pappso::masschroq::PeptideBase Class Reference

#include <peptidebase.h>

Inheritance diagram for pappso::masschroq::PeptideBase:

Public Member Functions
	PeptideBase (const pappso::PeptideSp &peptide_sp)
virtual	~PeptideBase ()
virtual const pappso::PeptideSp &	getPappsoPeptideSp () const
	get the peptide sequence
virtual void	computeIsotopologues (double ni_min_abundance)
	compute possible isotopes for this molecule
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

Protected Attributes
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

Todo

write docs

Definition at line 39 of file peptidebase.h.

Constructor & Destructor Documentation

PeptideBase()

pappso::masschroq::PeptideBase::PeptideBase

(

const pappso::PeptideSp &

peptide_sp

)

Default constructor

Definition at line 31 of file peptidebase.cpp.

  : msp_peptide(peptide_sp)
{
}

References msp_peptide.

Referenced by pappso::masschroq::Peptide::Peptide(), pappso::masschroq::Peptide::Peptide(), and pappso::masschroq::PeptideLabel::PeptideLabel().

~PeptideBase()

pappso::masschroq::PeptideBase::~PeptideBase ( )

virtual

Destructor

Definition at line 36 of file peptidebase.cpp.

{
}

Member Function Documentation

computeIsotopologues()

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

virtual

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 in pappso::masschroq::Peptide.

Definition at line 48 of file peptidebase.cpp.

{
  qDebug();
  if(ni_min_abundance > 0)
    {
      qDebug() << "if (_minimum_isotope_abundance > 0)";
      mpa_peptideNaturalIsotopeList =
        new pappso::PeptideNaturalIsotopeList(msp_peptide, 0.001);
    }
  qDebug();
}

References mpa_peptideNaturalIsotopeList, and msp_peptide.

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

getPappsoPeptideSp()

const pappso::PeptideSp & pappso::masschroq::PeptideBase::getPappsoPeptideSp ( ) const

virtual

get the peptide sequence

Returns

pappso::PeptideSp const reference

Definition at line 42 of file peptidebase.cpp.

{
  return msp_peptide;
}

References msp_peptide.

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

getPeptideNaturalIsotopeAverageSpList()

const std::vector< pappso::PeptideNaturalIsotopeAverageSp > & pappso::masschroq::PeptideBase::getPeptideNaturalIsotopeAverageSpList ( pappso::PrecisionPtr precision, std::uint8_t charge, double ni_min_abundance )

virtual

get possible and distinguishable masses of isotopes get list of distinguishable isotopes given the charge and mass precision

Parameters

precision	mass spectrometer MS1 precision
charge	number of H+
ni_min_abundance	select isotopes to regroup

Returns

std::vector<pappso::PeptideNaturalIsotopeAverageSp> list

Definition at line 68 of file peptidebase.cpp.

{
 
  QMutexLocker lock(&m_mutex);
  if(m_niMinAbundance == ni_min_abundance)
    {
    }
  else
    {
      m_peptideNaturalIsotopeAverageSpListByCharge.clear();
      m_niMinAbundance = ni_min_abundance;
    }
 
  auto it = m_peptideNaturalIsotopeAverageSpListByCharge.find(charge);
  if(it != m_peptideNaturalIsotopeAverageSpListByCharge.end())
    {
      if(it->second.size() == 0)
        {
          it->second = mpa_peptideNaturalIsotopeList->getByIntensityRatio(
            charge, precision, ni_min_abundance);
        }
 
      return it->second;
    }
  else
    {
      auto it_insert = m_peptideNaturalIsotopeAverageSpListByCharge.insert(
        {charge,
         mpa_peptideNaturalIsotopeList->getByIntensityRatio(
           charge, precision, ni_min_abundance)});
 
      return it_insert.first->second;
    }
}

References m_mutex, m_niMinAbundance, m_peptideNaturalIsotopeAverageSpListByCharge, and mpa_peptideNaturalIsotopeList.

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

getPeptideNaturalIsotopeList()

const pappso::PeptideNaturalIsotopeList * pappso::masschroq::PeptideBase::getPeptideNaturalIsotopeList ( ) const

virtual

get list of isotopes for this peptide needs computeIsotopologues before

Returns

pappso::PeptideNaturalIsotopeList pointer to all possible isotopes (C13, H2, N15...)

Definition at line 62 of file peptidebase.cpp.

{
  return mpa_peptideNaturalIsotopeList;
}

References mpa_peptideNaturalIsotopeList.

Member Data Documentation

m_mutex

QMutex pappso::masschroq::PeptideBase::m_mutex

protected

Definition at line 93 of file peptidebase.h.

Referenced by getPeptideNaturalIsotopeAverageSpList().

m_niMinAbundance

double pappso::masschroq::PeptideBase::m_niMinAbundance = 0

protected

Definition at line 92 of file peptidebase.h.

Referenced by getPeptideNaturalIsotopeAverageSpList().

m_peptideNaturalIsotopeAverageSpListByCharge

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

protected

Definition at line 91 of file peptidebase.h.

Referenced by getPeptideNaturalIsotopeAverageSpList().

mpa_peptideNaturalIsotopeList

pappso::PeptideNaturalIsotopeList* pappso::masschroq::PeptideBase::mpa_peptideNaturalIsotopeList = nullptr

protected

Definition at line 89 of file peptidebase.h.

Referenced by pappso::masschroq::Peptide::~Peptide(), pappso::masschroq::PeptideLabel::~PeptideLabel(), computeIsotopologues(), getPeptideNaturalIsotopeAverageSpList(), and getPeptideNaturalIsotopeList().

msp_peptide

const pappso::PeptideSp pappso::masschroq::PeptideBase::msp_peptide

protected

Definition at line 88 of file peptidebase.h.

Referenced by pappso::masschroq::Peptide::Peptide(), PeptideBase(), computeIsotopologues(), and getPappsoPeptideSp().

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

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