pappso::Aa Class Reference

#include <aa.h>

Inheritance diagram for pappso::Aa:

Public Member Functions
	Aa (char aa_letter)
	Aa (Enums::AminoAcidChar aa_char)
	Aa (const Aa &aa)
	Aa (Aa &&toCopy)
Aa &	operator= (const Aa &toCopy)
virtual	~Aa ()
pappso_double	getMass () const override
int	getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const override final
	get the number of atom C, O, N, H in the molecule
int	getNumberOfIsotope (Enums::Isotope isotope) const override final
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
unsigned int	getNumberOfModification (AaModificationP mod) const
const QString	toString () const
const QString	toAbsoluteString () const
const QString	toProForma () const
	get the amino acid in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md
void	addAaModification (AaModificationP aaModification)
void	removeAaModification (AaModificationP aaModification)
void	replaceAaModification (AaModificationP oldmod, AaModificationP newmod)
	replaces all occurences of a modification by a new one
void	removeAllButInternalModification ()
	remove all non internal modifications
const std::vector< AaModificationP > &	getModificationList () const
double	getTotalModificationMass () const
	get the sum of mass modifications
bool	isLesser (Aa const &r) const
bool	isAaEqual (Aa const &r) const
Public Member Functions inherited from pappso::AaBase
virtual const char &	getLetter () const
const Enums::AminoAcidChar &	getAminoAcidChar () const
virtual void	replaceLeucineIsoleucine ()
Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula	getChemicalFormula () const

Private Attributes
std::vector< AaModificationP >	m_listMod

Additional Inherited Members
Static Public Member Functions inherited from pappso::AaBase
static const std::vector< Enums::AminoAcidChar > &	getAminoAcidCharList ()
Protected Member Functions inherited from pappso::AaBase
	AaBase (char aa_letter)
	AaBase (Enums::AminoAcidChar aa_char)
	AaBase (const AaBase &aabase)
virtual	~AaBase ()
int	getNumberOfIsotope (Enums::Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
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)
{
}

References pappso::AaBase::AaBase().

Referenced by Aa(), Aa(), isAaEqual(), isLesser(), and operator=().

Aa() [2/4]

pappso::Aa::Aa

(

Enums::AminoAcidChar

aa_char

)

Definition at line 46 of file aa.cpp.

                                 : AaBase(aa_char)
{
}

References pappso::AaBase::AaBase().

Aa() [3/4]

pappso::Aa::Aa

(

const Aa &

aa

)

Definition at line 50 of file aa.cpp.

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

References Aa(), pappso::AaBase::AaBase(), and 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))
{
}

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

~Aa()

pappso::Aa::~Aa ( )

virtual

Definition at line 60 of file aa.cpp.

{
}

Member Function Documentation

addAaModification()

void pappso::Aa::addAaModification

(

AaModificationP

aaModification

)

Definition at line 189 of file aa.cpp.

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

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

getMass()

pappso_double pappso::Aa::getMass ( ) const

overridevirtual

Reimplemented from pappso::AaBase.

Definition at line 90 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::specglob::PeptideModel::checkForMutation(), pappso::AaModification::createInstanceMutation(), and pappso::specglob::PeptideModel::ltrimOnRemoval().

getModificationList()

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

(

)

const

Definition at line 73 of file aa.cpp.

{
  return m_listMod;
}

References m_listMod.

Referenced by pappso::specglob::PeptideModel::checkForAaModification(), and pappso::specglob::PeptideModel::checkForMutation().

getNumberOfAtom()

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

finaloverridevirtual

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

Reimplemented from pappso::AaBase.

Definition at line 206 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 ( Enums::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 220 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 233 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().

getTotalModificationMass()

double pappso::Aa::getTotalModificationMass

(

)

const

get the sum of mass modifications

Definition at line 79 of file aa.cpp.

{
  double mass = 0;
  for(auto &&mod : m_listMod)
    {
      mass += mod->getMass();
    }
  return mass;
}

References m_listMod.

Referenced by pappso::specglob::PeptideModel::checkForAaModification().

isAaEqual()

bool pappso::Aa::isAaEqual

(

Aa const &

r

)

const

Definition at line 279 of file aa.cpp.

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

References Aa(), pappso::AaBase::m_aaLetter, and m_listMod.

Referenced by pappso::operator==().

isLesser()

bool pappso::Aa::isLesser

(

Aa const &

r

)

const

Definition at line 254 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 Aa(), 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 Aa(), pappso::AaBase::m_aaLetter, and m_listMod.

removeAaModification()

void pappso::Aa::removeAaModification

(

AaModificationP

aaModification

)

Definition at line 177 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.

removeAllButInternalModification()

void pappso::Aa::removeAllButInternalModification

(

)

remove all non internal modifications

Definition at line 247 of file aa.cpp.

{
 
  m_listMod.clear();
}

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 199 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 104 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.

toProForma()

const QString pappso::Aa::toProForma

(

)

const

get the amino acid in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md

Returns

QString as described in ProForma

Definition at line 147 of file aa.cpp.

{
  QString seq = "";
  seq += this->getLetter();
 
  std::vector<AaModificationP> copy_mod_list = m_listMod;
  std::sort(copy_mod_list.begin(),
            copy_mod_list.end(),
            [](const AaModificationP &a, const AaModificationP &b) {
              return a->getAccession() < b->getAccession();
            });
  auto it(copy_mod_list.begin());
  if(it != copy_mod_list.end())
    {
      QStringList modification_str_list;
      while(it != copy_mod_list.end())
        {
          if(!(*it)->isInternal())
            {
              modification_str_list << (*it)->toProForma();
            }
          it++;
        }
      if(modification_str_list.size() > 0)
        seq += QString("[%1]").arg(modification_str_list.join("]["));
    }
  return seq;
}

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

toString()

const QString pappso::Aa::toString

(

)

const

Definition at line 124 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 98 of file aa.h.

Referenced by Aa(), Aa(), addAaModification(), getMass(), getModificationList(), getNumberOfAtom(), getNumberOfIsotope(), getNumberOfModification(), getTotalModificationMass(), isAaEqual(), isLesser(), operator=(), removeAaModification(), removeAllButInternalModification(), replaceAaModification(), toAbsoluteString(), toProForma(), and toString().

---

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

• pappsomspp/core/amino_acid/aa.h
• pappsomspp/core/amino_acid/aa.cpp