#include <mbrpeptidemeasurements.h>

Inheritance diagram for pappso::masschroq::MbrPeptideMeasurements:

Public Member Functions
	MbrPeptideMeasurements (const PeptideSp &peptide_sp)

	MbrPeptideMeasurements (const MbrPeptideMeasurements &other)

virtual	~MbrPeptideMeasurements ()

void	prepareMeasurements (const pappso::MsRunId &targeted_msrun, const MsRunGroup *msrun_group_p, const pappso::MsRunRetentionTime< QString > &msrun_retention_time, const QuantificationMethodSp &quantification_method)

virtual void	detectQuantifyPeaks (const QuantificationMethodSp &quantification_method) override

const PeptideSp &	getPeptideSp () 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
PeptideSp	msp_peptide

double	m_consensusMs2RetentionTime = 0

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

Todo: write docs

Definition at line 48 of file mbrpeptidemeasurements.h.

Constructor & Destructor Documentation

◆ MbrPeptideMeasurements() [1/2]

pappso::masschroq::MbrPeptideMeasurements::MbrPeptideMeasurements ( const PeptideSp & peptide_sp )

Default constructor

Definition at line 35 of file mbrpeptidemeasurements.cpp.

  : msp_peptide(peptide_sp)
{
  if(msp_peptide.get() == nullptr)
    {
      throw pappso::PappsoException("msp_peptide.get() == nullptr");
    }
}

References msp_peptide.

◆ MbrPeptideMeasurements() [2/2]

pappso::masschroq::MbrPeptideMeasurements::MbrPeptideMeasurements ( const MbrPeptideMeasurements & other )

Definition at line 46 of file mbrpeptidemeasurements.cpp.

  : PeptideMeasurementsBase(other)
{
  msp_peptide = other.msp_peptide;
  m_consensusMs2RetentionTime = other.m_consensusMs2RetentionTime;
}

References pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase(), m_consensusMs2RetentionTime, and msp_peptide.

◆ ~MbrPeptideMeasurements()

pappso::masschroq::MbrPeptideMeasurements::~MbrPeptideMeasurements ( )

virtual

Destructor

Definition at line 55 of file mbrpeptidemeasurements.cpp.

56{

57}

Member Function Documentation

◆ detectQuantifyPeaks()

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

overridevirtual

Implements pappso::masschroq::PeptideMeasurementsBase.

Definition at line 121 of file mbrpeptidemeasurements.cpp.

{
 
  qDebug();
  pappso::TracePeakList peak_list;
  std::vector<std::uint8_t> all_charge_states = msp_peptide.get()->getAllObservedChargeStateList();
 
 
  for(auto &measure_one : m_measurementList)
    {
      qDebug();
      double rt_target = measure_one.msp_xicCoord.get()->rtTarget;
      peak_list.clear();
      quantification_method.get()->getTraceDetectionInterfaceCstSPtr().get()->detect(
        *(measure_one.msp_xicCoord.get()->xicSptr.get()), peak_list, false);
 
      qDebug();
      measure_one.m_peakQualityCategory = PeakQualityCategory::missed;
      if(m_consensusMs2RetentionTime > 0)
        {
          qDebug();
          auto it_best_matched_peak = pappso::findTracePeakGivenRt(
            peak_list.begin(), peak_list.end(), m_consensusMs2RetentionTime);
 
          if(it_best_matched_peak != peak_list.end())
            {
              measure_one.m_tracePeakSp         = it_best_matched_peak->makeTracePeakCstSPtr();
              measure_one.m_peakQualityCategory = PeakQualityCategory::c;
              if(it_best_matched_peak->containsRt(rt_target))
                {
                  measure_one.m_peakQualityCategory = PeakQualityCategory::b;
                }
            }
          else
            {
 
              it_best_matched_peak =
                pappso::findTracePeakGivenRt(peak_list.begin(), peak_list.end(), rt_target);
 
              if(it_best_matched_peak != peak_list.end())
                {
                  measure_one.m_tracePeakSp         = it_best_matched_peak->makeTracePeakCstSPtr();
                  measure_one.m_peakQualityCategory = PeakQualityCategory::d;
                }
            }
        }
    }
}

References pappso::masschroq::b, pappso::masschroq::c, pappso::masschroq::d, pappso::findTracePeakGivenRt(), pappso::masschroq::QuantificationMethod::getTraceDetectionInterfaceCstSPtr(), m_consensusMs2RetentionTime, pappso::masschroq::PeptideMeasurementsBase::m_measurementList, pappso::masschroq::missed, and msp_peptide.

◆ getPeptideSp()

const pappso::masschroq::PeptideSp & pappso::masschroq::MbrPeptideMeasurements::getPeptideSp ( ) const

Definition at line 172 of file mbrpeptidemeasurements.cpp.

{
  return msp_peptide;
}

References msp_peptide.

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

◆ prepareMeasurements()

void pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements	(	const pappso::MsRunId &	targeted_msrun,
		const MsRunGroup *	msrun_group_p,
		const pappso::MsRunRetentionTime< QString > &	msrun_retention_time,
		const QuantificationMethodSp &	quantification_method )

Definition at line 61 of file mbrpeptidemeasurements.cpp.

{
  // for one peptide
  pappso::masschroq::Peptide *the_peptide_p = msp_peptide.get();
  //  1) charge states
  //  2) isotope list
  std::vector<std::uint8_t> charge_states = the_peptide_p->getAllObservedChargeStateList();
 
 
  m_consensusMs2RetentionTime = the_peptide_p->getConsensusMs2RetentionTime();
 
  if(msrun_retention_time.isAligned())
    {
      m_consensusMs2RetentionTime =
        msrun_retention_time.translateAligned2OriginalRetentionTime(m_consensusMs2RetentionTime);
    }
 
  double consensus_rt = the_peptide_p->getConsensusPeakRetentionTime();
 
  if(consensus_rt > 0)
    {
      if(msrun_retention_time.isAligned())
        {
          consensus_rt = msrun_retention_time.translateAligned2OriginalRetentionTime(consensus_rt);
        }
    }
  for(std::uint8_t charge : charge_states)
    {
 
      pappso::XicCoordSPtr best_xic_coord;
      if(msrun_group_p->getIonMobilityGridSp().get() != nullptr)
        {
          best_xic_coord = the_peptide_p->getBestIonMobilityXicCoordToExtractOverallMsRunGroup(
            *msrun_group_p, targeted_msrun, charge);
        }
      else
        {
          best_xic_coord =
            the_peptide_p->getBestXicCoordSPtrForChargeInMsRunGroup(msrun_group_p, charge);
        }
 
      if(best_xic_coord.get() == nullptr)
        {
          // We can not quantify it in this msrun group
        }
      else
        {
 
          prepareMeasurementsForPeptide(
            *the_peptide_p, quantification_method, best_xic_coord, charge, consensus_rt);
        }
    }
}

References pappso::masschroq::Peptide::getAllObservedChargeStateList(), pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup(), pappso::masschroq::Peptide::getBestXicCoordSPtrForChargeInMsRunGroup(), pappso::masschroq::Peptide::getConsensusMs2RetentionTime(), pappso::masschroq::Peptide::getConsensusPeakRetentionTime(), pappso::masschroq::MsRunGroup::getIonMobilityGridSp(), pappso::MsRunRetentionTime< T >::isAligned(), m_consensusMs2RetentionTime, msp_peptide, pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide(), and pappso::MsRunRetentionTime< T >::translateAligned2OriginalRetentionTime().

Referenced by pappso::masschroq::MsRunPeptideList::addMbrPeptideMeasurementsSp2XicCoordList().

Member Data Documentation

◆ m_consensusMs2RetentionTime

double pappso::masschroq::MbrPeptideMeasurements::m_consensusMs2RetentionTime = 0

private

Definition at line 78 of file mbrpeptidemeasurements.h.

Referenced by MbrPeptideMeasurements(), detectQuantifyPeaks(), and prepareMeasurements().

◆ msp_peptide

PeptideSp pappso::masschroq::MbrPeptideMeasurements::msp_peptide

private

Definition at line 76 of file mbrpeptidemeasurements.h.

Referenced by MbrPeptideMeasurements(), MbrPeptideMeasurements(), detectQuantifyPeaks(), getPeptideSp(), and prepareMeasurements().

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

pappsomspp/core/masschroq/mbrpeptidemeasurements.h
pappsomspp/core/masschroq/mbrpeptidemeasurements.cpp

Public Member Functions

Private Attributes

Additional Inherited Members