pappso::specglob::PeptideSpectrum Class Reference

#include <peptidespectrum.h>

Inheritance diagram for pappso::specglob::PeptideSpectrum:

Public Member Functions
	PeptideSpectrum (const pappso::PeptideSp peptide_sp)
	PeptideSpectrum (const PeptideSpectrum &other)
virtual	~PeptideSpectrum ()
std::vector< double >	getMassList () const
pappso::PeptideSp	getPeptideSp () const

Private Attributes
pappso::PeptideSp	msp_peptide

Detailed Description

Todo

write docs

Definition at line 62 of file peptidespectrum.h.

Constructor & Destructor Documentation

PeptideSpectrum() [1/2]

pappso::specglob::PeptideSpectrum::PeptideSpectrum

(

const pappso::PeptideSp

peptide_sp

)

Default constructor

Definition at line 46 of file peptidespectrum.cpp.

  : std::vector<PeptideSpectrumDataPoint>()
{
 
  if(peptide_sp.get()->size() < 2)
    {
      throw pappso::PappsoException(
        QObject::tr("PeptideSpectrum::PeptideSpectrum failed : peptide %1 is too small")
          .arg(peptide_sp.get()->toProForma()));
    }
  Enums::PeptideIon ion_type = Enums::PeptideIon::b;
  msp_peptide                = peptide_sp;
  std::list<Enums::PeptideIon> ion_list;
  ion_list.push_back(ion_type);
 
 
  pappso::PeptideFragmentIonListBase fragmented_ion_list(msp_peptide, ion_list);
 
  std::list<pappso::PeptideFragmentIonSp> peptide_ion_list =
    fragmented_ion_list.getPeptideFragmentIonSp(Enums::PeptideIon::b);
 
  push_back({pappso::MHPLUS, 0});
  // qDebug() << pappso::PeptideRawFragmentMasses::getDeltaMass(ion_type);
  for(auto &peptide_ion : peptide_ion_list)
    {
      push_back({peptide_ion.get()->getMz(1), 0});
    }
  push_back({(msp_peptide.get()->getMz(1) - pappso::MASSH2O +
              pappso::PeptideRawFragmentMasses::getDeltaMass(ion_type)),
             0});
  for(std::size_t i = 1; i < size(); i++)
    {
      at(i).diff_mz = (at(i).mz - at(i - 1).mz);
    }
}

References pappso::Enums::b, pappso::PeptideRawFragmentMasses::getDeltaMass(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), pappso::MASSH2O(), pappso::MHPLUS(), and msp_peptide.

Referenced by PeptideSpectrum().

PeptideSpectrum() [2/2]

pappso::specglob::PeptideSpectrum::PeptideSpectrum

(

const PeptideSpectrum &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 82 of file peptidespectrum.cpp.

  : std::vector<PeptideSpectrumDataPoint>(other)
{
  msp_peptide = other.msp_peptide;
}

References PeptideSpectrum(), and msp_peptide.

~PeptideSpectrum()

pappso::specglob::PeptideSpectrum::~PeptideSpectrum ( )

virtual

Destructor

Definition at line 88 of file peptidespectrum.cpp.

{
}

Member Function Documentation

getMassList()

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

(

)

const

Definition at line 93 of file peptidespectrum.cpp.

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

References pappso::specglob::PeptideSpectrumDataPoint::mz.

getPeptideSp()

pappso::PeptideSp pappso::specglob::PeptideSpectrum::getPeptideSp

(

)

const

Definition at line 105 of file peptidespectrum.cpp.

{
  return msp_peptide;
}

References msp_peptide.

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

Member Data Documentation

msp_peptide

pappso::PeptideSp pappso::specglob::PeptideSpectrum::msp_peptide

private

Definition at line 87 of file peptidespectrum.h.

Referenced by PeptideSpectrum(), PeptideSpectrum(), and getPeptideSp().

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

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