#include <peptidenaturalisotopeaverage.h>

Public Member Functions
	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)

	~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

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() [1/3]

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

Definition at line 32 of file peptidenaturalisotopeaverage.cpp.

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

◆ PeptideNaturalIsotopeAverage() [2/3]

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

Definition at line 46 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() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
   //       << "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(), m_abundanceRatio, m_averageMz, m_z, and recursiveDepletion().

◆ PeptideNaturalIsotopeAverage() [3/3]

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

Definition at line 159 of file peptidenaturalisotopeaverage.cpp.

   : mcsp_peptideSp(other.mcsp_peptideSp), mp_precision(other.mp_precision)
 {
  
   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;
 }

References m_abundanceRatio, m_averageMz, m_isotopeLevel, m_isotopeRank, m_peptideNaturalIsotopeSpList, and m_z.

◆ ~PeptideNaturalIsotopeAverage()

pappso::PeptideNaturalIsotopeAverage::~PeptideNaturalIsotopeAverage ( )

Definition at line 173 of file peptidenaturalisotopeaverage.cpp.

174 {

175 }

Member Function Documentation

◆ getCharge()

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

Definition at line 190 of file peptidenaturalisotopeaverage.cpp.

 {
   return m_z;
 }

References m_z.

◆ getComponents()

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

Definition at line 208 of file peptidenaturalisotopeaverage.cpp.

 {
   return m_peptideNaturalIsotopeSpList;
 }

References m_peptideNaturalIsotopeSpList.

◆ getIntensityRatio()

pappso_double pappso::PeptideNaturalIsotopeAverage::getIntensityRatio ( ) const

Definition at line 184 of file peptidenaturalisotopeaverage.cpp.

 {
   return m_abundanceRatio;
 }

References m_abundanceRatio.

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

◆ getIsotopeNumber()

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

Definition at line 196 of file peptidenaturalisotopeaverage.cpp.

 {
   return m_isotopeLevel;
 }

References m_isotopeLevel.

◆ getIsotopeRank()

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

Definition at line 202 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 178 of file peptidenaturalisotopeaverage.cpp.

 {
   return m_averageMz;
 }

References m_averageMz.

Referenced by matchPeak(), and recursiveDepletion().

◆ getPeptideInterfaceSp()

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

Definition at line 214 of file peptidenaturalisotopeaverage.cpp.

 {
   return mcsp_peptideSp;
 }

References mcsp_peptideSp.

◆ getPrecision()

PrecisionPtr pappso::PeptideNaturalIsotopeAverage::getPrecision ( ) const

Definition at line 220 of file peptidenaturalisotopeaverage.cpp.

 {
   return mp_precision;
 }

References mp_precision.

◆ isEmpty()

bool pappso::PeptideNaturalIsotopeAverage::isEmpty ( ) const

Definition at line 235 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 154 of file peptidenaturalisotopeaverage.cpp.

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

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

◆ matchPeak()

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

finalvirtual

Definition at line 226 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 90 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;
     }
 }