#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 44 of file aa.h.

Constructor & Destructor Documentation

◆ Aa() [1/4]

pappso::Aa::Aa ( char aa_letter )

Definition at line 41 of file aa.cpp.

                      : AaBase(aa_letter)
 {
 }

◆ Aa() [2/4]

pappso::Aa::Aa ( AminoAcidChar aa_char )

Definition at line 46 of file aa.cpp.

                             : AaBase(aa_char)
 {
 }

◆ Aa() [3/4]

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

Definition at line 50 of file aa.cpp.

                       : AaBase(other), m_listMod(other.m_listMod)
 {
 }

◆ Aa() [4/4]

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

Definition at line 55 of file aa.cpp.

   : AaBase(toCopy), m_listMod(std::move(toCopy.m_listMod))
 {
 }

◆ ~Aa()

pappso::Aa::~Aa ( )

virtual

Definition at line 60 of file aa.cpp.

61 {

62 }

Member Function Documentation

◆ addAaModification()

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

Definition at line 150 of file aa.cpp.

 {
   qDebug() << "Aa::addAaModification begin";
   qDebug() << aaModification->getAccession();
   m_listMod.push_back(aaModification);
   sort(m_listMod.begin(), m_listMod.end());
 }

References pappso::AaModification::getAccession(), and m_listMod.

Referenced by pappso::Peptide::Peptide(), and pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition().

◆ getInternalCterModification()

AaModificationP pappso::Aa::getInternalCterModification ( ) const

Definition at line 218 of file aa.cpp.

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

References m_listMod.

◆ getInternalNterModification()

AaModificationP pappso::Aa::getInternalNterModification ( ) const

Definition at line 207 of file aa.cpp.

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

References m_listMod.

◆ getMass()

pappso_double pappso::Aa::getMass ( ) const

overridevirtual

Reimplemented from pappso::AaBase.

Definition at line 79 of file aa.cpp.

 {
   // qDebug() << "Aa::getMass() begin";
   pappso_double mass = AaBase::getMass();
   for(auto &&mod : m_listMod)
     {
       mass += mod->getMass();
     }
  
   // qDebug() << "Aa::getMass() end " << mass;
   return mass;
 }

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

Referenced by pappso::AaModification::createInstanceMutation().

◆ getModificationList()

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

Definition at line 73 of file aa.cpp.

 {
   return m_listMod;
 }

References 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 166 of file aa.cpp.

 {
   int number_of_carbon = AaBase::getNumberOfAtom(atom);
   for(auto &&mod : m_listMod)
     {
       number_of_carbon += mod->getNumberOfAtom(atom);
     }
  
   // qDebug() << "Aa::getMass() end " << mass;
   return number_of_carbon;
 }

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

Referenced by pappso::AaModification::createInstanceMutation().

◆ 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 180 of file aa.cpp.

 {
   int number = 0;
   for(auto &&mod : m_listMod)
     {
       number += mod->getNumberOfIsotope(isotope);
     }
  
   // qDebug() << "Aa::getMass() end " << mass;
   return number;
 }

References m_listMod.

◆ getNumberOfModification()

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

Definition at line 193 of file aa.cpp.

 {
   unsigned int number_of_mod = 0;
   for(auto &&modb : m_listMod)
     {
       if(modb == mod)
         number_of_mod += 1;
     }
  
   // qDebug() << "Aa::getMass() end " << mass;
   return number_of_mod;
 }

References m_listMod.

Referenced by pappso::PeptideModificatorBase::getModificationPositionList().

◆ isAaEqual()

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

Definition at line 272 of file aa.cpp.

 {
  
   return (std::tie(m_aaLetter, m_listMod) ==
           std::tie(r.m_aaLetter, r.m_listMod));
 }

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

Referenced by pappso::operator==().

◆ isLesser()

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

Definition at line 247 of file aa.cpp.

 {
   qDebug() << m_listMod << "//" << r.m_listMod;
   // qDebug() << "operator<(const Aa& l, const Aa& r)";
   if(m_aaLetter == r.m_aaLetter)
     {
       std::size_t a = m_listMod.size();
       std::size_t b = r.m_listMod.size();
  
       if(a == b)
         {
           return (m_listMod < r.m_listMod);
         }
       else
         {
           return (a < b);
         }
     }
   else
     {
       return (m_aaLetter < r.m_aaLetter);
     }
 }

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

Referenced by pappso::operator<().

◆ operator=()

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

Definition at line 65 of file aa.cpp.

 {
   m_aaLetter = toCopy.m_aaLetter;
   m_listMod  = toCopy.m_listMod;
   return *this;
 }

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

◆ removeAaModification()

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

Definition at line 137 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 << Qt::endl;
 }

References m_listMod.

Referenced by pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition().

◆ removeInternalCterModification()

void pappso::Aa::removeInternalCterModification ( )

Definition at line 238 of file aa.cpp.

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

References m_listMod.

◆ removeInternalNterModification()

void pappso::Aa::removeInternalNterModification ( )

Definition at line 229 of file aa.cpp.

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

References 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 159 of file aa.cpp.

 {
   std::replace(m_listMod.begin(), m_listMod.end(), oldmod, newmod);
   sort(m_listMod.begin(), m_listMod.end());
 }

References m_listMod.

◆ toAbsoluteString()

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

Definition at line 93 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())
         {
           modification_str_list << (*it)->getAccession();
           it++;
         }
       if(modification_str_list.size() > 0)
         seq += QString("(%1)").arg(modification_str_list.join(","));
     }
   return seq;
 }

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

◆ toString()

const QString pappso::Aa::toString ( ) 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(","));
     }
   return seq;
 }

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

Member Data Documentation

◆ m_listMod

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

private

Definition at line 89 of file aa.h.

Referenced by addAaModification(), getInternalCterModification(), getInternalNterModification(), getMass(), getModificationList(), getNumberOfAtom(), getNumberOfIsotope(), getNumberOfModification(), isAaEqual(), isLesser(), operator=(), removeAaModification(), removeInternalCterModification(), removeInternalNterModification(), replaceAaModification(), toAbsoluteString(), and toString().

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