#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)
{
}

References pappso::masschroq::PeptideBase::PeptideBase(), m_id, and m_proteinSpList.

Referenced by Peptide().

◆ 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 Peptide(), pappso::masschroq::PeptideBase::PeptideBase(), m_id, m_mods, m_proteinSpList, and pappso::masschroq::PeptideBase::msp_peptide.

◆ ~Peptide()

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

virtual

Destructor

Definition at line 49 of file peptide.cpp.

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

References pappso::masschroq::PeptideBase::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(), m_alignedPeakPositionElementList, pappso::masschroq::PeptideMeasurementsBase::Measurement::m_tracePeakSp, pappso::MsRunRetentionTime< T >::translateOriginal2AlignedRetentionTime(), pappso::masschroq::Peptide::AlignedPeakPositionElement::wide, and pappso::x.

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(), m_referenceMs2ObservationList, 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 272 of file peptide.cpp.

{
  m_msRunXicCoordChargeList.push_back(msrun_xic_coord);
}

References m_msRunXicCoordChargeList.

Referenced by pappso::masschroq::MsRunPeptideList::addPeptideScanNumberObservation(), and pappso::masschroq::MsRunPeptideList::addPeptideSpectrumIndexObservation().

◆ 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);
    }
}

References m_allObservedChargeStateList.

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

◆ 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);
    }
}

References m_observedInMsRunSpList.

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

◆ 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, pappso::masschroq::b, m_alignedPeakPositionElementList, m_consensusAlignedMs2RetentionTime, m_consensusAlignedPeakRetentionTime, and m_referenceMs2ObservationList.

◆ 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(), and m_peptideLabelMap.

◆ getAllObservedChargeStateList()

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

Definition at line 116 of file peptide.cpp.

{
  return m_allObservedChargeStateList;
}

References 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 351 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(), m_msRunXicCoordChargeList, 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 280 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(), and m_msRunXicCoordChargeList.

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 265 of file peptide.cpp.

{
  return m_consensusAlignedMs2RetentionTime;
}

References 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 259 of file peptide.cpp.

{
  return m_consensusAlignedPeakRetentionTime;
}

References 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;
}

References m_id.

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

◆ getMods()

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

get optional information as text

Definition at line 94 of file peptide.cpp.

{
  return m_mods;
}

References m_mods.

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

◆ 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;
}

References 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 433 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();
}

References m_id, and m_peptideLabelMap.

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

◆ getProteinSpList()

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

Definition at line 134 of file peptide.cpp.

{
  return m_proteinSpList;
}

References 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, and m_observedInMsRunSpList.

◆ 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 308 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 m_msRunXicCoordChargeList, and pappso::IonMobilityGrid::storeObservedIdentityBetween().

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

◆ setJsonLabelList()

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

build peptide label map from JSON label_list object

Definition at line 405 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 m_id, m_peptideLabelMap, and pappso::PeptideProFormaParser::parseString().

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

◆ 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;
}

References m_mods.

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

◆ 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 252 of file peptide.cpp.

{
  mp_referenceMsRunRetentionTime = msrun_retention_time_reference_p;
}

References mp_referenceMsRunRetentionTime.

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.

Referenced by addAlignedPeakMeasurement(), and computeConsensusRetentionTime().

◆ m_allObservedChargeStateList

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

private

Definition at line 240 of file peptide.h.

Referenced by addObservedChargeState(), and getAllObservedChargeStateList().

◆ m_consensusAlignedMs2RetentionTime

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

private

Definition at line 246 of file peptide.h.

Referenced by computeConsensusRetentionTime(), and getConsensusMs2RetentionTime().

◆ m_consensusAlignedPeakRetentionTime

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

private

Definition at line 245 of file peptide.h.

Referenced by computeConsensusRetentionTime(), and getConsensusPeakRetentionTime().

◆ m_id

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

private

Definition at line 237 of file peptide.h.

Referenced by Peptide(), Peptide(), getId(), getPeptideLabelPtr(), and setJsonLabelList().

◆ m_mods

QString pappso::masschroq::Peptide::m_mods

private

Definition at line 239 of file peptide.h.

Referenced by Peptide(), getMods(), and setMods().

◆ m_msRunXicCoordChargeList

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

private

Definition at line 251 of file peptide.h.

Referenced by addMsRunXicCoordCharge(), getBestIonMobilityXicCoordToExtractOverallMsRunGroup(), getBestXicCoordSPtrForChargeInMsRunGroup(), and populateIonMobilityGrid().

◆ m_observedInMsRunSpList

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

private

Definition at line 241 of file peptide.h.

Referenced by addObservedInMsRunSp(), and isObservedInMsRunSp().

◆ m_peptideLabelMap

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

private

Definition at line 253 of file peptide.h.

Referenced by computeIsotopologues(), getPeptideLabelMap(), getPeptideLabelPtr(), and setJsonLabelList().

◆ m_proteinSpList

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

private

Definition at line 238 of file peptide.h.

Referenced by Peptide(), Peptide(), and getProteinSpList().

◆ m_referenceMs2ObservationList

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

private

Definition at line 249 of file peptide.h.

Referenced by addAlignedPeptideObservation(), and computeConsensusRetentionTime().

◆ mp_referenceMsRunRetentionTime

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

private

Definition at line 248 of file peptide.h.

Referenced by setReferenceMsRunRetentionTimePtr().

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