pappso::PsmFeatures Class Reference

#include <psmfeatures.h>

Public Member Functions
	PsmFeatures (PrecisionPtr ms2precision, double minimumMz)
	compute psm features
	~PsmFeatures ()
void	setPeptideSpectrumCharge (const pappso::PeptideSp peptideSp, const MassSpectrum *p_spectrum, unsigned int parent_charge, unsigned int max_isotope_number)
double	getIntensityOfMatchedIon (Enums::PeptideIon ion_type)
	get the sum of intensity of a specific ion
double	getTotalIntensity () const
	sum of all peak intensities (matched or not)
double	getTotalIntensityOfMatchedIons () const
	sum of matched peak intensities
std::size_t	getNumberOfMatchedIons () const
	number of matched ions (peaks)
std::size_t	countMatchedIonComplementPairs () const
	count the number of matched ion complement
double	getTotalIntensityOfMatchedIonComplementPairs () const
	intensity of matched ion complement
const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > &	getPeakIonPairs () const
double	getMatchedMzDiffMean () const
	get mean deviation of matched peak mass delta
double	getMatchedMzDiffSd () const
	get standard deviation of matched peak mass delta
double	getMaxIntensityMatchedIonComplementPairPrecursorMassDelta () const
	get the precursor mass delta of the maximum intensity pair of complement ions
std::size_t	getMaxConsecutiveIon (Enums::PeptideIon ion_type)
	get the maximum consecutive fragments of one ion type
std::size_t	getAaSequenceCoverage (Enums::PeptideIon ion_type)
	number of amino acid covered by matched ions
std::size_t	getComplementPairsAaSequenceCoverage ()
	number of amino acid covered by matched complement pairs of ions
double	getMaxIntensityPeakIonMatch (Enums::PeptideIon ion_type) const
double	getIonPairPrecursorMassDelta (const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &ion_pair) const
LinearRegression	getIonIsotopeLinearRegression () const

Private Member Functions
void	findComplementIonPairs (const pappso::PeptideSp &peptideSp)

Private Attributes
std::shared_ptr< FilterResampleKeepGreater >	msp_filterKeepGreater
std::shared_ptr< PeptideIsotopeSpectrumMatch >	msp_peptideSpectrumMatch
pappso::PeptideSp	msp_peptide
PrecisionPtr	m_ms2precision
std::list< Enums::PeptideIon >	m_ionList
double	m_spectrumSumIntensity
double	m_precursorTheoreticalMz
double	m_precursorTheoreticalMass
unsigned int	m_parentCharge = 1
std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > >	m_peakIonPairs
double	m_matchedMzDiffMean = 0
double	m_matchedMzDiffMedian = 0
double	m_matchedMzDiffSd = 0

Detailed Description

Todo

write docs

Definition at line 45 of file psmfeatures.h.

Constructor & Destructor Documentation

PsmFeatures()

PsmFeatures::PsmFeatures	(	PrecisionPtr	ms2precision,
		double	minimumMz )

compute psm features

Parameters

ms2precision	precision of mass measurements for MS2 fragments
minimumMz	ignore mz values under this threshold

Definition at line 35 of file psmfeatures.cpp.

{
 
  m_ms2precision = ms2precision;
 
  m_ionList.push_back(Enums::PeptideIon::y);
  m_ionList.push_back(Enums::PeptideIon::b);
 
 
  msp_filterKeepGreater = std::make_shared<FilterResampleKeepGreater>(minimumMz);
 
  // msp_filterChargeDeconvolution =
  // std::make_shared<FilterChargeDeconvolution>(m_ms2precision);
  // msp_filterMzExclusion = std::make_shared<FilterMzExclusion>(
  // PrecisionFactory::getPrecisionPtrFractionInstance(m_ms2precision, 0.5));
}

References pappso::Enums::b, m_ionList, m_ms2precision, msp_filterKeepGreater, and pappso::Enums::y.

~PsmFeatures()

PsmFeatures::~PsmFeatures

(

)

Destructor

Definition at line 52 of file psmfeatures.cpp.

{
}

Member Function Documentation

countMatchedIonComplementPairs()

std::size_t pappso::PsmFeatures::countMatchedIonComplementPairs

(

)

const

count the number of matched ion complement

matched ion complement are ions with a sum compatible to the precursor mass

Definition at line 158 of file psmfeatures.cpp.

{
  return m_peakIonPairs.size();
}

References m_peakIonPairs.

findComplementIonPairs()

void pappso::PsmFeatures::findComplementIonPairs ( const pappso::PeptideSp & peptideSp )

private

Definition at line 343 of file psmfeatures.cpp.

{
  std::size_t peptide_size = peptideSp.get()->size();
  std::vector<PeakIonIsotopeMatch> ion_isotope_list(
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
  for(const pappso::PeakIonIsotopeMatch &peak_ion_ext : ion_isotope_list)
    {
      if(peptideIonIsNter(peak_ion_ext.getPeptideIonType()))
        {
          auto it = findComplementIonType(
            ion_isotope_list.begin(), ion_isotope_list.end(), peak_ion_ext, peptide_size);
          if(it != ion_isotope_list.end())
            { // contains the complementary ion
              m_peakIonPairs.push_back({peak_ion_ext, *it});
            }
        }
    }
}

References pappso::findComplementIonType(), m_peakIonPairs, msp_peptideSpectrumMatch, pappso::peptideIonIsNter(), and pappso::Peptide::size().

Referenced by setPeptideSpectrumCharge().

getAaSequenceCoverage()

std::size_t pappso::PsmFeatures::getAaSequenceCoverage

(

Enums::PeptideIon

ion_type

)

number of amino acid covered by matched ions

Definition at line 254 of file psmfeatures.cpp.

{
  std::vector<bool> covered;
  covered.resize(msp_peptide.get()->size(), false);
 
  for(auto &peak : msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
    {
      if(peak.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() == 0)
        { // only count with monotisotopic
          if(peak.getPeptideIonType() == ion_type)
            {
              covered[peak.getPeptideFragmentIonSp().get()->size() - 1] = true;
            }
        }
    }
  return std::count(covered.begin(), covered.end(), true);
}

References msp_peptide, and msp_peptideSpectrumMatch.

getComplementPairsAaSequenceCoverage()

std::size_t pappso::PsmFeatures::getComplementPairsAaSequenceCoverage

(

)

number of amino acid covered by matched complement pairs of ions

Definition at line 273 of file psmfeatures.cpp.

{
 
  std::vector<bool> covered;
  covered.resize(msp_peptide.get()->size(), false);
 
  for(auto &peak_pair : m_peakIonPairs)
    {
      std::size_t pos  = peak_pair.first.getPeptideFragmentIonSp().get()->size() - 1;
      covered[pos]     = true;
      covered[pos + 1] = true;
    }
  return std::count(covered.begin(), covered.end(), true);
}

References m_peakIonPairs, and msp_peptide.

getIntensityOfMatchedIon()

double PsmFeatures::getIntensityOfMatchedIon

(

Enums::PeptideIon

ion_type

)

get the sum of intensity of a specific ion

Parameters

ion_type

ion species (y, b, ...)

Definition at line 128 of file psmfeatures.cpp.

{
  double sum = 0;
  for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
    {
      if(peak_ion_match.getPeptideIonType() == ion_type)
        {
          sum += peak_ion_match.getPeak().y;
        }
    }
  return sum;
}

References msp_peptideSpectrumMatch.

getIonIsotopeLinearRegression()

LinearRegression pappso::PsmFeatures::getIonIsotopeLinearRegression

(

)

const

experimental use with caution

Definition at line 365 of file psmfeatures.cpp.

{
  std::size_t peptide_size = msp_peptide.get()->size();
  std::vector<PeakIonIsotopeMatch> ion_isotope_list(
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
 
  Trace scaterplot;
 
  for(Enums::PeptideIon ion_type : m_ionList)
    {
      std::vector<double> mono_th_intensities(peptide_size, 0);
      std::vector<double> isotope_th_intensities(peptide_size, 0);
 
      std::vector<double> mono_exp_intensities(peptide_size, 0);
      std::vector<double> isotope_exp_intensities(peptide_size, 0);
      for(const PeakIonIsotopeMatch &peak_ion_match : ion_isotope_list)
        {
          if(peak_ion_match.getPeptideIonType() == ion_type)
            {
              std::size_t vector_position =
                peak_ion_match.getPeptideFragmentIonSp().get()->size() - 1;
              PeptideNaturalIsotopeAverageSp iso_average_sp =
                peak_ion_match.getPeptideNaturalIsotopeAverageSp();
              if(iso_average_sp.get()->getIsotopeNumber() == 0)
                {
                  mono_th_intensities[vector_position]  = iso_average_sp.get()->getIntensityRatio();
                  mono_exp_intensities[vector_position] = peak_ion_match.getPeak().y;
                }
              else if(iso_average_sp.get()->getIsotopeNumber() == 1)
                {
                  isotope_th_intensities[vector_position] =
                    iso_average_sp.get()->getIntensityRatio();
                  isotope_exp_intensities[vector_position] = peak_ion_match.getPeak().y;
                }
            }
        }
 
      for(std::size_t i = 0; i < mono_th_intensities.size(); i++)
        {
          if((mono_th_intensities[i] != 0) && (isotope_th_intensities[i] != 0))
            {
              DataPoint xy(mono_th_intensities[i] / isotope_th_intensities[i],
                           mono_exp_intensities[i] / isotope_exp_intensities[i]);
              scaterplot.push_back(xy);
            }
        }
    }
 
  scaterplot.sortX();
 
  LinearRegression linear_regression(scaterplot);
 
  return linear_regression;
}

References pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), pappso::PeptideNaturalIsotopeAverage::getIsotopeNumber(), m_ionList, msp_peptide, msp_peptideSpectrumMatch, and pappso::Trace::sortX().

getIonPairPrecursorMassDelta()

double pappso::PsmFeatures::getIonPairPrecursorMassDelta

(

const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &

ion_pair

)

const

Definition at line 327 of file psmfeatures.cpp.

{
  qDebug() << m_precursorTheoreticalMz << " " << ion_pair.first.getPeak().x << " "
           << ion_pair.second.getPeak().x << " " << ion_pair.second.getCharge() << " "
           << ion_pair.first.getCharge() << " " << m_parentCharge;
  double diff = (m_precursorTheoreticalMass + (MHPLUS * ion_pair.first.getCharge())) /
                ion_pair.first.getCharge();
 
 
  return (diff - (ion_pair.first.getPeak().x + ion_pair.second.getPeak().x -
                  ((MHPLUS * ion_pair.first.getCharge())) / ion_pair.first.getCharge()));
}

References m_parentCharge, m_precursorTheoreticalMass, m_precursorTheoreticalMz, and pappso::MHPLUS().

Referenced by getMaxIntensityMatchedIonComplementPairPrecursorMassDelta().

getMatchedMzDiffMean()

double pappso::PsmFeatures::getMatchedMzDiffMean

(

)

const

get mean deviation of matched peak mass delta

Definition at line 189 of file psmfeatures.cpp.

{
  return m_matchedMzDiffMean;
}

References m_matchedMzDiffMean.

getMatchedMzDiffSd()

double pappso::PsmFeatures::getMatchedMzDiffSd

(

)

const

get standard deviation of matched peak mass delta

Definition at line 183 of file psmfeatures.cpp.

{
  return m_matchedMzDiffSd;
}

References m_matchedMzDiffSd.

getMaxConsecutiveIon()

std::size_t pappso::PsmFeatures::getMaxConsecutiveIon

(

Enums::PeptideIon

ion_type

)

get the maximum consecutive fragments of one ion type

Parameters

ion_type

ion species (y, b, ...)

Definition at line 202 of file psmfeatures.cpp.

{
  std::size_t max          = 0;
  auto peak_ion_match_list = msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
 
  peak_ion_match_list.erase(
    std::remove_if(peak_ion_match_list.begin(),
                   peak_ion_match_list.end(),
                   [ion_type](const PeakIonIsotopeMatch &a) {
                     if(a.getPeptideIonType() != ion_type)
                       return true;
                     if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() > 0)
                       return true;
                     return false;
                   }),
    peak_ion_match_list.end());
 
  peak_ion_match_list.sort([](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
    if(a.getCharge() < b.getCharge())
      return true;
    if(a.getPeptideIonType() < b.getPeptideIonType())
      return true;
    if(a.getPeptideFragmentIonSp().get()->size() < b.getPeptideFragmentIonSp().get()->size())
      return true;
    return false;
  });
 
  unsigned int charge = 0;
  std::size_t size    = 0;
  std::size_t count   = 0;
  for(std::list<PeakIonIsotopeMatch>::iterator it = peak_ion_match_list.begin();
      it != peak_ion_match_list.end();
      it++)
    {
      qDebug() << it->toString() << max << " " << it->getPeak().x << " "
               << it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
      count++;
      if((charge != it->getCharge()) || (size != (it->getPeptideFragmentIonSp().get()->size() - 1)))
        {
          count  = 1;
          charge = it->getCharge();
        }
      if(max < count)
        max = count;
 
      size = it->getPeptideFragmentIonSp().get()->size();
    }
 
  return max;
}

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

getMaxIntensityMatchedIonComplementPairPrecursorMassDelta()

double pappso::PsmFeatures::getMaxIntensityMatchedIonComplementPairPrecursorMassDelta

(

)

const

get the precursor mass delta of the maximum intensity pair of complement ions

Definition at line 309 of file psmfeatures.cpp.

{
  auto peak_it = std::max_element(
    m_peakIonPairs.begin(),
    m_peakIonPairs.end(),
    [](const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch> &a,
       const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch> &b) {
      return ((a.first.getPeak().y + a.second.getPeak().y) <
              (b.first.getPeak().y + b.second.getPeak().y));
    });
 
  if(peak_it == m_peakIonPairs.end())
    return 0;
 
  return getIonPairPrecursorMassDelta(*peak_it);
}

References pappso::a, pappso::b, getIonPairPrecursorMassDelta(), and m_peakIonPairs.

getMaxIntensityPeakIonMatch()

double pappso::PsmFeatures::getMaxIntensityPeakIonMatch

(

Enums::PeptideIon

ion_type

)

const

Definition at line 290 of file psmfeatures.cpp.

{
  std::list<pappso::PeakIonIsotopeMatch> peak_ion_type =
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
 
  peak_ion_type.remove_if(
    [ion_type](const PeakIonIsotopeMatch &a) { return (a.getPeptideIonType() != ion_type); });
  auto peak_it = std::max_element(peak_ion_type.begin(),
                                  peak_ion_type.end(),
                                  [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
                                    return (a.getPeak().y < b.getPeak().y);
                                  });
 
  if(peak_it == peak_ion_type.end())
    return 0;
  return peak_it->getPeak().y;
}

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

getNumberOfMatchedIons()

std::size_t pappso::PsmFeatures::getNumberOfMatchedIons

(

)

const

number of matched ions (peaks)

Definition at line 196 of file psmfeatures.cpp.

{
  return msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().size();
}

References msp_peptideSpectrumMatch.

getPeakIonPairs()

const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > & pappso::PsmFeatures::getPeakIonPairs

(

)

const

Definition at line 164 of file psmfeatures.cpp.

{
  return m_peakIonPairs;
}

References m_peakIonPairs.

getTotalIntensity()

double PsmFeatures::getTotalIntensity

(

)

const

sum of all peak intensities (matched or not)

Definition at line 152 of file psmfeatures.cpp.

{
  return m_spectrumSumIntensity;
}

References m_spectrumSumIntensity.

getTotalIntensityOfMatchedIonComplementPairs()

double pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs

(

)

const

intensity of matched ion complement

Definition at line 170 of file psmfeatures.cpp.

{
 
  double sum = 0;
  for(auto &peak_pairs : m_peakIonPairs)
    {
      sum += peak_pairs.first.getPeak().y;
      sum += peak_pairs.second.getPeak().y;
    }
  return sum;
}

References m_peakIonPairs.

getTotalIntensityOfMatchedIons()

double PsmFeatures::getTotalIntensityOfMatchedIons

(

)

const

sum of matched peak intensities

Definition at line 141 of file psmfeatures.cpp.

{
  double sum = 0;
  for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
    {
      sum += peak_ion_match.getPeak().y;
    }
  return sum;
}

References msp_peptideSpectrumMatch.

setPeptideSpectrumCharge()

void PsmFeatures::setPeptideSpectrumCharge	(	const pappso::PeptideSp	peptideSp,
		const MassSpectrum *	p_spectrum,
		unsigned int	parent_charge,
		unsigned int	max_isotope_number )

Definition at line 57 of file psmfeatures.cpp.

{
  m_peakIonPairs.clear();
  msp_peptide = peptideSp;
  MassSpectrum spectrum(*p_spectrum);
  msp_filterKeepGreater.get()->filter(spectrum);
  // msp_filterChargeDeconvolution.get()->filter(spectrum);
  // msp_filterMzExclusion.get()->filter(spectrum);
 
  msp_peptideSpectrumMatch = std::make_shared<PeptideIsotopeSpectrumMatch>(
    spectrum, peptideSp, parent_charge, m_ms2precision, m_ionList, max_isotope_number, 1);
 
  msp_peptideSpectrumMatch.get()->dropPeaksLackingMonoisotope();
  m_spectrumSumIntensity = spectrum.sumY();
 
 
  qDebug() << " accumulate";
  std::vector<double> delta_list;
 
 
  // TODO compute number of matched complementary peaks having m/z compatible
  // with the precursor
 
  m_precursorTheoreticalMz   = peptideSp.get()->getMz(parent_charge);
  m_precursorTheoreticalMass = peptideSp.get()->getMass();
  m_parentCharge             = parent_charge;
 
 
  findComplementIonPairs(peptideSp);
 
 
  for(const pappso::PeakIonIsotopeMatch &peak_ion :
      msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
    {
      delta_list.push_back(peak_ion.getPeptideFragmentIonSp().get()->getMz(peak_ion.getCharge()) -
                           peak_ion.getPeak().x);
    }
  pappso::pappso_double sum = std::accumulate(delta_list.begin(), delta_list.end(), 0);
 
  qDebug() << " delta_list.size()=" << delta_list.size();
  m_matchedMzDiffMean   = 0;
  m_matchedMzDiffMedian = 0;
  m_matchedMzDiffSd     = 0;
  if(delta_list.size() > 0)
    {
      m_matchedMzDiffMean = sum / ((pappso::pappso_double)delta_list.size());
 
      std::sort(delta_list.begin(), delta_list.end());
      m_matchedMzDiffMedian = delta_list[(delta_list.size() / 2)];
 
 
      qDebug() << " sd";
      m_matchedMzDiffSd = 0;
      for(pappso::pappso_double val : delta_list)
        {
          // sd = sd + ((val - mean) * (val - mean));
          m_matchedMzDiffSd += std::pow((val - m_matchedMzDiffMean), 2);
        }
      m_matchedMzDiffSd = m_matchedMzDiffSd / delta_list.size();
      m_matchedMzDiffSd = std::sqrt(m_matchedMzDiffSd);
    }
  else
    {
    }
}

References findComplementIonPairs(), pappso::Peptide::getMass(), pappso::Ion::getMz(), m_ionList, m_matchedMzDiffMean, m_matchedMzDiffMedian, m_matchedMzDiffSd, m_ms2precision, m_parentCharge, m_peakIonPairs, m_precursorTheoreticalMass, m_precursorTheoreticalMz, m_spectrumSumIntensity, msp_filterKeepGreater, msp_peptide, msp_peptideSpectrumMatch, and pappso::Trace::sumY().

Member Data Documentation

m_ionList

std::list<Enums::PeptideIon> pappso::PsmFeatures::m_ionList

private

Definition at line 149 of file psmfeatures.h.

Referenced by PsmFeatures(), getIonIsotopeLinearRegression(), and setPeptideSpectrumCharge().

m_matchedMzDiffMean

double pappso::PsmFeatures::m_matchedMzDiffMean = 0

private

Definition at line 159 of file psmfeatures.h.

Referenced by getMatchedMzDiffMean(), and setPeptideSpectrumCharge().

m_matchedMzDiffMedian

double pappso::PsmFeatures::m_matchedMzDiffMedian = 0

private

Definition at line 160 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

m_matchedMzDiffSd

double pappso::PsmFeatures::m_matchedMzDiffSd = 0

private

Definition at line 161 of file psmfeatures.h.

Referenced by getMatchedMzDiffSd(), and setPeptideSpectrumCharge().

m_ms2precision

PrecisionPtr pappso::PsmFeatures::m_ms2precision

private

Definition at line 148 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

m_parentCharge

unsigned int pappso::PsmFeatures::m_parentCharge = 1

private

Definition at line 155 of file psmfeatures.h.

Referenced by getIonPairPrecursorMassDelta(), and setPeptideSpectrumCharge().

m_peakIonPairs

std::vector<std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch> > pappso::PsmFeatures::m_peakIonPairs

private

Definition at line 157 of file psmfeatures.h.

Referenced by countMatchedIonComplementPairs(), findComplementIonPairs(), getComplementPairsAaSequenceCoverage(), getMaxIntensityMatchedIonComplementPairPrecursorMassDelta(), getPeakIonPairs(), getTotalIntensityOfMatchedIonComplementPairs(), and setPeptideSpectrumCharge().

m_precursorTheoreticalMass

double pappso::PsmFeatures::m_precursorTheoreticalMass

private

Definition at line 154 of file psmfeatures.h.

Referenced by getIonPairPrecursorMassDelta(), and setPeptideSpectrumCharge().

m_precursorTheoreticalMz

double pappso::PsmFeatures::m_precursorTheoreticalMz

private

Definition at line 153 of file psmfeatures.h.

Referenced by getIonPairPrecursorMassDelta(), and setPeptideSpectrumCharge().

m_spectrumSumIntensity

double pappso::PsmFeatures::m_spectrumSumIntensity

private

Definition at line 151 of file psmfeatures.h.

Referenced by getTotalIntensity(), and setPeptideSpectrumCharge().

msp_filterKeepGreater

std::shared_ptr<FilterResampleKeepGreater> pappso::PsmFeatures::msp_filterKeepGreater

private

Definition at line 143 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

msp_peptide

pappso::PeptideSp pappso::PsmFeatures::msp_peptide

private

Definition at line 146 of file psmfeatures.h.

Referenced by getAaSequenceCoverage(), getComplementPairsAaSequenceCoverage(), getIonIsotopeLinearRegression(), and setPeptideSpectrumCharge().

msp_peptideSpectrumMatch

std::shared_ptr<PeptideIsotopeSpectrumMatch> pappso::PsmFeatures::msp_peptideSpectrumMatch

private

Definition at line 145 of file psmfeatures.h.

Referenced by findComplementIonPairs(), getAaSequenceCoverage(), getIntensityOfMatchedIon(), getIonIsotopeLinearRegression(), getMaxConsecutiveIon(), getMaxIntensityPeakIonMatch(), getNumberOfMatchedIons(), getTotalIntensityOfMatchedIons(), and setPeptideSpectrumCharge().

---

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

• pappsomspp/core/psm/features/psmfeatures.h
• pappsomspp/core/psm/features/psmfeatures.cpp