#include <xtandemhyperscorebis.h>

Public Member Functions
	XtandemHyperscoreBis (bool refine_spectrum_synthesis, PrecisionPtr precision, const std::vector< Enums::PeptideIon > &ion_list)

	~XtandemHyperscoreBis ()

pappso_double	getHyperscore () const

unsigned int	getMatchedIons (Enums::PeptideIon ion_type) const

void	reset ()

bool	computeXtandemHyperscore (const MassSpectrum &spectrum, const Peptide &peptide, unsigned int parent_charge)

unsigned int	getTotalMatchedIons () const

Private Types
using	AaFactorMap = std::map<char, pappso_double>

Private Member Functions
unsigned int	getXtandemPredictedIonIntensityFactor (const QString &sequence, Enums::PeptideIon ion_type, unsigned int size) const

Private Attributes
bool	m_isRefineSpectrumSynthesis

PrecisionPtr	mp_precision

std::vector< Enums::PeptideIon >	m_ionList

unsigned int	m_totalMatchedIons = 0

unsigned int	m_ionCount [PEPTIDE_ION_TYPE_COUNT] = {0}

pappso_double	m_protoHyperscore

Static Private Attributes
static AaFactorMap	m_aaIonFactorY

static AaFactorMap	m_aaIonFactorBb

Detailed Description

Definition at line 40 of file xtandemhyperscorebis.h.

Member Typedef Documentation

◆ AaFactorMap

using pappso::XtandemHyperscoreBis::AaFactorMap = std::map<char, pappso_double>

private

Definition at line 42 of file xtandemhyperscorebis.h.

Constructor & Destructor Documentation

◆ XtandemHyperscoreBis()

XtandemHyperscoreBis::XtandemHyperscoreBis	(	bool	refine_spectrum_synthesis,
		PrecisionPtr	precision,
		const std::vector< Enums::PeptideIon > &	ion_list )

Definition at line 50 of file xtandemhyperscorebis.cpp.

{
 
  m_isRefineSpectrumSynthesis = refine_spectrum_synthesis;
  mp_precision                = precision;
  m_ionList                   = ion_list;
  m_totalMatchedIons          = 0;
}

References m_ionList, m_isRefineSpectrumSynthesis, m_totalMatchedIons, and mp_precision.

◆ ~XtandemHyperscoreBis()

XtandemHyperscoreBis::~XtandemHyperscoreBis ( )

Definition at line 62 of file xtandemhyperscorebis.cpp.

63{

64}

Member Function Documentation

◆ computeXtandemHyperscore()

bool XtandemHyperscoreBis::computeXtandemHyperscore	(	const MassSpectrum &	spectrum,
		const Peptide &	peptide,
		unsigned int	parent_charge )

Definition at line 85 of file xtandemhyperscorebis.cpp.

{
  try
    {
 
      unsigned int max_charge = parent_charge;
      if(parent_charge > 1)
        {
          max_charge = parent_charge - 1;
        }
      // PeptideSpectrumMatch psm (spectrum, peptideSp, max_charge, precision,
      // ion_list);
 
      PeptideRawFragmentMasses calc_mass_list(peptide,
                                              RawFragmentationMode::full);
 
      std::vector<SimplePeakIonMatch> match_products;
      unsigned int charge_i;
      for(Enums::PeptideIon &ion : m_ionList)
        {
          charge_i = max_charge;
          while(charge_i > 0)
            {
              calc_mass_list.pushBackMatchSpectrum(
                match_products, spectrum, mp_precision, ion, charge_i);
              charge_i--;
            }
        }
      m_totalMatchedIons = match_products.size();
      if(m_totalMatchedIons == 0)
        {
          m_protoHyperscore = 0;
        }
      else
        {
 
          unsigned int charge_ion_count[5][20] = {0};
 
          pappso_double charge_dot_product[5] = {0};
 
          QString sequence = peptide.getSequence();
 
          for(SimplePeakIonMatch &peptide_ion_match : match_products)
            {
              charge_dot_product[peptide_ion_match.ion_charge] +=
                peptide_ion_match.peak.y *
                getXtandemPredictedIonIntensityFactor(
                  sequence,
                  peptide_ion_match.ion_type,
                  peptide_ion_match.ion_size);
              charge_ion_count[peptide_ion_match.ion_charge]
                              [(std::int8_t)peptide_ion_match.ion_type] += 1;
              m_ionCount[(std::int8_t)peptide_ion_match.ion_type] += 1;
            }
          // take the 2 best component
          pappso_double sum_intensity = 0;
          for(unsigned int i = 1; i <= max_charge; i++)
            {
              sum_intensity += charge_dot_product[i];
            }
          for(auto count : m_ionCount)
            {
              sum_intensity *= factorial(count);
            }
 
          m_protoHyperscore = sum_intensity;
        }
      return true;
    }
  catch(PappsoException &exception_pappso)
    {
      QString errorStr =
        QObject::tr("ERROR computing hyperscore, PAPPSO exception:\n%1")
          .arg(exception_pappso.qwhat());
      qDebug() << "XtandemHyperscore::XtandemHyperscore PappsoException :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
  catch(std::exception &exception_std)
    {
      QString errorStr =
        QObject::tr("ERROR computing hyperscore, std exception:\n%1")
          .arg(exception_std.what());
      qDebug() << "XtandemHyperscore::XtandemHyperscore std::exception :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
}

References pappso::factorial(), pappso::full, pappso::Peptide::getSequence(), getXtandemPredictedIonIntensityFactor(), m_ionCount, m_ionList, m_protoHyperscore, m_totalMatchedIons, mp_precision, pappso::PeptideRawFragmentMasses::pushBackMatchSpectrum(), and pappso::PappsoException::qwhat().

◆ getHyperscore()

pappso_double XtandemHyperscoreBis::getHyperscore ( ) const

Definition at line 269 of file xtandemhyperscorebis.cpp.

{
  try
    {
      if(m_protoHyperscore == 0)
        return 0.0;
      return (log10(m_protoHyperscore) * 4);
    }
  catch(PappsoException &exception_pappso)
    {
      QString errorStr =
        QObject::tr("ERROR in getHyperscore, PAPPSO exception:\n%1")
          .arg(exception_pappso.qwhat());
      qDebug() << "XtandemHyperscore::getHyperscore PappsoException :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
  catch(std::exception &exception_std)
    {
      QString errorStr =
        QObject::tr("ERROR in getHyperscore, std exception:\n%1")
          .arg(exception_std.what());
      qDebug() << "XtandemHyperscore::getHyperscore std::exception :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
}

References m_protoHyperscore, and pappso::PappsoException::qwhat().

◆ getMatchedIons()

unsigned int XtandemHyperscoreBis::getMatchedIons ( Enums::PeptideIon ion_type ) const

Definition at line 67 of file xtandemhyperscorebis.cpp.

{
  return m_ionCount[(std::int8_t)ion_type];
}

References m_ionCount.

◆ getTotalMatchedIons()

unsigned int XtandemHyperscoreBis::getTotalMatchedIons ( ) const

Definition at line 263 of file xtandemhyperscorebis.cpp.

{
  return m_totalMatchedIons;
}

References m_totalMatchedIons.

◆ getXtandemPredictedIonIntensityFactor()

unsigned int XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor	(	const QString &	sequence,
		Enums::PeptideIon	ion_type,
		unsigned int	size ) const

private

Definition at line 208 of file xtandemhyperscorebis.cpp.

{
  unsigned int Pi(1);
 
  char last_aa_nter('_'), last_aa_cter('_');
 
  if(peptideIonIsNter(ion_type))
    {
      last_aa_nter = sequence[ion_size - 1].toLatin1();
      last_aa_cter = sequence[ion_size].toLatin1();
      if(ion_size == 2)
        {
          if(last_aa_nter == 'P')
            {
              Pi *= 10;
            }
          else
            {
              Pi *= 3;
            }
        }
    }
  else
    {
      unsigned int offset(sequence.size() - ion_size);
      last_aa_nter = sequence[offset - 1].toLatin1();
      last_aa_cter = sequence[offset].toLatin1();
      if((offset) == 2)
        {
          if(last_aa_nter == 'P')
            {
              Pi *= 10;
            }
          else
            {
              Pi *= 3;
            }
        }
    }
  // QDebug << " last_aa_nter=" << QChar(last_aa_nter) << "
  // m_aaIonFactorBb[last_aa_nter]="s ;
  // qDebug() << PeptideFragment::getPeptideIonDirectionName(ion_direction) << "
  // last_aa_nter=" << last_aa_nter << " m_aaIonFactorBb[last_aa_nter]=" <<
  // m_aaIonFactorBb[last_aa_nter] << " last_aa_cter=" << last_aa_cter << "
  // m_aaIonFactorY[last_aa_cter]=" << m_aaIonFactorY[last_aa_cter];
  if(m_isRefineSpectrumSynthesis)
    {
      Pi *= m_aaIonFactorBb[last_aa_nter] * m_aaIonFactorY[last_aa_cter];
    }
 
  return Pi;
}

References m_aaIonFactorBb, m_aaIonFactorY, m_isRefineSpectrumSynthesis, and pappso::peptideIonIsNter().

Referenced by computeXtandemHyperscore().

◆ reset()

void XtandemHyperscoreBis::reset ( )

Definition at line 74 of file xtandemhyperscorebis.cpp.

{
 
  std::fill(m_ionCount, m_ionCount + PEPTIDE_ION_TYPE_COUNT, 0);
 
  m_totalMatchedIons = 0;
  m_protoHyperscore  = 0;
}

References m_ionCount, m_protoHyperscore, m_totalMatchedIons, and PEPTIDE_ION_TYPE_COUNT.

Member Data Documentation

◆ m_aaIonFactorBb

XtandemHyperscoreBis::AaFactorMap XtandemHyperscoreBis::m_aaIonFactorBb

staticprivate

Initial value:

= [] {
  AaFactorMap ret;
  
  for(long c = 64; c < 126; c++)
    {
      ret.insert(std::pair<char, pappso_double>(c, pappso_double(1.0)));
    }
  ret['D'] = pappso_double(5.0);
  ret['N'] = pappso_double(2.0);
  ret['V'] = pappso_double(3.0);
  ret['E'] = pappso_double(3.0);
  ret['Q'] = pappso_double(2.0);
  ret['I'] = pappso_double(3.0);
  ret['L'] = pappso_double(3.0);
  return ret;
}()

Definition at line 59 of file xtandemhyperscorebis.h.

Referenced by getXtandemPredictedIonIntensityFactor().

◆ m_aaIonFactorY

XtandemHyperscoreBis::AaFactorMap XtandemHyperscoreBis::m_aaIonFactorY

staticprivate

Initial value:

= [] {
  AaFactorMap ret;
  
  for(long c = 64; c < 126; c++)
    {
      ret.insert(std::pair<char, pappso_double>(c, pappso_double(1.0)));
    }
  ret['P'] = pappso_double(5.0);
  return ret;
}()

Definition at line 58 of file xtandemhyperscorebis.h.

Referenced by getXtandemPredictedIonIntensityFactor().

◆ m_ionCount

unsigned int pappso::XtandemHyperscoreBis::m_ionCount[PEPTIDE_ION_TYPE_COUNT] = {0}

private

Definition at line 53 of file xtandemhyperscorebis.h.

53{0};

Referenced by computeXtandemHyperscore(), getMatchedIons(), and reset().

◆ m_ionList

std::vector<Enums::PeptideIon> pappso::XtandemHyperscoreBis::m_ionList

private

Definition at line 50 of file xtandemhyperscorebis.h.

Referenced by XtandemHyperscoreBis(), and computeXtandemHyperscore().

◆ m_isRefineSpectrumSynthesis

bool pappso::XtandemHyperscoreBis::m_isRefineSpectrumSynthesis

private

Definition at line 48 of file xtandemhyperscorebis.h.

Referenced by XtandemHyperscoreBis(), and getXtandemPredictedIonIntensityFactor().

◆ m_protoHyperscore

pappso_double pappso::XtandemHyperscoreBis::m_protoHyperscore

private

Definition at line 56 of file xtandemhyperscorebis.h.

Referenced by computeXtandemHyperscore(), getHyperscore(), and reset().

◆ m_totalMatchedIons

unsigned int pappso::XtandemHyperscoreBis::m_totalMatchedIons = 0

private

Definition at line 52 of file xtandemhyperscorebis.h.

Referenced by XtandemHyperscoreBis(), computeXtandemHyperscore(), getTotalMatchedIons(), and reset().

◆ mp_precision

PrecisionPtr pappso::XtandemHyperscoreBis::mp_precision

private

Definition at line 49 of file xtandemhyperscorebis.h.

Referenced by XtandemHyperscoreBis(), and computeXtandemHyperscore().

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

pappsomspp/core/psm/xtandem/xtandemhyperscorebis.h
pappsomspp/core/psm/xtandem/xtandemhyperscorebis.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ AaFactorMap

Constructor & Destructor Documentation

◆ XtandemHyperscoreBis()

◆ ~XtandemHyperscoreBis()

Member Function Documentation

◆ computeXtandemHyperscore()

◆ getHyperscore()

◆ getMatchedIons()

◆ getTotalMatchedIons()

◆ getXtandemPredictedIonIntensityFactor()

◆ reset()

Member Data Documentation

◆ m_aaIonFactorBb

◆ m_aaIonFactorY

◆ m_ionCount

◆ m_ionList

◆ m_isRefineSpectrumSynthesis

◆ m_protoHyperscore

◆ m_totalMatchedIons

◆ mp_precision