spectrum *pwiz_spectrum_ptr,
                     MassSpectrumId &mass_spectrum_id) const;
 
  protected:
  static QMutex m_mutex;
  pwiz::msdata::MSDataPtr msp_msData = nullptr;
 
 
  private:
  bool m_hasScanNumbers = false;
};
 
} // namespace pappso
 
 
// Q_DECLARE_METATYPE(pappso::PwizMsRunReader);
// extern int pwizMsRunReaderMetaTypeId;