pappso::masschroq::PeptideMeasurements Class Reference

#include <peptidemeasurements.h>

Inheritance diagram for pappso::masschroq::PeptideMeasurements:

Public Member Functions
	PeptideMeasurements (const PeptideObservationSp &peptide_observations)
	PeptideMeasurements (const PeptideMeasurements &other)
virtual	~PeptideMeasurements ()
void	prepareMeasurements (const pappso::MsRunId &targeted_msrun, const MsRunGroup *msrun_group_p, const QuantificationMethodSp &quantification_method)
virtual void	detectQuantifyPeaks (const QuantificationMethodSp &quantification_method) override
const PeptideObservationSp &	getPeptideObservationSp () const
Public Member Functions inherited from pappso::masschroq::PeptideMeasurementsBase
	PeptideMeasurementsBase ()
	PeptideMeasurementsBase (const PeptideMeasurementsBase &other)
virtual	~PeptideMeasurementsBase ()
virtual const std::vector< Measurement > &	getMeasurementList () const
virtual void	pushBackXicCoordList (std::vector< pappso::XicCoordSPtr > &xic_coord_list) const final
virtual void	flushXics () final
virtual void	clear () final
	clear the measurement vector

Private Attributes
PeptideObservationSp	msp_peptideObservation

Additional Inherited Members
Protected Member Functions inherited from pappso::masschroq::PeptideMeasurementsBase
virtual void	prepareMeasurementsForPeptide (Peptide &the_peptide, const QuantificationMethodSp &quantification_method, const pappso::XicCoordSPtr &best_xic_coord, std::uint8_t charge, double best_rt) final
virtual void	generateMeasurementsForIsotopeList (PeptideBase &peptide_base, const PeptideLabel *label_p, const QuantificationMethodSp &quantification_method, std::uint8_t charge, double isotope_minimum_ratio, const pappso::XicCoordSPtr &best_xic_coord, double best_rt) final
Protected Attributes inherited from pappso::masschroq::PeptideMeasurementsBase
std::vector< Measurement >	m_measurementList

Detailed Description

group together a peptide and measurements made on this peptide

Definition at line 57 of file peptidemeasurements.h.

Constructor & Destructor Documentation

PeptideMeasurements() [1/2]

pappso::masschroq::PeptideMeasurements::PeptideMeasurements

(

const PeptideObservationSp &

peptide_observations

)

Default constructor

Definition at line 35 of file peptidemeasurements.cpp.

{
  msp_peptideObservation = peptide;
}

References msp_peptideObservation.

Referenced by PeptideMeasurements().

PeptideMeasurements() [2/2]

pappso::masschroq::PeptideMeasurements::PeptideMeasurements

(

const PeptideMeasurements &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 41 of file peptidemeasurements.cpp.

  : PeptideMeasurementsBase(other)
{
  msp_peptideObservation = other.msp_peptideObservation;
}

References PeptideMeasurements(), pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase(), and msp_peptideObservation.

~PeptideMeasurements()

pappso::masschroq::PeptideMeasurements::~PeptideMeasurements ( )

virtual

Destructor

Definition at line 47 of file peptidemeasurements.cpp.

{
}

Member Function Documentation

detectQuantifyPeaks()

void pappso::masschroq::PeptideMeasurements::detectQuantifyPeaks ( const QuantificationMethodSp & quantification_method )

overridevirtual

Implements pappso::masschroq::PeptideMeasurementsBase.

Definition at line 101 of file peptidemeasurements.cpp.

{
 
  qDebug();
  pappso::TracePeakList peak_list;
  std::vector<double> observed_rt_list =
    msp_peptideObservation.get()->getObservedRetentionTimesOverallChargeStates();
 
  std::vector<std::uint8_t> observed_charge_states =
    msp_peptideObservation->getObservedChargeStates();
 
  for(auto &measure_one : m_measurementList)
    {
      qDebug();
      pappso::Xic *xic_p = measure_one.msp_xicCoord.get()->xicSptr.get();
      if(xic_p == nullptr)
        {
          throw pappso::PappsoException(QObject::tr("xic_p == nullptr"));
        }
      peak_list.clear();
      std::size_t nb_peaks = 0;
      quantification_method.get()->getTraceDetectionInterfaceCstSPtr().get()->detect(
        *xic_p, peak_list, false);
 
      qDebug();
      auto it_best_matched_peak = findBestTracePeakGivenRtList(
        peak_list.begin(), peak_list.end(), observed_rt_list, nb_peaks);
 
      qDebug();
      measure_one.m_peakQualityCategory       = PeakQualityCategory::missed;
      bool direct_charge_observation_in_msrun = true;
      if(observed_charge_states.end() ==
         find(observed_charge_states.begin(), observed_charge_states.end(), measure_one.m_charge))
        {
          direct_charge_observation_in_msrun = false;
        }
      if(it_best_matched_peak != peak_list.end())
        {
          measure_one.m_tracePeakSp = it_best_matched_peak->makeTracePeakCstSPtr();
          if(nb_peaks == 1)
            {
 
              measure_one.m_peakQualityCategory = PeakQualityCategory::za;
              if(direct_charge_observation_in_msrun)
                measure_one.m_peakQualityCategory = PeakQualityCategory::a;
 
              if(observed_rt_list.size() > 1)
                {
                  measure_one.m_peakQualityCategory = PeakQualityCategory::zaa;
                  if(direct_charge_observation_in_msrun)
                    measure_one.m_peakQualityCategory = PeakQualityCategory::aa;
                }
            }
          else if(nb_peaks > 1)
            {
              measure_one.m_peakQualityCategory = PeakQualityCategory::zab;
              if(direct_charge_observation_in_msrun)
                measure_one.m_peakQualityCategory = PeakQualityCategory::ab;
            }
        }
    }
}

References pappso::masschroq::a, pappso::masschroq::aa, pappso::masschroq::ab, pappso::findBestTracePeakGivenRtList(), pappso::masschroq::QuantificationMethod::getTraceDetectionInterfaceCstSPtr(), pappso::masschroq::PeptideMeasurementsBase::m_measurementList, pappso::masschroq::missed, msp_peptideObservation, pappso::masschroq::za, pappso::masschroq::zaa, and pappso::masschroq::zab.

getPeptideObservationSp()

const pappso::masschroq::PeptideObservationSp & pappso::masschroq::PeptideMeasurements::getPeptideObservationSp

(

)

const

Definition at line 166 of file peptidemeasurements.cpp.

{
  return msp_peptideObservation;
}

References msp_peptideObservation.

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

prepareMeasurements()

void pappso::masschroq::PeptideMeasurements::prepareMeasurements	(	const pappso::MsRunId &	targeted_msrun,
		const MsRunGroup *	msrun_group_p,
		const QuantificationMethodSp &	quantification_method )

Definition at line 52 of file peptidemeasurements.cpp.

{
  // for one peptide
  pappso::masschroq::Peptide *the_peptide_p = msp_peptideObservation.get()->getPeptideSp().get();
  //  1) charge states
  //  2) isotope list
  std::vector<std::uint8_t> charge_states = the_peptide_p->getAllObservedChargeStateList();
 
  double best_rt = msp_peptideObservation.get()->getBestRtOverallChargeStates();
 
 
  pappso::XicCoordSPtr best_xic_coord = msp_peptideObservation.get()->getBestXicCoord();
 
  if(best_xic_coord.get() == nullptr)
    {
      throw pappso::PappsoException("best_xic_coord.get() == nullptr");
    }
 
  for(std::uint8_t charge : charge_states)
    {
 
      if(msrun_group_p->getIonMobilityGridSp().get() != nullptr)
        {
          // Ion mobility TimsTOF coordinates
          best_xic_coord = msp_peptideObservation.get()->getBestXicCoordSPtrForCharge(charge);
 
          if(best_xic_coord.get() == nullptr)
            {
              // now in this ms run, we do not have ion mobility index for
              // this charge we must chek out in other msrun for this charge
              best_xic_coord = the_peptide_p->getBestIonMobilityXicCoordToExtractOverallMsRunGroup(
                *msrun_group_p, targeted_msrun, charge);
            }
          if(best_xic_coord.get() == nullptr)
            continue;
 
          best_xic_coord.get()->rtTarget = best_rt;
        }
 
      prepareMeasurementsForPeptide(
        *the_peptide_p, quantification_method, best_xic_coord, charge, best_rt);
    }
}

References pappso::masschroq::Peptide::getAllObservedChargeStateList(), pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup(), pappso::masschroq::MsRunGroup::getIonMobilityGridSp(), msp_peptideObservation, and pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide().

Referenced by pappso::masschroq::MsRunPeptideList::addPeptideObservation2XicCoordList().

Member Data Documentation

msp_peptideObservation

PeptideObservationSp pappso::masschroq::PeptideMeasurements::msp_peptideObservation

private

Definition at line 88 of file peptidemeasurements.h.

Referenced by PeptideMeasurements(), PeptideMeasurements(), detectQuantifyPeaks(), getPeptideObservationSp(), and prepareMeasurements().

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

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