pappso::PeptideRawFragmentMasses Class Reference

#include <peptiderawfragmentmasses.h>

Public Member Functions
	PeptideRawFragmentMasses (const Peptide &peptide, RawFragmentationMode mode)
	~PeptideRawFragmentMasses ()
void	pushBackIonMasses (std::vector< pappso_double > &mass_list, Enums::PeptideIon ion_type) const
void	pushBackIonMz (std::vector< pappso_double > &mass_list, Enums::PeptideIon ion_type, unsigned int charge) const
void	pushBackMatchSpectrum (std::vector< SimplePeakIonMatch > &peak_match_list, const MassSpectrum &spectrum, PrecisionPtr precision, Enums::PeptideIon ion_type, unsigned int charge) const

Static Public Member Functions
static pappso_double	getDeltaMass (Enums::PeptideIon ion_type)

Private Types
using	ionDeltatMzMassMap = pappso_double[20]

Private Attributes
std::vector< pappso_double >	m_cumulativeNterMasses
	cumulative Nter masses (without internal Nter modification)
std::vector< pappso_double >	m_cumulativeCterMasses
	cumulative Cter masses (without internal Cter modification)

Static Private Attributes
static ionDeltatMzMassMap	m_ionDeltaMz

Detailed Description

Definition at line 59 of file peptiderawfragmentmasses.h.

Member Typedef Documentation

ionDeltatMzMassMap

using pappso::PeptideRawFragmentMasses::ionDeltatMzMassMap = pappso_double[20]

private

Definition at line 61 of file peptiderawfragmentmasses.h.

Constructor & Destructor Documentation

PeptideRawFragmentMasses()

pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses	(	const Peptide &	peptide,
		RawFragmentationMode	mode )

Definition at line 62 of file peptiderawfragmentmasses.cpp.

{
 
  qDebug() ;
  std::vector<Aa>::const_iterator it(peptide.begin());
  std::vector<Aa>::const_iterator end(peptide.end());
  if(it == end)
    return;
 
  pappso_double nter_internal =
    peptide.getCleavageNterModification()->getMass();
  pappso_double cter_internal =
    peptide.getCleavageCterModification()->getMass();
  qDebug() ;
  pappso_double cumulative_mass = it->getMass();
  if (peptide.getNterModification() != nullptr) {
    cumulative_mass += peptide.getNterModification()->getMass();
  }
  qDebug() ;
  m_cumulativeNterMasses.push_back(cumulative_mass);
  it++;
 
  if(it != end)
    {
      end--;
      qDebug() ;
      while(it != end)
        {
 
          qDebug() 
                   << " cumulative_mass=" << cumulative_mass;
          cumulative_mass += it->getMass();
          if((mode == RawFragmentationMode::proline_effect) &&
             (it->getLetter() == 'P'))
            {
            }
          else
            {
              m_cumulativeNterMasses.push_back(cumulative_mass);
            }
          it++;
        }
    }
 
  qDebug() ;
  std::vector<Aa>::const_reverse_iterator rit(peptide.rbegin());
  std::vector<Aa>::const_reverse_iterator ritf(peptide.rbegin());
  std::vector<Aa>::const_reverse_iterator rend(peptide.rend());
  ritf++;
  cumulative_mass = rit->getMass();
  if (peptide.getCterModification() != nullptr) {
    cumulative_mass += peptide.getCterModification()->getMass();
  }
  if((mode == RawFragmentationMode::proline_effect) && (ritf != rend) &&
     (ritf->getLetter() == 'P'))
    {
    }
  else
    {
      m_cumulativeCterMasses.push_back(cumulative_mass);
    }
  qDebug() ;
 
  rit++;
  ritf++;
  if(rit != rend)
    {
      rend--;
      while(rit != rend)
        {
          cumulative_mass += rit->getMass();
          if((mode == RawFragmentationMode::proline_effect) &&
             (ritf != peptide.rend()) && (ritf->getLetter() == 'P'))
            {
            }
          else
            {
              m_cumulativeCterMasses.push_back(cumulative_mass);
            }
          rit++;
          ritf++;
        }
    }
 
  qDebug() ;
}

References pappso::Peptide::begin(), pappso::Peptide::end(), pappso::Peptide::getCleavageCterModification(), pappso::Peptide::getCleavageNterModification(), pappso::Peptide::getCterModification(), pappso::AaModification::getMass(), pappso::Peptide::getNterModification(), m_cumulativeCterMasses, m_cumulativeNterMasses, pappso::proline_effect, pappso::Peptide::rbegin(), and pappso::Peptide::rend().

~PeptideRawFragmentMasses()

pappso::PeptideRawFragmentMasses::~PeptideRawFragmentMasses

(

)

Definition at line 231 of file peptiderawfragmentmasses.cpp.

{
}

Member Function Documentation

getDeltaMass()

pappso_double pappso::PeptideRawFragmentMasses::getDeltaMass ( Enums::PeptideIon ion_type )

static

Definition at line 56 of file peptiderawfragmentmasses.cpp.

{
  return m_ionDeltaMz[(std::int8_t)ion_type];
}

References m_ionDeltaMz.

Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), pappso::specglob::PeptideSpectrum::PeptideSpectrum(), and pappso::specglob::PeptideModel::generateTheoreticalPeaks().

pushBackIonMasses()

void pappso::PeptideRawFragmentMasses::pushBackIonMasses	(	std::vector< pappso_double > &	mass_list,
		Enums::PeptideIon	ion_type ) const

Definition at line 151 of file peptiderawfragmentmasses.cpp.

{
  const std::vector<pappso_double> *p_mass_list = &m_cumulativeCterMasses;
 
  if(peptideIonIsNter(ion_type))
    {
      // nter
      p_mass_list = &m_cumulativeNterMasses;
    }
 
  for(pappso_double mass : *p_mass_list)
    {
      mass_list.push_back(mass + m_ionDeltaMz[(std::int8_t)ion_type]);
    }
}

References m_cumulativeCterMasses, m_cumulativeNterMasses, m_ionDeltaMz, and pappso::peptideIonIsNter().

pushBackIonMz()

void pappso::PeptideRawFragmentMasses::pushBackIonMz	(	std::vector< pappso_double > &	mass_list,
		Enums::PeptideIon	ion_type,
		unsigned int	charge ) const

Definition at line 169 of file peptiderawfragmentmasses.cpp.

{
  const std::vector<pappso_double> *p_mass_list = &m_cumulativeCterMasses;
 
  if(peptideIonIsNter(ion_type))
    {
      // nter
      p_mass_list = &m_cumulativeNterMasses;
    }
 
  for(pappso_double mass : *p_mass_list)
    {
      mass_list.push_back(
        (mass + m_ionDeltaMz[(std::int8_t)ion_type] + (MHPLUS * charge)) /
        charge);
    }
}

References m_cumulativeCterMasses, m_cumulativeNterMasses, m_ionDeltaMz, pappso::MHPLUS(), and pappso::peptideIonIsNter().

Referenced by pappso::MorpheusScore::MorpheusScore(), and pushBackMatchSpectrum().

pushBackMatchSpectrum()

void pappso::PeptideRawFragmentMasses::pushBackMatchSpectrum	(	std::vector< SimplePeakIonMatch > &	peak_match_list,
		const MassSpectrum &	spectrum,
		PrecisionPtr	precision,
		Enums::PeptideIon	ion_type,
		unsigned int	charge ) const

Definition at line 190 of file peptiderawfragmentmasses.cpp.

{
  std::vector<pappso_double> mass_list;
  pushBackIonMz(mass_list, ion_type, charge);
 
  // no need to sort
  // std::sort(mass_list.begin(), mass_list.end());
 
  std::vector<pappso_double>::iterator it_mz     = mass_list.begin();
  std::vector<pappso_double>::iterator it_mz_end = mass_list.end();
 
  // scan products over each peak in spectrum :
  std::vector<DataPoint>::const_iterator it_peak     = spectrum.begin();
  std::vector<DataPoint>::const_iterator it_peak_end = spectrum.end();
  unsigned int ion_size                              = 1;
  while((it_peak != it_peak_end) && (it_mz != it_mz_end))
    {
      MzRange massrange(it_peak->x, precision);
      if((*it_mz) > massrange.upper())
        {
          it_peak++;
          continue;
        }
      if((*it_mz) < massrange.lower())
        {
          it_mz++;
          ion_size++;
          continue;
        }
      peak_match_list.push_back(
        {(*it_peak), ion_type, ion_size, charge, (*it_mz)});
      it_mz++;
      ion_size++;
    }
}

References pappso::MzRange::lower(), pushBackIonMz(), and pappso::MzRange::upper().

Referenced by pappso::XtandemHyperscoreBis::computeXtandemHyperscore().

Member Data Documentation

m_cumulativeCterMasses

std::vector<pappso_double> pappso::PeptideRawFragmentMasses::m_cumulativeCterMasses

private

cumulative Cter masses (without internal Cter modification)

Definition at line 72 of file peptiderawfragmentmasses.h.

Referenced by PeptideRawFragmentMasses(), pushBackIonMasses(), and pushBackIonMz().

m_cumulativeNterMasses

std::vector<pappso_double> pappso::PeptideRawFragmentMasses::m_cumulativeNterMasses

private

cumulative Nter masses (without internal Nter modification)

Definition at line 68 of file peptiderawfragmentmasses.h.

Referenced by PeptideRawFragmentMasses(), pushBackIonMasses(), and pushBackIonMz().

m_ionDeltaMz

PeptideRawFragmentMasses::ionDeltatMzMassMap pappso::PeptideRawFragmentMasses::m_ionDeltaMz

staticprivate

Initial value:

= {
    [(std::int8_t)Enums::PeptideIon::b]     = 0,
    [(std::int8_t)Enums::PeptideIon::bstar] = -MASSNH3,
    [(std::int8_t)Enums::PeptideIon::bo]    = -MASSH2O,
    [(std::int8_t)Enums::PeptideIon::a]     = -MASSCO,
    [(std::int8_t)Enums::PeptideIon::astar] = -MASSCO - MASSNH3,
    [(std::int8_t)Enums::PeptideIon::ao]    = -MASSCO - MASSH2O,
    [(std::int8_t)Enums::PeptideIon::bp]    = -1,
    [(std::int8_t)Enums::PeptideIon::c]     = MASSNH3,
    [(std::int8_t)Enums::PeptideIon::y]     = MASSH2O,
    [(std::int8_t)Enums::PeptideIon::ystar] = MASSH2O - MASSNH3,
    [(std::int8_t)Enums::PeptideIon::yo]    = 0,
    [(std::int8_t)Enums::PeptideIon::z]     = MASSOXYGEN - MASSNITROGEN - MPROTIUM,
    [(std::int8_t)Enums::PeptideIon::yp]    = -1,
    [(std::int8_t)Enums::PeptideIon::x]     = MASSCO + MASSOXYGEN}

Definition at line 64 of file peptiderawfragmentmasses.h.

Referenced by getDeltaMass(), pushBackIonMasses(), and pushBackIonMz().

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

• pappsomspp/core/peptide/peptiderawfragmentmasses.h
• pappsomspp/core/peptide/peptiderawfragmentmasses.cpp