mzcborspectrumcollectionreader.h

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/**
 * \file pappsomspp/core/processing/cbor/mzcbor/mzcborspectrumcollectionreader.h
 * \date 22/11/2025
 * \author Olivier Langella
 * \brief read mzcbor for spectrum collection handler
 */
 
/*******************************************************************************
 * Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
 *
 * This file is part of PAPPSOms-tools.
 *
 *     PAPPSOms-tools 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-tools 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-tools.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
 
#pragma once
 
#include "pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h"
#include "pappsomspp/core/msrun/spectrumcollectionhandlerinterface.h"
#include "pappsomspp/core/msrun/msrunreadconfig.h"
#include "pappsomspp/core/msrun/msrunid.h"
 
namespace pappso
{
namespace cbor
{
namespace mzcbor
{
/**
 * @todo write docs
 */
class PMSPP_LIB_DECL MzcborSpectrumCollectionReader : public MzcborReaderBase
{
  public:
  /**
   * Default constructor
   */
  MzcborSpectrumCollectionReader(const MsRunReadConfig &config,
                                 SpectrumCollectionHandlerInterface &handler);
 
  /**
   * Destructor
   */
  virtual ~MzcborSpectrumCollectionReader();
 
  void setMsRunId(const MsRunIdCstSPtr &msrun_id);
  void
  setNativeId2SpectrumIndexMapPtr(const std::map<QString, std::size_t> *nativeId2SpectrumIndexMap);
 
  protected:
  /** @brief read only the targeted msrun
   */
  virtual void readMsrun() override;
 
 
  /** @brief only the spectrum list of targeted msrun, then stop parsing
   */
  void readSpectrumListAndLeave();
 
  /** @brief read each spectrum in the targeted msrun (msrunId)
   */
  void readSpectrum(std::size_t index_count, bool want_binary_data);
 
 
  std::map<QString, CvParam> readScan();
 
  private:
  const MsRunReadConfig &m_msRunReadConfig;
  SpectrumCollectionHandlerInterface &m_SpectrumCollectionHandlerInterface;
  MsRunIdCstSPtr mcsp_msRunId;
  QString m_xmlMzMlRunId;
 
  const std::map<QString, std::size_t> *mp_nativeId2SpectrumIndexMap = nullptr;
};
} // namespace mzcbor
} // namespace cbor
} // namespace pappso