pappso::XtandemHyperscore Class Reference

#include <xtandemhyperscore.h>

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

Public Member Functions
	XtandemHyperscore (const MassSpectrum &spectrum, pappso::PeptideSp peptideSp, unsigned int parent_charge, PrecisionPtr precision, std::list< Enums::PeptideIon > ion_list, bool refine_spectrum_synthesis)
	XtandemHyperscore (const XtandemHyperscore &other)
	~XtandemHyperscore ()
pappso_double	getHyperscore () const
unsigned int	getMatchedIons (Enums::PeptideIon ion_type) const

Private Member Functions
unsigned int	getXtandemPredictedIonIntensityFactor (const QString &sequence, PeptideDirection ion_direction, unsigned int ion_size) const

Private Attributes
bool	_refine_spectrum_synthesis
pappso_double	_proto_hyperscore
std::map< Enums::PeptideIon, unsigned int >	_ion_count

Static Private Attributes
static AaFactorMap	_aa_ion_factor_y
static AaFactorMap	_aa_ion_factor_b

Detailed Description

Definition at line 42 of file xtandemhyperscore.h.

Member Typedef Documentation

AaFactorMap

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

Definition at line 45 of file xtandemhyperscore.h.

Constructor & Destructor Documentation

XtandemHyperscore() [1/2]

pappso::XtandemHyperscore::XtandemHyperscore	(	const MassSpectrum &	spectrum,
		pappso::PeptideSp	peptideSp,
		unsigned int	parent_charge,
		PrecisionPtr	precision,
		std::list< Enums::PeptideIon >	ion_list,
		bool	refine_spectrum_synthesis )

Definition at line 51 of file xtandemhyperscore.cpp.

  : _refine_spectrum_synthesis(refine_spectrum_synthesis)
{
  try
    {
      /*
      if ((peptide_ion_sp.get()->getPeptideIonType() == Enums::PeptideIon::c) ||
      (peptide_ion_sp.get()->getPeptideIonType() == Enums::PeptideIon::z)) {
                    if(current_max_charge > 2)  {
                        current_max_charge--;
                    }
                }*/
      unsigned int max_charge = parent_charge;
      if(parent_charge > 1)
        {
          max_charge = parent_charge - 1;
        }
      PeptideSpectrumMatch psm(spectrum, peptideSp, max_charge, precision, ion_list);
 
      _ion_count = {{Enums::PeptideIon::a, 0},
                    {Enums::PeptideIon::b, 0},
                    {Enums::PeptideIon::bo, 0},
                    {Enums::PeptideIon::bstar, 0},
                    {Enums::PeptideIon::c, 0},
                    {Enums::PeptideIon::y, 0},
                    {Enums::PeptideIon::yo, 0},
                    {Enums::PeptideIon::ystar, 0},
                    {Enums::PeptideIon::z, 0}};
 
      std::map<Enums::PeptideIon, unsigned int> ion_count;
      for(auto &&ion_type : ion_list)
        {
          ion_count.insert(std::pair<Enums::PeptideIon, unsigned int>(ion_type, 0));
        }
 
      std::map<unsigned int, pappso_double> charge_dot_product;
      std::map<unsigned int, std::map<Enums::PeptideIon, unsigned int>> charge_ion_count;
      for(unsigned int i = 1; i <= max_charge; i++)
        {
          charge_dot_product.insert(std::pair<unsigned int, pappso_double>(i, 0));
          charge_ion_count.insert(
            std::pair<unsigned int, std::map<Enums::PeptideIon, unsigned int>>(i, ion_count));
        }
      QString sequence = peptideSp.get()->getSequence();
      for(auto &&peptide_ion_match : psm)
        {
          Enums::PeptideIon ion_type = peptide_ion_match.getPeptideIonType();
          unsigned int charge        = peptide_ion_match.getCharge();
          charge_dot_product[charge] +=
            peptide_ion_match.getPeak().y *
            getXtandemPredictedIonIntensityFactor(
              sequence,
              peptide_ion_match.getPeptideIonDirection(),
              peptide_ion_match.getPeptideFragmentIonSp().get()->size());
          charge_ion_count[charge][ion_type] += 1;
          _ion_count[ion_type] += 1;
        }
 
      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
               << " _ion_count[Enums::PeptideIon::y]=" << _ion_count[Enums::PeptideIon::y];
      // 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 : _ion_count)
        {
          sum_intensity *= factorial(count.second);
        }
 
      _proto_hyperscore = sum_intensity;
    }
  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 _ion_count, _proto_hyperscore, _refine_spectrum_synthesis, pappso::Enums::a, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bstar, pappso::Enums::c, pappso::factorial(), getXtandemPredictedIonIntensityFactor(), pappso::PappsoException::qwhat(), pappso::Enums::y, pappso::Enums::yo, pappso::Enums::ystar, and pappso::Enums::z.

Referenced by XtandemHyperscore().

XtandemHyperscore() [2/2]

pappso::XtandemHyperscore::XtandemHyperscore

(

const XtandemHyperscore &

other

)

Definition at line 145 of file xtandemhyperscore.cpp.

{
  _ion_count                 = other._ion_count;
  _proto_hyperscore          = other._proto_hyperscore;
  _refine_spectrum_synthesis = other._refine_spectrum_synthesis;
}

References XtandemHyperscore(), _ion_count, _proto_hyperscore, and _refine_spectrum_synthesis.

~XtandemHyperscore()

pappso::XtandemHyperscore::~XtandemHyperscore

(

)

Definition at line 157 of file xtandemhyperscore.cpp.

{
}

Member Function Documentation

getHyperscore()

pappso_double pappso::XtandemHyperscore::getHyperscore

(

)

const

Definition at line 251 of file xtandemhyperscore.cpp.

{
  try
    {
      qDebug() << " _proto_hyperscore=" << _proto_hyperscore;
      double hyperscore = (log10(_proto_hyperscore) * 4);
      if(hyperscore < 0)
        return 0;
      return hyperscore;
    }
  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 _proto_hyperscore, and pappso::PappsoException::qwhat().

Referenced by pappso::cbor::psm::PsmFeaturesScan::process().

getMatchedIons()

unsigned int pappso::XtandemHyperscore::getMatchedIons

(

Enums::PeptideIon

ion_type

)

const

Definition at line 153 of file xtandemhyperscore.cpp.

{
  return _ion_count.at(ion_type);
}

References _ion_count.

getXtandemPredictedIonIntensityFactor()

unsigned int pappso::XtandemHyperscore::getXtandemPredictedIonIntensityFactor ( const QString & sequence, PeptideDirection ion_direction, unsigned int ion_size ) const

private

Definition at line 193 of file xtandemhyperscore.cpp.

{
  unsigned int Pi(1);
 
  char last_aa_nter('_'), last_aa_cter('_');
 
  if(ion_direction == PeptideDirection::Nter)
    {
      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) << "
  // _aa_ion_factor_b[last_aa_nter]="s ;
  qDebug() << PeptideFragment::getPeptideIonDirectionName(ion_direction)
           << " last_aa_nter=" << last_aa_nter
           << " _aa_ion_factor_b[last_aa_nter]=" << _aa_ion_factor_b[last_aa_nter]
           << " last_aa_cter=" << last_aa_cter
           << " _aa_ion_factor_y[last_aa_cter]=" << _aa_ion_factor_y[last_aa_cter];
  if(_refine_spectrum_synthesis)
    {
      Pi *= _aa_ion_factor_b[last_aa_nter] * _aa_ion_factor_y[last_aa_cter];
    }
 
  return Pi;
}

References _aa_ion_factor_b, _aa_ion_factor_y, _refine_spectrum_synthesis, pappso::PeptideFragment::getPeptideIonDirectionName(), and pappso::Nter.

Referenced by XtandemHyperscore().

Member Data Documentation

_aa_ion_factor_b

XtandemHyperscore::AaFactorMap pappso::XtandemHyperscore::_aa_ion_factor_b

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 70 of file xtandemhyperscore.h.

Referenced by getXtandemPredictedIonIntensityFactor().

_aa_ion_factor_y

XtandemHyperscore::AaFactorMap pappso::XtandemHyperscore::_aa_ion_factor_y

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 69 of file xtandemhyperscore.h.

Referenced by getXtandemPredictedIonIntensityFactor().

_ion_count

std::map<Enums::PeptideIon, unsigned int> pappso::XtandemHyperscore::_ion_count

private

Definition at line 67 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), XtandemHyperscore(), and getMatchedIons().

_proto_hyperscore

pappso_double pappso::XtandemHyperscore::_proto_hyperscore

private

Definition at line 66 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), XtandemHyperscore(), and getHyperscore().

_refine_spectrum_synthesis

bool pappso::XtandemHyperscore::_refine_spectrum_synthesis

private

Definition at line 59 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), XtandemHyperscore(), and getXtandemPredictedIonIntensityFactor().

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

• pappsomspp/core/psm/xtandem/xtandemhyperscore.h
• pappsomspp/core/psm/xtandem/xtandemhyperscore.cpp