mzcborprecursorfinder.h

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/**
 * \file pappsomspp/core/processing/cbor/mzcbor/copyreplace/mzcborprecursorfinder.h
 * \date 2/10/2026
 * \author Olivier Langella
 * \brief read mzcbor stream or file, process it and write processed mzcbor output
 */
 
/*******************************************************************************
 * Copyright (c) 2026 Olivier Langella <Olivier.Langella@cnrs.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 "mzcborcopyreplacebase.h"
#include "pappsomspp/core/processing/cbor/mzcbor/copyreplace/qcborspectrum.h"
#include "pappsomspp/core/trace/trace.h"
#include <cstddef>
#include <cstdint>
#include <deque>
#include <limits>
#include <qcontainerfwd.h>
#include <qjsonobject.h>
#include <vector>
namespace pappso
{
namespace cbor
{
namespace mzcbor
{
/**
 * @brief base class to transform mzCBOR stream in a new mzCBOR output stream
 *
 * ensures stream read on regular file or any readable device
 */
class PMSPP_LIB_DECL MzcborPrecursorFinder : public MzcborCopyReplaceBase
{
  public:
  /**
   * Default constructor
   */
  MzcborPrecursorFinder(CborStreamWriter *cbor_output_p, const QJsonObject &json_params);
 
  /**
   * Destructor
   */
  virtual ~MzcborPrecursorFinder();
 
  void setRetentionTimeRangeInSeconds(double rt_start, double rt_stop);
 
 
  protected:
  virtual void processQcborSpectrum(SpectrumTube &spectrum_tube, QcborSpectrum &cbor_spectrum);
  std::vector<QcborSpectrum> findPotentialPrecursorIonData(const QcborSpectrum &ms1_spectrum,
                                                           const QcborSpectrum &ms2_spectrum,
                                                           const QcborSpectrumPrecursor &precursor);
 
  private:
  QJsonValue getParameterValue(const QString &name) const;
 
  private:
  QJsonObject m_parameters;
  std::vector<std::int8_t> m_potentialPrecursorChargeStateList = {1, 2, 3};
  double m_rtStart                                             = 0;
  double m_rtStop                                              = std::numeric_limits<double>::max();
 
  std::map<QString, QString> m_ms1idOldToNew;
  std::deque<std::pair<QString, QcborSpectrum>> m_spectrumMs1List;
  std::size_t m_maxSpectrumMs1ListSize = 100;
  pappso::PrecisionPtr m_ms2Tolerance;
  pappso::PrecisionPtr m_ms1Tolerance;
  double m_intensityRatioThreshold   = 0.3;
  std::size_t m_minimumComplementIon = 1;
  double m_ms2minimumMz              = 150;
  std::size_t m_ms2nMostIntense      = 60;
 
  std::deque<std::pair<const QcborSpectrum *, TraceSPtr>> m_cacheMs1Trace;
};
} // namespace mzcbor
} // namespace cbor
} // namespace pappso