#include <peptideisotopespectrummatch.h>

Public Types
typedef std::list< PeakIonIsotopeMatch >::const_iterator	const_iterator

Public Member Functions
	PeptideIsotopeSpectrumMatch (const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, const std::list< Enums::PeptideIon > &ion_type_list, unsigned int max_isotope_number, unsigned int max_isotope_rank)
	annotate spectrum with peptide ions and isotopes

	PeptideIsotopeSpectrumMatch (const MassSpectrum &spectrum, std::vector< PeptideNaturalIsotopeAverageSp > v_peptideIsotopeList, std::vector< PeptideFragmentIonSp > v_peptideIonList, PrecisionPtr precision)

	PeptideIsotopeSpectrumMatch (const PeptideIsotopeSpectrumMatch &other)

virtual	~PeptideIsotopeSpectrumMatch ()

const std::list< PeakIonIsotopeMatch > &	getPeakIonIsotopeMatchList () const

std::size_t	size () const

const_iterator	begin () const

const_iterator	end () const

void	dropPeaksLackingMonoisotope ()

Private Member Functions
virtual std::vector< DataPoint >::iterator	getBestPeakIterator (std::vector< DataPoint > &peak_list, const PeptideNaturalIsotopeAverage &ion) const

Private Attributes
PrecisionPtr	_precision

std::list< PeakIonIsotopeMatch >	_peak_ion_match_list

Detailed Description

Definition at line 39 of file peptideisotopespectrummatch.h.

Member Typedef Documentation

◆ const_iterator

typedef std::list<PeakIonIsotopeMatch>::const_iterator pappso::PeptideIsotopeSpectrumMatch::const_iterator

Definition at line 71 of file peptideisotopespectrummatch.h.

Constructor & Destructor Documentation

◆ PeptideIsotopeSpectrumMatch() [1/3]

pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch	(	const MassSpectrum &	spectrum,
		const PeptideSp &	peptide_sp,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		const std::list< Enums::PeptideIon > &	ion_type_list,
		unsigned int	max_isotope_number,
		unsigned int	max_isotope_rank )

annotate spectrum with peptide ions and isotopes

Parameters

spectrum	the spectrum to annotate
peptide_sp	peptide to fragment
parent_charge	charge of the ion parent
precision	MS2 mass measurement precision
ion_list	ion types to compute fragments
max_isotope_number	maximum isotope number to compute (0 means only monoisotope is computed)
max_isotope_rank	maximum rank inside isotope level to compute

Definition at line 31 of file peptideisotopespectrummatch.cpp.

  : _precision(precision)
{
 
  try
    {
      _peak_ion_match_list.clear();
      qDebug() << "peptideSp.get()->getSequence()=" << peptideSp.get()->getSequence()
               << " max_isotope_number=" << max_isotope_number
               << " spectrum.size=" << spectrum.size() << " parent_charge=" << parent_charge
               << " ion_type_list.size=" << ion_type_list_in.size()
               << " max_isotope_rank=" << max_isotope_rank;
      PeptideFragmentIonListBase fragmentIonList(peptideSp, ion_type_list_in);
      std::list<Enums::PeptideIon> ion_type_list(ion_type_list_in);
 
      ion_type_list.sort([](const Enums::PeptideIon &iona, const Enums::PeptideIon &ionb) {
        if(iona == Enums::PeptideIon::b)
          return true;
        if(ionb == Enums::PeptideIon::b)
          return false;
        if(iona == Enums::PeptideIon::y)
          return true;
        if(ionb == Enums::PeptideIon::y)
          return false;
        return iona > ionb;
      });
 
      qDebug() << " fragmentIonList.size()=" << fragmentIonList.size();
      std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
      for(auto ion_type : ion_type_list)
        {
          const std::list<PeptideFragmentIonSp> peptide_fragment_ion_list =
            fragmentIonList.getPeptideFragmentIonSp(ion_type);
          qDebug() << " peptide_fragment_ion_list.size()=" << peptide_fragment_ion_list.size();
 
          for(unsigned int charge = 1; charge <= parent_charge; charge++)
            {
              qDebug();
              for(auto &&peptide_fragment_ion : peptide_fragment_ion_list)
                {
                  qDebug() << "peptide_fragment_ion.get()->getMz(charge)="
                           << peptide_fragment_ion.get()->getMz(charge);
                  PeptideNaturalIsotopeList isotope_list(peptide_fragment_ion);
                  for(unsigned int isotope_number = 0; isotope_number <= max_isotope_number;
                      isotope_number++)
                    {
                      qDebug();
                      PeptideNaturalIsotopeAverage *p_isotopeIon;
                      if(max_isotope_rank == 0)
                        {
                          // fast constructor, no need to compute isotope ratio
                          p_isotopeIon = new PeptideNaturalIsotopeAverage(
                            peptide_fragment_ion, isotope_number, charge, precision);
                        }
                      else
                        {
                          p_isotopeIon = new PeptideNaturalIsotopeAverage(
                            isotope_list, max_isotope_rank, isotope_number, charge, precision);
                        }
 
                      qDebug() << "max_isotope_rank=" << max_isotope_rank
                               << " isotope_number=" << isotope_number << " charge=" << charge
                               << " precision=" << precision
                               << " p_isotopeIon->getMz()=" << p_isotopeIon->getMz() << " "
                               << isotope_number << " " << p_isotopeIon->toString();
 
                      std::vector<DataPoint>::iterator it_peak =
                        getBestPeakIterator(peak_list, *p_isotopeIon);
                      if(it_peak != peak_list.end())
                        {
                          _peak_ion_match_list.push_back(
                            PeakIonIsotopeMatch(*it_peak,
                                                p_isotopeIon->makePeptideNaturalIsotopeAverageSp(),
                                                peptide_fragment_ion));
                          peak_list.erase(it_peak);
 
                          qDebug()
                            << isotope_number << " " << _peak_ion_match_list.back().toString();
                        }
                      delete p_isotopeIon;
                    }
                }
            }
        }
    }
  catch(PappsoException &exception_pappso)
    {
      QString errorStr =
        QObject::tr("ERROR building PeptideIsotopeSpectrumMatch, PAPPSO exception:\n%1")
          .arg(exception_pappso.qwhat());
      qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
                  "PappsoException :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
  catch(std::exception &exception_std)
    {
      QString errorStr =
        QObject::tr("ERROR building PeptideIsotopeSpectrumMatch, std exception:\n%1")
          .arg(exception_std.what());
      qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
                  "std::exception :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
 
  qDebug() << "_peak_ion_match_list.size()=" << _peak_ion_match_list.size();
}

References _peak_ion_match_list, _precision, pappso::Enums::b, getBestPeakIterator(), pappso::PeptideNaturalIsotopeAverage::getMz(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp(), pappso::PappsoException::qwhat(), pappso::PeptideFragmentIonListBase::size(), pappso::PeptideNaturalIsotopeAverage::toString(), and pappso::Enums::y.

Referenced by PeptideIsotopeSpectrumMatch().

◆ PeptideIsotopeSpectrumMatch() [2/3]

pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch	(	const MassSpectrum &	spectrum,
		std::vector< PeptideNaturalIsotopeAverageSp >	v_peptideIsotopeList,
		std::vector< PeptideFragmentIonSp >	v_peptideIonList,
		PrecisionPtr	precision )

Definition at line 147 of file peptideisotopespectrummatch.cpp.

  : _precision(precision)
{
  qDebug() << " begin";
  if(v_peptideIsotopeList.size() != v_peptideIonList.size())
    {
      throw PappsoException(
        QObject::tr("v_peptideIsotopeList.size() %1 != v_peptideIonList.size() %2")
          .arg(v_peptideIsotopeList.size())
          .arg(v_peptideIonList.size()));
    }
 
  auto isotopeIt = v_peptideIsotopeList.begin();
  auto ionIt     = v_peptideIonList.begin();
  std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
 
  while(isotopeIt != v_peptideIsotopeList.end())
    {
      std::vector<DataPoint>::iterator it_peak =
        getBestPeakIterator(peak_list, *(isotopeIt->get()));
      if(it_peak != peak_list.end())
        {
          _peak_ion_match_list.push_back(PeakIonIsotopeMatch(*it_peak, *isotopeIt, *ionIt));
          peak_list.erase(it_peak);
        }
      isotopeIt++;
      ionIt++;
    }
  qDebug() << "_peak_ion_match_list.size()=" << _peak_ion_match_list.size() << " end";
}

References _peak_ion_match_list, _precision, and getBestPeakIterator().

◆ PeptideIsotopeSpectrumMatch() [3/3]

pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch ( const PeptideIsotopeSpectrumMatch & other )

Definition at line 183 of file peptideisotopespectrummatch.cpp.

  : _precision(other._precision), _peak_ion_match_list(other._peak_ion_match_list)
{
  qDebug();
}

References PeptideIsotopeSpectrumMatch(), _peak_ion_match_list, and _precision.

◆ ~PeptideIsotopeSpectrumMatch()

pappso::PeptideIsotopeSpectrumMatch::~PeptideIsotopeSpectrumMatch ( )

virtual

Definition at line 189 of file peptideisotopespectrummatch.cpp.

190{

191}

Member Function Documentation

◆ begin()

PeptideIsotopeSpectrumMatch::const_iterator pappso::PeptideIsotopeSpectrumMatch::begin ( ) const

Definition at line 235 of file peptideisotopespectrummatch.cpp.

{
  return _peak_ion_match_list.begin();
}

References _peak_ion_match_list.

◆ dropPeaksLackingMonoisotope()

void pappso::PeptideIsotopeSpectrumMatch::dropPeaksLackingMonoisotope ( )

Definition at line 246 of file peptideisotopespectrummatch.cpp.

{
  qDebug();
  _peak_ion_match_list.sort([](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
    if(a.getPeptideIonType() < b.getPeptideIonType())
      return true;
    if(a.getPeptideFragmentIonSp().get()->size() < b.getPeptideFragmentIonSp().get()->size())
      return true;
    if(a.getCharge() < b.getCharge())
      return true;
    if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() <
       b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
      return true;
    return false;
  });
  Enums::PeptideIon ion_type      = Enums::PeptideIon::b;
  std::size_t nserie       = 0;
  std::size_t isotopeserie = 0;
  unsigned int charge      = 0;
  for(std::list<PeakIonIsotopeMatch>::iterator it = _peak_ion_match_list.begin();
      it != _peak_ion_match_list.end();
      it++)
    {
      if((nserie != it->getPeptideFragmentIonSp().get()->size()) ||
         (ion_type != it->getPeptideIonType()) || (charge != it->getCharge()))
        {
          ion_type     = it->getPeptideIonType();
          isotopeserie = 0;
          nserie       = it->getPeptideFragmentIonSp().get()->size();
          charge       = it->getCharge();
        }
      if(isotopeserie <= it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
        {
          isotopeserie = it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
        }
      else
        {
          it = _peak_ion_match_list.erase(it);
        }
    }
  qDebug();
}

References _peak_ion_match_list, pappso::a, pappso::Enums::b, and pappso::b.

◆ end()

PeptideIsotopeSpectrumMatch::const_iterator pappso::PeptideIsotopeSpectrumMatch::end ( ) const

Definition at line 240 of file peptideisotopespectrummatch.cpp.

{
  return _peak_ion_match_list.end();
}

References _peak_ion_match_list.

◆ getBestPeakIterator()

std::vector< DataPoint >::iterator pappso::PeptideIsotopeSpectrumMatch::getBestPeakIterator	(	std::vector< DataPoint > &	peak_list,
		const PeptideNaturalIsotopeAverage &	ion ) const

privatevirtual

Definition at line 195 of file peptideisotopespectrummatch.cpp.

{
  // qDebug();
  std::vector<DataPoint>::iterator itpeak   = peak_list.begin();
  std::vector<DataPoint>::iterator itend    = peak_list.end();
  std::vector<DataPoint>::iterator itselect = peak_list.end();
 
  pappso_double best_intensity = 0;
 
  while(itpeak != itend)
    {
      // qDebug() << itpeak->x;
      if(ion.matchPeak(itpeak->x))
        {
          if(itpeak->y > best_intensity)
            {
              best_intensity = itpeak->y;
              itselect       = itpeak;
            }
        }
      itpeak++;
    }
  // qDebug();
  return (itselect);
}

References pappso::PeptideNaturalIsotopeAverage::matchPeak().

Referenced by PeptideIsotopeSpectrumMatch(), and PeptideIsotopeSpectrumMatch().

◆ getPeakIonIsotopeMatchList()

const std::list< PeakIonIsotopeMatch > & pappso::PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList ( ) const

Definition at line 223 of file peptideisotopespectrummatch.cpp.

{
  qDebug() << "_peak_ion_match_list.size()=" << _peak_ion_match_list.size();
  return _peak_ion_match_list;
}

References _peak_ion_match_list.

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), and pappso::MassSpectrumWidget::peptideAnnotate().

◆ size()

std::size_t pappso::PeptideIsotopeSpectrumMatch::size ( ) const

Definition at line 230 of file peptideisotopespectrummatch.cpp.

{
  return _peak_ion_match_list.size();
}

References _peak_ion_match_list.

Member Data Documentation

◆ _peak_ion_match_list

std::list<PeakIonIsotopeMatch> pappso::PeptideIsotopeSpectrumMatch::_peak_ion_match_list

private

Definition at line 85 of file peptideisotopespectrummatch.h.

Referenced by PeptideIsotopeSpectrumMatch(), PeptideIsotopeSpectrumMatch(), PeptideIsotopeSpectrumMatch(), begin(), dropPeaksLackingMonoisotope(), end(), getPeakIonIsotopeMatchList(), and size().

◆ _precision

PrecisionPtr pappso::PeptideIsotopeSpectrumMatch::_precision

private

Definition at line 84 of file peptideisotopespectrummatch.h.

Referenced by PeptideIsotopeSpectrumMatch(), PeptideIsotopeSpectrumMatch(), and PeptideIsotopeSpectrumMatch().

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

pappsomspp/core/psm/peptideisotopespectrummatch.h
pappsomspp/core/psm/peptideisotopespectrummatch.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ const_iterator

Constructor & Destructor Documentation

◆ PeptideIsotopeSpectrumMatch() [1/3]

◆ PeptideIsotopeSpectrumMatch() [2/3]

◆ PeptideIsotopeSpectrumMatch() [3/3]

◆ ~PeptideIsotopeSpectrumMatch()

Member Function Documentation

◆ begin()

◆ dropPeaksLackingMonoisotope()

◆ end()

◆ getBestPeakIterator()

◆ getPeakIonIsotopeMatchList()

◆ size()

Member Data Documentation

◆ _peak_ion_match_list

◆ _precision