pappso::PeptideFragment Class Reference

#include <peptidefragment.h>

Inheritance diagram for pappso::PeptideFragment:

Public Member Functions
	PeptideFragment (const PeptideSp &sp_peptide, PeptideDirection direction, unsigned int size)
	PeptideFragment (const PeptideFragment &other)
	PeptideFragment (PeptideFragment &&toCopy)
virtual	~PeptideFragment ()
virtual const PeptideSp &	getPeptideSp () const
virtual unsigned int	size () const override
virtual const QString	getSequence () const override
	amino acid sequence without modification
virtual pappso_double	getMass () const override
PeptideDirection	getPeptideIonDirection () const
virtual int	getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const override
	get the number of atom C, O, N, H in the molecule
virtual int	getNumberOfIsotope (Enums::Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
virtual bool	isPalindrome () const override
	tells if the peptide sequence is a palindrome
Public Member Functions inherited from pappso::PeptideInterface
virtual const QString	getSequenceLi () const
	amino acid sequence without modification where L are replaced by I
virtual const QString	getName () const
virtual const ChemicalFormula	getChemicalFormulaCharge (unsigned int charge) const
virtual const QString	getFormula (unsigned int charge) const final
virtual bool	matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
	tells if the peptide m/z matches a given experimental mass
Public Member Functions inherited from pappso::Ion
	Ion ()
	~Ion ()
virtual pappso_double	getMz (unsigned int charge) const final
Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula	getChemicalFormula () const

Static Public Member Functions
static const QString	getPeptideIonDirectionName (PeptideDirection direction)

Private Attributes
const PeptideSp	msp_peptide
const PeptideDirection	m_direction
const unsigned int	m_size = 0
pappso_double	m_mass = 0

Detailed Description

Definition at line 47 of file peptidefragment.h.

Constructor & Destructor Documentation

PeptideFragment() [1/3]

pappso::PeptideFragment::PeptideFragment	(	const PeptideSp &	sp_peptide,
		PeptideDirection	direction,
		unsigned int	size )

Definition at line 38 of file peptidefragment.cpp.

  : msp_peptide(sp_peptide), m_direction(direction), m_size(size)
{
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          m_mass += it->getMass();
          it++;
          i++;
        }
 
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          m_mass += msp_peptide.get()->getNterModification()->getMass();
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          m_mass += it->getMass();
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          m_mass += msp_peptide.get()->getCterModification()->getMass();
        }
    }
 
  m_mass += msp_peptide.get()->getCleavageNterModification()->getMass();
  m_mass += msp_peptide.get()->getCleavageCterModification()->getMass();
}

References getMass(), m_direction, m_mass, m_size, msp_peptide, pappso::Nter, and size().

Referenced by PeptideFragment(), and PeptideFragment().

PeptideFragment() [2/3]

pappso::PeptideFragment::PeptideFragment

(

const PeptideFragment &

other

)

Definition at line 82 of file peptidefragment.cpp.

  : msp_peptide(other.msp_peptide), m_direction(other.m_direction), m_size(other.m_size)
{
  m_mass = other.m_mass;
}

References PeptideFragment(), m_direction, m_mass, m_size, and msp_peptide.

PeptideFragment() [3/3]

pappso::PeptideFragment::PeptideFragment

(

PeptideFragment &&

toCopy

)

Definition at line 89 of file peptidefragment.cpp.

  : msp_peptide(std::move(toCopy.msp_peptide)),
    m_direction(toCopy.m_direction),
    m_size(toCopy.m_size),
    m_mass(toCopy.m_mass)
{
}

References PeptideFragment(), m_direction, m_mass, m_size, and msp_peptide.

~PeptideFragment()

pappso::PeptideFragment::~PeptideFragment ( )

virtual

Definition at line 98 of file peptidefragment.cpp.

{
}

Member Function Documentation

getMass()

pappso_double pappso::PeptideFragment::getMass ( ) const

overridevirtual

Implements pappso::Ion.

Definition at line 234 of file peptidefragment.cpp.

{
  return m_mass;
}

References m_mass.

Referenced by PeptideFragment().

getNumberOfAtom()

int pappso::PeptideFragment::getNumberOfAtom ( Enums::AtomIsotopeSurvey atom ) const

overridevirtual

get the number of atom C, O, N, H in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 137 of file peptidefragment.cpp.

{
  int number = 0;
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfAtom(atom);
          it++;
          i++;
        }
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          number += msp_peptide.get()->getNterModification()->getNumberOfAtom(atom);
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfAtom(atom);
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          number += msp_peptide.get()->getCterModification()->getNumberOfAtom(atom);
        }
    }
  number += msp_peptide.get()->getCleavageNterModification()->getNumberOfAtom(atom);
  number += msp_peptide.get()->getCleavageCterModification()->getNumberOfAtom(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_direction, m_size, msp_peptide, and pappso::Nter.

getNumberOfIsotope()

int pappso::PeptideFragment::getNumberOfIsotope ( Enums::Isotope isotope ) const

overridevirtual

get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 179 of file peptidefragment.cpp.

{
  int number = 0;
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfIsotope(isotope);
          it++;
          i++;
        }
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          number += msp_peptide.get()->getNterModification()->getNumberOfIsotope(isotope);
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfIsotope(isotope);
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          number += msp_peptide.get()->getCterModification()->getNumberOfIsotope(isotope);
        }
    }
  number += msp_peptide.get()->getCleavageNterModification()->getNumberOfIsotope(isotope);
  number += msp_peptide.get()->getCleavageCterModification()->getNumberOfIsotope(isotope);
  // number += m_nterCterCleavage->getNumberOfIsotope(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_direction, m_size, msp_peptide, and pappso::Nter.

getPeptideIonDirection()

PeptideDirection pappso::PeptideFragment::getPeptideIonDirection

(

)

const

Definition at line 240 of file peptidefragment.cpp.

{
  return m_direction;
}

References m_direction.

getPeptideIonDirectionName()

const QString pappso::PeptideFragment::getPeptideIonDirectionName ( PeptideDirection direction )

static

Definition at line 103 of file peptidefragment.cpp.

{
  switch(direction)
    {
      case PeptideDirection::Cter:
        return "Cter";
        break;
      case PeptideDirection::Nter:
        return "Nter";
        break;
      default:
        throw PappsoException(QString("direction name not implemented"));
        break;
    }
}

References pappso::Cter, and pappso::Nter.

Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), and pappso::XtandemHyperscore::getXtandemPredictedIonIntensityFactor().

getPeptideSp()

const PeptideSp & pappso::PeptideFragment::getPeptideSp ( ) const

virtual

Definition at line 223 of file peptidefragment.cpp.

{
  return msp_peptide;
};

References msp_peptide.

getSequence()

const QString pappso::PeptideFragment::getSequence ( ) const

overridevirtual

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 120 of file peptidefragment.cpp.

{
  QString sequence = msp_peptide.get()->getSequence();
  int diffSize     = msp_peptide.get()->size() - m_size;
  if(m_direction == PeptideDirection::Nter)
    {
      sequence = sequence.mid(0, m_size);
    }
  else
    {
      sequence = sequence.mid(diffSize, m_size);
    }
  return sequence;
}

References m_direction, m_size, msp_peptide, and pappso::Nter.

isPalindrome()

bool pappso::PeptideFragment::isPalindrome ( ) const

overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 246 of file peptidefragment.cpp.

{
  return msp_peptide.get()->isPalindrome();
}

References msp_peptide.

size()

unsigned int pappso::PeptideFragment::size ( ) const

overridevirtual

Implements pappso::PeptideInterface.

Definition at line 228 of file peptidefragment.cpp.

{
  return m_size;
}

References m_size.

Referenced by PeptideFragment().

Member Data Documentation

m_direction

const PeptideDirection pappso::PeptideFragment::m_direction

private

Definition at line 73 of file peptidefragment.h.

Referenced by PeptideFragment(), PeptideFragment(), PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideIonDirection(), and getSequence().

m_mass

pappso_double pappso::PeptideFragment::m_mass = 0

private

Definition at line 76 of file peptidefragment.h.

Referenced by PeptideFragment(), PeptideFragment(), PeptideFragment(), and getMass().

m_size

const unsigned int pappso::PeptideFragment::m_size = 0

private

Definition at line 74 of file peptidefragment.h.

Referenced by PeptideFragment(), PeptideFragment(), PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getSequence(), and size().

msp_peptide

const PeptideSp pappso::PeptideFragment::msp_peptide

private

Definition at line 72 of file peptidefragment.h.

Referenced by PeptideFragment(), PeptideFragment(), PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideSp(), getSequence(), and isPalindrome().

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

• pappsomspp/core/peptide/peptidefragment.h
• pappsomspp/core/peptide/peptidefragment.cpp