#include <peptidenaturalisotopeaverage.h>

Public Member Functions
	PeptideNaturalIsotopeAverage (const PeptideInterfaceSp &peptide, unsigned int isotopeNumber, unsigned int charge, PrecisionPtr precision)
	fast constructor simple isotope build, not computing isotope ratio
	PeptideNaturalIsotopeAverage (const PeptideInterfaceSp &peptide, unsigned int askedIsotopeRank, unsigned int isotopeLevel, unsigned int charge, PrecisionPtr precision)
	PeptideNaturalIsotopeAverage (const PeptideNaturalIsotopeList &isotopeList, unsigned int askedIsotopeRank, unsigned int isotopeLevel, unsigned int charge, PrecisionPtr precision)
	PeptideNaturalIsotopeAverage (const PeptideNaturalIsotopeAverage &other)
virtual	~PeptideNaturalIsotopeAverage ()
PeptideNaturalIsotopeAverageSp	makePeptideNaturalIsotopeAverageSp () const
pappso_double	getMz () const
pappso_double	getIntensityRatio () const
unsigned int	getCharge () const
unsigned int	getIsotopeNumber () const
unsigned int	getIsotopeRank () const
const std::vector< PeptideNaturalIsotopeSp > &	getComponents () const
const PeptideInterfaceSp &	getPeptideInterfaceSp () const
PrecisionPtr	getPrecision () const
virtual bool	matchPeak (pappso_double peak_mz) const final
bool	isEmpty () const
virtual QString	toString () const

Private Member Functions
void	recursiveDepletion (std::vector< PeptideNaturalIsotopeSp > &v_isotope_list, unsigned int rank)

Private Attributes
const PeptideInterfaceSp	mcsp_peptideSp
std::vector< PeptideNaturalIsotopeSp >	m_peptideNaturalIsotopeSpList
pappso_double	m_averageMz
pappso_double	m_abundanceRatio
unsigned int	m_isotopeLevel
unsigned int	m_isotopeRank = 1
unsigned int	m_z
PrecisionPtr	mp_precision = nullptr

Detailed Description

Definition at line 42 of file peptidenaturalisotopeaverage.h.

Constructor & Destructor Documentation

◆ PeptideNaturalIsotopeAverage() [1/4]

pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage	(	const PeptideInterfaceSp &	peptide,
		unsigned int	isotopeNumber,
		unsigned int	charge,
		PrecisionPtr	precision )

fast constructor simple isotope build, not computing isotope ratio

Definition at line 34 of file peptidenaturalisotopeaverage.cpp.

  : mcsp_peptideSp(peptide),
    m_isotopeLevel(isotopeNumber),
    m_isotopeRank(1),
    m_z(charge),
    mp_precision(precision)
{
 
  m_peptideNaturalIsotopeSpList.clear();
 
  double diffC13 = ((double)isotopeNumber * DIFFC12C13) / (double)charge;
 
  m_averageMz      = peptide.get()->getMz(charge) + diffC13;
  m_abundanceRatio = 0;
}

References pappso::DIFFC12C13(), getMz(), m_abundanceRatio, m_averageMz, m_isotopeLevel, m_isotopeRank, m_peptideNaturalIsotopeSpList, m_z, mcsp_peptideSp, and mp_precision.

Referenced by PeptideNaturalIsotopeAverage(), and PeptideNaturalIsotopeAverage().

◆ PeptideNaturalIsotopeAverage() [2/4]

pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage	(	const PeptideInterfaceSp &	peptide,
		unsigned int	askedIsotopeRank,
		unsigned int	isotopeLevel,
		unsigned int	charge,
		PrecisionPtr	precision )

Definition at line 53 of file peptidenaturalisotopeaverage.cpp.

  : PeptideNaturalIsotopeAverage(
      PeptideNaturalIsotopeList(peptide), askedIsotopeRank, isotopeLevel, charge, precision)
{
}

References PeptideNaturalIsotopeAverage().

◆ PeptideNaturalIsotopeAverage() [3/4]

pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage	(	const PeptideNaturalIsotopeList &	isotopeList,
		unsigned int	askedIsotopeRank,
		unsigned int	isotopeLevel,
		unsigned int	charge,
		PrecisionPtr	precision )

Definition at line 63 of file peptidenaturalisotopeaverage.cpp.

  : mcsp_peptideSp(isotopeList.getPeptideInterfaceSp()),
    m_isotopeLevel(isotope_number),
    m_isotopeRank(askedIsotopeRank),
    m_z(charge),
    mp_precision(precision)
{ // get the askedIsotopeRank :
  std::vector<PeptideNaturalIsotopeSp> v_isotope_list(
    isotopeList.getByIsotopeNumber(isotope_number, m_z));
 
  qDebug() << "v_isotope_list.size()=" << v_isotope_list.size() << " " << isotope_number << " "
           << askedIsotopeRank;
  m_abundanceRatio = 0;
  m_averageMz      = 0;
  if(askedIsotopeRank > v_isotope_list.size())
    {
      // there is no isotope at this rank
      return;
      // throw PappsoException(QObject::tr("askedIsotopeRank greater than
      // v_isotope_list.size() %1 vs
      // %2").arg(askedIsotopeRank).arg(v_isotope_list.size()));
    }
  else if(askedIsotopeRank < 1)
    {
      throw PappsoException(
        QObject::tr("askedIsotopeRank must be 1 or more and not %1").arg(askedIsotopeRank));
    }
 
  unsigned int rank = 0;
 
  recursiveDepletion(v_isotope_list, rank);
 
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References pappso::PeptideNaturalIsotopeList::getByIsotopeNumber(), getPeptideInterfaceSp(), m_abundanceRatio, m_averageMz, m_isotopeLevel, m_isotopeRank, m_z, mcsp_peptideSp, mp_precision, and recursiveDepletion().

◆ PeptideNaturalIsotopeAverage() [4/4]

pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage ( const PeptideNaturalIsotopeAverage & other )

Definition at line 171 of file peptidenaturalisotopeaverage.cpp.

  : mcsp_peptideSp(other.mcsp_peptideSp), mp_precision(other.mp_precision)
{
 
  qDebug();
  m_peptideNaturalIsotopeSpList = other.m_peptideNaturalIsotopeSpList;
 
  m_averageMz      = other.m_averageMz;
  m_abundanceRatio = other.m_abundanceRatio;
  m_isotopeLevel   = other.m_isotopeLevel;
  m_isotopeRank    = other.m_isotopeRank;
  m_z              = other.m_z;
  qDebug();
}

References PeptideNaturalIsotopeAverage(), m_abundanceRatio, m_averageMz, m_isotopeLevel, m_isotopeRank, m_peptideNaturalIsotopeSpList, m_z, mcsp_peptideSp, and mp_precision.

◆ ~PeptideNaturalIsotopeAverage()

pappso::PeptideNaturalIsotopeAverage::~PeptideNaturalIsotopeAverage ( )

virtual

Definition at line 187 of file peptidenaturalisotopeaverage.cpp.

188{

189}

Member Function Documentation

◆ getCharge()

unsigned int pappso::PeptideNaturalIsotopeAverage::getCharge ( ) const

Definition at line 204 of file peptidenaturalisotopeaverage.cpp.

{
  return m_z;
}

References m_z.

Referenced by toString().

◆ getComponents()

const std::vector< PeptideNaturalIsotopeSp > & pappso::PeptideNaturalIsotopeAverage::getComponents ( ) const

Definition at line 222 of file peptidenaturalisotopeaverage.cpp.

{
  return m_peptideNaturalIsotopeSpList;
}

References m_peptideNaturalIsotopeSpList.

◆ getIntensityRatio()

pappso_double pappso::PeptideNaturalIsotopeAverage::getIntensityRatio ( ) const

Definition at line 198 of file peptidenaturalisotopeaverage.cpp.

{
  return m_abundanceRatio;
}

References m_abundanceRatio.

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), pappso::MassSpectrumWidget::computeIsotopeMassList(), pappso::PeptideNaturalIsotopeList::getByIntensityRatio(), and pappso::PsmFeatures::getIonIsotopeLinearRegression().

◆ getIsotopeNumber()

unsigned int pappso::PeptideNaturalIsotopeAverage::getIsotopeNumber ( ) const

Definition at line 210 of file peptidenaturalisotopeaverage.cpp.

{
  return m_isotopeLevel;
}

References m_isotopeLevel.

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), pappso::findComplementIonType(), pappso::PsmFeatures::getIonIsotopeLinearRegression(), and toString().

◆ getIsotopeRank()

unsigned int pappso::PeptideNaturalIsotopeAverage::getIsotopeRank ( ) const

Definition at line 216 of file peptidenaturalisotopeaverage.cpp.

{
  return m_isotopeRank;
}

References m_isotopeRank.

Referenced by pappso::MassSpectrumWidget::computeIsotopeMassList(), pappso::PeptideNaturalIsotopeList::getByIntensityRatio(), and pappso::getByIntensityRatioByIsotopeNumber().

◆ getMz()

pappso_double pappso::PeptideNaturalIsotopeAverage::getMz ( ) const

Definition at line 192 of file peptidenaturalisotopeaverage.cpp.

{
  return m_averageMz;
}

References m_averageMz.

Referenced by pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(), PeptideNaturalIsotopeAverage(), pappso::QCPSpectrum::addMassDelta(), matchPeak(), pappso::MassSpectrumWidget::plot(), recursiveDepletion(), and toString().

◆ getPeptideInterfaceSp()

const PeptideInterfaceSp & pappso::PeptideNaturalIsotopeAverage::getPeptideInterfaceSp ( ) const

Definition at line 228 of file peptidenaturalisotopeaverage.cpp.

{
  return mcsp_peptideSp;
}

References mcsp_peptideSp.

Referenced by PeptideNaturalIsotopeAverage(), and toString().

◆ getPrecision()

PrecisionPtr pappso::PeptideNaturalIsotopeAverage::getPrecision ( ) const

Definition at line 234 of file peptidenaturalisotopeaverage.cpp.

{
  return mp_precision;
}

References mp_precision.

◆ isEmpty()

bool pappso::PeptideNaturalIsotopeAverage::isEmpty ( ) const

Definition at line 249 of file peptidenaturalisotopeaverage.cpp.

{
  return (m_peptideNaturalIsotopeSpList.size() == 0);
}

References m_peptideNaturalIsotopeSpList.

Referenced by pappso::getByIntensityRatioByIsotopeNumber().

◆ makePeptideNaturalIsotopeAverageSp()

PeptideNaturalIsotopeAverageSp pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp ( ) const

Definition at line 166 of file peptidenaturalisotopeaverage.cpp.

{
  return std::make_shared<PeptideNaturalIsotopeAverage>(*this);
}

Referenced by pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(), pappso::MassSpectrumWidget::computeIsotopeMassList(), pappso::PeptideNaturalIsotopeList::getByIntensityRatio(), and pappso::getByIntensityRatioByIsotopeNumber().

◆ matchPeak()

bool pappso::PeptideNaturalIsotopeAverage::matchPeak ( pappso_double peak_mz ) const

finalvirtual

Definition at line 240 of file peptidenaturalisotopeaverage.cpp.

{
  // qDebug() << "PeptideNaturalIsotopeAverage::matchPeak";
  // qDebug() << "PeptideNaturalIsotopeAverage::matchPeak precision " <<
  // mp_precision.getDelta(200);
  return (MzRange(getMz(), mp_precision).contains(peak_mz));
}

References getMz(), and mp_precision.

Referenced by pappso::PeptideIsotopeSpectrumMatch::getBestPeakIterator().

◆ recursiveDepletion()

void pappso::PeptideNaturalIsotopeAverage::recursiveDepletion	(	std::vector< PeptideNaturalIsotopeSp > &	v_isotope_list,
		unsigned int	rank )

private

Definition at line 105 of file peptidenaturalisotopeaverage.cpp.

{
  rank++;
 
  m_abundanceRatio = 0;
  m_averageMz      = 0;
  m_peptideNaturalIsotopeSpList.clear();
  std::vector<PeptideNaturalIsotopeSp> peptide_list;
  // select neighbors in the precision range :
  MzRange mz_range(v_isotope_list[0].get()->getMz(m_z), mp_precision);
 
  for(auto &isotope_sp : v_isotope_list)
    {
      if(mz_range.contains(isotope_sp.get()->getMz(m_z)))
        {
          peptide_list.push_back(isotope_sp);
          m_abundanceRatio += isotope_sp.get()->getIntensityRatio(m_z);
          m_averageMz += (isotope_sp.get()->getMz(m_z) * isotope_sp.get()->getIntensityRatio(m_z));
        }
    }
 
  if(peptide_list.size() > 0)
    {
      m_averageMz = m_averageMz / m_abundanceRatio;
 
      // depletion
      auto it_remove =
        std::remove_if(v_isotope_list.begin(),
                       v_isotope_list.end(),
                       [peptide_list](const PeptideNaturalIsotopeSp &isotope_sp) {
                         auto it = std::find(peptide_list.begin(), peptide_list.end(), isotope_sp);
                         return (it != peptide_list.end());
                       });
      v_isotope_list.erase(it_remove, v_isotope_list.end());
 
      if(rank == m_isotopeRank)
        {
          m_peptideNaturalIsotopeSpList = peptide_list;
          return;
        }
      else
        {
          unsigned int charge = m_z;
          std::sort(v_isotope_list.begin(),
                    v_isotope_list.end(),
                    [charge](const PeptideNaturalIsotopeSp &m, const PeptideNaturalIsotopeSp &n) {
                      return (m.get()->getIntensityRatio(charge) >
                              n.get()->getIntensityRatio(charge));
                    });
          recursiveDepletion(v_isotope_list, rank);
        }
    }
  else
    {
      m_abundanceRatio = 0;
      m_averageMz      = 0;
    }
}

References pappso::MzRange::contains(), getMz(), m_abundanceRatio, m_averageMz, m_isotopeRank, m_peptideNaturalIsotopeSpList, m_z, mp_precision, and recursiveDepletion().

Referenced by PeptideNaturalIsotopeAverage(), and recursiveDepletion().

◆ toString()

QString pappso::PeptideNaturalIsotopeAverage::toString ( ) const

virtual

Definition at line 255 of file peptidenaturalisotopeaverage.cpp.

{
  return QString("%1 l%2 mz%3 z%4 N%5")
    .arg(getPeptideInterfaceSp().get()->getSequence())
    .arg(getPeptideInterfaceSp().get()->size())
    .arg(getMz())
    .arg(getCharge())
    .arg(getIsotopeNumber());
}