pappso::PeptideSpectrumMatch Class Reference

#include <peptidespectrummatch.h>

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

Public Member Functions
	PeptideSpectrumMatch (const MassSpectrum &spectrum, const pappso::PeptideSp &peptideSp, unsigned int parent_charge, PrecisionPtr precision, const std::list< Enums::PeptideIon > &ion_type_list)
	PeptideSpectrumMatch (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &peptide_fragment_ion_list, unsigned int parent_charge, PrecisionPtr precision, const std::list< Enums::PeptideIon > &ion_type_list)
	PeptideSpectrumMatch (const MassSpectrum &spectrum, std::vector< PeptideFragmentIonSp > &v_peptide_fragment_ion, std::vector< unsigned int > &v_peptide_fragment_ion_charge, PrecisionPtr precision)
	PeptideSpectrumMatch (const PeptideSpectrumMatch &other)
virtual	~PeptideSpectrumMatch ()
bool	contains (const PeptideFragmentIon *peptideFragmentIonSp, unsigned int z) const
unsigned int	size () const
const_iterator	begin () const
const_iterator	end () const
unsigned int	countTotalMatchedIons () const
const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > &	getIonTypeCountArray () const

Private Member Functions
void	privMatchIonList (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &fragmentIonList, unsigned int max_charge, const std::list< Enums::PeptideIon > &ion_type_list)
virtual std::list< DataPoint >::iterator	getBestPeakIterator (std::list< DataPoint > &peak_list, const PeptideFragmentIonSp &ion, unsigned int charge) const

Private Attributes
PrecisionPtr	_precision
std::list< PeakIonMatch >	_peak_ion_match_list
std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT >	_ion_type_count = {{0}}

Detailed Description

Definition at line 43 of file peptidespectrummatch.h.

Member Typedef Documentation

const_iterator

typedef std::list<PeakIonMatch>::const_iterator pappso::PeptideSpectrumMatch::const_iterator

Definition at line 69 of file peptidespectrummatch.h.

Constructor & Destructor Documentation

PeptideSpectrumMatch() [1/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch	(	const MassSpectrum &	spectrum,
		const pappso::PeptideSp &	peptideSp,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		const std::list< Enums::PeptideIon > &	ion_type_list )

Definition at line 149 of file peptidespectrummatch.cpp.

  : _precision(precision)
{
  PeptideFragmentIonListBase fragmentIonList(peptideSp, ion_type_list);
  privMatchIonList(spectrum, fragmentIonList, parent_charge, ion_type_list);
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
           << " _ion_type_count[PeptideIon::y]=" << _ion_type_count[(std::int8_t)Enums::PeptideIon::y];
}

References _ion_type_count, _precision, privMatchIonList(), and pappso::Enums::y.

Referenced by PeptideSpectrumMatch().

PeptideSpectrumMatch() [2/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch	(	const MassSpectrum &	spectrum,
		const PeptideFragmentIonListBase &	peptide_fragment_ion_list,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		const std::list< Enums::PeptideIon > &	ion_type_list )

Definition at line 137 of file peptidespectrummatch.cpp.

  : _precision(precision)
{
  privMatchIonList(spectrum, fragmentIonList, max_charge, ion_type_list);
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
           << " _ion_type_count[PeptideIon::y]=" << _ion_type_count[(std::int8_t)Enums::PeptideIon::y];
}

References _ion_type_count, _precision, privMatchIonList(), and pappso::Enums::y.

PeptideSpectrumMatch() [3/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch	(	const MassSpectrum &	spectrum,
		std::vector< PeptideFragmentIonSp > &	v_peptide_fragment_ion,
		std::vector< unsigned int > &	v_peptide_fragment_ion_charge,
		PrecisionPtr	precision )

Definition at line 95 of file peptidespectrummatch.cpp.

  : _precision(precision)
{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  // throw PappsoException(QObject::tr("v_peptideIsotopeList.size() %1 !=
  // v_peptideIonList.size()
  // %2").arg(v_peptideIsotopeList.size()).arg(v_peptideIonList.size()));
  if(v_peptide_fragment_ion.size() != v_peptide_fragment_ion_charge.size())
    {
      throw PappsoException(QObject::tr("v_peptide_fragment_ion.size() != "
                                        "v_peptide_fragment_ion_charge.size() %2")
                              .arg(v_peptide_fragment_ion.size())
                              .arg(v_peptide_fragment_ion_charge.size()));
    }
 
 
  auto ionIt    = v_peptide_fragment_ion.begin();
  auto chargeIt = v_peptide_fragment_ion_charge.begin();
  std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
 
  while(ionIt != v_peptide_fragment_ion.end())
    {
      std::list<DataPoint>::iterator it_peak = getBestPeakIterator(peak_list, *ionIt, *chargeIt);
      if(it_peak != peak_list.end())
        {
          _peak_ion_match_list.push_back(PeakIonMatch(*it_peak, *ionIt, *chargeIt));
          _ion_type_count[(std::int8_t)ionIt->get()->getPeptideIonType()]++;
          peak_list.erase(it_peak);
        }
 
      ionIt++;
      chargeIt++;
    }
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
           << " _ion_type_count[PeptideIon::y]=" << _ion_type_count[(std::int8_t)Enums::PeptideIon::y];
}

References _ion_type_count, _peak_ion_match_list, _precision, getBestPeakIterator(), and pappso::Enums::y.

PeptideSpectrumMatch() [4/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch

(

const PeptideSpectrumMatch &

other

)

Definition at line 163 of file peptidespectrummatch.cpp.

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

References PeptideSpectrumMatch(), _peak_ion_match_list, and _precision.

~PeptideSpectrumMatch()

pappso::PeptideSpectrumMatch::~PeptideSpectrumMatch ( )

virtual

Definition at line 202 of file peptidespectrummatch.cpp.

{
}

Member Function Documentation

begin()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::begin

(

)

const

Definition at line 214 of file peptidespectrummatch.cpp.

{
  return _peak_ion_match_list.begin();
}

References _peak_ion_match_list.

contains()

bool pappso::PeptideSpectrumMatch::contains	(	const PeptideFragmentIon *	peptideFragmentIonSp,
		unsigned int	z ) const

Definition at line 237 of file peptidespectrummatch.cpp.

{
  auto it = _peak_ion_match_list.begin();
  while(it != _peak_ion_match_list.end())
    {
      const PeakIonMatch &ref = *it;
      if((ref.getCharge() == z) && (ref.getPeptideFragmentIonSp().get() == peptideFragmentIonSp))
        {
          return true;
        }
      it++;
    }
  return false;
}

References _peak_ion_match_list, pappso::PeakIonMatch::getCharge(), pappso::PeakIonMatch::getPeptideFragmentIonSp(), and pappso::z.

countTotalMatchedIons()

unsigned int pappso::PeptideSpectrumMatch::countTotalMatchedIons

(

)

const

Definition at line 225 of file peptidespectrummatch.cpp.

{
  return std::accumulate(_ion_type_count.begin(), _ion_type_count.end(), 0);
}

References _ion_type_count.

end()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::end

(

)

const

Definition at line 219 of file peptidespectrummatch.cpp.

{
  return _peak_ion_match_list.end();
}

References _peak_ion_match_list.

getBestPeakIterator()

std::list< DataPoint >::iterator pappso::PeptideSpectrumMatch::getBestPeakIterator ( std::list< DataPoint > & peak_list, const PeptideFragmentIonSp & ion, unsigned int charge ) const

privatevirtual

Definition at line 169 of file peptidespectrummatch.cpp.

{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
  //         << " peak_list.size()=" << peak_list.size();
  std::list<DataPoint>::iterator itpeak   = peak_list.begin();
  std::list<DataPoint>::iterator itend    = peak_list.end();
  std::list<DataPoint>::iterator itselect = peak_list.end();
 
  pappso_double best_intensity = 0;
 
  while(itpeak != itend)
    {
 
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
      //         << " itpeak->x=" << itpeak->x;
      if(ion.get()->matchPeak(_precision, itpeak->x, charge))
        {
          // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
          //         << " ion.get()->matchPeak";
          if(itpeak->y > best_intensity)
            {
              best_intensity = itpeak->y;
              itselect       = itpeak;
            }
        }
      itpeak++;
    }
 
  return (itselect);
}

References _precision.

Referenced by PeptideSpectrumMatch(), and privMatchIonList().

getIonTypeCountArray()

const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > & pappso::PeptideSpectrumMatch::getIonTypeCountArray

(

)

const

Definition at line 231 of file peptidespectrummatch.cpp.

{
  return _ion_type_count;
}

References _ion_type_count.

privMatchIonList()

void pappso::PeptideSpectrumMatch::privMatchIonList ( const MassSpectrum & spectrum, const PeptideFragmentIonListBase & fragmentIonList, unsigned int max_charge, const std::list< Enums::PeptideIon > & ion_type_list )

private

Definition at line 45 of file peptidespectrummatch.cpp.

{
 
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
  //         << " ion_type_list.size()=" << ion_type_list.size();
  std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
  //         << " peak_list.size()=" << peak_list.size();
  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;
  });
  for(auto ion_type : ion_type_list)
    {
      auto ion_list = fragmentIonList.getPeptideFragmentIonSp(ion_type);
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
      //         << " ion_list.size()=" << ion_list.size();
      for(unsigned int charge = 1; charge <= max_charge; charge++)
        {
          for(auto &&ion : ion_list)
            {
              std::list<DataPoint>::iterator it_peak = getBestPeakIterator(peak_list, ion, charge);
 
              if(it_peak != peak_list.end())
                {
 
                  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " <<
                  // __LINE__
                  //        << " peak FOUND";
                  _peak_ion_match_list.push_back(PeakIonMatch(*it_peak, ion, charge));
                  _ion_type_count[(std::int8_t)ion->getPeptideIonType()]++;
                  peak_list.erase(it_peak);
                }
            }
        }
    }
}

References _ion_type_count, _peak_ion_match_list, pappso::Enums::b, getBestPeakIterator(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), and pappso::Enums::y.

Referenced by PeptideSpectrumMatch(), and PeptideSpectrumMatch().

size()

unsigned int pappso::PeptideSpectrumMatch::size

(

)

const

Definition at line 208 of file peptidespectrummatch.cpp.

{
  return _peak_ion_match_list.size();
}

References _peak_ion_match_list.

Member Data Documentation

_ion_type_count

std::array<unsigned int, PEPTIDE_ION_TYPE_COUNT> pappso::PeptideSpectrumMatch::_ion_type_count = {{0}}

private

Definition at line 96 of file peptidespectrummatch.h.

{{0}};

Referenced by PeptideSpectrumMatch(), PeptideSpectrumMatch(), PeptideSpectrumMatch(), countTotalMatchedIons(), getIonTypeCountArray(), and privMatchIonList().

_peak_ion_match_list

std::list<PeakIonMatch> pappso::PeptideSpectrumMatch::_peak_ion_match_list

private

Definition at line 94 of file peptidespectrummatch.h.

Referenced by PeptideSpectrumMatch(), PeptideSpectrumMatch(), begin(), contains(), end(), privMatchIonList(), and size().

_precision

PrecisionPtr pappso::PeptideSpectrumMatch::_precision

private

Definition at line 92 of file peptidespectrummatch.h.

Referenced by PeptideSpectrumMatch(), PeptideSpectrumMatch(), PeptideSpectrumMatch(), PeptideSpectrumMatch(), and getBestPeakIterator().

---

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

• pappsomspp/core/psm/peptidespectrummatch.h
• pappsomspp/core/psm/peptidespectrummatch.cpp