pappso::specglob::ExperimentalSpectrum Class Reference

#include <experimentalspectrum.h>

Inheritance diagram for pappso::specglob::ExperimentalSpectrum:

Public Member Functions
	ExperimentalSpectrum (const pappso::QualifiedMassSpectrum &qmass_spectrum, pappso::PrecisionPtr precision_ptr)
	ExperimentalSpectrum (const pappso::QualifiedMassSpectrum &qmass_spectrum, pappso::PrecisionPtr precision_ptr, double precursor_mass_error)
	ExperimentalSpectrum (const ExperimentalSpectrum &other)
virtual	~ExperimentalSpectrum ()
std::vector< double >	getMassList () const
double	getSymetricMz (double mz) const
	compute the symmetric mass for debuggin purpose
double	getTargetMzSum () const
double	getPrecursorMass () const
std::vector< double >	getMassList (ExperimentalSpectrumDataPointType type) const
QString	toString () const
const pappso::QualifiedMassSpectrum &	getQualifiedMassSpectrum () const
std::vector< ExperimentalSpectrumDataPoint >::const_reverse_iterator	reverseFindDiffMz (std::size_t start_position, const pappso::MzRange &targeted_mass_range) const
	find the peak for wich mass difference from rbegin corresponds to aaTheoMass Find if a peak back in the peak list has a mass difference that corresponds to the targeted mass

Private Member Functions
void	createSymetricPeakList ()
	add symmetric peaks to the spectrum Create a SymetricPeakList that contain symmetric peaks and the information if a peak is the initial peak, the symmetric peak, or both if already exist. assuming fragment ion charge is 1
void	createSymetricPeakList (double precursor_mass_error)
std::vector< pappso::DataPoint >::const_iterator	findMz (double mz)
	find the correspondin mz in the mass spectrum (given the precision)

Private Attributes
pappso::QualifiedMassSpectrum	m_qualifiedMassSpectrum
double	m_targetMzSum
double	m_precursorMass
pappso::PrecisionPtr	m_precisionPtr

Detailed Description

Todo

write docs

Definition at line 63 of file experimentalspectrum.h.

Constructor & Destructor Documentation

ExperimentalSpectrum() [1/3]

pappso::specglob::ExperimentalSpectrum::ExperimentalSpectrum	(	const pappso::QualifiedMassSpectrum &	qmass_spectrum,
		pappso::PrecisionPtr	precision_ptr )

Default constructor

Definition at line 45 of file experimentalspectrum.cpp.

  : std::vector<ExperimentalSpectrumDataPoint>()
{
  m_qualifiedMassSpectrum = qmass_spectrum;
  m_precisionPtr          = precision_ptr;
  createSymetricPeakList();
}

References createSymetricPeakList(), m_precisionPtr, and m_qualifiedMassSpectrum.

Referenced by ExperimentalSpectrum().

ExperimentalSpectrum() [2/3]

pappso::specglob::ExperimentalSpectrum::ExperimentalSpectrum	(	const pappso::QualifiedMassSpectrum &	qmass_spectrum,
		pappso::PrecisionPtr	precision_ptr,
		double	precursor_mass_error )

specpeptidoms post-processing constructor

Definition at line 54 of file experimentalspectrum.cpp.

  : std::vector<ExperimentalSpectrumDataPoint>()
{
  m_qualifiedMassSpectrum = qmass_spectrum;
  m_precisionPtr          = precision_ptr;
  createSymetricPeakList(precursor_mass_error);
}

References createSymetricPeakList(), m_precisionPtr, and m_qualifiedMassSpectrum.

ExperimentalSpectrum() [3/3]

pappso::specglob::ExperimentalSpectrum::ExperimentalSpectrum

(

const ExperimentalSpectrum &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 64 of file experimentalspectrum.cpp.

  : std::vector<ExperimentalSpectrumDataPoint>(other)
{
  m_targetMzSum           = other.m_targetMzSum;
  m_qualifiedMassSpectrum = other.m_qualifiedMassSpectrum;
  m_precisionPtr          = other.m_precisionPtr;
}

References ExperimentalSpectrum(), m_precisionPtr, m_qualifiedMassSpectrum, and m_targetMzSum.

~ExperimentalSpectrum()

pappso::specglob::ExperimentalSpectrum::~ExperimentalSpectrum ( )

virtual

Destructor

Definition at line 72 of file experimentalspectrum.cpp.

{
}

Member Function Documentation

createSymetricPeakList() [1/2]

void pappso::specglob::ExperimentalSpectrum::createSymetricPeakList ( )

private

add symmetric peaks to the spectrum Create a SymetricPeakList that contain symmetric peaks and the information if a peak is the initial peak, the symmetric peak, or both if already exist. assuming fragment ion charge is 1

Definition at line 77 of file experimentalspectrum.cpp.

{
  createSymetricPeakList(0);
}

References createSymetricPeakList().

Referenced by ExperimentalSpectrum(), ExperimentalSpectrum(), and createSymetricPeakList().

createSymetricPeakList() [2/2]

void pappso::specglob::ExperimentalSpectrum::createSymetricPeakList ( double precursor_mass_error )

private

Definition at line 83 of file experimentalspectrum.cpp.

{
 
  bool ok;
  auto charge = m_qualifiedMassSpectrum.getPrecursorCharge(&ok);
  if(!ok)
    {
      throw pappso::PappsoException(
        QObject::tr("precursor charge is not defined in spectrum %1")
          .arg(m_qualifiedMassSpectrum.getMassSpectrumId().getNativeId()));
    }
 
  double mz_prec = m_qualifiedMassSpectrum.getPrecursorMz(&ok);
  if(!ok)
    {
      throw pappso::PappsoException(
        QObject::tr("precursor m/z is not defined in spectrum %1")
          .arg(m_qualifiedMassSpectrum.getMassSpectrumId().getNativeId()));
    }
 
  // compute precursor mass given the charge state
  m_precursorMass = mz_prec * (double)charge - precursor_mass_error;
  m_precursorMass -= pappso::MHPLUS * (double)charge;
  m_targetMzSum = m_precursorMass + pappso::MHPLUS + pappso::MHPLUS;
 
  std::vector<double> mz_list = m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->xValues();
 
  std::size_t mz_current_indice = 0;
  auto itend                    = m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->end();
  for(std::vector<pappso::DataPoint>::const_iterator it =
        m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->begin();
      it != itend;
      it++)
    {
      double current_mz = it->x;
 
      double symmetric_current_mz = getSymetricMz(current_mz);
 
      auto itpair_symmetric = findMz(symmetric_current_mz);
      if(itpair_symmetric != itend)
        {
          // there is a counterpart
          push_back({ExperimentalSpectrumDataPointType::both, it->x, 0});
          qDebug() << "current_mz=" << current_mz << " both";
        }
      else
        {
          // there is no counterpart
          push_back({ExperimentalSpectrumDataPointType::native, it->x, 0});
          push_back({ExperimentalSpectrumDataPointType::symmetric, symmetric_current_mz, 0});
          qDebug() << "current_mz=" << current_mz << " symmetrics";
        }
 
      mz_current_indice++;
    }
 
  // we add a peak with NT mass (1.0078) if it is not detected, to give better
  // chance to align the first amino acid in b if it is present
  if(findMz(pappso::MPROTIUM) == itend)
    {
      push_back({ExperimentalSpectrumDataPointType::synthetic, pappso::MPROTIUM, 0});
    }
 
  // We add the B peak corresponding to the precursor (complete peptide)
  double precusorBion = m_targetMzSum - pappso::MASSH2O - pappso::MPROTIUM;
 
  if(findMz(precusorBion) == itend)
    {
      push_back({ExperimentalSpectrumDataPointType::synthetic, precusorBion, 0});
    }
 
  std::sort(begin(),
            end(),
            [](const ExperimentalSpectrumDataPoint &a, const ExperimentalSpectrumDataPoint &b) {
              return (a.peak_mz < b.peak_mz);
            });
 
  std::size_t i = 0;
  for(auto &data_point : *this)
    {
      data_point.indice = i;
      i++;
    }
}

References pappso::a, pappso::b, pappso::specglob::both, findMz(), getSymetricMz(), m_precursorMass, m_qualifiedMassSpectrum, m_targetMzSum, pappso::MASSH2O(), pappso::MHPLUS(), pappso::MPROTIUM(), pappso::specglob::native, pappso::specglob::symmetric, and pappso::specglob::synthetic.

findMz()

std::vector< pappso::DataPoint >::const_iterator pappso::specglob::ExperimentalSpectrum::findMz ( double mz )

private

find the correspondin mz in the mass spectrum (given the precision)

Definition at line 169 of file experimentalspectrum.cpp.

{
  pappso::MzRange mz_range(mz, m_precisionPtr);
  auto itend = m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->end();
  auto it =
    findFirstEqualOrGreaterX(m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->begin(),
                             m_qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->end(),
                             mz_range.lower());
 
  if(it != itend)
    {
      if(it->x <= mz_range.upper())
        {
          return it;
        }
    }
  return itend;
}

References pappso::findFirstEqualOrGreaterX(), pappso::MzRange::lower(), m_precisionPtr, m_qualifiedMassSpectrum, and pappso::MzRange::upper().

Referenced by createSymetricPeakList().

getMassList() [1/2]

std::vector< double > pappso::specglob::ExperimentalSpectrum::getMassList

(

)

const

Definition at line 195 of file experimentalspectrum.cpp.

{
  std::vector<double> mass_list;
  for(const ExperimentalSpectrumDataPoint &n : *this)
    {
      mass_list.push_back(n.peak_mz);
    }
 
  return mass_list;
}

References pappso::specglob::ExperimentalSpectrumDataPoint::peak_mz.

getMassList() [2/2]

std::vector< double > pappso::specglob::ExperimentalSpectrum::getMassList

(

ExperimentalSpectrumDataPointType

type

)

const

Definition at line 213 of file experimentalspectrum.cpp.

{
  std::vector<double> mass_list;
  for(const ExperimentalSpectrumDataPoint &n : *this)
    {
      if(n.type == type)
        mass_list.push_back(n.peak_mz);
    }
 
  return mass_list;
}

References pappso::specglob::ExperimentalSpectrumDataPoint::peak_mz, and pappso::specglob::ExperimentalSpectrumDataPoint::type.

getPrecursorMass()

double pappso::specglob::ExperimentalSpectrum::getPrecursorMass

(

)

const

Definition at line 237 of file experimentalspectrum.cpp.

{
  return m_precursorMass;
}

References m_precursorMass.

getQualifiedMassSpectrum()

const pappso::QualifiedMassSpectrum & pappso::specglob::ExperimentalSpectrum::getQualifiedMassSpectrum

(

)

const

Definition at line 284 of file experimentalspectrum.cpp.

{
  return m_qualifiedMassSpectrum;
}

References m_qualifiedMassSpectrum.

getSymetricMz()

double pappso::specglob::ExperimentalSpectrum::getSymetricMz

(

double

mz

)

const

compute the symmetric mass for debuggin purpose

Definition at line 207 of file experimentalspectrum.cpp.

{
  return m_targetMzSum - mz;
}

References m_targetMzSum.

Referenced by createSymetricPeakList().

getTargetMzSum()

double pappso::specglob::ExperimentalSpectrum::getTargetMzSum

(

)

const

Definition at line 189 of file experimentalspectrum.cpp.

{
  return m_targetMzSum;
}

References m_targetMzSum.

reverseFindDiffMz()

std::vector< ExperimentalSpectrumDataPoint >::const_reverse_iterator pappso::specglob::ExperimentalSpectrum::reverseFindDiffMz	(	std::size_t	start_position,
		const pappso::MzRange &	targeted_mass_range ) const

find the peak for wich mass difference from rbegin corresponds to aaTheoMass Find if a peak back in the peak list has a mass difference that corresponds to the targeted mass

Parameters

start_position	reverse iterator on the reference peak to look for mass difference from
targeted_mass_range	the mass difference to look forconst pappso::PeptideSp peptide_sp

Returns

a reverse iterator on the peak (found) or the end of the search (not found)

Definition at line 243 of file experimentalspectrum.cpp.

{
 
  qDebug() << "start_position" << start_position << " lookfor=" << aaTheoMzRange.getMz();
  std::vector<ExperimentalSpectrumDataPoint>::const_reverse_iterator itrbegin =
    rbegin() + (size() - 1 - start_position);
 
  qDebug() << itrbegin->indice << "mz=" << itrbegin->peak_mz;
  double eperimentalMzReference = itrbegin->peak_mz;
  auto itrend                   = this->rend();
  // We check all row from j to 0
  qDebug();
  for(auto itr = itrbegin + 1; itr != itrend; ++itr)
    {
      qDebug() << itr->indice;
      double experimentalMzDifference = eperimentalMzReference - itr->peak_mz;
 
      if(experimentalMzDifference > aaTheoMzRange.upper())
        {
          // if we pass the mass of the theoretical amino acid, we stop to not
          // over
          // calculate
          qDebug() << experimentalMzDifference << ">" << aaTheoMzRange.upper();
          return itrend;
        }
      else if(experimentalMzDifference < aaTheoMzRange.lower())
        {
          continue;
        }
 
      qDebug() << itr->indice << " diff=" << experimentalMzDifference;
      // if we found that j-k give an amino acid, we keep k value
      return itr;
    }
  qDebug() << "rend";
  return itrend; // a value of -1 to show that
                 // there is no k value
}

References pappso::MzRange::getMz(), pappso::MzRange::lower(), and pappso::MzRange::upper().

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

toString()

QString pappso::specglob::ExperimentalSpectrum::toString

(

)

const

Definition at line 226 of file experimentalspectrum.cpp.

{
  QStringList all_element;
  for(const ExperimentalSpectrumDataPoint &n : *this)
    {
      all_element << QString("%1 %2").arg(n.peak_mz).arg((std::uint8_t)n.type);
    }
  return QString("[%1]").arg(all_element.join("] ["));
}

References pappso::specglob::ExperimentalSpectrumDataPoint::peak_mz, and pappso::specglob::ExperimentalSpectrumDataPoint::type.

Member Data Documentation

m_precisionPtr

pappso::PrecisionPtr pappso::specglob::ExperimentalSpectrum::m_precisionPtr

private

Definition at line 141 of file experimentalspectrum.h.

Referenced by ExperimentalSpectrum(), ExperimentalSpectrum(), ExperimentalSpectrum(), and findMz().

m_precursorMass

double pappso::specglob::ExperimentalSpectrum::m_precursorMass

private

Definition at line 140 of file experimentalspectrum.h.

Referenced by createSymetricPeakList(), and getPrecursorMass().

m_qualifiedMassSpectrum

pappso::QualifiedMassSpectrum pappso::specglob::ExperimentalSpectrum::m_qualifiedMassSpectrum

private

Definition at line 138 of file experimentalspectrum.h.

Referenced by ExperimentalSpectrum(), ExperimentalSpectrum(), ExperimentalSpectrum(), createSymetricPeakList(), findMz(), and getQualifiedMassSpectrum().

m_targetMzSum

double pappso::specglob::ExperimentalSpectrum::m_targetMzSum

private

Definition at line 139 of file experimentalspectrum.h.

Referenced by ExperimentalSpectrum(), createSymetricPeakList(), getSymetricMz(), and getTargetMzSum().

---

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

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