pappso::masschroq::PeptideMeasurementsBase Class Reference

#include <peptidemeasurementsbase.h>

Inheritance diagram for pappso::masschroq::PeptideMeasurementsBase:

Classes
struct	Measurement

Public Member Functions
	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	detectQuantifyPeaks (const QuantificationMethodSp &quantification_method)=0
virtual void	flushXics () final
virtual void	clear () final
	clear the measurement vector

Protected Member Functions
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
std::vector< Measurement >	m_measurementList

Detailed Description

Todo:

write docs

Definition at line 48 of file peptidemeasurementsbase.h.

Constructor & Destructor Documentation

PeptideMeasurementsBase() [1/2]

pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase

(

)

Default constructor

Definition at line 34 of file peptidemeasurementsbase.cpp.

{
}

PeptideMeasurementsBase() [2/2]

pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase

(

const PeptideMeasurementsBase &

other

)

Definition at line 42 of file peptidemeasurementsbase.cpp.

{
  m_measurementList = other.m_measurementList;
}

References m_measurementList.

~PeptideMeasurementsBase()

pappso::masschroq::PeptideMeasurementsBase::~PeptideMeasurementsBase ( )

virtual

Destructor

Definition at line 38 of file peptidemeasurementsbase.cpp.

{
}

Member Function Documentation

clear()

void pappso::masschroq::PeptideMeasurementsBase::clear ( )

finalvirtual

clear the measurement vector

Definition at line 199 of file peptidemeasurementsbase.cpp.

{
  m_measurementList.clear();
}

detectQuantifyPeaks()

virtual void pappso::masschroq::PeptideMeasurementsBase::detectQuantifyPeaks ( const QuantificationMethodSp &  quantification_method )

pure virtual

Implemented in pappso::masschroq::MbrPeptideMeasurements, and pappso::masschroq::PeptideMeasurements.

flushXics()

void pappso::masschroq::PeptideMeasurementsBase::flushXics ( )

finalvirtual

Definition at line 189 of file peptidemeasurementsbase.cpp.

{
 
  for(auto &measure_one : m_measurementList)
    {
      measure_one.msp_xicCoord.get()->xicSptr = nullptr;
    }
}

generateMeasurementsForIsotopeList()

void pappso::masschroq::PeptideMeasurementsBase::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  )

finalprotectedvirtual

Definition at line 56 of file peptidemeasurementsbase.cpp.

{
 
  qDebug();
  const std::vector<pappso::PeptideNaturalIsotopeAverageSp> &natural_isotope_average_list =
    peptide_base.getPeptideNaturalIsotopeAverageSpList(
      quantification_method.get()->getXicExtractionMeanPrecisionPtr(),
      charge,
      isotope_minimum_ratio);
 
  for(pappso::PeptideNaturalIsotopeAverageSp isotope_average_sp : natural_isotope_average_list)
    {
      pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
      xic_coord.get()->rtTarget      = best_rt;
      xic_coord.get()->mzRange =
        quantification_method.get()->getXicExtractionMzRange(isotope_average_sp.get()->getMz());
 
 
      m_measurementList.push_back(
        {charge, xic_coord, PeakQualityCategory::nomatch, label_p, nullptr, isotope_average_sp});
    }
 
  qDebug() << m_measurementList.size();
}

References pappso::masschroq::PeptideBase::getPeptideNaturalIsotopeAverageSpList(), and pappso::masschroq::nomatch.

getMeasurementList()

const std::vector< pappso::masschroq::PeptideMeasurementsBase::Measurement > & pappso::masschroq::PeptideMeasurementsBase::getMeasurementList ( ) const

virtual

Definition at line 50 of file peptidemeasurementsbase.cpp.

{
  return m_measurementList;
}

Referenced by pappso::masschroq::CborOutputStream::writeMbrPeptideMeasurements(), and pappso::masschroq::CborOutputStream::writePeptideMeasurements().

prepareMeasurementsForPeptide()

void pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide ( Peptide &  the_peptide, const QuantificationMethodSp &  quantification_method, const pappso::XicCoordSPtr &  best_xic_coord, std::uint8_t  charge, double  best_rt  )

finalprotectedvirtual

Definition at line 89 of file peptidemeasurementsbase.cpp.

{
 
  double isotope_minimum_ratio = quantification_method.get()->getIsotopeMinimumRatio();
 
 
  auto label_map = the_peptide.getPeptideLabelMap();
 
  if(isotope_minimum_ratio > 0)
    {
      //  isotope
      if(label_map.size() > 0)
        {
          // isotope, label
 
          for(auto &peptide_label_pair : label_map)
            {
              // for each label
              qDebug();
              generateMeasurementsForIsotopeList(*(peptide_label_pair.second.get()),
                                                 peptide_label_pair.second.get(),
                                                 quantification_method,
                                                 charge,
                                                 isotope_minimum_ratio,
                                                 best_xic_coord,
                                                 best_rt);
            }
        }
      else
        {
          // isotope, no label
          generateMeasurementsForIsotopeList(the_peptide,
                                             nullptr,
                                             quantification_method,
                                             charge,
                                             isotope_minimum_ratio,
                                             best_xic_coord,
                                             best_rt);
        }
    }
  else
    {
      // no isotope
      if(label_map.size() > 0)
        {
          // no isotope, label
          for(auto &peptide_label_pair : label_map)
            {
              // for each label
              qDebug();
              double mz = peptide_label_pair.second->getPappsoPeptideSp().get()->getMz(charge);
              pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
              xic_coord.get()->rtTarget      = best_rt;
              xic_coord.get()->mzRange = quantification_method.get()->getXicExtractionMzRange(mz);
 
 
              m_measurementList.push_back({charge,
                                           xic_coord,
                                           PeakQualityCategory::nomatch,
                                           peptide_label_pair.second.get(),
                                           nullptr,
                                           nullptr});
            }
        }
      else
        {
          // no isotope, no label
          double mz                      = the_peptide.getPappsoPeptideSp().get()->getMz(charge);
          pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
          xic_coord.get()->rtTarget      = best_rt;
          xic_coord.get()->mzRange       = quantification_method.get()->getXicExtractionMzRange(mz);
 
 
          m_measurementList.push_back(
            {charge, xic_coord, PeakQualityCategory::nomatch, nullptr, nullptr, nullptr});
        }
    }
}

References pappso::masschroq::PeptideBase::getPappsoPeptideSp(), pappso::masschroq::Peptide::getPeptideLabelMap(), and pappso::masschroq::nomatch.

pushBackXicCoordList()

void pappso::masschroq::PeptideMeasurementsBase::pushBackXicCoordList ( std::vector< pappso::XicCoordSPtr > &  xic_coord_list ) const

finalvirtual

Definition at line 175 of file peptidemeasurementsbase.cpp.

{
  for(auto &measure : m_measurementList)
    {
      if(measure.msp_xicCoord.get()->rtTarget > 0)
        {
          xic_coord_list.push_back(measure.msp_xicCoord);
        }
    }
}

Member Data Documentation

m_measurementList

std::vector<Measurement> pappso::masschroq::PeptideMeasurementsBase::m_measurementList

protected

Definition at line 117 of file peptidemeasurementsbase.h.

Referenced by PeptideMeasurementsBase().

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

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