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< PeptideIon > &ion_type_list)
	PeptideSpectrumMatch (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &peptide_fragment_ion_list, unsigned int parent_charge, PrecisionPtr precision, const std::list< 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)
	~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< 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 62 of file peptidespectrummatch.h.

Member Typedef Documentation

const_iterator

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

Definition at line 108 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< PeptideIon > &	ion_type_list
	)

Definition at line 166 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;

PeptideSpectrumMatch() [2/4]

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

Definition at line 152 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)PeptideIon::y];
}
 
 
PeptideSpectrumMatch::PeptideSpectrumMatch(const PeptideSpectrumMatch &other)
  : _precision(other._precision),
    _peak_ion_match_list(other._peak_ion_match_list)

References pappso::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 106 of file peptidespectrummatch.cpp.

    {
      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)PeptideIon::y];
}
 
 
PeptideSpectrumMatch::PeptideSpectrumMatch(
  const MassSpectrum &spectrum,
  const PeptideFragmentIonListBase &fragmentIonList,
  unsigned int max_charge,
  PrecisionPtr precision,
  const std::list<PeptideIon> &ion_type_list)
  : _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)PeptideIon::y];
}
 
PeptideSpectrumMatch::PeptideSpectrumMatch(
  const MassSpectrum &spectrum,
  const pappso::PeptideSp &peptideSp,
  unsigned int parent_charge,

References _ion_type_count, _peak_ion_match_list, and getBestPeakIterator().

PeptideSpectrumMatch() [4/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch

(

const PeptideSpectrumMatch &

other

)

Definition at line 182 of file peptidespectrummatch.cpp.

    {
 
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
      //         << " itpeak->x=" << itpeak->x;
      if(ion.get()->matchPeak(_precision, itpeak->x, charge))

References _precision.

~PeptideSpectrumMatch()

pappso::PeptideSpectrumMatch::~PeptideSpectrumMatch

(

)

Definition at line 222 of file peptidespectrummatch.cpp.

Member Function Documentation

begin()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::begin

(

)

const

Definition at line 234 of file peptidespectrummatch.cpp.

{

contains()

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

Definition at line 257 of file peptidespectrummatch.cpp.

countTotalMatchedIons()

unsigned int pappso::PeptideSpectrumMatch::countTotalMatchedIons

(

)

const

Definition at line 245 of file peptidespectrummatch.cpp.

        {
          return true;
        }

end()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::end

(

)

const

Definition at line 239 of file peptidespectrummatch.cpp.

{
  auto it = _peak_ion_match_list.begin();
  while(it != _peak_ion_match_list.end())
    {

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

getBestPeakIterator()

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

privatevirtual

Definition at line 189 of file peptidespectrummatch.cpp.

            {
              best_intensity = itpeak->y;
              itselect       = itpeak;
            }
        }
      itpeak++;
    }
 
  return (itselect);
}
 
PeptideSpectrumMatch::~PeptideSpectrumMatch()
{
}
 
 
unsigned int
PeptideSpectrumMatch::size() const
{
  return _peak_ion_match_list.size();
}
 
PeptideSpectrumMatch::const_iterator
PeptideSpectrumMatch::begin() const
{
  return _peak_ion_match_list.begin();
}
PeptideSpectrumMatch::const_iterator
PeptideSpectrumMatch::end() const
{

Referenced by PeptideSpectrumMatch(), and privMatchIonList().

getIonTypeCountArray()

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

(

)

const

Definition at line 251 of file peptidespectrummatch.cpp.

privMatchIonList()

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

private

Definition at line 65 of file peptidespectrummatch.cpp.

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

References _ion_type_count, _peak_ion_match_list, and getBestPeakIterator().

size()

unsigned int pappso::PeptideSpectrumMatch::size

(

)

const

Definition at line 228 of file peptidespectrummatch.cpp.

{

Member Data Documentation

_ion_type_count

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

private

Definition at line 135 of file peptidespectrummatch.h.

Referenced by PeptideSpectrumMatch(), and privMatchIonList().

_peak_ion_match_list

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

private

Definition at line 133 of file peptidespectrummatch.h.

Referenced by end(), PeptideSpectrumMatch(), and privMatchIonList().

_precision

PrecisionPtr pappso::PeptideSpectrumMatch::_precision

private

Definition at line 131 of file peptidespectrummatch.h.

Referenced by PeptideSpectrumMatch().

---

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

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