pappso::Aa Class Reference

#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 65 of file aa.h.

Constructor & Destructor Documentation

Aa() [1/4]

pappso::Aa::Aa

(

char

aa_letter

)

Definition at line 62 of file aa.cpp.

Aa() [2/4]

pappso::Aa::Aa

(

AminoAcidChar

aa_char

)

Definition at line 67 of file aa.cpp.

Aa() [3/4]

pappso::Aa::Aa

(

const Aa &

aa

)

Definition at line 71 of file aa.cpp.

{

References m_listMod.

Aa() [4/4]

pappso::Aa::Aa

(

Aa &&

toCopy

)

Definition at line 76 of file aa.cpp.

{

~Aa()

pappso::Aa::~Aa ( )

virtual

Definition at line 81 of file aa.cpp.

                 : m_listMod)

Member Function Documentation

addAaModification()

void pappso::Aa::addAaModification

(

AaModificationP

aaModification

)

Definition at line 171 of file aa.cpp.

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

getInternalCterModification()

AaModificationP pappso::Aa::getInternalCterModification

(

)

const

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_");
    });
}
 
bool
Aa::isLesser(Aa const &r) const

References m_listMod.

getInternalNterModification()

AaModificationP pappso::Aa::getInternalNterModification

(

)

const

Definition at line 227 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.

getMass()

pappso_double pappso::Aa::getMass ( ) const

overridevirtual

Reimplemented from pappso::AaBase.

Definition at line 100 of file aa.cpp.

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

getModificationList()

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

(

)

const

Definition at line 94 of file aa.cpp.

{
  QString seq = "";
  seq += this->getLetter();
  auto it(m_listMod.begin());

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 186 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 200 of file aa.cpp.

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

getNumberOfModification()

unsigned int pappso::Aa::getNumberOfModification

(

AaModificationP

mod

)

const

Definition at line 213 of file aa.cpp.

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

isAaEqual()

bool pappso::Aa::isAaEqual

(

Aa const &

r

)

const

Definition at line 292 of file aa.cpp.

isLesser()

bool pappso::Aa::isLesser

(

Aa const &

r

)

const

Definition at line 267 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);
}
} /* namespace pappso */

operator=()

Aa & pappso::Aa::operator=

(

const Aa &

toCopy

)

Definition at line 86 of file aa.cpp.

removeAaModification()

void pappso::Aa::removeAaModification

(

AaModificationP

aaModification

)

Definition at line 158 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);
  for(auto &&mod : m_listMod)

References m_listMod.

removeInternalCterModification()

void pappso::Aa::removeInternalCterModification

(

)

Definition at line 258 of file aa.cpp.

        {
          return (a < b);
        }
    }
  else

removeInternalNterModification()

void pappso::Aa::removeInternalNterModification

(

)

Definition at line 249 of file aa.cpp.

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

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 180 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 114 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 134 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();
  m_listMod.push_back(aaModification);

References m_listMod.

Member Data Documentation

m_listMod

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

private

Definition at line 131 of file aa.h.

Referenced by Aa(), getInternalCterModification(), getInternalNterModification(), getModificationList(), removeAaModification(), 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