pappso::Peptide Class Reference

#include <peptide.h>

Inheritance diagram for pappso::Peptide:

Public Member Functions
	Peptide (const QString &pepstr)
virtual	~Peptide ()
	Peptide (const Peptide &peptide)
	Peptide (Peptide &&toCopy)
PeptideSp	makePeptideSp () const
NoConstPeptideSp	makeNoConstPeptideSp () const
void	addAaModification (AaModificationP aaModification, unsigned int position)
	adds a modification to amino acid sequence More...
std::vector< Aa >::iterator	begin ()
std::vector< Aa >::iterator	end ()
std::vector< Aa >::const_iterator	begin () const
std::vector< Aa >::const_iterator	end () const
std::vector< Aa >::const_reverse_iterator	rbegin () const
std::vector< Aa >::const_reverse_iterator	rend () const
Aa &	getAa (unsigned int position)
const Aa &	getConstAa (unsigned int position) const
pappso_double	getMass ()
pappso_double	getMass () const override
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...
const QString	getSequence () const override
	print amino acid sequence without modifications More...
unsigned int	size () const override
unsigned int	getNumberOfModification (AaModificationP mod) const
	count modification occurence More...
unsigned int	countModificationOnAa (AaModificationP mod, const std::vector< char > &aa_list) const
	count modification occurence More...
void	replaceAaModification (AaModificationP oldmod, AaModificationP newmod)
	replaces all occurences of a modification by a new one More...
void	removeAaModification (AaModificationP mod)
	removes all occurences of a modification More...
std::vector< unsigned int >	getModificationPositionList (AaModificationP mod) const
	get modification positions More...
std::vector< unsigned int >	getModificationPositionList (AaModificationP mod, const std::vector< char > &aa_list) const
	get modification positions More...
std::vector< unsigned int >	getAaPositionList (char aa) const
	get positions of one amino acid in peptide More...
std::vector< unsigned int >	getAaPositionList (std::list< char > list_aa) const
const QString	toString () const
	print modification except internal modifications More...
const QString	toAbsoluteString () const
	print all modifications More...
const QString	getLiAbsoluteString () const
	get all sequence string with modifications and converting Leucine to Isoleucine More...
AaModificationP	getInternalNterModification () const
AaModificationP	getInternalCterModification () const
void	removeInternalNterModification ()
void	removeInternalCterModification ()
void	setInternalNterModification (AaModificationP mod)
void	setInternalCterModification (AaModificationP mod)
void	rotate ()
void	reverse ()
virtual bool	isPalindrome () const override
	tells if the peptide sequence is a palindrome More...
void	replaceLeucineIsoleucine ()
void	removeNterAminoAcid ()
void	removeCterAminoAcid ()
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

Protected Attributes
std::vector< Aa >	m_aaVec
pappso_double	m_proxyMass = -1

Friends
bool	operator< (const Peptide &l, const Peptide &r)
bool	operator== (const Peptide &l, const Peptide &r)

Detailed Description

Definition at line 113 of file peptide.h.

Constructor & Destructor Documentation

Peptide() [1/3]

pappso::Peptide::Peptide

(

const QString &

pepstr

)

Definition at line 84 of file peptide.cpp.

                                           :Cter_hydrolytic_cleavage_HO"));
      getMass();
      qDebug() << "blabla " << m_aaVec.back().toString();
    }
}
 
Peptide::~Peptide()
{
}
 
Peptide::Peptide(const Peptide &peptide)
  : m_aaVec(peptide.m_aaVec), m_proxyMass(peptide.m_proxyMass)
{
}
 
 
Peptide::Peptide(Peptide &&toCopy) // move constructor
  : m_aaVec(std::move(toCopy.m_aaVec)), m_proxyMass(toCopy.m_proxyMass)
{
}
 
 
PeptideSp
Peptide::makePeptideSp() const
{
  return std::make_shared<const Peptide>(*this);

~Peptide()

pappso::Peptide::~Peptide ( )

virtual

Definition at line 113 of file peptide.cpp.

{

Peptide() [2/3]

pappso::Peptide::Peptide

(

const Peptide &

peptide

)

Definition at line 117 of file peptide.cpp.

Peptide() [3/3]

pappso::Peptide::Peptide

(

Peptide &&

toCopy

)

Definition at line 123 of file peptide.cpp.

{
  if(position >= size())
    {
      throw ExceptionOutOfRange(

References m_proxyMass, and size().

Member Function Documentation

addAaModification()

void pappso::Peptide::addAaModification	(	AaModificationP	aaModification,
		unsigned int	position
	)

adds a modification to amino acid sequence

Parameters

aaModification	pointer on modification to add
position	position in the amino acid sequence (starts at 0)

Definition at line 142 of file peptide.cpp.

    {
      seq += it->getLetter();
      it++;
    }
  return seq;
}
const QString
Peptide::toAbsoluteString() const
{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {

Referenced by pappso::PeptideFixedModificationBuilder::setPeptideSp().

begin() [1/2]

std::vector<Aa>::iterator pappso::Peptide::begin ( )

inline

Definition at line 147 of file peptide.h.

  {

begin() [2/2]

std::vector<Aa>::const_iterator pappso::Peptide::begin ( ) const

inline

Definition at line 159 of file peptide.h.

  {

countModificationOnAa()

unsigned int pappso::Peptide::countModificationOnAa	(	AaModificationP	mod,
		const std::vector< char > &	aa_list
	)		const

count modification occurence

Parameters

mod	modification to look for
aa_list	amino acid list targets (one letter code)

Returns

number of occurences

Definition at line 271 of file peptide.cpp.

    {
      it->replaceAaModification(oldmod, newmod);
      it++;
    }
  m_proxyMass = -1;
  getMass();
}
void
Peptide::removeAaModification(AaModificationP mod)
{
  std::vector<Aa>::iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {

end() [1/2]

std::vector<Aa>::iterator pappso::Peptide::end ( )

inline

Definition at line 153 of file peptide.h.

  {

end() [2/2]

std::vector<Aa>::const_iterator pappso::Peptide::end ( ) const

inline

Definition at line 165 of file peptide.h.

  {

getAa()

Aa & pappso::Peptide::getAa

(

unsigned int

position

)

Definition at line 540 of file peptide.cpp.

{
 
  std::vector<Aa>::iterator it(m_aaVec.begin());
  std::vector<Aa>::iterator itend(m_aaVec.end());
  for(; it != itend; it++)
    {
      it->replaceLeucineIsoleucine();

References m_aaVec.

getAaPositionList() [1/2]

std::vector< unsigned int > pappso::Peptide::getAaPositionList

(

char

aa

)

const

get positions of one amino acid in peptide

Parameters

aa	the one letter code of the amino acid

Returns

vector containing positions (from 0 to size-1)

Definition at line 365 of file peptide.cpp.

    {
 
      bool found =
        (std::find(list_aa.begin(), list_aa.end(), it->getLetter()) !=
         list_aa.end());
      if(found)
        {
          position_list.push_back(number);
        }
      number++;
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;

getAaPositionList() [2/2]

std::vector< unsigned int > pappso::Peptide::getAaPositionList

(

std::list< char >

list_aa

)

const

Definition at line 382 of file peptide.cpp.

{
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  if(it != m_aaVec.end())
    {
      return it->getInternalNterModification();
    }
 
  return nullptr;
}
AaModificationP
Peptide::getInternalCterModification() const
{
  std::vector<Aa>::const_iterator it(m_aaVec.end());
  it--;
  if(it != m_aaVec.end())
    {
      return it->getInternalCterModification();
    }

References m_aaVec.

getConstAa()

const Aa & pappso::Peptide::getConstAa

(

unsigned int

position

)

const

Definition at line 550 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.begin());
  if(it != m_aaVec.end())
    {

getInternalCterModification()

AaModificationP pappso::Peptide::getInternalCterModification

(

)

const

Definition at line 416 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.end());
  it--;
  if(it != m_aaVec.end())
    {
      m_proxyMass -= it->getMass();
      it->removeInternalCterModification();
      m_proxyMass += it->getMass();

References m_aaVec, and m_proxyMass.

Referenced by removeNterAminoAcid().

getInternalNterModification()

AaModificationP pappso::Peptide::getInternalNterModification

(

)

const

Definition at line 405 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.begin());
  if(it != m_aaVec.end())
    {
      m_proxyMass -= it->getMass();
      it->removeInternalNterModification();
      m_proxyMass += it->getMass();
    }

References m_aaVec, and m_proxyMass.

getLiAbsoluteString()

const QString pappso::Peptide::getLiAbsoluteString

(

)

const

get all sequence string with modifications and converting Leucine to Isoleucine

Definition at line 185 of file peptide.cpp.

{
  qDebug() << "Aa::getMass() begin";
  if(m_proxyMass < 0)
    {

getMass() [1/2]

pappso_double pappso::Peptide::getMass

(

)

Definition at line 212 of file peptide.cpp.

    {
      number += it->getNumberOfAtom(atom);
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
int
Peptide::getNumberOfIsotope(Isotope isotope) const
{
  int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())

Referenced by removeNterAminoAcid().

getMass() [2/2]

pappso_double pappso::Peptide::getMass ( ) const

inlineoverridevirtual

Implements pappso::Ion.

Definition at line 188 of file peptide.h.

getModificationPositionList() [1/2]

std::vector< unsigned int > pappso::Peptide::getModificationPositionList

(

AaModificationP

mod

)

const

get modification positions

Parameters

mod	modification to look for

Returns

vector containing positions (from 0 to size-1)

Definition at line 318 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int position = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(std::find(aa_list.begin(), aa_list.end(), it->getLetter()) !=
         aa_list.end())
        {
          unsigned int number = 0;
          number += it->getNumberOfModification(mod);
          for(unsigned int j = 0; j < number; j++)
            {
              position_list.push_back(position);
            }
        }
      it++;

References m_aaVec.

getModificationPositionList() [2/2]

std::vector< unsigned int > pappso::Peptide::getModificationPositionList	(	AaModificationP	mod,
		const std::vector< char > &	aa_list
	)		const

get modification positions

Parameters

mod	modification to look for
aa_list	amino acid list targets (one letter code)

Returns

vector containing positions (from 0 to size-1)

Definition at line 339 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(it->getLetter() == aa)
        position_list.push_back(number);
      number++;
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}
 
std::vector<unsigned int>
Peptide::getAaPositionList(std::list<char> list_aa) const
{

getNumberOfAtom()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 228 of file peptide.cpp.

{
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());

getNumberOfIsotope()

int pappso::Peptide::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 242 of file peptide.cpp.

{
  unsigned int number = 0;

getNumberOfModification()

unsigned int pappso::Peptide::getNumberOfModification

(

AaModificationP

mod

)

const

count modification occurence

Parameters

mod	modification to look for

Returns

number of occurences

Definition at line 257 of file peptide.cpp.

        {
          number += it->getNumberOfModification(mod);
        }
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
void

getSequence()

const QString pappso::Peptide::getSequence ( ) const

overridevirtual

print amino acid sequence without modifications

Implements pappso::PeptideInterface.

Definition at line 160 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      seq += it->toAbsoluteString();

Referenced by pappso::XtandemHyperscoreBis::computeXtandemHyperscore().

isPalindrome()

bool pappso::Peptide::isPalindrome ( ) const

overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 525 of file peptide.cpp.

{
  if(position >= m_aaVec.size())
    {
      throw ExceptionOutOfRange(
        QObject::tr("no AA at position %1").arg(position));
    }
  return m_aaVec.at(position);
}

makeNoConstPeptideSp()

NoConstPeptideSp pappso::Peptide::makeNoConstPeptideSp

(

)

const

Definition at line 136 of file peptide.cpp.

{

makePeptideSp()

PeptideSp pappso::Peptide::makePeptideSp

(

)

const

Definition at line 130 of file peptide.cpp.

Referenced by pappso::PeptideModificatorPipeline::setPeptide(), and pappso::PeptideFixedModificationBuilder::setPeptideSp().

rbegin()

std::vector<Aa>::const_reverse_iterator pappso::Peptide::rbegin ( ) const

inline

Definition at line 171 of file peptide.h.

  {

removeAaModification()

void pappso::Peptide::removeAaModification

(

AaModificationP

mod

)

removes all occurences of a modification

Parameters

mod	modification to remove

Definition at line 304 of file peptide.cpp.

        {
          position_list.push_back(position);
        }
      it++;
      position++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}
 

removeCterAminoAcid()

void pappso::Peptide::removeCterAminoAcid

(

)

Definition at line 598 of file peptide.cpp.

removeInternalCterModification()

void pappso::Peptide::removeInternalCterModification

(

)

Definition at line 438 of file peptide.cpp.

        {
          it->addAaModification(mod);
        }
      else
        {
          throw ExceptionOutOfRange(QObject::tr("peptide is empty"));
        }
    }
  else
    {
      throw ExceptionNotPossible(

removeInternalNterModification()

void pappso::Peptide::removeInternalNterModification

(

)

Definition at line 427 of file peptide.cpp.

{
  if(mod->getAccession().startsWith("internal:Nter_"))
    {
      removeInternalNterModification();
      std::vector<Aa>::iterator it(m_aaVec.begin());

removeNterAminoAcid()

void pappso::Peptide::removeNterAminoAcid

(

)

Definition at line 575 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.end());
  it--;
  if(it != m_aaVec.end())
    {
      AaModificationP cter_modification = getInternalCterModification();
      m_aaVec.erase(it);
      if(cter_modification != nullptr)
        {
          it = m_aaVec.end();
          it--;
          it->addAaModification(cter_modification);
        }
      m_proxyMass = -1;
      getMass();
    }
  else

References getInternalCterModification(), getMass(), m_aaVec, and m_proxyMass.

rend()

std::vector<Aa>::const_reverse_iterator pappso::Peptide::rend ( ) const

inline

Definition at line 177 of file peptide.h.

  {
    return m_aaVec.size();

replaceAaModification()

void pappso::Peptide::replaceAaModification	(	AaModificationP	oldmod,
		AaModificationP	newmod
	)

replaces all occurences of a modification by a new one

Parameters

oldmod	modification to change
newmod	new modification

Definition at line 290 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int position = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())

replaceLeucineIsoleucine()

void pappso::Peptide::replaceLeucineIsoleucine

(

)

Definition at line 562 of file peptide.cpp.

        {
          m_aaVec.begin()->addAaModification(nter_modification);
        }
 
      m_proxyMass = -1;
      getMass();
    }
  else
    {
      throw ExceptionOutOfRange(QObject::tr("peptide is empty"));

References m_aaVec.

reverse()

void pappso::Peptide::reverse

(

)

Definition at line 512 of file peptide.cpp.

{
  if(position >= m_aaVec.size())

rotate()

void pappso::Peptide::rotate

(

)

Definition at line 500 of file peptide.cpp.

{
  std::size_t size = m_aaVec.size();
  std::size_t k    = (size - 1);
  for(std::size_t i = 0; i < (size / 2); i++, k--)
    {

setInternalCterModification()

void pappso::Peptide::setInternalCterModification

(

AaModificationP

mod

)

Definition at line 475 of file peptide.cpp.

{
  AaModificationP modNter = getInternalNterModification();
  AaModificationP modCter = getInternalCterModification();
  m_aaVec.begin()->removeInternalNterModification();
  (m_aaVec.end() - 1)->removeInternalCterModification();
  std::rotate(m_aaVec.begin(), m_aaVec.begin() + 1, m_aaVec.end());
  m_aaVec.begin()->addAaModification(modNter);
  (m_aaVec.end() - 1)->addAaModification(modCter);
}
 
void
Peptide::reverse()
{
  AaModificationP modNter = getInternalNterModification();
  AaModificationP modCter = getInternalCterModification();
  m_aaVec.begin()->removeInternalNterModification();
  (m_aaVec.end() - 1)->removeInternalCterModification();
  std::reverse(m_aaVec.begin(), m_aaVec.end());

setInternalNterModification()

void pappso::Peptide::setInternalNterModification

(

AaModificationP

mod

)

Definition at line 452 of file peptide.cpp.

{
  if(mod->getAccession().startsWith("internal:Cter_"))
    {
      removeInternalCterModification();
      std::vector<Aa>::iterator it(m_aaVec.end());
      it--;
      if(it != m_aaVec.end())
        {
          it->addAaModification(mod);
        }
      else
        {
          throw ExceptionOutOfRange(QObject::tr("peptide is empty"));
        }
    }
  else
    {
      throw ExceptionNotPossible(
        QObject::tr("modification is not an internal Cter modification : %1")

size()

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

inlineoverridevirtual

Implements pappso::PeptideInterface.

Definition at line 199 of file peptide.h.

Referenced by Peptide(), and pappso::PeptideFixedModificationBuilder::setPeptideSp().

toAbsoluteString()

const QString pappso::Peptide::toAbsoluteString

(

)

const

print all modifications

Definition at line 172 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())

toString()

const QString pappso::Peptide::toString

(

)

const

print modification except internal modifications

Definition at line 199 of file peptide.cpp.

{
  int number = 0;

Friends And Related Function Documentation

operator<

bool operator< ( const Peptide &  l, const Peptide &  r  )

friend

Definition at line 123 of file peptide.h.

  {

operator==

bool operator== ( const Peptide &  l, const Peptide &  r  )

friend

Definition at line 129 of file peptide.h.

  {

Member Data Documentation

m_aaVec

std::vector<Aa> pappso::Peptide::m_aaVec

protected

Definition at line 116 of file peptide.h.

Referenced by getAa(), getAaPositionList(), getInternalCterModification(), getInternalNterModification(), getModificationPositionList(), pappso::getPeptideIonDirection(), removeNterAminoAcid(), and replaceLeucineIsoleucine().

m_proxyMass

pappso_double pappso::Peptide::m_proxyMass = -1

protected

Definition at line 117 of file peptide.h.

Referenced by getInternalCterModification(), getInternalNterModification(), Peptide(), and removeNterAminoAcid().

---

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

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