#include <msrunxicextractor.h>

Inheritance diagram for pappso::MsRunXicExtractor:

Classes
struct	MsRunXicExtractorPoints
class	MsRunXicExtractorReadPoints
	class to read retention time points of MsRun More...

Public Member Functions
	MsRunXicExtractor (const MsRunXicExtractor &other)
virtual	~MsRunXicExtractor ()
Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (Enums::XicExtractMethod method)
	set the XIC extraction method
void	setRetentionTimeAroundTarget (double range_in_seconds)
	set the retention time range in seconds around the target rt
virtual void	extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
	extract a list of XIC given a list of xic coordinates to extract
virtual void	extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
	multithreaded XIC extraction
const MsRunIdCstSPtr &	getMsRunId () const
const MsRunReaderSPtr &	getMsRunReaderSPtr () const
	get the msrunreader currently used for XIC extraction
void	setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
	filter interface to apply just after XIC extration on each trace

Protected Member Functions
	MsRunXicExtractor (MsRunReaderSPtr &msrun_reader)
virtual void	getXicFromPwizMSDataFile (std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)
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 Member Functions inherited from pappso::MsRunXicExtractorInterface
	MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
	constructor is private, use the MsRunXicExtractorFactory
	MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
virtual	~MsRunXicExtractorInterface ()
virtual void	postExtractionProcess (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)
	possible post extraction process, eventually trace filters

Protected Attributes
std::vector< MsRunXicExtractorPoints >	m_msrun_points
Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr	msp_msrun_reader
Enums::XicExtractMethod	m_xicExtractMethod = Enums::XicExtractMethod::max
double	m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
pappso::FilterInterfaceCstSPtr	mcsp_postExtractionTraceFilter = nullptr

Private Member Functions
void	extractOneXicCoord (XicCoord &xic_coord)

Private Attributes
friend	MsRunXicExtractorFactory

Detailed Description

Definition at line 42 of file msrunxicextractor.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractor() [1/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( const MsRunXicExtractor & other )

Definition at line 73 of file msrunxicextractor.cpp.

  : MsRunXicExtractorInterface(other)
{
  m_msrun_points = other.m_msrun_points;
}

References MsRunXicExtractor(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface(), and m_msrun_points.

Referenced by MsRunXicExtractor(), pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), and pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk().

◆ ~MsRunXicExtractor()

pappso::MsRunXicExtractor::~MsRunXicExtractor ( )

virtual

Definition at line 68 of file msrunxicextractor.cpp.

69{

70}

◆ MsRunXicExtractor() [2/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( MsRunReaderSPtr & msrun_reader )

protected

Definition at line 43 of file msrunxicextractor.cpp.

  : pappso::MsRunXicExtractorInterface(msrun_reader)
{
 
  MsRunXicExtractorReadPoints get_msrun_points(m_msrun_points);
 
 
  pappso::MsRunReadConfig config;
  config.setNeedPeakList(true);
  config.setMsLevels({1});
 
  msp_msrun_reader.get()->readSpectrumCollection2(config, get_msrun_points);
 
  std::sort(
    m_msrun_points.begin(),
    m_msrun_points.end(),
    [](const MsRunXicExtractorPoints &a, const MsRunXicExtractorPoints &b) { return a.rt < b.rt; });
 
 
  if(m_msrun_points.size() == 0)
    {
      throw pappso::PappsoException(
        QObject::tr("error extracting XIC: no MS level 1 in data file"));
    }
}

References pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface(), pappso::a, pappso::b, m_msrun_points, pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::setNeedPeakList().

Member Function Documentation

◆ extractOneXicCoord()

void pappso::MsRunXicExtractor::extractOneXicCoord ( XicCoord & xic_coord )

private

Definition at line 106 of file msrunxicextractor.cpp.

{
  FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(), xic_coord.mzRange.upper());
  std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
 
  double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
  double rt_end   = xic_coord.rtTarget + m_retentionTimeAroundTarget;
 
 
  auto itpoints = m_msrun_points.begin();
 
  // find startint retention time :
  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
    {
      itpoints++;
    }
  MassSpectrumSPtr spectrum;
  DataPoint peak;
  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
    {
      spectrum = msp_msrun_reader.get()->massSpectrumSPtr(itpoints->spectrum_index);
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
      // << spectrum->size(); spectrum->debugPrintValues();
 
      qDebug() << " spectrum->size()=" << spectrum->size();
      keep_range.filter(*(spectrum.get()));
      qDebug() << " spectrum->size()=" << spectrum->size();
 
      peak.x = itpoints->rt;
 
      if(m_xicExtractMethod == Enums::XicExtractMethod::max)
        {
          peak.y = 0;
          if(spectrum->size() > 0)
            {
              peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
 
              qDebug() << " peak.y=" << peak.y << " spectrum->size()=" << spectrum->size();
            }
        }
      else
        {
          peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
        }
      msrunxic_sp->push_back(peak);
 
      itpoints++;
    }
}

References pappso::FilterResampleKeepXRange::filter(), pappso::MzRange::lower(), m_msrun_points, pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::Enums::max, pappso::maxYDataPoint(), pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::sumYTrace(), pappso::MzRange::upper(), pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.

Referenced by protectedExtractXicCoordSPtrList().

◆ getXicFromPwizMSDataFile()

void pappso::MsRunXicExtractor::getXicFromPwizMSDataFile	(	std::vector< Xic * > &	xic_list,
		const std::vector< MzRange > &	mass_range_list,
		pappso::pappso_double	rt_begin,
		pappso::pappso_double	rt_end )

protectedvirtual

Definition at line 157 of file msrunxicextractor.cpp.

{
  qDebug();
 
  std::vector<DataPoint> peak_for_mass;
  for(const MzRange &mass_range : mass_range_list)
    {
      peak_for_mass.push_back(DataPoint());
      qDebug() << " mass_range=" << mass_range.getMz();
    }
 
 
  qDebug();
 
  auto itpoints = m_msrun_points.begin();
 
  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
    {
      itpoints++;
    }
 
  MassSpectrumCstSPtr spectrum;
  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
    {
      spectrum = msp_msrun_reader.get()->massSpectrumCstSPtr(itpoints->spectrum_index);
 
      for(DataPoint &peak : peak_for_mass)
        {
          peak.x = itpoints->rt;
          peak.y = 0;
        }
 
 
      // iterate through the m/z-intensity pairs
      for(auto &&spectrum_point : *(spectrum.get()))
        {
          // qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz <<
          // " it->intensity" << it->intensity;
          for(std::size_t i = 0; i < mass_range_list.size(); i++)
            {
              if(mass_range_list[i].contains(spectrum_point.x))
                {
                  if(m_xicExtractMethod == Enums::XicExtractMethod::max)
                    {
                      if(peak_for_mass[i].y < spectrum_point.y)
                        {
                          peak_for_mass[i].y = spectrum_point.y;
                        }
                    }
                  else
                    {
                      peak_for_mass[i].y += spectrum_point.y;
                    }
                }
            }
        }
 
      for(std::size_t i = 0; i < mass_range_list.size(); i++)
        {
          // qDebug() << "getXicFromPwizMSDataFile push_back " <<
          // peak_for_mass[i].rt;
          xic_list[i]->push_back(peak_for_mass[i]);
        }
 
      itpoints++;
    }
 
 
  qDebug();
} // namespace pappso

References m_msrun_points, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::Enums::max, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and pappso::y.

◆ protectedExtractXicCoordSPtrList()

void pappso::MsRunXicExtractor::protectedExtractXicCoordSPtrList	(	UiMonitorInterface &	monitor,
		std::vector< XicCoordSPtr >::iterator	it_xic_coord_list_begin,
		std::vector< XicCoordSPtr >::iterator	it_xic_coord_list_end )

overrideprotectedvirtual

Implements pappso::MsRunXicExtractorInterface.

Reimplemented in pappso::MsRunXicExtractorDisk.

Definition at line 81 of file msrunxicextractor.cpp.

{
 
  // sort xic by mz:
  std::sort(it_xic_coord_list_begin, it_xic_coord_list_end, [](XicCoordSPtr &a, XicCoordSPtr &b) {
    return a.get()->rtTarget < b.get()->rtTarget;
  });
 
  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
    {
      // XicCoord *p_xic_coord = sp_xic_coord.get();
      extractOneXicCoord(*(it->get()));
      monitor.count();
      if(monitor.shouldIstop())
        {
          throw pappso::ExceptionInterrupted(QObject::tr("Xic extraction process interrupted"));
        }
    }
}

References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), extractOneXicCoord(), and pappso::UiMonitorInterface::shouldIstop().

Member Data Documentation

◆ m_msrun_points

std::vector<MsRunXicExtractorPoints> pappso::MsRunXicExtractor::m_msrun_points

protected

Definition at line 105 of file msrunxicextractor.h.

Referenced by MsRunXicExtractor(), MsRunXicExtractor(), extractOneXicCoord(), getXicFromPwizMSDataFile(), and pappso::MsRunXicExtractorDisk::serializeMsRun().

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractor::MsRunXicExtractorFactory

private

Definition at line 44 of file msrunxicextractor.h.

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

pappsomspp/core/xicextractor/private/msrunxicextractor.h
pappsomspp/core/xicextractor/private/msrunxicextractor.cpp

Classes

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Protected Member Functions

Protected Attributes

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Private Attributes