#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 111 of file peptide.h.

Constructor & Destructor Documentation

◆ Peptide() [1/3]

pappso::Peptide::Peptide ( const QString & pepstr )

Definition at line 83 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
 {

◆ ~Peptide()

pappso::Peptide::~Peptide ( )

virtual

Definition at line 112 of file peptide.cpp.

◆ Peptide() [2/3]

pappso::Peptide::Peptide ( const Peptide & peptide )

Definition at line 116 of file peptide.cpp.

 {
   return std::make_shared<Peptide>(*this);
 }
  

◆ Peptide() [3/3]

pappso::Peptide::Peptide ( Peptide && toCopy )

Definition at line 122 of file peptide.cpp.

 {
   if(position >= size())
     {

References 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 141 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())

◆ begin() [1/2]

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

inline

Definition at line 145 of file peptide.h.

   {
     return m_aaVec.end();
   }
  

◆ begin() [2/2]

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

inline

Definition at line 157 of file peptide.h.

   {
     return m_aaVec.rend();
   }
  

◆ 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 270 of file peptide.cpp.

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

References getMass(), m_aaVec, and m_proxyMass.

◆ end() [1/2]

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

inline

Definition at line 151 of file peptide.h.

   {
     return m_aaVec.rbegin();
   }
  

Referenced by pappso::PeptideFragment::PeptideFragment().

◆ end() [2/2]

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

inline

Definition at line 163 of file peptide.h.

168 {

◆ getAa()

Aa & pappso::Peptide::getAa ( unsigned int position )

Definition at line 539 of file peptide.cpp.

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

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 364 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++;
     }

◆ getAaPositionList() [2/2]

std::vector< unsigned int > pappso::Peptide::getAaPositionList ( std::list< char > list_aa ) const

Definition at line 381 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();

◆ getConstAa()

const Aa & pappso::Peptide::getConstAa ( unsigned int position ) const

Definition at line 549 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 415 of file peptide.cpp.

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

Referenced by removeNterAminoAcid().

◆ getInternalNterModification()

AaModificationP pappso::Peptide::getInternalNterModification ( ) const

Definition at line 404 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();

◆ getLiAbsoluteString()

const QString pappso::Peptide::getLiAbsoluteString ( ) const

get all sequence string with modifications and converting Leucine to Isoleucine

Definition at line 184 of file peptide.cpp.

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

◆ getMass() [1/2]

pappso_double pappso::Peptide::getMass ( )

Definition at line 211 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());

Referenced by countModificationOnAa(), and removeNterAminoAcid().

◆ getMass() [2/2]

pappso_double pappso::Peptide::getMass ( ) const

inlineoverridevirtual

Implements pappso::Ion.

Definition at line 186 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 317 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);
             }
         }

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 338 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 227 of file peptide.cpp.

237 {

238 unsigned int number = 0;

◆ 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 241 of file peptide.cpp.

     {
       number += it->getNumberOfModification(mod);
       it++;
     }
   // qDebug() << "Aa::getMass() end " << mass;
   return number;
 }
  
 unsigned int
 Peptide::countModificationOnAa(AaModificationP mod,
                                const std::vector<char> &aa_list) const
 {

◆ 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 256 of file peptide.cpp.

     {
       if(std::find(aa_list.begin(), aa_list.end(), it->getLetter()) !=
          aa_list.end())
         {
           number += it->getNumberOfModification(mod);
         }
       it++;
     }
   // qDebug() << "Aa::getMass() end " << mass;
   return number;
 }
  

◆ getSequence()

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

overridevirtual

print amino acid sequence without modifications

Implements pappso::PeptideInterface.

Definition at line 159 of file peptide.cpp.

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

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 524 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 135 of file peptide.cpp.

◆ makePeptideSp()

PeptideSp pappso::Peptide::makePeptideSp ( ) const

Definition at line 129 of file peptide.cpp.

Referenced by pappso::PeptideModificatorPipeline::setPeptide().

◆ rbegin()

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

inline

Definition at line 169 of file peptide.h.

179 {

◆ removeAaModification()

void pappso::Peptide::removeAaModification ( AaModificationP mod )

removes all occurences of a modification

Parameters

mod	modification to remove

Definition at line 303 of file peptide.cpp.

     {
       unsigned int number = 0;
       number += it->getNumberOfModification(mod);
       for(unsigned int j = 0; j < number; j++)
         {
           position_list.push_back(position);
         }
       it++;
       position++;
     }
   // qDebug() << "Aa::getMass() end " << mass;
   return position_list;
 }

◆ removeCterAminoAcid()

void pappso::Peptide::removeCterAminoAcid ( )

Definition at line 597 of file peptide.cpp.

◆ removeInternalCterModification()

void pappso::Peptide::removeInternalCterModification ( )

Definition at line 437 of file peptide.cpp.

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

◆ removeInternalNterModification()

void pappso::Peptide::removeInternalNterModification ( )

Definition at line 426 of file peptide.cpp.

 {
   if(mod->getAccession().startsWith("internal:Nter_"))
     {
       removeInternalNterModification();

◆ removeNterAminoAcid()

void pappso::Peptide::removeNterAminoAcid ( )

Definition at line 574 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();
     }

References pappso::AaModificationP, getInternalCterModification(), getMass(), m_aaVec, and m_proxyMass.

◆ rend()

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

inline

Definition at line 175 of file peptide.h.

179 {

◆ 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 289 of file peptide.cpp.

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

◆ replaceLeucineIsoleucine()

void pappso::Peptide::replaceLeucineIsoleucine ( )

Definition at line 561 of file peptide.cpp.

         {
           m_aaVec.begin()->addAaModification(nter_modification);
         }
  
       m_proxyMass = -1;
       getMass();
     }
   else
     {

References m_aaVec.

◆ reverse()

void pappso::Peptide::reverse ( )

Definition at line 511 of file peptide.cpp.

         {
           return false;
         }
     }
   return true;
 }
  
 Aa &
 Peptide::getAa(unsigned int position)
 {

◆ rotate()

void pappso::Peptide::rotate ( )

Definition at line 499 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 474 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();

◆ setInternalNterModification()

void pappso::Peptide::setInternalNterModification ( AaModificationP mod )

Definition at line 451 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(

◆ size()

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

inlineoverridevirtual

Implements pappso::PeptideInterface.

Definition at line 197 of file peptide.h.

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

◆ toAbsoluteString()

const QString pappso::Peptide::toAbsoluteString ( ) const

print all modifications

Definition at line 171 of file peptide.cpp.

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

◆ toString()

const QString pappso::Peptide::toString ( ) const

print modification except internal modifications

Definition at line 198 of file peptide.cpp.

         {
           m_proxyMass += aa.getMass();
         }
     }
   qDebug() << "Aa::getMass() end " << m_proxyMass;
   return m_proxyMass;
 }
  
 int
 Peptide::getNumberOfAtom(AtomIsotopeSurvey atom) const
 {

References m_proxyMass.

Friends And Related Function Documentation

◆ operator<

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

friend

Definition at line 122 of file peptide.h.

127 {

◆ operator==

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

friend

Definition at line 127 of file peptide.h.

   {
     return m_aaVec.begin();
   }
  

Member Data Documentation

◆ m_aaVec

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

protected

Definition at line 114 of file peptide.h.

Referenced by countModificationOnAa(), getAa(), getModificationPositionList(), pappso::getPeptideIonDirection(), removeNterAminoAcid(), and replaceLeucineIsoleucine().

◆ m_proxyMass

pappso_double pappso::Peptide::m_proxyMass = -1

protected

Definition at line 115 of file peptide.h.

Referenced by countModificationOnAa(), removeNterAminoAcid(), and toString().

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

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

Public Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Peptide() [1/3]

◆ ~Peptide()

◆ Peptide() [2/3]

◆ Peptide() [3/3]

Member Function Documentation

◆ addAaModification()

◆ begin() [1/2]

◆ begin() [2/2]

◆ countModificationOnAa()

◆ end() [1/2]

◆ end() [2/2]

◆ getAa()

◆ getAaPositionList() [1/2]

◆ getAaPositionList() [2/2]

◆ getConstAa()

◆ getInternalCterModification()

◆ getInternalNterModification()

◆ getLiAbsoluteString()

◆ getMass() [1/2]

◆ getMass() [2/2]

◆ getModificationPositionList() [1/2]

◆ getModificationPositionList() [2/2]

◆ getNumberOfAtom()

◆ getNumberOfIsotope()

◆ getNumberOfModification()

◆ getSequence()

◆ isPalindrome()

◆ makeNoConstPeptideSp()

◆ makePeptideSp()

◆ rbegin()

◆ removeAaModification()

◆ removeCterAminoAcid()

◆ removeInternalCterModification()

◆ removeInternalNterModification()

◆ removeNterAminoAcid()

◆ rend()

◆ replaceAaModification()

◆ replaceLeucineIsoleucine()

◆ reverse()

◆ rotate()

◆ setInternalCterModification()

◆ setInternalNterModification()

◆ size()

◆ toAbsoluteString()

◆ toString()

Friends And Related Function Documentation

◆ operator<

◆ operator==

Member Data Documentation

◆ m_aaVec

◆ m_proxyMass