base class to transform mzCBOR stream in a new mzCBOR output stream More...

#include <mzcborprecursorfinder.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborPrecursorFinder:

Public Member Functions
	MzcborPrecursorFinder (CborStreamWriter *cbor_output_p, const QJsonObject &json_params)
virtual	~MzcborPrecursorFinder ()
void	setRetentionTimeRangeInSeconds (double rt_start, double rt_stop)
Public Member Functions inherited from pappso::cbor::mzcbor::MzcborCopyReplaceBase
	MzcborCopyReplaceBase (CborStreamWriter *cbor_output_p, const QString &operation)
virtual	~MzcborCopyReplaceBase ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR file
virtual void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR from any device (memory buffer or else)
virtual void	close ()
	convenient function to clean pointer before leaving
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
virtual void	processQcborSpectrum (SpectrumTube &spectrum_tube, QcborSpectrum &cbor_spectrum)
std::vector< QcborSpectrum >	findPotentialPrecursorIonData (const QcborSpectrum &ms1_spectrum, const QcborSpectrum &ms2_spectrum, const QcborSpectrumPrecursor &precursor)
Protected Member Functions inherited from pappso::cbor::mzcbor::MzcborCopyReplaceBase
void	readRoot (pappso::UiMonitorInterface &monitor)
void	readCbor (pappso::UiMonitorInterface &monitor)
void	readRun (pappso::UiMonitorInterface &monitor)
void	readSpectrumList (pappso::UiMonitorInterface &monitor)
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

Private Member Functions
QJsonValue	getParameterValue (const QString &name) const

Private Attributes
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

Additional Inherited Members
Protected Attributes inherited from pappso::cbor::mzcbor::MzcborCopyReplaceBase
bool	m_stopParsing = false
CborStreamWriter *	mp_cborOutput
QString	m_operation
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader *	mpa_cborReader = nullptr
QString	m_expectedString
QByteArray	m_data

Detailed Description

base class to transform mzCBOR stream in a new mzCBOR output stream

ensures stream read on regular file or any readable device

Definition at line 51 of file mzcborprecursorfinder.h.

Constructor & Destructor Documentation

◆ MzcborPrecursorFinder()

pappso::cbor::mzcbor::MzcborPrecursorFinder::MzcborPrecursorFinder	(	CborStreamWriter *	cbor_output_p,
		const QJsonObject &	json_params )

Default constructor

Definition at line 54 of file mzcborprecursorfinder.cpp.

  : MzcborCopyReplaceBase(cbor_output_p, "precursor_finder")
{
  m_parameters = json_params;
 
 
  if(getParameterValue("ms1_tolerance_unit").toString() == "dalton")
    {
      m_ms1Tolerance =
        pappso::PrecisionFactory::getDaltonInstance(getParameterValue("ms1_tolerance").toDouble());
    }
  else if(getParameterValue("ms1_tolerance_unit").toString() == "ppm")
    {
      m_ms1Tolerance =
        pappso::PrecisionFactory::getPpmInstance(getParameterValue("ms1_tolerance").toDouble());
    }
  else
    {
      throw pappso::ExceptionNotFound(QObject::tr("ms1_tolerance_unit %1 not known")
                                        .arg(getParameterValue("ms1_tolerance_unit").toString()));
    }
 
  if(getParameterValue("ms2_tolerance_unit").toString() == "dalton")
    {
      m_ms2Tolerance =
        pappso::PrecisionFactory::getDaltonInstance(getParameterValue("ms2_tolerance").toDouble());
    }
  else if(getParameterValue("ms2_tolerance_unit").toString() == "ppm")
    {
      m_ms2Tolerance =
        pappso::PrecisionFactory::getPpmInstance(getParameterValue("ms2_tolerance").toDouble());
    }
  else
    {
      throw pappso::ExceptionNotFound(QObject::tr("ms2_tolerance_unit %1 not known")
                                        .arg(getParameterValue("ms2_tolerance_unit").toString()));
    }
 
  m_minimumComplementIon    = getParameterValue("minimum_complement_ion").toInt();
  m_intensityRatioThreshold = getParameterValue("intensity_ratio_threshold").toDouble();
 
  m_ms2nMostIntense = getParameterValue("ms2_max_peaks").toInt();
 
  m_potentialPrecursorChargeStateList.clear();
  QJsonArray charge_arr = getParameterValue("potential_charge_states").toArray();
  for(auto charge : charge_arr)
    {
      m_potentialPrecursorChargeStateList.push_back(charge.toInt());
    }
}

References pappso::cbor::mzcbor::MzcborCopyReplaceBase::MzcborCopyReplaceBase(), pappso::PrecisionFactory::getDaltonInstance(), getParameterValue(), pappso::PrecisionFactory::getPpmInstance(), m_intensityRatioThreshold, m_minimumComplementIon, m_ms1Tolerance, m_ms2nMostIntense, m_ms2Tolerance, m_parameters, and m_potentialPrecursorChargeStateList.

◆ ~MzcborPrecursorFinder()

pappso::cbor::mzcbor::MzcborPrecursorFinder::~MzcborPrecursorFinder ( )

virtual

Destructor

Definition at line 105 of file mzcborprecursorfinder.cpp.

106{

107}

Member Function Documentation

◆ findPotentialPrecursorIonData()

std::vector< QcborSpectrum > pappso::cbor::mzcbor::MzcborPrecursorFinder::findPotentialPrecursorIonData	(	const QcborSpectrum &	ms1_spectrum,
		const QcborSpectrum &	ms2_spectrum,
		const QcborSpectrumPrecursor &	precursor )

protected

Definition at line 251 of file mzcborprecursorfinder.cpp.

{
 
  pappso::TraceSPtr ms1_trace_sp;
 
  auto it_cache_ms1_trace =
    std::find_if(m_cacheMs1Trace.cbegin(),
                 m_cacheMs1Trace.cend(),
                 [ms1_spectrum](const auto &item) { return item.first == &ms1_spectrum; });
 
  if(it_cache_ms1_trace == m_cacheMs1Trace.end())
    {
      ms1_trace_sp = std::make_shared<Trace>();
      ms1_spectrum.decodeTrace(*ms1_trace_sp.get());
      m_cacheMs1Trace.push_back({&ms1_spectrum, ms1_trace_sp});
      if(m_cacheMs1Trace.size() > m_maxSpectrumMs1ListSize)
        {
          m_cacheMs1Trace.pop_front();
        }
    }
  else
    {
      ms1_trace_sp = it_cache_ms1_trace->second;
    }
  pappso::Trace ms1_trace(*ms1_trace_sp.get());
  pappso::Trace ms2_trace;
  ms2_spectrum.decodeTrace(ms2_trace);
 
  // MS2 filters
  pappso::FilterChargeDeconvolution(m_ms2Tolerance).filter(ms2_trace);
  pappso::FilterResampleKeepGreater(m_ms2minimumMz).filter(ms2_trace);
  pappso::FilterGreatestY(m_ms2nMostIntense).filter(ms2_trace);
  // END MS2 filters
 
 
  std::vector<QcborSpectrum> potential_precursors;
  double precursor_intensity                 = 0;
  std::vector<SelectedIon> selected_ion_list = precursor.getSelectedIonList();
  if(selected_ion_list.size() != 1)
    {
      throw pappso::PappsoException("ERROR: selected_ion_list.size() != 1");
    }
  bool is_ok          = false;
  precursor_intensity = selected_ion_list.at(0).getIntensity(&is_ok);
  if(!is_ok)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: precursor intensity not found in spectrum %1")
          .arg(ms2_spectrum.getId()));
      precursor_intensity = 0;
    }
 
  qDebug();
  FilterMs1WindowSelection window(precursor);
  qDebug();
  window.filter(ms1_trace);
  pappso::FilterHighPass(precursor_intensity * m_intensityRatioThreshold).filter(ms1_trace);
 
  for(const pappso::DataPoint &data_point : ms1_trace)
    {
      for(int charge : m_potentialPrecursorChargeStateList)
        {
          double intensity = data_point.y;
          double mz        = data_point.x;
 
          FilterComplement complement(mz * (double)charge, m_ms2Tolerance);
          pappso::Trace ms2(ms2_trace);
          complement.filter(ms2);
          if(ms2.size() > (std::size_t)m_minimumComplementIon)
            {
              QcborSpectrum new_ms2(ms2_spectrum);
 
              QcborSpectrumPrecursor copy_precursor(precursor);
              copy_precursor.setSelectedIon(mz, intensity, charge);
 
              std::vector<QcborSpectrumPrecursor> precursor_list;
              precursor_list.push_back(copy_precursor);
 
              qDebug() << copy_precursor;
              new_ms2.setPrecursorList(precursor_list);
 
              qDebug() << new_ms2;
              potential_precursors.push_back(new_ms2);
            }
        }
    }
 
 
  return potential_precursors;
}

References pappso::cbor::mzcbor::QcborSpectrum::decodeTrace(), FilterComplement::filter(), FilterMs1WindowSelection::filter(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterGreatestY::filter(), pappso::FilterHighPass::filter(), pappso::FilterResampleKeepGreater::filter(), pappso::cbor::mzcbor::QcborSpectrum::getId(), pappso::cbor::mzcbor::QcborSpectrumPrecursor::getSelectedIonList(), m_cacheMs1Trace, m_intensityRatioThreshold, m_maxSpectrumMs1ListSize, m_minimumComplementIon, m_ms2minimumMz, m_ms2nMostIntense, m_ms2Tolerance, m_potentialPrecursorChargeStateList, pappso::cbor::mzcbor::QcborSpectrum::setPrecursorList(), and pappso::cbor::mzcbor::QcborSpectrumPrecursor::setSelectedIon().

Referenced by processQcborSpectrum().

◆ getParameterValue()

QJsonValue pappso::cbor::mzcbor::MzcborPrecursorFinder::getParameterValue ( const QString & name ) const

private

Definition at line 111 of file mzcborprecursorfinder.cpp.

{
  QJsonValue value;
  if(m_parameters.contains(name))
    {
      return m_parameters.value(name);
    }
  else
    {
      throw pappso::ExceptionNotFound(QObject::tr("parameter %1 not defined precursor finder JSON "
                                                  "parameters")
                                        .arg(name));
    }
  return value;
}

References m_parameters.

Referenced by MzcborPrecursorFinder().

◆ processQcborSpectrum()

void pappso::cbor::mzcbor::MzcborPrecursorFinder::processQcborSpectrum	(	SpectrumTube &	spectrum_tube,
		QcborSpectrum &	cbor_spectrum )

protectedvirtual

Reimplemented from pappso::cbor::mzcbor::MzcborCopyReplaceBase.

Definition at line 134 of file mzcborprecursorfinder.cpp.

{
  if(cbor_spectrum.getMsLevel() == 1)
    {
      QString old_ms1_id = cbor_spectrum.getId();
      m_spectrumMs1List.push_back({old_ms1_id, cbor_spectrum});
      if(m_spectrumMs1List.size() > m_maxSpectrumMs1ListSize)
        {
          m_spectrumMs1List.pop_front();
        }
      QString new_ms1_id = spectrum_tube.push_back(cbor_spectrum);
 
      m_ms1idOldToNew.insert({old_ms1_id, new_ms1_id});
    }
  else
    {
      double rt = cbor_spectrum.getRetentionTimeInSeconds();
      if((rt > m_rtStart) && (rt < m_rtStop))
        {
 
          std::vector<QcborSpectrumPrecursor> precursor_list = cbor_spectrum.getPrecursorList();
          if(precursor_list.size() == 1)
            {
              //"spectrumRef":"controllerType=0 controllerNumber=1 scan=2711",
              QString spectrum_ref = precursor_list.at(0).getSpectrumRef();
 
              auto it_ms1 =
                std::find_if(m_spectrumMs1List.begin(),
                             m_spectrumMs1List.end(),
                             [spectrum_ref](const std::pair<QString, QcborSpectrum> &pair) {
                               return pair.first == spectrum_ref;
                             });
              if(it_ms1 != m_spectrumMs1List.end())
                {
 
                  // replace with new spectrum_ref
                  QString new_spectrum_ref = m_ms1idOldToNew.at(spectrum_ref);
 
 
                  QcborSpectrumPrecursor precursor = precursor_list.at(0);
 
                  pappso::MzRange original_ms1_peak_range(
                    precursor.getSelectedIonList().at(0).getMz(), m_ms1Tolerance);
                  // qWarning() << "original precursor charge="
                  //            << precursor.getSelectedIonList().at(0).getChargeState();
                  precursor.setSpectrumRef(new_spectrum_ref);
                  std::vector<QcborSpectrumPrecursor> new_precursor_list;
                  new_precursor_list.push_back(precursor);
                  cbor_spectrum.setPrecursorList(new_precursor_list);
 
 
                  std::vector<QcborSpectrum> spectrum_list =
                    findPotentialPrecursorIonData(it_ms1->second, cbor_spectrum, precursor);
 
                  int i                         = 0;
                  bool report_original_spectrum = true;
                  for(QcborSpectrum &spectrum : spectrum_list)
                    {
                      QcborSpectrumPrecursor candidate_precursor =
                        spectrum.getPrecursorList().at(0);
 
                      // qWarning() << "candidate_precursor charge="
                      //            <<
                      //            candidate_precursor.getSelectedIonList().at(0).getChargeState();
                      if(candidate_precursor.getSelectedIonList().at(0).getChargeState() ==
                         precursor.getSelectedIonList().at(0).getChargeState())
                        {
                          if(original_ms1_peak_range.contains(
                               candidate_precursor.getSelectedIonList().at(0).getMz()))
                            {
                              report_original_spectrum = false;
                            }
                        }
 
                      QString new_id = spectrum_tube.push_back(spectrum);
                      // qWarning() << " id=" << new_id << " candidate_precursor charge="
                      //            << spectrum.getPrecursorList()
                      //                 .at(0)
                      //                 .getSelectedIonList()
                      //                 .at(0)
                      //                 .getChargeState();
                      i++;
                    }
                  if(report_original_spectrum)
                    {
                      QString new_id = spectrum_tube.push_back(cbor_spectrum);
                      // qWarning() << "orig id=" << new_id
                      //            << " spectrum_list.size()=" << spectrum_list.size()
                      //            << " candidate_precursor charge="
                      //            << cbor_spectrum.getPrecursorList()
                      //                 .at(0)
                      //                 .getSelectedIonList()
                      //                 .at(0)
                      //                 .getChargeState();
                    }
                }
              else
                {
                  throw pappso::ExceptionNotFound(
                    QObject::tr("ERROR: precursor ref %1 not found for current spectrum %2")
                      .arg(spectrum_ref)
                      .arg(cbor_spectrum.getId()));
                }
            }
          else
            {
              qDebug() << cbor_spectrum.getId();
              throw pappso::PappsoException(
                QObject::tr("ERROR: precursor_list.size() != 1 (%1)").arg(precursor_list.size()));
            }
        }
    }
}

◆ setRetentionTimeRangeInSeconds()

void pappso::cbor::mzcbor::MzcborPrecursorFinder::setRetentionTimeRangeInSeconds	(	double	rt_start,
		double	rt_stop )

Definition at line 128 of file mzcborprecursorfinder.cpp.

{
  m_rtStart = rt_start;
  m_rtStop  = rt_stop;
}

References m_rtStart, and m_rtStop.

Member Data Documentation

◆ m_cacheMs1Trace

std::deque<std::pair<const QcborSpectrum *, TraceSPtr> > pappso::cbor::mzcbor::MzcborPrecursorFinder::m_cacheMs1Trace

private

Definition at line 92 of file mzcborprecursorfinder.h.

Referenced by findPotentialPrecursorIonData().

◆ m_intensityRatioThreshold

double pappso::cbor::mzcbor::MzcborPrecursorFinder::m_intensityRatioThreshold = 0.3

private

Definition at line 87 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and findPotentialPrecursorIonData().

◆ m_maxSpectrumMs1ListSize

std::size_t pappso::cbor::mzcbor::MzcborPrecursorFinder::m_maxSpectrumMs1ListSize = 100

private

Definition at line 84 of file mzcborprecursorfinder.h.

Referenced by findPotentialPrecursorIonData(), and processQcborSpectrum().

◆ m_minimumComplementIon

std::size_t pappso::cbor::mzcbor::MzcborPrecursorFinder::m_minimumComplementIon = 1

private

Definition at line 88 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and findPotentialPrecursorIonData().

◆ m_ms1idOldToNew

std::map<QString, QString> pappso::cbor::mzcbor::MzcborPrecursorFinder::m_ms1idOldToNew

private

Definition at line 82 of file mzcborprecursorfinder.h.

Referenced by processQcborSpectrum().

◆ m_ms1Tolerance

pappso::PrecisionPtr pappso::cbor::mzcbor::MzcborPrecursorFinder::m_ms1Tolerance

private

Definition at line 86 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and processQcborSpectrum().

◆ m_ms2minimumMz

double pappso::cbor::mzcbor::MzcborPrecursorFinder::m_ms2minimumMz = 150

private

Definition at line 89 of file mzcborprecursorfinder.h.

Referenced by findPotentialPrecursorIonData().

◆ m_ms2nMostIntense

std::size_t pappso::cbor::mzcbor::MzcborPrecursorFinder::m_ms2nMostIntense = 60

private

Definition at line 90 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and findPotentialPrecursorIonData().

◆ m_ms2Tolerance

pappso::PrecisionPtr pappso::cbor::mzcbor::MzcborPrecursorFinder::m_ms2Tolerance

private

Definition at line 85 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and findPotentialPrecursorIonData().

◆ m_parameters

QJsonObject pappso::cbor::mzcbor::MzcborPrecursorFinder::m_parameters

private

Definition at line 77 of file mzcborprecursorfinder.h.

Referenced by MzcborPrecursorFinder(), and getParameterValue().

◆ m_potentialPrecursorChargeStateList

std::vector<std::int8_t> pappso::cbor::mzcbor::MzcborPrecursorFinder::m_potentialPrecursorChargeStateList = {1, 2, 3}

private

Definition at line 78 of file mzcborprecursorfinder.h.

78{1, 2, 3};

Referenced by MzcborPrecursorFinder(), and findPotentialPrecursorIonData().

◆ m_rtStart

double pappso::cbor::mzcbor::MzcborPrecursorFinder::m_rtStart = 0

private

Definition at line 79 of file mzcborprecursorfinder.h.

Referenced by processQcborSpectrum(), and setRetentionTimeRangeInSeconds().

◆ m_rtStop

double pappso::cbor::mzcbor::MzcborPrecursorFinder::m_rtStop = std::numeric_limits<double>::max()

private

Definition at line 80 of file mzcborprecursorfinder.h.

Referenced by processQcborSpectrum(), and setRetentionTimeRangeInSeconds().

◆ m_spectrumMs1List

std::deque<std::pair<QString, QcborSpectrum> > pappso::cbor::mzcbor::MzcborPrecursorFinder::m_spectrumMs1List

private

Definition at line 83 of file mzcborprecursorfinder.h.

Referenced by processQcborSpectrum().

The documentation for this class was generated from the following files:

pappsomspp/core/processing/cbor/mzcbor/copyreplace/mzcborprecursorfinder.h
pappsomspp/core/processing/cbor/mzcbor/copyreplace/mzcborprecursorfinder.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzcborPrecursorFinder()

◆ ~MzcborPrecursorFinder()

Member Function Documentation

◆ findPotentialPrecursorIonData()

◆ getParameterValue()

◆ processQcborSpectrum()

◆ setRetentionTimeRangeInSeconds()

Member Data Documentation

◆ m_cacheMs1Trace

◆ m_intensityRatioThreshold

◆ m_maxSpectrumMs1ListSize

◆ m_minimumComplementIon

◆ m_ms1idOldToNew

◆ m_ms1Tolerance

◆ m_ms2minimumMz

◆ m_ms2nMostIntense

◆ m_ms2Tolerance

◆ m_parameters

◆ m_potentialPrecursorChargeStateList

◆ m_rtStart

◆ m_rtStop

◆ m_spectrumMs1List