pappso::masschroq::MsRunPeptideList Class Reference

#include <msrunpeptidelist.h>

Public Member Functions
	MsRunPeptideList (MsRunSp msrun)
	MsRunPeptideList (const MsRunPeptideList &other)
virtual	~MsRunPeptideList ()
void	addPeptideSpectrumIndexObservation (PeptideSp peptide_sp, PeptideLabel *p_label, std::size_t spectrum_index, std::uint8_t charge)
void	addPeptideScanNumberObservation (PeptideSp peptide_sp, PeptideLabel *p_label, std::size_t spectrum_index, std::uint8_t charge)
void	quantify (const MsRunGroup *msrun_group_p, const QString &tmp_dir, pappso::UiMonitorInterface &m_uiMonitor, const QuantificationMethodSp &quantification_method)
void	quantifyMatchBetweenRun (const MsRunGroup *msrun_group_p, const std::vector< PeptideSp > &peptide_mbr_list, const QString &tmp_dir, pappso::UiMonitorInterface &m_uiMonitor, const QuantificationMethodSp &quantification_method)
const MsRunSp &	getMsRunSp () const
void	flushChromatogramTraces ()
void	clearMeasurements ()
	clear all measurements MBR or not Clearing measurements also removes every chromatogram
std::shared_ptr< pappso::MsRunRetentionTime< QString > > &	buildMsRunRetentionTimeSpOnPeptideObservations (const AlignmentMethodSp &alignment_method)
	build a retention time vector with seamarks using MS2 best intensities
void	collectPeptidePeakRetentionTime (const pappso::MsRunRetentionTime< QString > *msrun_retention_time_reference_p) const
	collect peak retention times collect all quantified peptides retention times and convert it to the reference time to store it for each peptides
void	collectPeptideMs2RetentionTime (const pappso::MsRunRetentionTime< QString > *msrun_retention_time_reference_p) const
	collect ms2 retention times collect all MS2 events retention times and convert it to the reference time to store it for each peptides
const pappso::MsRunRetentionTime< QString > *	getMsRunRetentionTimeConstPtr () const
pappso::MsRunRetentionTime< QString > *	getMsRunRetentionTimePtr () const
const std::vector< PeptideMeasurementsSp > &	getPeptideMeasurementsList () const
const std::vector< MbrPeptideMeasurementsSp > &	getMbrPeptideMeasurementsList () const

Private Member Functions
std::vector< pappso::XicCoordSPtr >	buildXicCoordList (const MsRunGroup *msrun_group_p, const QuantificationMethodSp &quantification_method)
void	detectQuantifyPeaks (pappso::UiMonitorInterface &m_uiMonitor, const QuantificationMethodSp &quantification_method)
void	mbrDetectQuantifyPeaks (pappso::UiMonitorInterface &m_uiMonitor, const QuantificationMethodSp &quantification_method)
void	addPeptideObservation2XicCoordList (const MsRunGroup *msrun_group_p, const QuantificationMethodSp &quantification_method, const PeptideObservationSp &peptide_events_sp, std::vector< pappso::XicCoordSPtr > &xic_coord_list)
void	addMbrPeptideMeasurementsSp2XicCoordList (const MsRunGroup *msrun_group_p, const QuantificationMethodSp &quantification_method, const PeptideSp &peptide, std::vector< pappso::XicCoordSPtr > &xic_coord_list)

Private Attributes
MsRunSp	msp_msRun
std::map< Peptide *, PeptideObservationSp >	m_peptideObservationList
std::vector< PeptideMeasurementsSp >	m_peptideMeasurementsList
std::shared_ptr< pappso::MsRunRetentionTime< QString > >	msp_msRunRetentionTime = nullptr
std::vector< MbrPeptideMeasurementsSp >	m_mbrPeptideMeasurementsList

Detailed Description

group together an msrun, available peptide observations, and peptide measurements

Definition at line 53 of file msrunpeptidelist.h.

Constructor & Destructor Documentation

MsRunPeptideList() [1/2]

pappso::masschroq::MsRunPeptideList::MsRunPeptideList

(

MsRunSp

msrun

)

Default constructor

Definition at line 34 of file msrunpeptidelist.cpp.

{
  msp_msRun = msrun;
}

References msp_msRun.

MsRunPeptideList() [2/2]

pappso::masschroq::MsRunPeptideList::MsRunPeptideList

(

const MsRunPeptideList &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 39 of file msrunpeptidelist.cpp.

{
  msp_msRun = other.msp_msRun;
}

References msp_msRun.

~MsRunPeptideList()

pappso::masschroq::MsRunPeptideList::~MsRunPeptideList ( )

virtual

Destructor

Definition at line 45 of file msrunpeptidelist.cpp.

{
}

Member Function Documentation

addMbrPeptideMeasurementsSp2XicCoordList()

void pappso::masschroq::MsRunPeptideList::addMbrPeptideMeasurementsSp2XicCoordList ( const MsRunGroup * msrun_group_p, const QuantificationMethodSp & quantification_method, const PeptideSp & peptide, std::vector< pappso::XicCoordSPtr > & xic_coord_list )

private

Definition at line 438 of file msrunpeptidelist.cpp.

{
  MbrPeptideMeasurementsSp mbr_peptide_measurements =
    std::make_shared<pappso::masschroq::MbrPeptideMeasurements>(peptide_sp);
 
  m_mbrPeptideMeasurementsList.push_back(mbr_peptide_measurements);
 
  mbr_peptide_measurements.get()->prepareMeasurements(
    *(msp_msRun.get()->getMsRunReaderSPtr().get()->getMsRunId().get()),
    msrun_group_p,
    *(msp_msRunRetentionTime.get()),
    quantification_method);
  mbr_peptide_measurements.get()->pushBackXicCoordList(xic_coord_list);
}

References m_mbrPeptideMeasurementsList, msp_msRun, msp_msRunRetentionTime, pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurementsBase::pushBackXicCoordList().

Referenced by quantifyMatchBetweenRun().

addPeptideObservation2XicCoordList()

void pappso::masschroq::MsRunPeptideList::addPeptideObservation2XicCoordList ( const MsRunGroup * msrun_group_p, const QuantificationMethodSp & quantification_method, const PeptideObservationSp & peptide_events_sp, std::vector< pappso::XicCoordSPtr > & xic_coord_list )

private

Definition at line 174 of file msrunpeptidelist.cpp.

{
  PeptideMeasurementsSp peptide_measurements =
    std::make_shared<pappso::masschroq::PeptideMeasurements>(peptide_events_sp);
 
  m_peptideMeasurementsList.push_back(peptide_measurements);
 
  peptide_measurements.get()->prepareMeasurements(
    *(msp_msRun.get()->getMsRunReaderSPtr().get()->getMsRunId().get()),
    msrun_group_p,
    quantification_method);
  peptide_measurements.get()->pushBackXicCoordList(xic_coord_list);
}

References m_peptideMeasurementsList, msp_msRun, pappso::masschroq::PeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurementsBase::pushBackXicCoordList().

Referenced by buildXicCoordList().

addPeptideScanNumberObservation()

void pappso::masschroq::MsRunPeptideList::addPeptideScanNumberObservation	(	PeptideSp	peptide_sp,
		PeptideLabel *	p_label,
		std::size_t	spectrum_index,
		std::uint8_t	charge )

Definition at line 71 of file msrunpeptidelist.cpp.

{
 
  auto it = m_peptideObservationList.insert(
    {peptide_sp.get(), std::make_shared<pappso::masschroq::PeptideObservation>(peptide_sp)});
  pappso::masschroq::PrecursorSp precursor_sp =
    msp_msRun.get()->getPrecursorSPtrByScanNumber(scan_number);
  it.first->second.get()->addObservation({scan_number, charge, precursor_sp, false, p_label});
 
  peptide_sp.get()->addMsRunXicCoordCharge({msp_msRun.get(),
                                            precursor_sp.get()->getXicCoordSPtr(),
                                            charge,
                                            precursor_sp.get()->getIntensity()});
  qDebug() << "m_peptideObservationList.size()=" << m_peptideObservationList.size();
}

References pappso::masschroq::Peptide::addMsRunXicCoordCharge(), pappso::masschroq::Precursor::getIntensity(), pappso::masschroq::Precursor::getXicCoordSPtr(), m_peptideObservationList, and msp_msRun.

Referenced by pappso::masschroq::JsonInput::read_msrun_peptide_observations().

addPeptideSpectrumIndexObservation()

void pappso::masschroq::MsRunPeptideList::addPeptideSpectrumIndexObservation	(	PeptideSp	peptide_sp,
		PeptideLabel *	p_label,
		std::size_t	spectrum_index,
		std::uint8_t	charge )

Definition at line 50 of file msrunpeptidelist.cpp.

{
 
  auto it = m_peptideObservationList.insert(
    {peptide_sp.get(), std::make_shared<pappso::masschroq::PeptideObservation>(peptide_sp)});
  pappso::masschroq::PrecursorSp precursor_sp =
    msp_msRun.get()->getPrecursorSPtrBySpectrumIndex(spectrum_index);
  it.first->second.get()->addObservation({spectrum_index, charge, precursor_sp, true, p_label});
 
  peptide_sp.get()->addMsRunXicCoordCharge({msp_msRun.get(),
                                            precursor_sp.get()->getXicCoordSPtr(),
                                            charge,
                                            precursor_sp.get()->getIntensity()});
  qDebug() << "m_peptideObservationList.size()=" << m_peptideObservationList.size();
}

References pappso::masschroq::Peptide::addMsRunXicCoordCharge(), pappso::masschroq::Precursor::getIntensity(), pappso::masschroq::Precursor::getXicCoordSPtr(), m_peptideObservationList, and msp_msRun.

Referenced by pappso::masschroq::JsonInput::read_msrun_peptide_observations().

buildMsRunRetentionTimeSpOnPeptideObservations()

std::shared_ptr< pappso::MsRunRetentionTime< QString > > & pappso::masschroq::MsRunPeptideList::buildMsRunRetentionTimeSpOnPeptideObservations

(

const AlignmentMethodSp &

alignment_method

)

build a retention time vector with seamarks using MS2 best intensities

Parameters

alignment_method

parameters to use for alignment

Definition at line 243 of file msrunpeptidelist.cpp.

{
  msp_msRunRetentionTime =
    std::make_shared<pappso::MsRunRetentionTime<QString>>(msp_msRun->getRetentionTimeLine());
 
  msp_msRunRetentionTime.get()->setMs2MedianFilter(
    pappso::FilterMorphoMedian(alignment_method.get()->getMs2TendencyWindow()));
  msp_msRunRetentionTime.get()->setMs2MeanFilter(
    pappso::FilterMorphoMean(alignment_method.get()->getMs2SmoothingWindow()));
  msp_msRunRetentionTime.get()->setMs1MeanFilter(
    pappso::FilterMorphoMean(alignment_method.get()->getMs1SmoothingWindow()));
 
 
  for(const auto &observation_pair : m_peptideObservationList)
    {
      QString peptide_id = observation_pair.first->getId();
 
      for(std::uint8_t charge : observation_pair.second->getObservedChargeStates())
        {
 
          msp_msRunRetentionTime.get()->addPeptideAsSeamark(
            QString("%1-%2").arg(peptide_id).arg(charge),
            observation_pair.second.get()->getBestXicCoordSPtrForCharge(charge).get()->rtTarget,
            1);
        }
    }
  /*
for(auto &one_xic_measure : measures.get()->getMeasurementList())
{
if((one_xic_measure.m_peakQualityCategory ==
PeakQualityCategory::aa) ||
(one_xic_measure.m_peakQualityCategory == PeakQualityCategory::a))
{
msp_msRunRetentionTime.get()->addPeptideAsSeamark(
peptide_id,
one_xic_measure.m_tracePeakSp.get()->getMaxXicElement().x,
one_xic_measure.m_tracePeakSp.get()->getMaxXicElement().y);
}
}
*/
 
 
  msp_msRunRetentionTime.get()->computeSeamarks();
 
  return msp_msRunRetentionTime;
}

References pappso::masschroq::AlignmentMethod::getMs1SmoothingWindow(), pappso::masschroq::AlignmentMethod::getMs2SmoothingWindow(), pappso::masschroq::AlignmentMethod::getMs2TendencyWindow(), m_peptideObservationList, msp_msRun, and msp_msRunRetentionTime.

buildXicCoordList()

std::vector< pappso::XicCoordSPtr > pappso::masschroq::MsRunPeptideList::buildXicCoordList ( const MsRunGroup * msrun_group_p, const QuantificationMethodSp & quantification_method )

private

Definition at line 154 of file msrunpeptidelist.cpp.

{
  std::vector<pappso::XicCoordSPtr> xic_coord_list;
 
  for(auto pair_peptide : m_peptideObservationList)
    {
      pappso::masschroq::PeptideObservationSp peptide_events_sp = pair_peptide.second;
 
      addPeptideObservation2XicCoordList(
        msrun_group_p, quantification_method, pair_peptide.second, xic_coord_list);
      // peptide_events_sp.get()
    }
 
 
  return xic_coord_list;
}

References addPeptideObservation2XicCoordList(), and m_peptideObservationList.

Referenced by quantify().

clearMeasurements()

void pappso::masschroq::MsRunPeptideList::clearMeasurements

(

)

clear all measurements MBR or not Clearing measurements also removes every chromatogram

Definition at line 513 of file msrunpeptidelist.cpp.

{
 
  for(auto &measure : m_peptideMeasurementsList)
    {
      measure.get()->flushXics();
    }
 
  for(auto &mbr_measure : m_mbrPeptideMeasurementsList)
    {
      mbr_measure.get()->flushXics();
    }
}

References m_mbrPeptideMeasurementsList, and m_peptideMeasurementsList.

collectPeptideMs2RetentionTime()

void pappso::masschroq::MsRunPeptideList::collectPeptideMs2RetentionTime

(

const pappso::MsRunRetentionTime< QString > *

msrun_retention_time_reference_p

)

const

collect ms2 retention times collect all MS2 events retention times and convert it to the reference time to store it for each peptides

Definition at line 320 of file msrunpeptidelist.cpp.

{
  // collect only peptides that were selected for measurement in the first pass
  for(const pappso::masschroq::PeptideMeasurementsSp &measures : m_peptideMeasurementsList)
    {
      try
        {
 
          pappso::masschroq::Peptide *peptide_p =
            measures.get()->getPeptideObservationSp().get()->getPeptideSp().get();
          peptide_p->setReferenceMsRunRetentionTimePtr(msrun_retention_time_reference_p);
          peptide_p->addAlignedPeptideObservation(
            *(measures.get()->getPeptideObservationSp().get()), *(msp_msRunRetentionTime.get()));
        }
      catch(const pappso::PappsoException &error)
        {
          throw pappso::PappsoException(
            QObject::tr("error collecting MS2 retention time in msrun %1 :\n%2")
              .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId()->getXmlId())
              .arg(error.qwhat()));
        }
    }
}

References pappso::masschroq::Peptide::addAlignedPeptideObservation(), m_peptideMeasurementsList, msp_msRun, msp_msRunRetentionTime, pappso::PappsoException::qwhat(), and pappso::masschroq::Peptide::setReferenceMsRunRetentionTimePtr().

collectPeptidePeakRetentionTime()

void pappso::masschroq::MsRunPeptideList::collectPeptidePeakRetentionTime

(

const pappso::MsRunRetentionTime< QString > *

msrun_retention_time_reference_p

)

const

collect peak retention times collect all quantified peptides retention times and convert it to the reference time to store it for each peptides

Definition at line 292 of file msrunpeptidelist.cpp.

{
  for(const pappso::masschroq::PeptideMeasurementsSp &measures : m_peptideMeasurementsList)
    {
      try
        {
          pappso::masschroq::Peptide *peptide_p =
            measures.get()->getPeptideObservationSp().get()->getPeptideSp().get();
          peptide_p->setReferenceMsRunRetentionTimePtr(msrun_retention_time_reference_p);
          for(auto &one_xic_measure : measures.get()->getMeasurementList())
            {
              peptide_p->addAlignedPeakMeasurement(one_xic_measure,
                                                   *(msp_msRunRetentionTime.get()));
            }
        }
      catch(const pappso::PappsoException &error)
        {
          throw pappso::PappsoException(
            QObject::tr("error collecting peak retention time in msrun %1 :\n%2")
              .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId()->getXmlId())
              .arg(error.qwhat()));
        }
    }
}

References pappso::masschroq::Peptide::addAlignedPeakMeasurement(), m_peptideMeasurementsList, msp_msRun, msp_msRunRetentionTime, pappso::PappsoException::qwhat(), and pappso::masschroq::Peptide::setReferenceMsRunRetentionTimePtr().

detectQuantifyPeaks()

void pappso::masschroq::MsRunPeptideList::detectQuantifyPeaks ( pappso::UiMonitorInterface & m_uiMonitor, const QuantificationMethodSp & quantification_method )

private

Definition at line 193 of file msrunpeptidelist.cpp.

{
 
  m_uiMonitor.appendText(QString("Detect and quantify peak"));
  /*
    for(auto &measure : m_peptideMeasurementsList)
      {
        measure->detectQuantifyPeaks(quantification_method);
      }
  */
 
  std::function<void(const pappso::masschroq::PeptideMeasurementsSp &)> mapdetectQuantifyPeaks =
    [quantification_method](const pappso::masschroq::PeptideMeasurementsSp &measure) {
      measure->detectQuantifyPeaks(quantification_method);
    };
 
 
  QFuture<void> res =
    QtConcurrent::map<std::vector<pappso::masschroq::PeptideMeasurementsSp>::iterator>(
      m_peptideMeasurementsList.begin(), m_peptideMeasurementsList.end(), mapdetectQuantifyPeaks);
  res.waitForFinished();
 
 
  m_uiMonitor.appendText(QString("Detect and quantify peak done"));
}

References pappso::UiMonitorInterface::appendText(), and m_peptideMeasurementsList.

Referenced by quantify().

flushChromatogramTraces()

void pappso::masschroq::MsRunPeptideList::flushChromatogramTraces

(

)

flush (remove) transient chromatogram traces after peak detection to save space in memory

Definition at line 228 of file msrunpeptidelist.cpp.

{
 
  for(auto &measure : m_peptideMeasurementsList)
    {
      measure.get()->flushXics();
    }
 
  for(auto &mbr_measure : m_mbrPeptideMeasurementsList)
    {
      mbr_measure.get()->flushXics();
    }
}

References m_mbrPeptideMeasurementsList, and m_peptideMeasurementsList.

getMbrPeptideMeasurementsList()

const std::vector< pappso::masschroq::MbrPeptideMeasurementsSp > & pappso::masschroq::MsRunPeptideList::getMbrPeptideMeasurementsList

(

)

const

Definition at line 507 of file msrunpeptidelist.cpp.

{
  return m_mbrPeptideMeasurementsList;
}

References m_mbrPeptideMeasurementsList.

Referenced by pappso::masschroq::CborOutputStream::writeQrDataBlock().

getMsRunRetentionTimeConstPtr()

const pappso::MsRunRetentionTime< QString > * pappso::masschroq::MsRunPeptideList::getMsRunRetentionTimeConstPtr

(

)

const

Definition at line 495 of file msrunpeptidelist.cpp.

{
  return msp_msRunRetentionTime.get();
}

References msp_msRunRetentionTime.

Referenced by pappso::masschroq::CborOutputStream::writeQrDataBlock().

getMsRunRetentionTimePtr()

pappso::MsRunRetentionTime< QString > * pappso::masschroq::MsRunPeptideList::getMsRunRetentionTimePtr

(

)

const

Definition at line 490 of file msrunpeptidelist.cpp.

{
  return msp_msRunRetentionTime.get();
}

References msp_msRunRetentionTime.

getMsRunSp()

const pappso::masschroq::MsRunSp & pappso::masschroq::MsRunPeptideList::getMsRunSp

(

)

const

Definition at line 222 of file msrunpeptidelist.cpp.

{
  return msp_msRun;
}

References msp_msRun.

Referenced by pappso::masschroq::JsonInput::read_msrun_peptide_observations(), and pappso::masschroq::CborOutputStream::writeQrDataBlock().

getPeptideMeasurementsList()

const std::vector< pappso::masschroq::PeptideMeasurementsSp > & pappso::masschroq::MsRunPeptideList::getPeptideMeasurementsList

(

)

const

Definition at line 501 of file msrunpeptidelist.cpp.

{
  return m_peptideMeasurementsList;
}

References m_peptideMeasurementsList.

Referenced by pappso::masschroq::CborOutputStream::writeQrDataBlock().

mbrDetectQuantifyPeaks()

void pappso::masschroq::MsRunPeptideList::mbrDetectQuantifyPeaks ( pappso::UiMonitorInterface & m_uiMonitor, const QuantificationMethodSp & quantification_method )

private

Definition at line 458 of file msrunpeptidelist.cpp.

{
 
  m_uiMonitor.appendText(QString("MBR Detect and quantify peak"));
  /*
    for(auto &measure : m_peptideMeasurementsList)
      {
        measure->detectQuantifyPeaks(quantification_method);
      }
  */
 
  std::function<void(const pappso::masschroq::MbrPeptideMeasurementsSp &)> mapdetectQuantifyPeaks =
    [quantification_method](const pappso::masschroq::MbrPeptideMeasurementsSp &measure) {
      measure->detectQuantifyPeaks(quantification_method);
    };
 
 
  QFuture<void> res =
    QtConcurrent::map<std::vector<pappso::masschroq::MbrPeptideMeasurementsSp>::iterator>(
      m_mbrPeptideMeasurementsList.begin(),
      m_mbrPeptideMeasurementsList.end(),
      mapdetectQuantifyPeaks);
  res.waitForFinished();
 
 
  m_uiMonitor.appendText(QString("Detect and quantify peak done"));
}

References pappso::UiMonitorInterface::appendText(), and m_mbrPeptideMeasurementsList.

Referenced by quantifyMatchBetweenRun().

quantify()

void pappso::masschroq::MsRunPeptideList::quantify	(	const MsRunGroup *	msrun_group_p,
		const QString &	tmp_dir,
		pappso::UiMonitorInterface &	m_uiMonitor,
		const QuantificationMethodSp &	quantification_method )

Definition at line 92 of file msrunpeptidelist.cpp.

{
  m_peptideMeasurementsList.clear();
  ui_monitor.appendText(
    QString("Starting quantification for msrun %1")
      .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId().get()->getFileName()));
 
  qDebug() << m_peptideObservationList.size();
  pappso::MsRunXicExtractorFactory::getInstance().setTmpDir(tmp_dir);
 
  qDebug();
  pappso::MsRunXicExtractorFactory::getInstance().setMsRunXicExtractorFactoryType(
    pappso::MsRunXicExtractorFactoryType::diskbuffer);
 
  qDebug();
  ui_monitor.appendText(QString("Preparing extraction list"));
  std::vector<pappso::XicCoordSPtr> xic_coord_list =
    buildXicCoordList(msrun_group_p, quantification_method);
 
  ui_monitor.appendText(QString("Preparing extraction list done"));
 
  ui_monitor.appendText(QString("Building XIC extractor"));
  pappso::MsRunXicExtractorInterfaceSp extractor_pwiz =
    pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(
      msp_msRun.get()->getMsRunReaderSPtr());
 
  qDebug();
  extractor_pwiz->setXicExtractMethod(quantification_method.get()->getXicExtractMethod());
 
  // qWarning() << quantification_method.get()->getXicExtractionRtRange();
 
  extractor_pwiz.get()->setRetentionTimeAroundTarget(
    quantification_method.get()->getXicExtractionRtRange());
 
  qDebug();
  pappso::FilterInterfaceCstSPtr csp_filter_suite = quantification_method.get()->getXicFilter();
 
  qDebug();
  extractor_pwiz.get()->setPostExtractionTraceFilterCstSPtr(csp_filter_suite);
 
  qDebug();
 
  ui_monitor.appendText(QString("Building XIC extractor done"));
  ui_monitor.appendText(QString("Extracting"));
  extractor_pwiz.get()->extractXicCoordSPtrListParallelized(ui_monitor, xic_coord_list);
 
  // qWarning() << "size of first xic=" << xic_coord_list.at(0).get()->xicSptr.get()->size();
  qDebug();
 
  detectQuantifyPeaks(ui_monitor, quantification_method);
 
 
  ui_monitor.appendText(
    QString("Quantification for msrun %1 done")
      .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId().get()->getFileName()));
}

References pappso::UiMonitorInterface::appendText(), pappso::MsRunXicExtractorFactory::buildMsRunXicExtractorSp(), buildXicCoordList(), detectQuantifyPeaks(), pappso::diskbuffer, pappso::MsRunXicExtractorFactory::getInstance(), pappso::masschroq::QuantificationMethod::getXicExtractionRtRange(), pappso::masschroq::QuantificationMethod::getXicExtractMethod(), pappso::masschroq::QuantificationMethod::getXicFilter(), m_peptideMeasurementsList, m_peptideObservationList, msp_msRun, pappso::MsRunXicExtractorFactory::setMsRunXicExtractorFactoryType(), and pappso::MsRunXicExtractorFactory::setTmpDir().

quantifyMatchBetweenRun()

void pappso::masschroq::MsRunPeptideList::quantifyMatchBetweenRun	(	const MsRunGroup *	msrun_group_p,
		const std::vector< PeptideSp > &	peptide_mbr_list,
		const QString &	tmp_dir,
		pappso::UiMonitorInterface &	m_uiMonitor,
		const QuantificationMethodSp &	quantification_method )

Definition at line 347 of file msrunpeptidelist.cpp.

{
  try
    {
      m_peptideMeasurementsList.clear();
      ui_monitor.appendText(
        QString("Starting quantification for msrun %1 (MBR)")
          .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId().get()->getFileName()));
 
      qDebug();
      pappso::MsRunXicExtractorFactory::getInstance().setTmpDir(tmp_dir);
 
      qDebug();
      pappso::MsRunXicExtractorFactory::getInstance().setMsRunXicExtractorFactoryType(
        pappso::MsRunXicExtractorFactoryType::diskbuffer);
 
      qDebug();
      ui_monitor.appendText(
        QString("MBR Preparing extraction list (%1)").arg(peptide_mbr_list.size()));
 
 
      std::vector<pappso::XicCoordSPtr> xic_coord_list;
 
      for(auto &peptide_sp : peptide_mbr_list)
        {
          /*
          pappso::masschroq::PeptideObservationSp peptide_events_sp = pair_peptide.second;
 
          addPeptideObservation2XicCoordList(quantification_method,
                                             pair_peptide.second,
                                             xic_coord_list,
                                             ni_minimum_abundance);
                                             */
          addMbrPeptideMeasurementsSp2XicCoordList(
            msrun_group_p, quantification_method, peptide_sp, xic_coord_list);
          // peptide_events_sp.get()
        }
 
 
      ui_monitor.appendText(QString("MBR Preparing extraction list done (%1 %2)")
                              .arg(m_mbrPeptideMeasurementsList.size())
                              .arg(xic_coord_list.size()));
 
      ui_monitor.appendText(QString("MBR Building XIC extractor"));
      pappso::MsRunXicExtractorInterfaceSp extractor_pwiz =
        pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(
          msp_msRun.get()->getMsRunReaderSPtr());
 
      qDebug();
      extractor_pwiz->setXicExtractMethod(quantification_method.get()->getXicExtractMethod());
 
      qDebug();
 
      extractor_pwiz.get()->setRetentionTimeAroundTarget(
        quantification_method.get()->getXicExtractionRtRange());
 
      qDebug();
      pappso::FilterInterfaceCstSPtr csp_filter_suite = quantification_method.get()->getXicFilter();
 
      qDebug();
      extractor_pwiz.get()->setPostExtractionTraceFilterCstSPtr(csp_filter_suite);
 
      qDebug();
 
      ui_monitor.appendText(QString("MBR Building XIC extractor done"));
      ui_monitor.appendText(QString("MBR Extracting"));
      extractor_pwiz.get()->extractXicCoordSPtrListParallelized(ui_monitor, xic_coord_list);
 
      qDebug();
 
      mbrDetectQuantifyPeaks(ui_monitor, quantification_method);
 
 
      ui_monitor.appendText(
        QString("MBR Quantification for msrun %1 done")
          .arg(msp_msRun.get()->getMsRunReaderSPtr()->getMsRunId().get()->getFileName()));
    }
  catch(const pappso::PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("error in %1 :\n%2").arg(__FUNCTION__).arg(error.qwhat()));
    }
}

References addMbrPeptideMeasurementsSp2XicCoordList(), pappso::UiMonitorInterface::appendText(), pappso::MsRunXicExtractorFactory::buildMsRunXicExtractorSp(), pappso::diskbuffer, pappso::MsRunXicExtractorFactory::getInstance(), pappso::masschroq::QuantificationMethod::getXicExtractionRtRange(), pappso::masschroq::QuantificationMethod::getXicExtractMethod(), pappso::masschroq::QuantificationMethod::getXicFilter(), m_mbrPeptideMeasurementsList, m_peptideMeasurementsList, mbrDetectQuantifyPeaks(), msp_msRun, pappso::PappsoException::qwhat(), pappso::MsRunXicExtractorFactory::setMsRunXicExtractorFactoryType(), and pappso::MsRunXicExtractorFactory::setTmpDir().

Member Data Documentation

m_mbrPeptideMeasurementsList

std::vector<MbrPeptideMeasurementsSp> pappso::masschroq::MsRunPeptideList::m_mbrPeptideMeasurementsList

private

Definition at line 169 of file msrunpeptidelist.h.

Referenced by addMbrPeptideMeasurementsSp2XicCoordList(), clearMeasurements(), flushChromatogramTraces(), getMbrPeptideMeasurementsList(), mbrDetectQuantifyPeaks(), and quantifyMatchBetweenRun().

m_peptideMeasurementsList

std::vector<PeptideMeasurementsSp> pappso::masschroq::MsRunPeptideList::m_peptideMeasurementsList

private

Definition at line 164 of file msrunpeptidelist.h.

Referenced by addPeptideObservation2XicCoordList(), clearMeasurements(), collectPeptideMs2RetentionTime(), collectPeptidePeakRetentionTime(), detectQuantifyPeaks(), flushChromatogramTraces(), getPeptideMeasurementsList(), quantify(), and quantifyMatchBetweenRun().

m_peptideObservationList

std::map<Peptide *, PeptideObservationSp> pappso::masschroq::MsRunPeptideList::m_peptideObservationList

private

Definition at line 162 of file msrunpeptidelist.h.

Referenced by addPeptideScanNumberObservation(), addPeptideSpectrumIndexObservation(), buildMsRunRetentionTimeSpOnPeptideObservations(), buildXicCoordList(), and quantify().

msp_msRun

MsRunSp pappso::masschroq::MsRunPeptideList::msp_msRun

private

Definition at line 160 of file msrunpeptidelist.h.

Referenced by MsRunPeptideList(), MsRunPeptideList(), addMbrPeptideMeasurementsSp2XicCoordList(), addPeptideObservation2XicCoordList(), addPeptideScanNumberObservation(), addPeptideSpectrumIndexObservation(), buildMsRunRetentionTimeSpOnPeptideObservations(), collectPeptideMs2RetentionTime(), collectPeptidePeakRetentionTime(), getMsRunSp(), quantify(), and quantifyMatchBetweenRun().

msp_msRunRetentionTime

std::shared_ptr<pappso::MsRunRetentionTime<QString> > pappso::masschroq::MsRunPeptideList::msp_msRunRetentionTime = nullptr

private

Definition at line 166 of file msrunpeptidelist.h.

Referenced by addMbrPeptideMeasurementsSp2XicCoordList(), buildMsRunRetentionTimeSpOnPeptideObservations(), collectPeptideMs2RetentionTime(), collectPeptidePeakRetentionTime(), getMsRunRetentionTimeConstPtr(), and getMsRunRetentionTimePtr().

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

• pappsomspp/core/masschroq/msrunpeptidelist.h
• pappsomspp/core/masschroq/msrunpeptidelist.cpp