#include <peptide.h>

Inheritance diagram for pappso::masschroq::Peptide:

Classes
struct	AlignedPeakPositionElement
	internal structure to compute consensus retention times More...

struct	MsRunXicCoordCharge
	internal structure to store msrun + charge + intensity + xic coordinate More...

Public Member Functions
	Peptide (const QString &id, const pappso::PeptideSp &peptide_sp, const std::vector< ProteinSp > &protein_list)
	constructor

	Peptide (const Peptide &other)

virtual	~Peptide ()

virtual void	computeIsotopologues (double ni_min_abundance) override
	compute possible isotopes for this molecule

const QString &	getId () const
	get peptide unique identifier

void	setMods (const QString &mods)
	set optional information as text to this peptide

const QString &	getMods () const
	get optional information as text

void	addObservedChargeState (std::uint8_t charge)

void	addObservedInMsRunSp (const MsRunSp &msrun_sp)

const std::vector< std::uint8_t > &	getAllObservedChargeStateList () const

const std::vector< ProteinSp > &	getProteinSpList () const

void	addAlignedPeakMeasurement (const PeptideMeasurements::Measurement &one_xic_measure, const pappso::MsRunRetentionTime< QString > &msrun_retention_time)
	accumulate retention time information for MS1 peak measurement

void	addAlignedPeptideObservation (const PeptideObservation &peptide_observation, const pappso::MsRunRetentionTime< QString > &msrun_retention_time)
	accumulate retention time information for MS2 observation convenient function used while collecting data from first pass quantification process

void	computeConsensusRetentionTime ()
	compute consensus retention time (on MS2 observations and MS1 peak measurements) the computation is based on data collected during the first pass of quantification

bool	isObservedInMsRunSp (const MsRun *msrun_p)
	tell if this peptide is observed (MS2 fragmentation and identification) in this msrun

pappso::XicCoordSPtr	getBestXicCoordSPtrForChargeInMsRunGroup (const MsRunGroup *msrun_group_p, std::uint8_t charge) const
	get the XIC coordinates of the higher observed intensity for this peptide and charge in other MS run in the group

pappso::XicCoordSPtr	getBestIonMobilityXicCoordToExtractOverallMsRunGroup (const MsRunGroup &msrun_group, const pappso::MsRunId &targeted_msrun, std::uint8_t charge) const
	get ion mobility coordinates corrected against other MSruns in the group

void	setReferenceMsRunRetentionTimePtr (const pappso::MsRunRetentionTime< QString > *msrun_retention_time_reference_p)
	sets the current msrun retention time reference

double	getConsensusPeakRetentionTime () const
	get consensus retention time based on XIC peak measurements

double	getConsensusMs2RetentionTime () const
	get consensus retention time based on MS2 fragmenation and identification events

void	addMsRunXicCoordCharge (const MsRunXicCoordCharge &msrun_xic_coord)

void	populateIonMobilityGrid (pappso::IonMobilityGrid *ion_mobility_grid_p) const
	Populate ion mobility grid with observed XIC coordinates for this peptide on all MSruns The ion mobility grid only works with Tims TOF mobility index.

void	setJsonLabelList (const QJsonObject &json_label_list)
	build peptide label map from JSON label_list object

PeptideLabel *	getPeptideLabelPtr (const QString &label) const
	get a peptide label pointer with the corresponding label identifier

const std::map< QString, PeptideLabelSp > &	getPeptideLabelMap () const
	get the peptide label label_list

Public Member Functions inherited from pappso::masschroq::PeptideBase
	PeptideBase (const pappso::PeptideSp &peptide_sp)

virtual	~PeptideBase ()

virtual const pappso::PeptideSp &	getPappsoPeptideSp () const
	get the peptide sequence

virtual const pappso::PeptideNaturalIsotopeList *	getPeptideNaturalIsotopeList () const
	get list of isotopes for this peptide needs computeIsotopologues before

virtual const std::vector< pappso::PeptideNaturalIsotopeAverageSp > &	getPeptideNaturalIsotopeAverageSpList (pappso::PrecisionPtr precision, std::uint8_t charge, double ni_min_abundance)
	get possible and distinguishable masses of isotopes get list of distinguishable isotopes given the charge and mass precision

Private Attributes
const QString	m_id

const std::vector< ProteinSp >	m_proteinSpList

QString	m_mods

std::vector< std::uint8_t >	m_allObservedChargeStateList

std::vector< MsRunSp >	m_observedInMsRunSpList

std::vector< AlignedPeakPositionElement >	m_alignedPeakPositionElementList

double	m_consensusAlignedPeakRetentionTime = 0

double	m_consensusAlignedMs2RetentionTime = 0

const pappso::MsRunRetentionTime< QString > *	mp_referenceMsRunRetentionTime = nullptr

std::vector< double >	m_referenceMs2ObservationList

std::vector< MsRunXicCoordCharge >	m_msRunXicCoordChargeList

std::map< QString, PeptideLabelSp >	m_peptideLabelMap

Additional Inherited Members
Protected Attributes inherited from pappso::masschroq::PeptideBase
const pappso::PeptideSp	msp_peptide

pappso::PeptideNaturalIsotopeList *	mpa_peptideNaturalIsotopeList = nullptr

std::map< std::uint8_t, std::vector< pappso::PeptideNaturalIsotopeAverageSp > >	m_peptideNaturalIsotopeAverageSpListByCharge

double	m_niMinAbundance = 0

QMutex	m_mutex

Detailed Description

unique studied entity representing the molecule we want to measure

Definition at line 57 of file peptide.h.

Constructor & Destructor Documentation

◆ Peptide() [1/2]

pappso::masschroq::Peptide::Peptide	(	const QString &	id,
		const pappso::PeptideSp &	peptide_sp,
		const std::vector< ProteinSp > &	protein_list
	)

constructor

Parameters

id	unique identifier for this peptide
msp_peptide	peptide sequence
protein_list	vector of protein shared pointer linked to this peptide^

Definition at line 36 of file peptide.cpp.

  : PeptideBase(peptide_sp), m_id(id), m_proteinSpList(protein_list)
{
}

◆ Peptide() [2/2]

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

Copy constructor

Parameters

other TODO

Definition at line 43 of file peptide.cpp.

  : PeptideBase(other.msp_peptide), m_id(other.m_id), m_proteinSpList(other.m_proteinSpList)
{
  m_mods = other.m_mods;
}

References m_mods.

◆ ~Peptide()

pappso::masschroq::Peptide::~Peptide ( )

virtual

Destructor

Definition at line 49 of file peptide.cpp.

{
  if(mpa_peptideNaturalIsotopeList != nullptr)
    delete mpa_peptideNaturalIsotopeList;
}

Member Function Documentation

◆ addAlignedPeakMeasurement()

void pappso::masschroq::Peptide::addAlignedPeakMeasurement	(	const PeptideMeasurements::Measurement &	one_xic_measure,
		const pappso::MsRunRetentionTime< QString > &	msrun_retention_time
	)

accumulate retention time information for MS1 peak measurement

convenient function used while collecting data from first pass quantification process

Parameters

one_xic_measure	a peak to process
msrun_retention_time	the msrun retention time converter for this msrun

Definition at line 140 of file peptide.cpp.

{
  if(one_xic_measure.m_tracePeakSp.get() != nullptr)
    {
      AlignedPeakPositionElement position;
      position.intensity = one_xic_measure.m_tracePeakSp.get()->getMaxXicElement().y;
      if(msrun_retention_time.isAligned())
        {
          position.alignedRetentionTime =
            msrun_retention_time.translateOriginal2AlignedRetentionTime(
              one_xic_measure.m_tracePeakSp.get()->getMaxXicElement().x);
          position.alignedRetentionTimeCenter =
            msrun_retention_time.translateOriginal2AlignedRetentionTime(
              (one_xic_measure.m_tracePeakSp.get()->getLeftBoundary().x +
               one_xic_measure.m_tracePeakSp.get()->getRightBoundary().x) /
              2);
        }
      else
        {
          position.alignedRetentionTime = one_xic_measure.m_tracePeakSp.get()->getMaxXicElement().x;
          position.alignedRetentionTimeCenter =
            ((one_xic_measure.m_tracePeakSp.get()->getLeftBoundary().x +
              one_xic_measure.m_tracePeakSp.get()->getRightBoundary().x) /
             2);
        }
      /*
    position.alignedRetentionTime =
      position.alignedRetentionTime +
      ((position.alignedRetentionTimeCenter - position.alignedRetentionTime) /
       4);*/
      position.wide = one_xic_measure.m_tracePeakSp.get()->getArea();
      //  one_xic_measure.m_tracePeakSp.get()->getRightBoundary().x -
      //  one_xic_measure.m_tracePeakSp.get()->getLeftBoundary().x;
      m_alignedPeakPositionElementList.push_back(position);
    }
}

References pappso::masschroq::Peptide::AlignedPeakPositionElement::alignedRetentionTime, pappso::masschroq::Peptide::AlignedPeakPositionElement::alignedRetentionTimeCenter, pappso::masschroq::Peptide::AlignedPeakPositionElement::intensity, pappso::MsRunRetentionTime< T >::isAligned(), pappso::masschroq::PeptideMeasurementsBase::Measurement::m_tracePeakSp, pappso::MsRunRetentionTime< T >::translateOriginal2AlignedRetentionTime(), and pappso::masschroq::Peptide::AlignedPeakPositionElement::wide.

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

◆ addAlignedPeptideObservation()

void pappso::masschroq::Peptide::addAlignedPeptideObservation	(	const PeptideObservation &	peptide_observation,
		const pappso::MsRunRetentionTime< QString > &	msrun_retention_time
	)

accumulate retention time information for MS2 observation convenient function used while collecting data from first pass quantification process

Parameters

peptide_observation	an MS2 observation
msrun_retention_time	the msrun retention time converter for this msrun

Definition at line 180 of file peptide.cpp.

{
  double best_rt = peptide_observation.getBestXicCoord().get()->rtTarget;
  if(msrun_retention_time.isAligned())
    {
      best_rt = msrun_retention_time.translateOriginal2AlignedRetentionTime(best_rt);
    }
 
  m_referenceMs2ObservationList.push_back(best_rt);
}

References pappso::masschroq::PeptideObservation::getBestXicCoord(), pappso::MsRunRetentionTime< T >::isAligned(), and pappso::MsRunRetentionTime< T >::translateOriginal2AlignedRetentionTime().

Referenced by pappso::masschroq::MsRunPeptideList::collectPeptideMs2RetentionTime().

◆ addMsRunXicCoordCharge()

void pappso::masschroq::Peptide::addMsRunXicCoordCharge ( const MsRunXicCoordCharge & msrun_xic_coord )

Definition at line 271 of file peptide.cpp.

{
  m_msRunXicCoordChargeList.push_back(msrun_xic_coord);
}

◆ addObservedChargeState()

void pappso::masschroq::Peptide::addObservedChargeState ( std::uint8_t charge )

Definition at line 106 of file peptide.cpp.

{
  if(m_allObservedChargeStateList.end() ==
     std::find(m_allObservedChargeStateList.begin(), m_allObservedChargeStateList.end(), charge))
    {
      m_allObservedChargeStateList.push_back(charge);
    }
}

◆ addObservedInMsRunSp()

void pappso::masschroq::Peptide::addObservedInMsRunSp ( const MsRunSp & msrun_sp )

Definition at line 123 of file peptide.cpp.

{
  auto it = std::find(m_observedInMsRunSpList.begin(), m_observedInMsRunSpList.end(), msrun_sp);
  if(it == m_observedInMsRunSpList.end())
    {
      m_observedInMsRunSpList.push_back(msrun_sp);
    }
}

◆ computeConsensusRetentionTime()

void pappso::masschroq::Peptide::computeConsensusRetentionTime ( )

compute consensus retention time (on MS2 observations and MS1 peak measurements) the computation is based on data collected during the first pass of quantification

Definition at line 194 of file peptide.cpp.

{
  m_consensusAlignedPeakRetentionTime = 0;
 
  if(m_alignedPeakPositionElementList.size() > 0)
    {
      std::sort(m_alignedPeakPositionElementList.begin(),
                m_alignedPeakPositionElementList.end(),
                [](AlignedPeakPositionElement const &a, AlignedPeakPositionElement const &b) {
                  return a.wide > b.wide;
                });
 
      // take only the 90% best measures
      std::size_t limit = m_alignedPeakPositionElementList.size() * 0.9;
      if(limit < 5)
        {
          limit = m_alignedPeakPositionElementList.size();
          //  throw pappso::PappsoException("limit < 3");
        }
      double total_intensity = std::accumulate(m_alignedPeakPositionElementList.begin(),
                                               m_alignedPeakPositionElementList.begin() + limit,
                                               (double)0.0,
                                               [](double sum, AlignedPeakPositionElement &element) {
                                                 sum += element.intensity;
                                                 return (sum);
                                               });
      double sum_rt          = std::accumulate(m_alignedPeakPositionElementList.begin(),
                                      m_alignedPeakPositionElementList.begin() + limit,
                                      (double)0.0,
                                      [](double sum, AlignedPeakPositionElement &element) {
                                        sum += element.intensity * element.alignedRetentionTime;
                                        return (sum);
                                      });
 
      m_consensusAlignedPeakRetentionTime = sum_rt / total_intensity;
    }
  m_alignedPeakPositionElementList.clear();
 
  double sum_rt = std::accumulate(
    m_referenceMs2ObservationList.begin(), m_referenceMs2ObservationList.end(), (double)0.0);
  m_consensusAlignedMs2RetentionTime = sum_rt / (double)m_referenceMs2ObservationList.size();
 
  m_referenceMs2ObservationList.clear();
}

References pappso::masschroq::a, and pappso::masschroq::b.

◆ computeIsotopologues()

void pappso::masschroq::Peptide::computeIsotopologues ( double ni_min_abundance )

overridevirtual

compute possible isotopes for this molecule

Parameters

ni_min_abundance the minimal isotop abundance proportion to cover (0.9 will compute isotopes to reach at least 90% of its theoretical abundance

Reimplemented from pappso::masschroq::PeptideBase.

Definition at line 56 of file peptide.cpp.

{
  qDebug();
  if(ni_min_abundance > 0)
    {
      if(m_peptideLabelMap.size() > 0)
        {
          qDebug();
          for(auto &pair_label : m_peptideLabelMap)
            {
              qDebug() << pair_label.second.get();
              pair_label.second->computeIsotopologues(ni_min_abundance);
              qDebug();
            }
          qDebug();
        }
      else
        {
          qDebug();
          PeptideBase::computeIsotopologues(ni_min_abundance);
        }
    }
  qDebug();
}

References pappso::masschroq::PeptideBase::computeIsotopologues().

◆ getAllObservedChargeStateList()

const std::vector< std::uint8_t > & pappso::masschroq::Peptide::getAllObservedChargeStateList ( ) const

Definition at line 116 of file peptide.cpp.

{
  return m_allObservedChargeStateList;
}

Referenced by pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurements::prepareMeasurements().

◆ getBestIonMobilityXicCoordToExtractOverallMsRunGroup()

pappso::XicCoordSPtr pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup	(	const MsRunGroup &	msrun_group,
		const pappso::MsRunId &	targeted_msrun,
		std::uint8_t	charge
	)		const

get ion mobility coordinates corrected against other MSruns in the group

Parameters

msrun_group_p	pointer on the msrun group
targeted_msrun	the xic coordinate target (required to adjust ion mobility to this msrun)
charge	the targeted charge

Returns: pappso::XicCoordSPtr shared pointer on xic coordinate

Definition at line 348 of file peptide.cpp.

{
  pappso::XicCoordSPtr xic_coord_mean;
  std::size_t count                            = 0;
  pappso::IonMobilityGrid *ion_mobility_grid_p = msrun_group.getIonMobilityGridSp().get();
 
  for(auto &msrun_xic_coord_charge : m_msRunXicCoordChargeList)
    {
      if(msrun_group.contains(msrun_xic_coord_charge.msrun_p))
        {
 
          if(msrun_xic_coord_charge.charge == charge)
            {
              // compute the mean coordinate :
              pappso::XicCoordSPtr xic_coord_to_add = msrun_xic_coord_charge.xic_coord_sp;
 
              if(ion_mobility_grid_p != nullptr)
                {
                  // ion mobility coordinate translation for the targeted msrun
                  xic_coord_to_add = ion_mobility_grid_p->translateXicCoordFromTo(
                    *xic_coord_to_add.get(),
                    *(msrun_xic_coord_charge.msrun_p->getMsRunReaderSPtr()
                        .get()
                        ->getMsRunId()
                        .get()),
                    targeted_msrun);
                }
 
              if(xic_coord_mean.get() == nullptr)
                {
                  xic_coord_mean = xic_coord_to_add.get()->initializeAndClone();
                }
              else
                {
                  xic_coord_mean = xic_coord_mean.get()->addition(xic_coord_to_add);
                }
              count++;
              qDebug() << " xic_coord_mean.get()->toString=" << xic_coord_mean.get()->toString();
            }
        }
    }
  if(xic_coord_mean.get() != nullptr)
    {
      xic_coord_mean = xic_coord_mean.get()->divideBy(count);
    }
 
 
  return xic_coord_mean;
}

References pappso::masschroq::MsRunGroup::contains(), pappso::masschroq::MsRunGroup::getIonMobilityGridSp(), and pappso::IonMobilityGrid::translateXicCoordFromTo().

Referenced by pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurements::prepareMeasurements().

◆ getBestXicCoordSPtrForChargeInMsRunGroup()

pappso::XicCoordSPtr pappso::masschroq::Peptide::getBestXicCoordSPtrForChargeInMsRunGroup	(	const MsRunGroup *	msrun_group_p,
		std::uint8_t	charge
	)		const

get the XIC coordinates of the higher observed intensity for this peptide and charge in other MS run in the group

Parameters

msrun_group_p	pointer on the msrun group
charge	the targeted charge

Returns: pappso::XicCoordSPtr shared pointer on xic coordinate

Definition at line 278 of file peptide.cpp.

{
  // get XIC coordinates of the most intense precursor
  pappso::pappso_double intensity = -1;
  pappso::XicCoordSPtr best_xic_coord;
 
  for(auto &xic_coord_charge : m_msRunXicCoordChargeList)
    {
      if(msrun_group_p->contains(xic_coord_charge.msrun_p))
        {
          if(xic_coord_charge.charge == charge)
            {
              if(xic_coord_charge.intensity > intensity)
                {
                  intensity      = xic_coord_charge.intensity;
                  best_xic_coord = xic_coord_charge.xic_coord_sp;
                  qDebug();
                }
            }
        }
    }
 
  return best_xic_coord;
}

References pappso::masschroq::MsRunGroup::contains().

Referenced by pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements().

◆ getConsensusMs2RetentionTime()

double pappso::masschroq::Peptide::getConsensusMs2RetentionTime ( ) const

get consensus retention time based on MS2 fragmenation and identification events

Returns: retention time in seconds

Definition at line 264 of file peptide.cpp.

{
  return m_consensusAlignedMs2RetentionTime;
}

Referenced by pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements().

◆ getConsensusPeakRetentionTime()

double pappso::masschroq::Peptide::getConsensusPeakRetentionTime ( ) const

get consensus retention time based on XIC peak measurements

Returns: retention time in seconds

Definition at line 258 of file peptide.cpp.

{
  return m_consensusAlignedPeakRetentionTime;
}

Referenced by pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements().

◆ getId()

const QString & pappso::masschroq::Peptide::getId ( ) const

get peptide unique identifier

Definition at line 82 of file peptide.cpp.

{
  return m_id;
}

◆ getMods()

const QString & pappso::masschroq::Peptide::getMods ( ) const

get optional information as text

Definition at line 94 of file peptide.cpp.

{
  return m_mods;
}

◆ getPeptideLabelMap()

const std::map< QString, pappso::masschroq::PeptideLabelSp > & pappso::masschroq::Peptide::getPeptideLabelMap ( ) const

get the peptide label label_list

Definition at line 100 of file peptide.cpp.

{
  return m_peptideLabelMap;
}

Referenced by pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide().

◆ getPeptideLabelPtr()

pappso::masschroq::PeptideLabel * pappso::masschroq::Peptide::getPeptideLabelPtr ( const QString & label ) const

get a peptide label pointer with the corresponding label identifier

Definition at line 430 of file peptide.cpp.

{
  auto it = m_peptideLabelMap.find(label);
  if(it == m_peptideLabelMap.end())
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR: label %1 not found in peptide %2").arg(label).arg(m_id));
    }
  return it->second.get();
}

◆ getProteinSpList()

const std::vector< pappso::masschroq::ProteinSp > & pappso::masschroq::Peptide::getProteinSpList ( ) const

Definition at line 134 of file peptide.cpp.

{
  return m_proteinSpList;
}

◆ isObservedInMsRunSp()

bool pappso::masschroq::Peptide::isObservedInMsRunSp ( const MsRun * msrun_p )

tell if this peptide is observed (MS2 fragmentation and identification) in this msrun

Parameters

msrun_p msrun pointer

Returns: true if observed, false otherwise

Definition at line 240 of file peptide.cpp.

{
  auto it = std::find_if(m_observedInMsRunSpList.begin(),
                         m_observedInMsRunSpList.end(),
                         [msrun_p](const pappso::masschroq::MsRunSp &a) { return (a.get() == msrun_p); });
  if(it == m_observedInMsRunSpList.end())
    return false;
  return true;
}

References pappso::masschroq::a.

◆ populateIonMobilityGrid()

void pappso::masschroq::Peptide::populateIonMobilityGrid ( pappso::IonMobilityGrid * ion_mobility_grid_p ) const

Populate ion mobility grid with observed XIC coordinates for this peptide on all MSruns The ion mobility grid only works with Tims TOF mobility index.

Definition at line 306 of file peptide.cpp.

{
 
  for(auto &xic_coord_charge_a : m_msRunXicCoordChargeList)
    {
      // qInfo() << " observed_in_a";
      const pappso::MsRunId &msrun_id_a =
        *(xic_coord_charge_a.msrun_p->getMsRunReaderSPtr().get()->getMsRunId().get());
      pappso::XicCoordSPtr xic_coord_a = xic_coord_charge_a.xic_coord_sp;
 
      for(auto &xic_coord_charge_b : m_msRunXicCoordChargeList)
        {
          if(&xic_coord_charge_a == &xic_coord_charge_b)
            {
              break;
            }
          else
            {
 
              // qInfo() << " observed_in_b";
              const pappso::MsRunId &msrun_id_b =
                *(xic_coord_charge_b.msrun_p->getMsRunReaderSPtr().get()->getMsRunId().get());
              if(msrun_id_b == msrun_id_a)
                {
                }
              else
                {
                  pappso::XicCoordSPtr xic_coord_b = xic_coord_charge_b.xic_coord_sp;
 
                  if(xic_coord_charge_a.charge == xic_coord_charge_b.charge)
                    {
                      ion_mobility_grid_p->storeObservedIdentityBetween(
                        msrun_id_a, xic_coord_a.get(), msrun_id_b, xic_coord_b.get());
                    }
                }
            }
        }
    }
}

References pappso::IonMobilityGrid::storeObservedIdentityBetween().

◆ setJsonLabelList()

void pappso::masschroq::Peptide::setJsonLabelList ( const QJsonObject & json_label_list )

build peptide label map from JSON label_list object

Definition at line 402 of file peptide.cpp.

{
  auto it = json_label_list.begin();
 
  while(it != json_label_list.end())
    {
      QString label = it.key();
 
      QString proforma = it.value().toObject().value("proforma").toString();
 
      pappso::masschroq::PeptideLabelSp peptide_label_sp;
 
      if(proforma.isEmpty())
        {
          throw pappso::ExceptionNotFound(
            QObject::tr("ERROR: label %1 %2 must contain proforma sequence").arg(label).arg(m_id));
        }
      else
        {
          peptide_label_sp = std::make_shared<pappso::masschroq::PeptideLabel>(
            pappso::PeptideProFormaParser::parseString(proforma), this, label);
        }
      m_peptideLabelMap.insert({label, peptide_label_sp});
      it++;
    }
}

References pappso::PeptideProFormaParser::parseString().

◆ setMods()

void pappso::masschroq::Peptide::setMods ( const QString & mods )

set optional information as text to this peptide

Definition at line 88 of file peptide.cpp.

{
  m_mods = mods;
}

◆ setReferenceMsRunRetentionTimePtr()

void pappso::masschroq::Peptide::setReferenceMsRunRetentionTimePtr ( const pappso::MsRunRetentionTime< QString > * msrun_retention_time_reference_p )

sets the current msrun retention time reference

Parameters

pappso::MsRunRetentionTime<QString> msrun run retention time reference

Definition at line 251 of file peptide.cpp.

{
  mp_referenceMsRunRetentionTime = msrun_retention_time_reference_p;
}

Referenced by pappso::masschroq::MsRunPeptideList::collectPeptideMs2RetentionTime(), and pappso::masschroq::MsRunPeptideList::collectPeptidePeakRetentionTime().

Member Data Documentation

◆ m_alignedPeakPositionElementList

std::vector<AlignedPeakPositionElement> pappso::masschroq::Peptide::m_alignedPeakPositionElementList

private

Definition at line 243 of file peptide.h.

◆ m_allObservedChargeStateList

std::vector<std::uint8_t> pappso::masschroq::Peptide::m_allObservedChargeStateList

private

Definition at line 240 of file peptide.h.

◆ m_consensusAlignedMs2RetentionTime

double pappso::masschroq::Peptide::m_consensusAlignedMs2RetentionTime = 0

private

Definition at line 246 of file peptide.h.

◆ m_consensusAlignedPeakRetentionTime

double pappso::masschroq::Peptide::m_consensusAlignedPeakRetentionTime = 0

private

Definition at line 245 of file peptide.h.

◆ m_id

const QString pappso::masschroq::Peptide::m_id

private

Definition at line 237 of file peptide.h.

◆ m_mods

QString pappso::masschroq::Peptide::m_mods

private

Definition at line 239 of file peptide.h.

Referenced by Peptide().

◆ m_msRunXicCoordChargeList

std::vector<MsRunXicCoordCharge> pappso::masschroq::Peptide::m_msRunXicCoordChargeList

private

Definition at line 251 of file peptide.h.

◆ m_observedInMsRunSpList

std::vector<MsRunSp> pappso::masschroq::Peptide::m_observedInMsRunSpList

private

Definition at line 241 of file peptide.h.

◆ m_peptideLabelMap

std::map<QString, PeptideLabelSp> pappso::masschroq::Peptide::m_peptideLabelMap

private

Definition at line 253 of file peptide.h.

◆ m_proteinSpList

const std::vector<ProteinSp> pappso::masschroq::Peptide::m_proteinSpList

private

Definition at line 238 of file peptide.h.

◆ m_referenceMs2ObservationList

std::vector<double> pappso::masschroq::Peptide::m_referenceMs2ObservationList

private

Definition at line 249 of file peptide.h.

◆ mp_referenceMsRunRetentionTime

const pappso::MsRunRetentionTime<QString>* pappso::masschroq::Peptide::mp_referenceMsRunRetentionTime = nullptr

private

Definition at line 248 of file peptide.h.

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

pappsomspp/core/masschroq/peptide.h
pappsomspp/core/masschroq/peptide.cpp

Classes

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Peptide() [1/2]

◆ Peptide() [2/2]

◆ ~Peptide()

Member Function Documentation

◆ addAlignedPeakMeasurement()

◆ addAlignedPeptideObservation()

◆ addMsRunXicCoordCharge()

◆ addObservedChargeState()

◆ addObservedInMsRunSp()

◆ computeConsensusRetentionTime()

◆ computeIsotopologues()

◆ getAllObservedChargeStateList()

◆ getBestIonMobilityXicCoordToExtractOverallMsRunGroup()

◆ getBestXicCoordSPtrForChargeInMsRunGroup()

◆ getConsensusMs2RetentionTime()

◆ getConsensusPeakRetentionTime()

◆ getId()

◆ getMods()

◆ getPeptideLabelMap()

◆ getPeptideLabelPtr()

◆ getProteinSpList()

◆ isObservedInMsRunSp()

◆ populateIonMobilityGrid()

◆ setJsonLabelList()

◆ setMods()

◆ setReferenceMsRunRetentionTimePtr()

Member Data Documentation

◆ m_alignedPeakPositionElementList

◆ m_allObservedChargeStateList

◆ m_consensusAlignedMs2RetentionTime

◆ m_consensusAlignedPeakRetentionTime

◆ m_id

◆ m_mods

◆ m_msRunXicCoordChargeList

◆ m_observedInMsRunSpList

◆ m_peptideLabelMap

◆ m_proteinSpList

◆ m_referenceMs2ObservationList

◆ mp_referenceMsRunRetentionTime