pappso::masschroq::PeptideObservation Class Reference

#include <peptideobservation.h>

Classes
struct	Observation

Public Member Functions
	PeptideObservation (PeptideSp peptide)
	PeptideObservation (const PeptideObservation &other)
virtual	~PeptideObservation ()
const PeptideSp &	getPeptideSp () const
void	addObservation (const PeptideObservation::Observation &observation)
std::vector< std::uint8_t >	getObservedChargeStates () const
double	getBestRtOverallChargeStates () const
std::vector< double >	getObservedRetentionTimesOverallChargeStates () const
pappso::XicCoordSPtr	getBestXicCoordSPtrForCharge (std::uint8_t charge) const
pappso::XicCoordSPtr	getBestXicCoord () const
const std::vector< Observation > &	getObservationList () const

Private Attributes
PeptideSp	msp_peptide
std::vector< Observation >	m_observationList

Detailed Description

Todo

group together one Peptide and observations on this peptide

Definition at line 47 of file peptideobservation.h.

Constructor & Destructor Documentation

PeptideObservation() [1/2]

pappso::masschroq::PeptideObservation::PeptideObservation

(

PeptideSp

peptide

)

Default constructor

Definition at line 34 of file peptideobservation.cpp.

  : msp_peptide(peptide)
{
}

References msp_peptide.

Referenced by PeptideObservation().

PeptideObservation() [2/2]

pappso::masschroq::PeptideObservation::PeptideObservation

(

const PeptideObservation &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 40 of file peptideobservation.cpp.

  : msp_peptide(other.msp_peptide)
{
  m_observationList = other.m_observationList;
}

References PeptideObservation(), m_observationList, and msp_peptide.

~PeptideObservation()

pappso::masschroq::PeptideObservation::~PeptideObservation ( )

virtual

Destructor

Definition at line 46 of file peptideobservation.cpp.

{
}

Member Function Documentation

addObservation()

void pappso::masschroq::PeptideObservation::addObservation

(

const PeptideObservation::Observation &

observation

)

Definition at line 51 of file peptideobservation.cpp.

{
  m_observationList.push_back(observation);
}

References m_observationList.

getBestRtOverallChargeStates()

double pappso::masschroq::PeptideObservation::getBestRtOverallChargeStates

(

)

const

Definition at line 78 of file peptideobservation.cpp.

{
  double best_rt   = 0;
  double intensity = -1;
  for(auto &observation : m_observationList)
    {
      if(observation.msp_precursor.get()->getIntensity() > intensity)
        {
          best_rt =
            observation.msp_precursor.get()->getXicCoordSPtr().get()->rtTarget;
          intensity = observation.msp_precursor.get()->getIntensity();
        }
    }
 
  return best_rt;
}

References m_observationList.

getBestXicCoord()

pappso::XicCoordSPtr pappso::masschroq::PeptideObservation::getBestXicCoord

(

)

const

Definition at line 121 of file peptideobservation.cpp.

{
 
  // get XIC coordinates of the most intense precursor
  pappso::pappso_double intensity = -1;
  pappso::XicCoordSPtr best_xic_coord;
 
  for(auto &observation : m_observationList)
    {
      if(observation.msp_precursor.get()->getIntensity() > intensity)
        {
          intensity      = observation.msp_precursor.get()->getIntensity();
          best_xic_coord = observation.msp_precursor.get()->getXicCoordSPtr();
          qDebug();
        }
    }
  return best_xic_coord;
}

References m_observationList.

Referenced by pappso::masschroq::Peptide::addAlignedPeptideObservation().

getBestXicCoordSPtrForCharge()

pappso::XicCoordSPtr pappso::masschroq::PeptideObservation::getBestXicCoordSPtrForCharge

(

std::uint8_t

charge

)

const

Definition at line 96 of file peptideobservation.cpp.

{
 
  // get XIC coordinates of the most intense precursor
  pappso::pappso_double intensity = -1;
  pappso::XicCoordSPtr best_xic_coord;
 
  for(auto &observation : m_observationList)
    {
      if(observation.m_charge == charge)
        {
          if(observation.msp_precursor.get()->getIntensity() > intensity)
            {
              intensity = observation.msp_precursor.get()->getIntensity();
              best_xic_coord =
                observation.msp_precursor.get()->getXicCoordSPtr();
              qDebug();
            }
        }
    }
  return best_xic_coord;
}

References m_observationList.

getObservationList()

const std::vector< pappso::masschroq::PeptideObservation::Observation > & pappso::masschroq::PeptideObservation::getObservationList

(

)

const

Definition at line 155 of file peptideobservation.cpp.

{
  return m_observationList;
}

References m_observationList.

getObservedChargeStates()

std::vector< std::uint8_t > pappso::masschroq::PeptideObservation::getObservedChargeStates

(

)

const

Definition at line 57 of file peptideobservation.cpp.

{
  std::vector<std::uint8_t> charge_list;
  for(auto &observation : m_observationList)
    {
      charge_list.push_back(observation.m_charge);
    }
  std::sort(charge_list.begin(), charge_list.end());
 
  charge_list.erase(std::unique(charge_list.begin(), charge_list.end()),
                    charge_list.end());
  return charge_list;
}

References m_observationList.

getObservedRetentionTimesOverallChargeStates()

std::vector< double > pappso::masschroq::PeptideObservation::getObservedRetentionTimesOverallChargeStates

(

)

const

Definition at line 142 of file peptideobservation.cpp.

{
  std::vector<double> rt_list;
  for(auto &observation : m_observationList)
    {
      rt_list.push_back(
        observation.msp_precursor.get()->getXicCoordSPtr().get()->rtTarget);
    }
 
  return rt_list;
}

References m_observationList.

getPeptideSp()

const pappso::masschroq::PeptideSp & pappso::masschroq::PeptideObservation::getPeptideSp

(

)

const

Definition at line 72 of file peptideobservation.cpp.

{
  return msp_peptide;
}

References msp_peptide.

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

Member Data Documentation

m_observationList

std::vector<Observation> pappso::masschroq::PeptideObservation::m_observationList

private

Definition at line 99 of file peptideobservation.h.

Referenced by PeptideObservation(), addObservation(), getBestRtOverallChargeStates(), getBestXicCoord(), getBestXicCoordSPtrForCharge(), getObservationList(), getObservedChargeStates(), and getObservedRetentionTimesOverallChargeStates().

msp_peptide

PeptideSp pappso::masschroq::PeptideObservation::msp_peptide

private

Definition at line 98 of file peptideobservation.h.

Referenced by PeptideObservation(), PeptideObservation(), and getPeptideSp().

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

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