#include <aa.h>

Inheritance diagram for pappso::Aa:

Public Member Functions
	Aa (char aa_letter)

	Aa (AminoAcidChar aa_char)

	Aa (const Aa &aa)

	Aa (Aa &&toCopy)

Aa &	operator= (const Aa &toCopy)

virtual	~Aa ()

pappso_double	getMass () const override

int	getNumberOfAtom (AtomIsotopeSurvey atom) const override final
	get the number of atom C, O, N, H in the molecule More...

int	getNumberOfIsotope (Isotope isotope) const override final
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...

unsigned int	getNumberOfModification (AaModificationP mod) const

const QString	toString () const

const QString	toAbsoluteString () const

void	addAaModification (AaModificationP aaModification)

void	removeAaModification (AaModificationP aaModification)

void	replaceAaModification (AaModificationP oldmod, AaModificationP newmod)
	replaces all occurences of a modification by a new one More...

AaModificationP	getInternalNterModification () const

AaModificationP	getInternalCterModification () const

void	removeInternalNterModification ()

void	removeInternalCterModification ()

const std::vector< AaModificationP > &	getModificationList () const

bool	isLesser (Aa const &r) const

bool	isAaEqual (Aa const &r) const

Public Member Functions inherited from pappso::AaBase
virtual const char &	getLetter () const

virtual void	replaceLeucineIsoleucine ()

Private Attributes
std::vector< AaModificationP >	m_listMod

Additional Inherited Members
Static Public Member Functions inherited from pappso::AaBase
static const std::vector< AminoAcidChar > &	getAminoAcidCharList ()

Protected Member Functions inherited from pappso::AaBase
	AaBase (char aa_letter)

	AaBase (AminoAcidChar aa_char)

	AaBase (const AaBase &aabase)

virtual	~AaBase ()

int	getNumberOfIsotope (Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...

Static Protected Member Functions inherited from pappso::AaBase
static pappso_double	getAaMass (char aa_letter)

Protected Attributes inherited from pappso::AaBase
char	m_aaLetter

Detailed Description

Definition at line 63 of file aa.h.

Constructor & Destructor Documentation

◆ Aa() [1/4]

pappso::Aa::Aa ( char aa_letter )

Definition at line 61 of file aa.cpp.

 {
 }
  

◆ Aa() [2/4]

pappso::Aa::Aa ( AminoAcidChar aa_char )

Definition at line 66 of file aa.cpp.

 {
   m_aaLetter = toCopy.m_aaLetter;
   m_listMod  = toCopy.m_listMod;

References pappso::AaBase::m_aaLetter, and m_listMod.

◆ Aa() [3/4]

pappso::Aa::Aa ( const Aa & aa )

Definition at line 70 of file aa.cpp.

◆ Aa() [4/4]

pappso::Aa::Aa ( Aa && toCopy )

Definition at line 75 of file aa.cpp.

◆ ~Aa()

pappso::Aa::~Aa ( )

virtual

Definition at line 80 of file aa.cpp.

 {
   qDebug() << "Aa::getMass() begin";
   pappso_double mass = AaBase::getMass();

References pappso::AaBase::getMass(), and m_listMod.

Member Function Documentation

◆ addAaModification()

void pappso::Aa::addAaModification ( AaModificationP aaModification )

Definition at line 170 of file aa.cpp.

Referenced by pappso::peptideIonIsNter(), and pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement().

◆ getInternalCterModification()

AaModificationP pappso::Aa::getInternalCterModification ( ) const

Definition at line 237 of file aa.cpp.

 {
   std::remove_if(
     m_listMod.begin(), m_listMod.end(), [](AaModificationP const &mod) {
       return mod->getAccession().startsWith("internal:Cter_");
     });
 }
  
 bool

References pappso::AaModificationP, and m_listMod.

◆ getInternalNterModification()

AaModificationP pappso::Aa::getInternalNterModification ( ) const

Definition at line 226 of file aa.cpp.

 {
   std::remove_if(
     m_listMod.begin(), m_listMod.end(), [](AaModificationP const &mod) {
       return mod->getAccession().startsWith("internal:Nter_");
     });
 }

References pappso::AaModificationP, and m_listMod.

◆ getMass()

pappso_double pappso::Aa::getMass ( ) const

overridevirtual

Reimplemented from pappso::AaBase.

Definition at line 99 of file aa.cpp.

     {
       QStringList modification_str_list;
       while(it != m_listMod.end())
         {
           modification_str_list << (*it)->getAccession();
           it++;
         }
       if(modification_str_list.size() > 0)
         seq += QString("(%1)").arg(modification_str_list.join(","));
     }
   return seq;
 }

References m_listMod.

◆ getModificationList()

const std::vector< AaModificationP > & pappso::Aa::getModificationList ( ) const

Definition at line 93 of file aa.cpp.

 {
   QString seq = "";
   seq += this->getLetter();

References pappso::AaBase::getLetter(), and m_listMod.

◆ getNumberOfAtom()

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

finaloverridevirtual

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

Reimplemented from pappso::AaBase.

Definition at line 185 of file aa.cpp.

 {
   unsigned int number_of_mod = 0;
   for(auto &&modb : m_listMod)

◆ getNumberOfIsotope()

int pappso::Aa::getNumberOfIsotope ( Isotope isotope ) const

finaloverridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 199 of file aa.cpp.

 {
   for(auto &&modb : m_listMod)
     {

◆ getNumberOfModification()

unsigned int pappso::Aa::getNumberOfModification ( AaModificationP mod ) const

Definition at line 212 of file aa.cpp.

 {
   for(auto &&modb : m_listMod)
     {
       if(modb->getAccession().startsWith("internal:Cter_"))
         return modb;
     }

◆ isAaEqual()

bool pappso::Aa::isAaEqual ( Aa const & r ) const

Definition at line 291 of file aa.cpp.

◆ isLesser()

bool pappso::Aa::isLesser ( Aa const & r ) const

Definition at line 266 of file aa.cpp.

 {
  
   return (std::tie(m_aaLetter, m_listMod) ==
           std::tie(r.m_aaLetter, r.m_listMod));
 }
  
 bool
 operator==(Aa const &l, Aa const &r)
 {
   return l.isAaEqual(r);
 }
  
 bool
 operator<(Aa const &l, Aa const &r)
 {
   return l.isLesser(r);
 }

◆ operator=()

Aa & pappso::Aa::operator= ( const Aa & toCopy )

Definition at line 85 of file aa.cpp.

◆ removeAaModification()

void pappso::Aa::removeAaModification ( AaModificationP aaModification )

Definition at line 157 of file aa.cpp.

 {
   std::replace(m_listMod.begin(), m_listMod.end(), oldmod, newmod);
 }
  
 int
 Aa::getNumberOfAtom(AtomIsotopeSurvey atom) const
 {
   int number_of_carbon = AaBase::getNumberOfAtom(atom);

References m_listMod.

◆ removeInternalCterModification()

void pappso::Aa::removeInternalCterModification ( )

Definition at line 257 of file aa.cpp.

         {
           return (a < b);
         }
     }

◆ removeInternalNterModification()

void pappso::Aa::removeInternalNterModification ( )

Definition at line 248 of file aa.cpp.

     {
       std::size_t a = m_listMod.size();
       std::size_t b = r.m_listMod.size();
  

References pappso::a, pappso::b, and m_listMod.

◆ replaceAaModification()

void pappso::Aa::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 179 of file aa.cpp.

 {
   int number = 0;
   for(auto &&mod : m_listMod)

References m_listMod.

◆ toAbsoluteString()

const QString pappso::Aa::toAbsoluteString ( ) const

Definition at line 113 of file aa.cpp.

 {
   QString seq = "";
   seq += this->getLetter();
   auto it(m_listMod.begin());
   if(it != m_listMod.end())
     {
       QStringList modification_str_list;
       while(it != m_listMod.end())
         {
           if(!(*it)->isInternal())
             {
               modification_str_list << (*it)->getAccession();
             }
           it++;
         }
       if(modification_str_list.size() > 0)
         seq += QString("(%1)").arg(modification_str_list.join(","));

References pappso::AaBase::getLetter(), and m_listMod.

◆ toString()

const QString pappso::Aa::toString ( ) const

Definition at line 133 of file aa.cpp.

 {
   std::vector<AaModificationP>::iterator it =
     std::find(m_listMod.begin(), m_listMod.end(), mod);
   if(it != m_listMod.end())
     {
       m_listMod.erase(it);
     }
  
   qDebug() << m_listMod << endl;
 }
  
 void
 Aa::addAaModification(AaModificationP aaModification)
 {
   qDebug() << "Aa::addAaModification begin";
   qDebug() << aaModification->getAccession();

Member Data Documentation

◆ m_listMod

std::vector<AaModificationP> pappso::Aa::m_listMod

private

Definition at line 128 of file aa.h.

Referenced by Aa(), getInternalCterModification(), getInternalNterModification(), getMass(), getModificationList(), removeAaModification(), removeInternalNterModification(), replaceAaModification(), toAbsoluteString(), and ~Aa().

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

pappsomspp/amino_acid/aa.h
pappsomspp/amino_acid/aa.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Aa() [1/4]

◆ Aa() [2/4]

◆ Aa() [3/4]

◆ Aa() [4/4]

◆ ~Aa()

Member Function Documentation

◆ addAaModification()

◆ getInternalCterModification()

◆ getInternalNterModification()

◆ getMass()

◆ getModificationList()

◆ getNumberOfAtom()

◆ getNumberOfIsotope()

◆ getNumberOfModification()

◆ isAaEqual()

◆ isLesser()

◆ operator=()

◆ removeAaModification()

◆ removeInternalCterModification()

◆ removeInternalNterModification()

◆ replaceAaModification()

◆ toAbsoluteString()

◆ toString()

Member Data Documentation

◆ m_listMod