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 More...
virtual pappso_double	getMass () const override
PeptideDirection	getPeptideIonDirection () const
virtual int	getNumberOfAtom (AtomIsotopeSurvey atom) const override
	get the number of atom C, O, N, H in the molecule More...
virtual int	getNumberOfIsotope (Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...
virtual bool	isPalindrome () const override
	tells if the peptide sequence is a palindrome More...
Public Member Functions inherited from pappso::PeptideInterface
virtual const QString	getSequenceLi () const
	amino acid sequence without modification where L are replaced by I More...
virtual const QString	getName () const
virtual const QString	getFormula (unsigned int charge) const final
virtual bool	matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
Public Member Functions inherited from pappso::Ion
	Ion ()
	~Ion ()
virtual pappso_double	getMz (unsigned int charge) const final

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
AaModificationP	m_nterCterCleavage
pappso_double	m_mass = 0

Detailed Description

Definition at line 66 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 57 of file peptidefragment.cpp.

    {
      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++;
        }
      m_nterCterCleavage =
        AaModification::getInstance("internal:Nter_hydrolytic_cleavage_H");
    }
  m_mass += m_nterCterCleavage->getMass();
}
 
 
PeptideFragment::PeptideFragment(const PeptideFragment &other)
  : msp_peptide(other.msp_peptide),
    m_direction(other.m_direction),
    m_size(other.m_size)
{
  m_mass = other.m_mass;
}
 
 
PeptideFragment::PeptideFragment(PeptideFragment &&toCopy) // move constructor
  : msp_peptide(std::move(toCopy.msp_peptide)),
    m_direction(toCopy.m_direction),
    m_size(toCopy.m_size),
    m_mass(toCopy.m_mass)
{
}
 

References pappso::Peptide::end(), and pappso::AaModification::getInstance().

PeptideFragment() [2/3]

pappso::PeptideFragment::PeptideFragment

(

const PeptideFragment &

other

)

Definition at line 94 of file peptidefragment.cpp.

{
}
 
const QString
PeptideFragment::getPeptideIonDirectionName(PeptideDirection direction)
{
  switch(direction)

PeptideFragment() [3/3]

pappso::PeptideFragment::PeptideFragment

(

PeptideFragment &&

toCopy

)

Definition at line 103 of file peptidefragment.cpp.

                               :
        return "Nter";
        break;
      default:
        throw PappsoException(QString("direction name not implemented"));

~PeptideFragment()

pappso::PeptideFragment::~PeptideFragment ( )

virtual

Definition at line 112 of file peptidefragment.cpp.

Member Function Documentation

getMass()

pappso_double pappso::PeptideFragment::getMass ( ) const

overridevirtual

Implements pappso::Ion.

Definition at line 229 of file peptidefragment.cpp.

getNumberOfAtom()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 151 of file peptidefragment.cpp.

        {
          number += it->getNumberOfAtom(atom);
          it++;
          i++;
        }
    }
  number += m_nterCterCleavage->getNumberOfAtom(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
int
PeptideFragment::getNumberOfIsotope(Isotope isotope) const
{
  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++;
        }
    }
  else
    {

getNumberOfIsotope()

int pappso::PeptideFragment::getNumberOfIsotope ( 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 184 of file peptidefragment.cpp.

        {
          number += it->getNumberOfIsotope(isotope);
          it++;
          i++;
        }
    }
  // number += m_nterCterCleavage->getNumberOfIsotope(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
 
const PeptideSp &
PeptideFragment::getPeptideSp() const
{
  return msp_peptide;
};
unsigned int
PeptideFragment::size() const
{
  return m_size;
}
 
pappso_double
PeptideFragment::getMass() const
{
  return m_mass;
}
 

getPeptideIonDirection()

PeptideDirection pappso::PeptideFragment::getPeptideIonDirection

(

)

const

Definition at line 235 of file peptidefragment.cpp.

getPeptideIonDirectionName()

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

static

Definition at line 117 of file peptidefragment.cpp.

    {
      sequence = sequence.mid(0, m_size);
    }
  else
    {
      sequence = sequence.mid(diffSize, m_size);
    }
  return sequence;
}
 
 
int

References m_size.

getPeptideSp()

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

virtual

Definition at line 218 of file peptidefragment.cpp.

getSequence()

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

overridevirtual

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 134 of file peptidefragment.cpp.

    {
      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++;
        }
    }
  else

References m_size, and msp_peptide.

isPalindrome()

bool pappso::PeptideFragment::isPalindrome ( ) const

overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 241 of file peptidefragment.cpp.

size()

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

overridevirtual

Implements pappso::PeptideInterface.

Definition at line 223 of file peptidefragment.cpp.

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

References msp_peptide.

Member Data Documentation

m_direction

const PeptideDirection pappso::PeptideFragment::m_direction

private

Definition at line 94 of file peptidefragment.h.

m_mass

pappso_double pappso::PeptideFragment::m_mass = 0

private

Definition at line 100 of file peptidefragment.h.

m_nterCterCleavage

AaModificationP pappso::PeptideFragment::m_nterCterCleavage

private

Definition at line 98 of file peptidefragment.h.

m_size

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

private

Definition at line 95 of file peptidefragment.h.

Referenced by getPeptideIonDirectionName(), and getSequence().

msp_peptide

const PeptideSp pappso::PeptideFragment::msp_peptide

private

Definition at line 93 of file peptidefragment.h.

Referenced by getSequence(), and size().

---

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

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