msrunxicextractor.h

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/**
 * \file pappsomspp/xicextractor/private/msrunxicextractorpwiz.h
 * \date 07/05/2018
 * \author Olivier Langella
 * \brief simple proteowizard based XIC extractor
 */
 
/*******************************************************************************
 * 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 "../msrunxicextractorinterface.h"
 
class MsRunXicExtractorFactory;
 
namespace pappso
{
 
 
class MsRunXicExtractor : public MsRunXicExtractorInterface
{
  friend MsRunXicExtractorFactory;
 
  public:
  MsRunXicExtractor(const MsRunXicExtractor &other);
  virtual ~MsRunXicExtractor();
 
  protected:
  MsRunXicExtractor(MsRunReaderSPtr &msrun_reader);
 
  virtual void protectedExtractXicCoordSPtrList(
    UiMonitorInterface &monitor,
    std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
    std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end) override;
 
 
  protected:
  struct MsRunXicExtractorPoints
  {
    std::size_t spectrum_index;
    double rt;
  };
 
  /** @brief class to read retention time points of MsRun
   */
  class MsRunXicExtractorReadPoints : public SpectrumCollectionHandlerInterface
  {
    private:
    std::vector<MsRunXicExtractorPoints> &m_msrun_points;
 
    public:
    MsRunXicExtractorReadPoints(std::vector<MsRunXicExtractorPoints> &msrun_points)
      : m_msrun_points(msrun_points) {};
 
    virtual void
    setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override
    {
      if(spectrum.getMsLevel() == 1)
        {
          qDebug() << spectrum.getMassSpectrumId().getSpectrumIndex();
          m_msrun_points.push_back(
            {spectrum.getMassSpectrumId().getSpectrumIndex(), spectrum.getRtInSeconds()});
        }
    }
    virtual bool
    needPeakList() const override
    {
      return false;
    }
    virtual void
    loadingEnded() override
    {
    }
  };
 
 
  protected:
  std::vector<MsRunXicExtractorPoints> m_msrun_points;
 
  private:
  void extractOneXicCoord(XicCoord &xic_coord);
};
 
 
} // namespace pappso