pappso::specglob::PeptideModel Class Reference

#include <peptidemodel.h>

Inheritance diagram for pappso::specglob::PeptideModel:

Public Member Functions
	PeptideModel (const pappso::QualifiedMassSpectrum &qmass_spectrum, const pappso::Peptide &peptide)
	PeptideModel ()
	PeptideModel (const PeptideModel &other)
virtual	~PeptideModel ()
QString	toString () const
double	getMass () const
pappso_double	getMz (unsigned int charge) const
	get the m/z peptide model mass
double	getMassDelta () const
	mass delta between experimental and theoretical mass
std::size_t	modifCount () const
void	setBeginMassDelta (double)
void	matchExperimentalPeaks (pappso::PrecisionPtr precision)
std::vector< double >	getTheoreticalIonMassList () const
std::size_t	getCountSharedPeaks () const
double	getIntensitySharedPeaks () const
double	getIntensityExperimentalPeaks () const
void	assignResidualMass2Cter ()
bool	eliminateComplementaryDelta (pappso::PrecisionPtr precision)
bool	checkForMutations (const std::vector< Enums::AminoAcidChar > &aa_list, pappso::PrecisionPtr precision)
	try to replace mass differences with corresponding mutations mass delta
bool	checkForMutation (const pappso::Aa &amino_acid_candidate, pappso::PrecisionPtr precision)
	try to replace mass differences with corresponding mutation mass delta
bool	checkForAaModification (const pappso::Aa &aa_modified, pappso::PrecisionPtr precision)
	try to replace mass differences with the given modifications on a specific amino acid
bool	checkForAaModificationP (pappso::AaModificationP modification, pappso::PrecisionPtr precision)
	try to replace mass differences with the given modification
PeptideModel &	operator= (const PeptideModel &other)
PeptideModel &	copyDeep (const PeptideModel &other)
bool	eliminateNegativeOffset (pappso::PrecisionPtr precision)
bool	removeBracketsForAlignedAA ()
const std::vector< TheoreticalPeakDataPoint > &	getTheoreticalPeakDataPointList () const
QString	getTheoreticalPeakDataPointListToString () const
QString	toProForma () const
	get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md
bool	hasRemoval () const
bool	ltrimOnRemoval ()
	try to remove left amino acid if there is a removal

Private Member Functions
void	generateTheoreticalPeaks (pappso::PrecisionPtr precision)

Private Attributes
std::vector< TheoreticalPeakDataPoint >	m_theoreticalPeakList
double	m_experimentalPrecursorMass
double	m_beginMassDelta = 0
pappso::MassSpectrumCstSPtr	mcsp_peakList = nullptr
pappso::AaModificationP	m_nterModification
pappso::AaModificationP	m_cterModification
std::size_t	m_countSharedPeaks = 0
double	m_intensitySharedPeaks = 0
double	m_intensityExperimentalPeaks = 0

Detailed Description

Todo

write docs

Definition at line 72 of file peptidemodel.h.

Constructor & Destructor Documentation

PeptideModel() [1/3]

pappso::specglob::PeptideModel::PeptideModel	(	const pappso::QualifiedMassSpectrum &	qmass_spectrum,
		const pappso::Peptide &	peptide )

Default constructor

Definition at line 53 of file peptidemodel.cpp.

  : std::vector<AminoAcidModel>()
{
  m_experimentalPrecursorMass = qmass_spectrum.getPrecursorMass();
  mcsp_peakList               = qmass_spectrum.getMassSpectrumCstSPtr();
  m_nterModification          = peptide.getCleavageNterModification();
  m_cterModification          = peptide.getCleavageCterModification();
  for(auto aa_pep : peptide)
    {
 
      push_back({aa_pep, SpectralAlignmentType::nonAlign, false, 0.0});
    }
 
  // internal:Nter_hydrolytic_cleavage_H
 
  // internal:Cter_hydrolytic_cleavage_HO
  //
}

References pappso::Peptide::getCleavageCterModification(), pappso::Peptide::getCleavageNterModification(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getPrecursorMass(), m_cterModification, m_experimentalPrecursorMass, m_nterModification, mcsp_peakList, and pappso::specglob::nonAlign.

Referenced by PeptideModel(), copyDeep(), and operator=().

PeptideModel() [2/3]

pappso::specglob::PeptideModel::PeptideModel

(

)

Definition at line 48 of file peptidemodel.cpp.

{
  // not valid
}

PeptideModel() [3/3]

pappso::specglob::PeptideModel::PeptideModel

(

const PeptideModel &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 73 of file peptidemodel.cpp.

                                                    : std::vector<AminoAcidModel>(other)
{
  m_experimentalPrecursorMass = other.m_experimentalPrecursorMass;
  mcsp_peakList               = other.mcsp_peakList;
 
  m_experimentalPrecursorMass = other.m_experimentalPrecursorMass;
  m_beginMassDelta            = other.m_beginMassDelta;
 
  m_nterModification           = other.m_nterModification;
  m_cterModification           = other.m_cterModification;
  m_countSharedPeaks           = other.m_countSharedPeaks;
  m_intensitySharedPeaks       = other.m_intensitySharedPeaks;
  m_intensityExperimentalPeaks = other.m_intensityExperimentalPeaks;
}

References PeptideModel(), m_beginMassDelta, m_countSharedPeaks, m_cterModification, m_experimentalPrecursorMass, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_nterModification, and mcsp_peakList.

~PeptideModel()

pappso::specglob::PeptideModel::~PeptideModel ( )

virtual

Destructor

Definition at line 117 of file peptidemodel.cpp.

{
}

Member Function Documentation

assignResidualMass2Cter()

void pappso::specglob::PeptideModel::assignResidualMass2Cter

(

)

Definition at line 458 of file peptidemodel.cpp.

{
  back().mass_difference = getMassDelta();
}

References getMassDelta().

checkForAaModification()

bool pappso::specglob::PeptideModel::checkForAaModification	(	const pappso::Aa &	aa_modified,
		pappso::PrecisionPtr	precision )

try to replace mass differences with the given modifications on a specific amino acid

Parameters

aa_modified	the modified amino acid
precision	The mass spectrometer precision

Returns

true if model is modified

Definition at line 769 of file peptidemodel.cpp.

{
 
  bool modif = false;
 
  double mass_difference = m_beginMassDelta;
  for(auto &aa_model : *this)
    {
      mass_difference += aa_model.mass_difference;
      auto aa_ref = aa_model.amino_acid;
      if(aa_ref.getLetter() == aa_modified.getLetter())
        {
          if(mass_difference != 0.0)
            {
              double mass_modification = aa_modified.getTotalModificationMass();
              if(std::abs(mass_modification - mass_difference) < precision->getNominal())
                {
                  aa_model.mass_difference = 0;
                  for(auto &modification : aa_modified.getModificationList())
                    {
                      aa_model.amino_acid.addAaModification(modification);
                    }
                  modif = true;
                }
            }
        }
      mass_difference = 0;
    }
  return modif;
}

References pappso::AaBase::getLetter(), pappso::Aa::getModificationList(), pappso::PrecisionBase::getNominal(), pappso::Aa::getTotalModificationMass(), and m_beginMassDelta.

checkForAaModificationP()

bool pappso::specglob::PeptideModel::checkForAaModificationP	(	pappso::AaModificationP	modification,
		pappso::PrecisionPtr	precision )

try to replace mass differences with the given modification

Parameters

modification	: The proposed modification pointer
precision	: The mass spectrometer precision

Returns

true if model is modified

Definition at line 742 of file peptidemodel.cpp.

{
 
  bool modif = false;
 
  double mass_difference = m_beginMassDelta;
  for(auto &aa_model : *this)
    {
      mass_difference += aa_model.mass_difference;
      auto aa_ref = aa_model.amino_acid;
      if(mass_difference != 0.0)
        {
          if(std::abs(modification->getMass() - mass_difference) < precision->getNominal())
            {
              aa_model.mass_difference = 0;
              aa_model.amino_acid.addAaModification(modification);
              modif = true;
            }
        }
      mass_difference = 0;
    }
  return modif;
}

References pappso::AaModification::getMass(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.

checkForMutation()

bool pappso::specglob::PeptideModel::checkForMutation	(	const pappso::Aa &	amino_acid_candidate,
		pappso::PrecisionPtr	precision )

try to replace mass differences with corresponding mutation mass delta

amino acid candidate tested could bear some modifications

Parameters

amino_acid_candidate	: The amino acid candidate to check
precision	: The mass spectrometer precision

Returns

true if model is modified

Definition at line 643 of file peptidemodel.cpp.

{
  bool modif                  = false;
  double total_mass_to_insert = amino_acid_candidate.getMass();
  auto insert_aa_modification =
    AaModification::getInstanceInsertionAccessionByAaLetter(amino_acid_candidate.getLetter());
 
  double mass_difference = m_beginMassDelta;
  for(auto &aa_model : *this)
    {
      mass_difference += aa_model.mass_difference;
      auto aa_ref = aa_model.amino_acid;
      if(mass_difference != 0.0)
        {
          mass_difference += aa_ref.getTotalModificationMass();
          AaModificationP aa_ref_remove =
            AaModification::getInstanceRemovalAccessionByAaLetter(aa_model.amino_acid.getLetter());
          // check for possible mutation
          double current_diff = (aa_ref_remove->getMass() - mass_difference) + total_mass_to_insert;
 
 
          qDebug() << "current_diff=" << current_diff;
          if(std::abs(current_diff) < precision->getNominal())
            {
              qDebug() << "modif = true=";
              aa_model.mass_difference = 0;
              aa_model.amino_acid.removeAllButInternalModification();
              aa_model.amino_acid.addAaModification(aa_ref_remove);
              aa_model.amino_acid.addAaModification(insert_aa_modification);
              for(auto &mod : amino_acid_candidate.getModificationList())
                {
                  aa_model.amino_acid.addAaModification(mod);
                }
              modif = true;
            }
        }
      mass_difference = 0;
    }
  return modif;
}

References pappso::AaModification::getInstanceInsertionAccessionByAaLetter(), pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), pappso::AaBase::getLetter(), pappso::Aa::getMass(), pappso::AaModification::getMass(), pappso::Aa::getModificationList(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.

checkForMutations()

bool pappso::specglob::PeptideModel::checkForMutations	(	const std::vector< Enums::AminoAcidChar > &	aa_list,
		pappso::PrecisionPtr	precision )

try to replace mass differences with corresponding mutations mass delta

amino acid list is tested as raw (no modification)

Parameters

aa_list	amno acid list to test (beware of cysteine + carbamidomethyl)
precision	: The mass spectrometer precision

Returns

true if model is modified

Definition at line 686 of file peptidemodel.cpp.

{
  bool modif = false;
  // AaModificationP carbamido = AaModification::getInstance("MOD:00397");
  // AaModificationP metox = AaModification::getInstance("MOD:00719");
 
  std::vector<AaModificationP> modificationInsertList;
  for(const auto aa : aa_list)
    {
      modificationInsertList.push_back(
        AaModification::getInstanceInsertionAccessionByAaLetter((char)aa));
    }
  double mass_difference = m_beginMassDelta;
  for(auto &aa_model : *this)
    {
      mass_difference += aa_model.mass_difference;
      auto aa_ref = aa_model.amino_acid;
      if(mass_difference != 0.0)
        {
          mass_difference += aa_ref.getTotalModificationMass();
          AaModificationP aa_ref_remove =
            AaModification::getInstanceRemovalAccessionByAaLetter(aa_model.amino_acid.getLetter());
          AaModificationP aa_ref_insert = nullptr;
          double better_diff            = 10;
          // check for possible mutation
          for(const auto aaInsertion : modificationInsertList)
            {
              double current_diff =
                (aa_ref_remove->getMass() - mass_difference) + aaInsertion->getMass();
              qDebug() << aa_model.amino_acid.getLetter() << " " << aaInsertion->getName() << " "
                       << aaInsertion->getMass() << " " << current_diff;
              if(std::abs(current_diff) < std::abs(better_diff))
                {
                  aa_ref_insert = aaInsertion;
                  better_diff   = current_diff;
                }
            }
          qDebug() << "better_diff=" << better_diff;
          if((aa_ref_insert != nullptr) && (std::abs(better_diff) < precision->getNominal()))
            {
 
              qDebug() << "modif = true=";
              aa_model.mass_difference = 0;
              aa_model.amino_acid.removeAllButInternalModification();
              aa_model.amino_acid.addAaModification(aa_ref_remove);
              aa_model.amino_acid.addAaModification(aa_ref_insert);
              modif = true;
            }
        }
      mass_difference = 0;
    }
  return modif;
}

References pappso::AaModification::getInstanceInsertionAccessionByAaLetter(), pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), pappso::AaModification::getMass(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.

copyDeep()

PeptideModel & pappso::specglob::PeptideModel::copyDeep

(

const PeptideModel &

other

)

Definition at line 109 of file peptidemodel.cpp.

{
  operator=(other);
 
  m_theoreticalPeakList = other.m_theoreticalPeakList;
  return *this;
}

References PeptideModel(), m_theoreticalPeakList, and operator=().

Referenced by pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().

eliminateComplementaryDelta()

bool pappso::specglob::PeptideModel::eliminateComplementaryDelta

(

pappso::PrecisionPtr

precision

)

Use to delete offset when there is two opposite mass in the hit modified example : [150.2]SDS[-150.2]KR --> SDSKR

Parameters

precision

: The mass spectrometer precision

Returns

true if model is modified

Definition at line 464 of file peptidemodel.cpp.

{
  double precision_ref                                 = precision->getNominal();
  double offset                                        = 0;
  bool modified                                        = false;
  std::vector<AminoAcidModel>::iterator it_begin_block = end();
  if(std::abs(m_beginMassDelta) > precision_ref)
    {
      it_begin_block = begin();
      offset         = m_beginMassDelta;
 
      qDebug() << " new block offset=" << offset;
    }
  qDebug() << offset;
  for(auto it = begin(); it != end(); it++)
    {
      qDebug() << " it->mass_difference=" << it->mass_difference;
      if(it_begin_block == end())
        {
 
          if(std::abs(it->mass_difference) > precision_ref)
            {
              // new block
              it_begin_block = it;
              offset         = it->mass_difference;
            }
          qDebug() << " new block offset=" << offset;
        }
      if(it_begin_block != end())
        {
          // existing block
          qDebug() << " existing block offset=" << offset;
          if(it == begin())
            {
              offset += it->mass_difference;
            }
          else
            {
              // where is the end of the block ?
              qDebug() << " where is the end of the block ? offset=" << offset;
              auto it_end_block =
                std::find_if(it, end(), [offset, precision_ref](const AminoAcidModel &point) {
                  qDebug() << point.mass_difference << " " << offset + point.mass_difference;
                  if(std::abs(offset + point.mass_difference) <= precision_ref)
                    return true;
                  return false;
                });
 
              if(it_end_block != end())
                {
                  // eliminate mass mass_difference
                  modified = true;
                  if(it_begin_block == begin())
                    m_beginMassDelta = 0;
                  it_begin_block->mass_difference = 0.0;
                  it_end_block->mass_difference   = 0.0;
                  // start new block search
                  it_begin_block = end();
                  offset         = 0;
                  qDebug() << " existing block end block found";
                }
              else
                {
                  qDebug() << " existing block end block not found offset=" << offset;
                  // close block
                  it_begin_block = end();
                  offset         = 0;
                }
            }
        }
    }
  qDebug() << toString();
  return modified;
}

References pappso::PrecisionBase::getNominal(), m_beginMassDelta, pappso::specglob::AminoAcidModel::mass_difference, and toString().

Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel(), and pappso::specglob::SpectralAlignment::rtrim().

eliminateNegativeOffset()

bool pappso::specglob::PeptideModel::eliminateNegativeOffset

(

pappso::PrecisionPtr

precision

)

Use to try to explain negative offset with deletion of amino acids

Parameters

precision

: The mass spectrometer precision

Returns

true if model is modified

Definition at line 541 of file peptidemodel.cpp.

{ // System.out.println("Elimination des neg offsets");
  double precision_ref = precision->getNominal();
  auto it_reverse      = rbegin();
  bool modified        = false;
 
  while(it_reverse != rend())
    {
      if(it_reverse->remove)
        {
          // this is a part of already removed block
        }
      else
        {
          double mass_difference = it_reverse->mass_difference;
          if(mass_difference < 0)
            {
              // try to find an amino acid blocl of that mass
              double cumul_mass_aa = 0;
              auto it_block_end    = it_reverse;
              while(it_block_end != rend())
                {
                  cumul_mass_aa += it_block_end->amino_acid.getMass();
                  it_block_end++;
                  if(std::abs(mass_difference + cumul_mass_aa) < precision_ref)
                    {
                      modified = true;
                      // block found -> remove this range
                      for(auto it_block = it_reverse; it_block != it_block_end; it_block++)
                        {
                          it_block->remove = true;
                        }
                    }
                  else
                    {
                      if((it_block_end != rend()) && (it_block_end->mass_difference != 0.0))
                        {
                          // interrupted block
                          break;
                        }
                    }
                }
            }
        }
      it_reverse++;
    }
 
  return modified;
}

References pappso::PrecisionBase::getNominal().

Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel().

generateTheoreticalPeaks()

void pappso::specglob::PeptideModel::generateTheoreticalPeaks ( pappso::PrecisionPtr precision )

private

Definition at line 387 of file peptidemodel.cpp.

{
  m_theoreticalPeakList.clear();
  double cumul_mass =
    m_beginMassDelta + m_nterModification->getMass() - pappso::MPROTIUM + pappso::MHPLUS;
 
 
  auto it_expe_peaks_end = mcsp_peakList.get()->end();
  std::size_t i          = 0;
  for(auto aa_model : *this)
    {
      // compute B ions
      cumul_mass += aa_model.amino_acid.getMass() + aa_model.mass_difference;
 
      qDebug() << cumul_mass;
      m_theoreticalPeakList.push_back(
        {pappso::MzRange(cumul_mass, precision), it_expe_peaks_end, i});
      i++;
    }
  // remove the complete ion B (entire peptide, no fragment):
  m_theoreticalPeakList.pop_back();
 
  std::size_t bmaxindice = m_theoreticalPeakList.size();
  double yion_delta      = pappso::PeptideRawFragmentMasses::getDeltaMass(Enums::PeptideIon::y);
  cumul_mass += yion_delta + pappso::MHPLUS;
  for(std::size_t i = 0; i < bmaxindice; i++)
    {
      m_theoreticalPeakList.push_back(
        {pappso::MzRange(cumul_mass - m_theoreticalPeakList[i].mz_range.getMz(), precision),
         it_expe_peaks_end,
         i + 1});
      qDebug() << m_theoreticalPeakList.back().mz_range.getMz();
    }
 
  std::sort(m_theoreticalPeakList.begin(),
            m_theoreticalPeakList.end(),
            [](const TheoreticalPeakDataPoint &a, const TheoreticalPeakDataPoint &b) {
              return a.mz_range.getMz() < b.mz_range.getMz();
            });
}

References pappso::a, pappso::b, pappso::PeptideRawFragmentMasses::getDeltaMass(), m_beginMassDelta, m_nterModification, m_theoreticalPeakList, mcsp_peakList, pappso::MHPLUS(), pappso::MPROTIUM(), and pappso::Enums::y.

Referenced by matchExperimentalPeaks().

getCountSharedPeaks()

std::size_t pappso::specglob::PeptideModel::getCountSharedPeaks

(

)

const

Definition at line 440 of file peptidemodel.cpp.

{
  return m_countSharedPeaks;
}

References m_countSharedPeaks.

Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::cbor::psm::PsmSpecGlobScan::process(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().

getIntensityExperimentalPeaks()

double pappso::specglob::PeptideModel::getIntensityExperimentalPeaks

(

)

const

Definition at line 452 of file peptidemodel.cpp.

{
  return m_intensityExperimentalPeaks;
}

References m_intensityExperimentalPeaks.

getIntensitySharedPeaks()

double pappso::specglob::PeptideModel::getIntensitySharedPeaks

(

)

const

Definition at line 446 of file peptidemodel.cpp.

{
  return m_intensitySharedPeaks;
}

References m_intensitySharedPeaks.

getMass()

double pappso::specglob::PeptideModel::getMass

(

)

const

Definition at line 277 of file peptidemodel.cpp.

{
  double mass = m_beginMassDelta;
  if(m_cterModification != nullptr)
    mass += m_cterModification->getMass();
  if(m_nterModification != nullptr)
    mass += m_nterModification->getMass();
 
  for(auto aa_model : *this)
    {
      mass += aa_model.amino_acid.getMass() + aa_model.mass_difference;
    }
  return mass;
}

References m_beginMassDelta, m_cterModification, and m_nterModification.

Referenced by getMassDelta(), and getMz().

getMassDelta()

double pappso::specglob::PeptideModel::getMassDelta

(

)

const

mass delta between experimental and theoretical mass

Definition at line 293 of file peptidemodel.cpp.

{
  return m_experimentalPrecursorMass - getMass();
}

References getMass(), and m_experimentalPrecursorMass.

Referenced by assignResidualMass2Cter(), toProForma(), and toString().

getMz()

double pappso::specglob::PeptideModel::getMz

(

unsigned int

charge

)

const

get the m/z peptide model mass

Definition at line 122 of file peptidemodel.cpp.

{
  return ((getMass() + (pappso::MHPLUS * charge)) / (double)charge);
}

References getMass(), and pappso::MHPLUS().

getTheoreticalIonMassList()

std::vector< double > pappso::specglob::PeptideModel::getTheoreticalIonMassList

(

)

const

Definition at line 429 of file peptidemodel.cpp.

{
  std::vector<double> mass_list;
  for(auto &datapoint : m_theoreticalPeakList)
    {
      mass_list.push_back(datapoint.mz_range.getMz());
    }
  return mass_list;
}

References m_theoreticalPeakList.

getTheoreticalPeakDataPointList()

const std::vector< TheoreticalPeakDataPoint > & pappso::specglob::PeptideModel::getTheoreticalPeakDataPointList

(

)

const

Definition at line 615 of file peptidemodel.cpp.

{
  return m_theoreticalPeakList;
}

References m_theoreticalPeakList.

getTheoreticalPeakDataPointListToString()

QString pappso::specglob::PeptideModel::getTheoreticalPeakDataPointListToString

(

)

const

Definition at line 621 of file peptidemodel.cpp.

{
 
  auto it_expe_peaks_end = mcsp_peakList.get()->end();
  QString str;
  for(auto &theo_peak : m_theoreticalPeakList)
    {
      double intensity = 0;
      if(theo_peak.it_experimental_peak_match != it_expe_peaks_end)
        {
          intensity = theo_peak.it_experimental_peak_match->y;
        }
      str.append(QString("{%1,%2,%3,%4}")
                   .arg(theo_peak.mz_range.getMz())
                   .arg(intensity)
                   .arg(theo_peak.aa_indice)
                   .arg(at(theo_peak.aa_indice).amino_acid.toString()));
    }
  return str;
}

References m_theoreticalPeakList, and mcsp_peakList.

hasRemoval()

bool pappso::specglob::PeptideModel::hasRemoval

(

)

const

Definition at line 173 of file peptidemodel.cpp.

{
  for(auto aa_model : *this)
    {
      if(std::abs(aa_model.amino_acid.getMass() + aa_model.mass_difference) < 0.001)
        return true;
    }
  return false;
}

ltrimOnRemoval()

bool pappso::specglob::PeptideModel::ltrimOnRemoval

(

)

try to remove left amino acid if there is a removal

Returns

true if peptide model is modified

Definition at line 184 of file peptidemodel.cpp.

{
  AminoAcidModel *amino_acid_to_remove = nullptr;
  int pos                              = -1;
  for(auto aa_model : *this)
    {
      pos++;
      if(std::abs(aa_model.amino_acid.getMass() + aa_model.mass_difference) < 0.001)
        {
          amino_acid_to_remove = &aa_model;
          break;
        }
    }
  if(amino_acid_to_remove != nullptr)
    {
      if(std::abs(front().amino_acid.getMass() - amino_acid_to_remove->amino_acid.getMass()) <
         0.001)
        {
          erase(begin());
          if(pos > 0)
            at(pos - 1).mass_difference = 0;
          return true;
        }
    }
  return false;
}

References pappso::specglob::AminoAcidModel::amino_acid, and pappso::Aa::getMass().

Referenced by pappso::specglob::SpectralAlignment::rtrim().

matchExperimentalPeaks()

void pappso::specglob::PeptideModel::matchExperimentalPeaks

(

pappso::PrecisionPtr

precision

)

Definition at line 319 of file peptidemodel.cpp.

{
  if(m_theoreticalPeakList.size() == 0)
    {
      m_intensityExperimentalPeaks = mcsp_peakList.get()->totalIonCurrent();
      generateTheoreticalPeaks(precision);
    }
  auto it_expe_peaks_end = mcsp_peakList.get()->end();
  auto it_expe_peaks     = mcsp_peakList.get()->begin();
  auto it_theo_peaks     = m_theoreticalPeakList.begin();
  while((it_expe_peaks != mcsp_peakList.get()->end()) &&
        (it_theo_peaks != m_theoreticalPeakList.end()))
    {
      while((it_expe_peaks != mcsp_peakList.get()->end()) &&
            (it_expe_peaks->x < it_theo_peaks->mz_range.lower()))
        { // find the first possible ion hit
          it_expe_peaks++;
        }
      if(it_expe_peaks == mcsp_peakList.get()->end())
        continue;
 
      if(it_expe_peaks->x < it_theo_peaks->mz_range.upper())
        {
          // ok, we've got a hit
          auto it_theo_peaks_loop = it_theo_peaks;
          while((it_theo_peaks_loop != m_theoreticalPeakList.end()) &&
                (it_theo_peaks_loop->mz_range.contains(it_expe_peaks->x)))
            {
              if((it_theo_peaks_loop->it_experimental_peak_match == it_expe_peaks_end) ||
                 (it_theo_peaks_loop->it_experimental_peak_match->y < it_expe_peaks->y))
                {
                  it_theo_peaks_loop->it_experimental_peak_match = it_expe_peaks;
                  qDebug() << "match: mz=" << it_expe_peaks->x << " intensity=" << it_expe_peaks->y;
                  break;
                }
              it_theo_peaks_loop++;
            }
          it_expe_peaks++;
        }
      else
        {
          it_theo_peaks++;
        }
      // it_expe_peaks++;
    }
 
  // get number of shared peaks
  m_countSharedPeaks     = 0;
  m_intensitySharedPeaks = 0;
  std::vector<std::vector<pappso::DataPoint>::const_iterator> matched_experimental_peaks;
  for(auto &theo_peak : m_theoreticalPeakList)
    {
      if(theo_peak.it_experimental_peak_match != it_expe_peaks_end)
        {
          matched_experimental_peaks.push_back(theo_peak.it_experimental_peak_match);
          // m_countSharedPeaks++;
        }
    }
  auto it_end = std::unique(matched_experimental_peaks.begin(), matched_experimental_peaks.end());
  m_countSharedPeaks     = std::distance(matched_experimental_peaks.begin(), it_end);
  m_intensitySharedPeaks = std::accumulate(
    matched_experimental_peaks.begin(),
    it_end,
    0.0,
    [](double k, const std::vector<pappso::DataPoint>::const_iterator &l) { return (k + l->y); });
}

References generateTheoreticalPeaks(), m_countSharedPeaks, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_theoreticalPeakList, and mcsp_peakList.

Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().

modifCount()

std::size_t pappso::specglob::PeptideModel::modifCount

(

)

const

Definition at line 299 of file peptidemodel.cpp.

{
  std::size_t count = 0;
  if(m_beginMassDelta != 0.0)
    count++;
  for(auto aa_model : *this)
    {
      if(aa_model.mass_difference != 0.0)
        count++;
    }
  return count;
}

References m_beginMassDelta.

operator=()

PeptideModel & pappso::specglob::PeptideModel::operator=

(

const PeptideModel &

other

)

Definition at line 89 of file peptidemodel.cpp.

{
 
  assign(other.begin(), other.end());
  m_experimentalPrecursorMass = other.m_experimentalPrecursorMass;
  mcsp_peakList               = other.mcsp_peakList;
 
  m_experimentalPrecursorMass = other.m_experimentalPrecursorMass;
  m_beginMassDelta            = other.m_beginMassDelta;
 
  m_nterModification           = other.m_nterModification;
  m_cterModification           = other.m_cterModification;
  m_countSharedPeaks           = other.m_countSharedPeaks;
  m_intensitySharedPeaks       = other.m_intensitySharedPeaks;
  m_intensityExperimentalPeaks = other.m_intensityExperimentalPeaks;
  m_theoreticalPeakList.clear();
  return *this;
}

References PeptideModel(), m_beginMassDelta, m_countSharedPeaks, m_cterModification, m_experimentalPrecursorMass, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_nterModification, m_theoreticalPeakList, and mcsp_peakList.

Referenced by copyDeep().

removeBracketsForAlignedAA()

bool pappso::specglob::PeptideModel::removeBracketsForAlignedAA

(

)

Use to remove brackets around not found Amino acids when the B or Y peak corresponding to the amino acid in the sequence is in the experimental peak list

Parameters

betterModified	: The better sequence of hit Modified
experimentalMassList	: The list of mass that are in the experimental spectrum
precision	: The precision of the mass spectrometer

Returns

the new sequence without brackets around found amino acids after all post treatments

Definition at line 592 of file peptidemodel.cpp.

{
  if(m_theoreticalPeakList.size() == 0)
    {
      throw pappso::PappsoException("missing peak matching");
    }
  bool modified          = false;
  auto it_expe_peaks_end = mcsp_peakList.get()->end();
  for(auto &theo_peak : m_theoreticalPeakList)
    {
      if(theo_peak.it_experimental_peak_match != it_expe_peaks_end)
        {
          if(at(theo_peak.aa_indice).bracket == true)
            {
              modified                        = true;
              at(theo_peak.aa_indice).bracket = false;
            }
        }
    }
  return modified;
}

References m_theoreticalPeakList, and mcsp_peakList.

setBeginMassDelta()

void pappso::specglob::PeptideModel::setBeginMassDelta

(

double

delta

)

Definition at line 313 of file peptidemodel.cpp.

{
  m_beginMassDelta = delta;
}

References m_beginMassDelta.

Referenced by pappso::specglob::SpectralAlignment::buildPeptideModel().

toProForma()

QString pappso::specglob::PeptideModel::toProForma

(

)

const

get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md

Returns

QString as described in ProForma

Definition at line 213 of file peptidemodel.cpp.

{
  QString peptide_str("[");
 
  // if(m_beginMassDelta != 0.0)
  //   peptide_str.append(
  //    QString("[%1]").arg(QString::number(m_beginMassDelta, 'f', 2)));
  // ProForma version 2 unexplained mass delta :
  //  peptide_str.append(
  //  QString("_[%1]").arg(QString::number(getMassDelta(), 'f', 2)));
 
  if(getMassDelta() > 0)
    {
      peptide_str.append("+");
    }
  peptide_str.append(QString("%1]?").arg(QString::number(getMassDelta(), 'f', 4)));
  peptide_str.replace("[+0.0000]?", "");
  peptide_str.replace("[-0.0000]?", "");
 
 
  double mass_diff = m_beginMassDelta;
  for(auto aa_model : *this)
    {
      qDebug() << " aa_model.amino_acid.toString()=" << aa_model.amino_acid.toAbsoluteString()
               << " aa_model.alignment_type=" << Utils::toString(aa_model.alignment_type)
               << " aa_model.mass_difference=" << aa_model.mass_difference
               << " aa_model.bracket=" << aa_model.bracket;
 
      if(aa_model.bracket)
        {
        }
 
      if(aa_model.remove)
        {
          peptide_str.append(aa_model.amino_acid.getLetter());
 
          peptide_str.append(
            "[" +
            AaModification::getInstanceRemovalAccessionByAaLetter(aa_model.amino_acid.getLetter())
              ->getAccession() +
            "]");
        }
      else
        {
          peptide_str.append(aa_model.amino_acid.toProForma());
 
          mass_diff += aa_model.mass_difference;
          if(mass_diff != 0.0)
            {
              if(mass_diff > 0)
                {
                  peptide_str.append(QString("[+%1]").arg(QString::number(mass_diff, 'f', 4)));
                }
              else
                {
                  peptide_str.append(QString("[%1]").arg(QString::number(mass_diff, 'f', 4)));
                }
            }
        }
      mass_diff = 0.0;
    }
  return peptide_str;
}

References pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), getMassDelta(), m_beginMassDelta, and pappso::Utils::toString().

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

toString()

QString pappso::specglob::PeptideModel::toString

(

)

const

Definition at line 128 of file peptidemodel.cpp.

{
  QString peptide_str;
 
  if(m_beginMassDelta != 0.0)
    peptide_str.append(QString("[%1]").arg(QString::number(m_beginMassDelta, 'f', 2)));
 
  for(auto aa_model : *this)
    {
      qDebug() << " aa_model.amino_acid.toString()=" << aa_model.amino_acid.toAbsoluteString()
               << " aa_model.alignment_type=" << Utils::toString(aa_model.alignment_type)
               << " aa_model.mass_difference=" << aa_model.mass_difference
               << " aa_model.bracket=" << aa_model.bracket;
 
      if(aa_model.remove)
        peptide_str.append("-(");
      if(aa_model.bracket)
        {
          peptide_str.append(QString("[%1]").arg(aa_model.amino_acid.toString()));
        }
      else
        {
          peptide_str.append(aa_model.amino_acid.toString());
        }
 
 
      if(aa_model.mass_difference != 0.0)
        {
          peptide_str.append(
            QString("[%1]").arg(QString::number(aa_model.mass_difference, 'f', 2)));
        }
 
      if(aa_model.remove)
        peptide_str.append(")");
    }
 
  peptide_str.replace(")-(", "");
  peptide_str.append(QString("_[%1]").arg(QString::number(getMassDelta(), 'f', 2)));
  peptide_str.replace("_[0.00]", "");
  peptide_str.replace("_[-0.00]", "");
  return peptide_str;
}

References getMassDelta(), m_beginMassDelta, and pappso::Utils::toString().

Referenced by eliminateComplementaryDelta(), pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::cbor::psm::PsmSpecGlobScan::process(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().

Member Data Documentation

m_beginMassDelta

double pappso::specglob::PeptideModel::m_beginMassDelta = 0

private

Definition at line 224 of file peptidemodel.h.

Referenced by PeptideModel(), checkForAaModification(), checkForAaModificationP(), checkForMutation(), checkForMutations(), eliminateComplementaryDelta(), generateTheoreticalPeaks(), getMass(), modifCount(), operator=(), setBeginMassDelta(), toProForma(), and toString().

m_countSharedPeaks

std::size_t pappso::specglob::PeptideModel::m_countSharedPeaks = 0

private

Definition at line 230 of file peptidemodel.h.

Referenced by PeptideModel(), getCountSharedPeaks(), matchExperimentalPeaks(), and operator=().

m_cterModification

pappso::AaModificationP pappso::specglob::PeptideModel::m_cterModification

private

Definition at line 228 of file peptidemodel.h.

Referenced by PeptideModel(), PeptideModel(), getMass(), and operator=().

m_experimentalPrecursorMass

double pappso::specglob::PeptideModel::m_experimentalPrecursorMass

private

Definition at line 223 of file peptidemodel.h.

Referenced by PeptideModel(), PeptideModel(), getMassDelta(), and operator=().

m_intensityExperimentalPeaks

double pappso::specglob::PeptideModel::m_intensityExperimentalPeaks = 0

private

Definition at line 232 of file peptidemodel.h.

Referenced by PeptideModel(), getIntensityExperimentalPeaks(), matchExperimentalPeaks(), and operator=().

m_intensitySharedPeaks

double pappso::specglob::PeptideModel::m_intensitySharedPeaks = 0

private

Definition at line 231 of file peptidemodel.h.

Referenced by PeptideModel(), getIntensitySharedPeaks(), matchExperimentalPeaks(), and operator=().

m_nterModification

pappso::AaModificationP pappso::specglob::PeptideModel::m_nterModification

private

Definition at line 227 of file peptidemodel.h.

Referenced by PeptideModel(), PeptideModel(), generateTheoreticalPeaks(), getMass(), and operator=().

m_theoreticalPeakList

std::vector<TheoreticalPeakDataPoint> pappso::specglob::PeptideModel::m_theoreticalPeakList

private

Definition at line 221 of file peptidemodel.h.

Referenced by copyDeep(), generateTheoreticalPeaks(), getTheoreticalIonMassList(), getTheoreticalPeakDataPointList(), getTheoreticalPeakDataPointListToString(), matchExperimentalPeaks(), operator=(), and removeBracketsForAlignedAA().

mcsp_peakList

pappso::MassSpectrumCstSPtr pappso::specglob::PeptideModel::mcsp_peakList = nullptr

private

Definition at line 225 of file peptidemodel.h.

Referenced by PeptideModel(), PeptideModel(), generateTheoreticalPeaks(), getTheoreticalPeakDataPointListToString(), matchExperimentalPeaks(), operator=(), and removeBracketsForAlignedAA().

---

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

• pappsomspp/core/processing/specglob/peptidemodel.h
• pappsomspp/core/processing/specglob/peptidemodel.cpp