qcborspectrumprecursor.cpp

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/**
 * \file pappsomspp/core/processing/cbor/mzcbor/copyreplace/qcborspectrumprecursor.cpp
 * \date 2/10/2026
 * \author Olivier Langella
 * \brief Low level CBOR map to store an mzCBOR Spectrum object
 *  */
 
/*******************************************************************************
 * 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/>.
 *
 ******************************************************************************/
 
 
#include "qcborspectrumprecursor.h"
#include "pappsomspp/core/exception/exceptionnotfound.h"
#include "pappsomspp/core/processing/cbor/mzcbor/precursor.h"
#include <QCborArray>
#include <qcborarray.h>
#include <qcbormap.h>
#include <qcborvalue.h>
#include <qlogging.h>
 
namespace pappso
{
namespace cbor
{
namespace mzcbor
{
QcborSpectrumPrecursor::QcborSpectrumPrecursor(const QCborMap &cbor_map) : QCborMap(cbor_map)
{
}
QcborSpectrumPrecursor::QcborSpectrumPrecursor(const QcborSpectrumPrecursor &other)
  : QCborMap(other)
{
}
QString
QcborSpectrumPrecursor::getSpectrumRef() const
{
  //"spectrumRef":"controllerType=0 controllerNumber=1 scan=2711",
  //
  auto it = constFind(QCborValue("spectrumRef"));
  if(it != end())
    {
      return it.value().toString();
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR: no spectrumRef in QcborSpectrumPrecursor"));
    }
}
 
void
QcborSpectrumPrecursor::setSpectrumRef(const QString &spectrum_ref)
{
  auto it = find(QCborValue("spectrumRef"));
  if(it != end())
    {
      insert(QCborValue("spectrumRef"), spectrum_ref);
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR: no spectrumRef in QcborSpectrumPrecursor"));
    }
}
 
 
IsolationWindow
QcborSpectrumPrecursor::getIsolationWindow() const
{
  auto it = constFind(QCborValue("isolationWindow"));
  if(it != end())
    {
      IsolationWindow isolation_window;
      isolation_window.fromQCborMap(it->toMap());
      return isolation_window;
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no isolationWindow in QcborSpectrumPrecursor"));
    }
}
 
void
QcborSpectrumPrecursor::setSelectedIon(double mz, double intensity, int charge)
{
  auto it = find(QCborValue("selectedIonList"));
  if(it != end())
    {
      QCborMap new_selected_ion_list;
      new_selected_ion_list.insert(QString("count"), 1);
 
      QCborMap new_selected_ion;
      // <cvParam cvRef="MS" accession="MS:1000041" value="3" name="charge state"/>
      QCborArray cv_param_list;
      QCborMap cv_param;
      cv_param.insert(QString("cvRef"), QCborValue("MS"));
      cv_param.insert(QString("accession"), QCborValue("MS:1000041"));
      cv_param.insert(QString("value"), QCborValue(charge));
      cv_param.insert(QString("name"), QCborValue("charge state"));
      cv_param_list.push_back(cv_param);
      // <cvParam cvRef="MS" accession="MS:1000042" value="248032.25" name="peak intensity"
      // unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
      //
      QCborMap cv_param_intensity;
      cv_param_intensity.insert(QString("cvRef"), QCborValue("MS"));
      cv_param_intensity.insert(QString("accession"), QCborValue("MS:1000042"));
      cv_param_intensity.insert(QString("value"), QCborValue(intensity));
      cv_param_intensity.insert(QString("name"), QCborValue("peak intensity"));
      cv_param_list.push_back(cv_param_intensity);
      // <cvParam
      // cvRef="MS" accession="MS:1000744" value="506.2513" name="selected ion m/z"
      // unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
      QCborMap cv_param_mz;
      cv_param_mz.insert(QString("cvRef"), QCborValue("MS"));
      cv_param_mz.insert(QString("accession"), QCborValue("MS:1000744"));
      cv_param_mz.insert(QString("value"), QCborValue(mz));
      cv_param_mz.insert(QString("name"), QCborValue("selected ion m/z"));
      cv_param_list.push_back(cv_param_mz);
 
      new_selected_ion.insert(QString("cvParam"), cv_param_list);
 
 
      QCborArray new_selected_ion_arr;
      new_selected_ion_arr.push_back(new_selected_ion);
 
 
      new_selected_ion_list.insert(QString("selectedIon"), new_selected_ion_arr);
      qDebug();
      // it.value() = new_selected_ion_list;
      insert(QCborValue("selectedIonList"), new_selected_ion_list);
      qDebug();
    }
 
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no selectedIonList in QcborSpectrumPrecursor"));
    }
}
std::vector<SelectedIon>
QcborSpectrumPrecursor::getSelectedIonList() const
{
  std::vector<SelectedIon> selected_ion_list;
  auto itout = constFind(QCborValue("selectedIonList"));
  if(itout != end())
    {
      auto it = itout.value().toMap().constFind(QCborValue("selectedIon"));
      if(it != end())
        {
          for(auto it_cv = it->toArray().cbegin(); it_cv != it->toArray().cend(); it_cv++)
            {
              SelectedIon precursor;
              precursor.fromQCborMap(it_cv->toMap());
              selected_ion_list.push_back(precursor);
            }
          return selected_ion_list;
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: no selectedIon array in QcborSpectrumPrecursor"));
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no selectedIonList in QcborSpectrumPrecursor"));
    }
}
} // namespace mzcbor
} // namespace cbor
} // namespace pappso