#include <morpheusscore.h>

Public Member Functions
	MorpheusScore (const MassSpectrum &spectrum, pappso::PeptideSp peptideSp, unsigned int parent_charge, PrecisionPtr precision, std::vector< Enums::PeptideIon > ion_list, RawFragmentationMode fragmentation_mode)

	~MorpheusScore ()

pappso::pappso_double	getMorpheusScore () const

Private Attributes
pappso::pappso_double	_morpheus_score

Detailed Description

Definition at line 40 of file morpheusscore.h.

Constructor & Destructor Documentation

◆ MorpheusScore()

pappso::MorpheusScore::MorpheusScore	(	const MassSpectrum &	spectrum,
		pappso::PeptideSp	peptideSp,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		std::vector< Enums::PeptideIon >	ion_list,
		RawFragmentationMode	fragmentation_mode )

Definition at line 39 of file morpheusscore.cpp.

{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  PeptideRawFragmentMasses calc_mass_list_proline(*peptide_sp.get(),
                                                  fragmentation_mode);
 
  std::vector<pappso_double> ion_products;
  unsigned int charge = parent_charge;
  while(charge > 0)
    {
      for(Enums::PeptideIon &ion : ion_list)
        {
          calc_mass_list_proline.pushBackIonMz(ion_products, ion, charge);
        }
      charge--;
    }
 
 
  // compute the number of matched peaks
  unsigned int number_of_matched_peaks = 0;
 
  std::sort(ion_products.begin(), ion_products.end());
 
 
  // compute ratio of matched peaks on total peaks
  std::vector<pappso_double>::const_iterator it_theoretical =
    ion_products.begin();
  std::vector<pappso_double>::const_iterator it_theoretical_end =
    ion_products.end();
  std::vector<DataPoint>::const_iterator it_spectrum     = spectrum.begin();
  std::vector<DataPoint>::const_iterator it_spectrum_end = spectrum.end();
  pappso::pappso_double sum_intensities                  = 0;
  pappso::pappso_double sum_matched_intensities          = 0;
  // unsigned int peak_number                               = spectrum.size();
  while((it_spectrum != it_spectrum_end) &&
        (it_theoretical != it_theoretical_end))
    {
      sum_intensities += it_spectrum->y;
      MzRange peak_range(it_spectrum->x, precision);
 
      while((it_theoretical != it_theoretical_end) &&
            (*it_theoretical < peak_range.lower()))
        {
          it_theoretical++;
        }
      while((it_theoretical != it_theoretical_end) &&
            peak_range.contains(*it_theoretical))
        {
          sum_matched_intensities += it_spectrum->y;
          number_of_matched_peaks++;
          it_theoretical++;
        }
      it_spectrum++;
    }
  while(it_spectrum != it_spectrum_end)
    {
      sum_intensities += it_spectrum->y;
      it_spectrum++;
    }
 
 
  // compute the sum of matching peak intensities
 
  // morpheus score = number of matched peaks + matching intensities ratio
 
  _morpheus_score = (pappso_double)number_of_matched_peaks +
                    (sum_matched_intensities / sum_intensities);
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References _morpheus_score, pappso::MzRange::contains(), pappso::MzRange::lower(), and pappso::PeptideRawFragmentMasses::pushBackIonMz().

◆ ~MorpheusScore()

pappso::MorpheusScore::~MorpheusScore ( )

Definition at line 115 of file morpheusscore.cpp.

116{

117}

Member Function Documentation

◆ getMorpheusScore()

pappso::pappso_double pappso::MorpheusScore::getMorpheusScore ( ) const

Definition at line 120 of file morpheusscore.cpp.

{
  return _morpheus_score;
}

References _morpheus_score.

Member Data Documentation

◆ _morpheus_score

pappso::pappso_double pappso::MorpheusScore::_morpheus_score

private

Definition at line 54 of file morpheusscore.h.

Referenced by MorpheusScore(), and getMorpheusScore().

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

pappsomspp/core/psm/morpheus/morpheusscore.h
pappsomspp/core/psm/morpheus/morpheusscore.cpp

Public Member Functions

Private Attributes