pappso::IonIsotopeRatioScore Class Reference

#include <ionisotoperatioscore.h>

Public Member Functions
	IonIsotopeRatioScore (const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, std::vector< Enums::PeptideIon > ion_list)
virtual	~IonIsotopeRatioScore ()
pappso::pappso_double	getIonIsotopeRatioScore () const

Private Attributes
pappso::pappso_double	m_ionIsotopeRatioScore

Detailed Description

Definition at line 36 of file ionisotoperatioscore.h.

Constructor & Destructor Documentation

IonIsotopeRatioScore()

IonIsotopeRatioScore::IonIsotopeRatioScore	(	const MassSpectrum &	spectrum,
		const PeptideSp &	peptide_sp,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		std::vector< Enums::PeptideIon >	ion_list )

Definition at line 34 of file ionisotoperatioscore.cpp.

{
  std::list<Enums::PeptideIon> ion_list(ion_vector.begin(), ion_vector.end());
  PeptideIsotopeSpectrumMatch psm_match(
    spectrum, peptide_sp, parent_charge, precision, ion_list, 1, 1);
 
  Trace scaterplot;
 
  for(Enums::PeptideIon ion_type : ion_vector)
    {
      std::vector<double> mono_th_intensities(peptide_sp.get()->size(), 0);
      std::vector<double> isotope_th_intensities(peptide_sp.get()->size(), 0);
 
      std::vector<double> mono_exp_intensities(peptide_sp.get()->size(), 0);
      std::vector<double> isotope_exp_intensities(peptide_sp.get()->size(), 0);
      for(const PeakIonIsotopeMatch &peak_ion_match :
          psm_match.getPeakIonIsotopeMatchList())
        {
          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);
 
  m_ionIsotopeRatioScore = linear_regression.getCoefficientOfDetermination();
}

References pappso::LinearRegression::getCoefficientOfDetermination(), pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), pappso::PeptideNaturalIsotopeAverage::getIsotopeNumber(), pappso::PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList(), m_ionIsotopeRatioScore, pappso::Peptide::size(), and pappso::Trace::sortX().

~IonIsotopeRatioScore()

IonIsotopeRatioScore::~IonIsotopeRatioScore ( )

virtual

Definition at line 99 of file ionisotoperatioscore.cpp.

{
}

Member Function Documentation

getIonIsotopeRatioScore()

pappso::pappso_double IonIsotopeRatioScore::getIonIsotopeRatioScore

(

)

const

Definition at line 104 of file ionisotoperatioscore.cpp.

{
  return m_ionIsotopeRatioScore;
}

References m_ionIsotopeRatioScore.

Member Data Documentation

m_ionIsotopeRatioScore

pappso::pappso_double pappso::IonIsotopeRatioScore::m_ionIsotopeRatioScore

private

Definition at line 49 of file ionisotoperatioscore.h.

Referenced by IonIsotopeRatioScore(), and getIonIsotopeRatioScore().

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

• pappsomspp/core/psm/experimental/ionisotoperatioscore.h
• pappsomspp/core/psm/experimental/ionisotoperatioscore.cpp